HISTORICAL PROCESSES AND GENETIC IMPLICATIONS OF LIMB REDUCTION AND LOSS IN AN ISLAND SKINK LINEAGE BY Cameron D. Siler Submitted to the graduate degree program in Ecology and Evolutionary Biology of the University of Kansas in partial fulfillment of the requirements for the degree of Doctor of Philosophy. Chair: __________________________ Committee Members: __________________________ __________________________ __________________________ __________________________ Date defended: __________________________ ii The dissertation committee for Cameron D. Siler certifies that this is the approved version of the following dissertation: HISTORICAL PROCESSES AND GENETIC IMPLICATIONS OF LIMB REDUCTION AND LOSS IN AN ISLAND SKINK LINEAGE Committee: Chair: __________________________ Committee Members: __________________________ __________________________ __________________________ __________________________ Date approved: __________________________ iii ACKNOWLEDGMENTS This body of work resulted from collaborative assistance from numerous individuals and institutions in the Philippines and in the United States. Without this assistance, the success of this avenue of research would not have been feasible. I am grateful for the help and support that all colleagues and friends have provided. The chapters making up this dissertation have been co-authored by a varying group of colleagues, including Rafe Brown, Arvin Diesmos, Mae Diesmos, Angel Alcala, Allison Fuiten, and Robin Jones. Numerous other researchers have provided assistance and feedback. I am indebted to the U.S. Department of Education and the Philippines-American Education Foundation (PAEF), who supported my research in the form of a Fulbright and Fulbright-Hayes Fellowship. The incredible sampling achieved for this research was made possible by these two awards. I would like to extend a special thank you to Charles Bankart, Esmeralda Cunanan, Yolly Casas, Marge Tolentino, G. Dizon, Con Valdecanas, and Hodgie Bricke. The University of Kansas turned out to be an absolutely perfect fit for graduate school, and I cannot express enough gratitude to all of the people who have supported me over the course of my graduate degree. A special thank you to the ever-changing community of herpetologists at KU, including Bill Duellman and Linda Trueb who have always provided sound advice and encouragement. I am not sure how the EEB department and the Biodiversity Institute put up with all of my requests, but I sincerely appreciate their support. I would like to extend a special thank you to Jaime Keeler, Lori Schlenker, Leonard Krishtalka, Dorothy Johanning, and Chris Haufler. Many individuals have made contributions to fieldwork, including Angel Alcala, Ely Alcala, Arthur Ong, Leonardo Averia, Philip Alviola, Nonito Antoque, Danilo Balete, Jerry iv Cantil, Arvin Diesmos, Liza Duya, Mariano Duya, Jason “Tungao” Fernandez, Boying Fernandez, Vicente Yngente, Mark Yngente, Marvic Yngente, Mae Diesmos, Charles Linkem, Kyle Hesed, David McLeod, Luke Welton, Jessi Siler, Andrew Faso, Joey Brown, Carl Oliveros, Edmund Rico, Rob Moyle, Fred Sheldon, Maklarin Lakim, Lee Grismer, and Jake Esselstyn. I extend a special thank you to my advisor and close friend and colleague, Rafe Brown, who is the reason I started working in the Philippines. Rafe’s support over the last six years has been instrumental in the success of my developing research program. I thank all members of my Ph.D. committee (Linda Trueb, Rob Moyle, Maria Orive, and David Frayer) for their continued support over the last six years. I am grateful for all of my committee’s suggestions, forward-thinking strategies for success, and willingness to attend early meetings on an annual basis (even if it was for the coffee and bagels). I thank the Protected Areas and Wildlife Bureau (PAWB) of the Philippine Department of Environment and Natural Resources (DENR) for facilitating collecting and export permits necessary for this and related studies; we are particularly grateful to M. Lim, C. Custodio, and A. Tagtag. Financial support for fieldwork was provided by several Panorama Fund grants from The University of Kansas Biodiversity Institute, travel funds form The University of Kansas Department of Ecology and Evolutionary Biology, a Madison and Lila Self Graduate Fellowship from the University of Kansas, a Fulbright Fellowship, a Fulbright-Hayes Fellowship, NSF DEB 0804115 to CDS, and DEB 0743491, and NSF EF-0334952 to Rafe Brown. For the loans of specimens I sincerely appreciate the support of J. Vindum and A. Leviton (California Academy of Sciences), R. Sison, V. Palpal-latoc, and J. Barnes (Philippine National Museum), J. Ferner (Cincinnati Museum Center), A. Resetar (Field Museum of Natural History), R. Crombie and K. de Queiroz (United States Natural History Museum), T. LaDuc (Texas Memorial Natural History v Museum), J. Rosado (MCZ), and M. Lakim (Sabah Parks). I am grateful for all critical reviews of these chapters provided by Jens Vindum, Jake Esselstyn, David McLeod, Linda Trueb, David Blackburn, Allison Fuiten, Luke Welton, Rafe Brown, Arvin Diesmos, Ron Crombie, Matt Brandley, Lee Grismer, Jesse Grismer, Anthony Barley, Jeet Sukumaran, Jamie Oaks, Mark Holder, Charles Linkem, and many anonymous reviewers. I am indebted to the CAS’s Stearns Fellowship and the MCZ’s Ernst Mayr Fellowship for funding multiple visits to examine comparative material. During visits to CAS, I was always particularly appreciative of the support of Jens Vindum, who creatively applied new common, albeit snarky, names for my focal organisms. I would like to thank my both of my families, the Siler Clan, and the Faso-Kuehn Gruppo Familiare. Whether I am in Colorado, Texas, or abroad, you provided a level of support above anything I could have asked for. My parents, Cherie and Eric, and my Sister Tess, supported my strange pursuits since childhood, and I am grateful for their love and encouragement. My Texas family was there for me through the dark years when I was addicted to queso, and I am forever grateful. Finally, and most importantly, I want to thank my wife Jessi for her endless support through many long years of fieldwork and research. Your patience, support, encouragement, and love are what got me through many rough patches along the way. Not to mention you are an expert Brachymeles catcher! Now we have a lovely daughter, Stella Blue, to share our next series of adventures with. vi ABSTRACT Evolutionary simplification, or loss of complex characters, is a major theme in studies of body form evolution. The apparently infrequent evolutionary reacquisition of complex characters has led to the assertion (Dollo’s Law) that once lost, complex characters may be impossible to re-evolve, at least via the exact same evolutionary process. The spectacular, virtually endemic radiation of Philippine semi-fossorial skinks of the genus Brachymeles represent one of the few radiations of scincid lizards to possess both fully limbed and limbless species. And yet, nothing is known of the phylogenetic relationships of this exceptional group. Morphologically similar body plans have made it difficult to assess species-level diversity, and the genus has long been recognized as one of the more modest radiations of southeast Asian lizards. However, taxonomic studies indicate that the diversity within the genus Brachymeles is grossly underestimated. Here I provide one of the most comprehensive, fine-scale analyses of squamate body-form evolution to date, introducing a new model system of closely related, morphologically variable, lizards. In this study I provide the first robust estimate of phylogenetic relationships within the genus Brachymeles using a multi-locus dataset and nearly complete taxonomic sampling. Systematic revisions guided by robust estimates of phylogeny subsequently result in a 125% increase in species diversity. I provide statistical tests of monophyly for all polytypic species and two widespread limb-reduced species and our results indicate wholesale deviations from past summaries and taxonomic evaluations of the genus. A Bayesian reconstruction of ancestral areas indicates strong statistical support for a minimum of five major dispersal events that have given rise to a major component of the observed species diversity across the archipelago. Our phylogenetic results support independent instances of complete limb loss as well as multiple instances of digit and external ear opening loss and re-acquisition. Even more vii striking, I find strong statistical support for the re-acquisition of a pentadactyl body form from a digit-reduced ancestor. Our findings have broad, general implications for body form evolution in burrowing vertebrates: whatever constraints have shaped trends in morphological evolution among other squamate groups (excluding Bipes) have been lost in this one exemplary clade. viii TABLE OF CONTENTS Title Page ................................................................................................................................... i Acknowledgments ..................................................................................................................... iii Abstract ...................................................................................................................................... vi List of Figures ............................................................................................................................ ix List of Tables ............................................................................................................................. xi List of Appendices ..................................................................................................................... xiii Introduction ............................................................................................................................... 1 Chapter 1 ................................................................................................................................... 5 Chapter 2 ................................................................................................................................... 42 Chapter 3 ................................................................................................................................... 97 Chapter 4 ................................................................................................................................... 220 Chapter 5 ................................................................................................................................... 302 Literature Cited ........................................................................................................................ 389 Appendix I ................................................................................................................................. 414 Appendix II ................................................................................................................................ 424 Appendix III .............................................................................................................................. 451 Appendix IV .............................................................................................................................. 454 Appendix V ................................................................................................................................ 461 Appendix VI .............................................................................................................................. 470 ix LIST OF FIGURES Figure 1.1 Map of the Philippines .............................................................................................. 8 Figure 1.2 Maps of the Philippines with Distribution of Samples ............................................. 13 Figure 1.3 Summary of Taxonomy-Based Hypothesis Tests .................................................... 20 Figure 1.4 Species-Level Phylogeny of Brachymeles ............................................................... 27 Figure 1.5 Ancestral Area Reconstructions ............................................................................... 31 Figure 2.1 Species-Level Phylogeny and Summary of Body Form Diversity of Brachymeles ..................................................................................................... 46 Figure 2.2 Summary of Morphology-Based Hypothesis Tests .................................................. 67 Figure 2.3 Summary of Phylogenetic Signal for Morphometric Variables ............................... 72 Figure 2.4 Multivariate Plots for Phylogenetic Principal Component Analysis ........................ 74 Figure 2.5 Bivariate Scatter Plots of Morphological Thresholds ............................................... 76 Figure 2.6 Ancestral State Reconstructions for Limb and Ear States ........................................ 89 Figure 2.7 Ancestral State Reconstructions for Digit States ...................................................... 91 Figure 3.1 Map of the Philippines .............................................................................................. 100 Figure 3.2 Phylogeny of Focal Species of Brachymeles ............................................................ 110 Figure 3.3 Distribution Map of Brachymeles boholensis, B. boulengeri, B. mindorensis, and B. taylori ............................................................................................... 119 Figure 3.4 Distribution Map of Brachymeles orientalis, B. schadenbergi, and B. vindumi ...................................................................................................................... 121 Figure 3.5 Distribution Map of Brachymeles kadwa, B. tungaoi, and B. talinis ....................... 123 Figure 3.6 Illustrations of Head Views of Brachymeles boholensis and B. boulengeri .................................................................................................................. 209 Figure 3.7 Illustrations of Head Views of Brachymeles mindorensis and B. taylori ......................................................................................................................... 211 Figure 3.8 Illustrations of Head Views of Brachymeles orientalis x and B. schadenbergi .............................................................................................................. 213 Figure 3.9 Illustrations of Head Views of Brachymeles talinis and B. kadwa ......................................................................................................................... 215 Figure 3.10 Illustrations of Head Views of Brachymeles tungaoi and B. vindumi ...................................................................................................................... 217 Figure 3.11 Photographs in Life of Focal Species of Brachymeles ........................................... 219 Figure 4.1 Map of the Philippines .............................................................................................. 222 Figure 4.2 Phylogeny of Focal Species of Brachymeles ............................................................ 233 Figure 4.3 Distribution Map of Focal Species of Brachymeles ................................................. 235 Figure 4.4 Illustrations of Head Views of Brachymeles samarensis and B. tatlo ...................... 293 Figure 4.5 Illustrations of Head Views of Brachymeles lima and B. apat ................................. 295 Figure 4.6 Illustrations of Head Views of Brachymeles dalawa and B. isa .............................. 297 Figure 4.7 Photograph in Life of Brachymeles isa .................................................................... 299 Figure 4.8 Photographs in Life of Brachymeles dalawa ............................................................ 301 Figure 5.1 Map of the Philippines .............................................................................................. 308 Figure 5.2 Phylogeny of Focal Species of Brachymeles ............................................................ 322 Figure 5.3 Distribution Map of Focal Species of Brachymeles ................................................. 324 Figure 5.4 Illustrations of Head Views of Brachymeles gracilis and B. pito ............................ 382 Figure 5.5 Illustrations of Head Views of Brachymeles sampu and B. anim ............................ 384 Figure 5.6 Illustrations of Head Views of Brachymeles syam and B. walo ............................... 386 Figure 5.7 Photograph in Life of Brachymeles syam ................................................................. 388 Supplementary Figure of Appendix III Multivariate Plots for Non-Phylogenetic Principal Component Analysis ............................................................... 453 xi LIST OF TABLES Table 1.1 Primers and Annealing Temperatures ........................................................................ 14 Table 1.2 Models of Sequence Evolution .................................................................................. 17 Table 2.1 Summary of Specimens Examined ........................................................................... 52 Table 2.2 Summary of Bivariate Regression Analyses of Size-Corrected Meristic and Mensural Variables ........................................................................................................ 64 Table 2.3 Summary of Bivariate Regression Analyses of Non-Size-Corrected Meristic and Mensural Variables ........................................................................................................ 65 Table 2.4 Summary of Correlation Analyses ............................................................................. 69 Table 2.5 Summary of Exploration of BayesTraits Models of Digit Evolution ........................ 80 Table 2.6 Summary of Results of Ancestral State Reconstructions ........................................... 82 Table 3.1 List of Samples Used in Chapter 3 ............................................................................. 106 Table 3.2 Models of Sequence Evolution .................................................................................. 108 Table 3.3 Uncorrected Pairwise Sequence Divergences ............................................................ 117 Table 3.4 Summary of Meristic and Mensural Characters ......................................................... 154 Table 3.5 Summary of Qualitative Diagnostic Characters ......................................................... 157 Table 3.6 Summary of Intraspecific Univariate Morphological Variation ............................... 160 Table 4.1 List of Samples Used in Chapter 3 ............................................................................. 237 Table 4.2 Models of Sequence Evolution .................................................................................. 238 Table 4.3 Uncorrected Pairwise Sequence Divergences ............................................................ 240 Table 4.4 Summary of Meristic and Mensural Characters ......................................................... 261 Table 4.5 Summary of Qualitative Diagnostic Characters ......................................................... 264 Table 4.6 Summary of Intraspecific Univariate Morphological Variation ............................... 266 xii Table 5.1 List of Samples Used in Chapter 3 ............................................................................. 314 Table 5.2 Models of Sequence Evolution .................................................................................. 315 Table 5.3 Uncorrected Pairwise Sequence Divergences ............................................................ 317 Table 5.4 Summary of Meristic and Mensural Characters ......................................................... 326 Table 5.5 Summary of Qualitative Diagnostic Characters ......................................................... 329 Table 5.6 Summary of Intraspecific Univariate Morphological Variation ............................... 331 xiii LIST OF APPENDICES Appendix I: List of Samples Used in Chapter 1 ....................................................................... 414 Appendix II: Summary of Genbank Voucher Numbers Published with Chapter 1 ................. 424 Appendix III: Supplementary Information Published with Chapter 2 ..................................... 451 Appendix IV: List of Specimens Examined for Chapter 3 ....................................................... 454 Appendix V: List of Specimens Examined for Chapter 4 ........................................................ 461 Appendix VI: List of Specimens Examined for Chapter 5 ....................................................... 470 1 INTRODUCTION Only four genera of scincid lizards are known to possess both fully limbed and limbless species (Brachymeles, Chalcides, Lerista, and Scelotes; Lande, 1978; Wiens and Slingluff, 2001; Brandley et al., 2008). Of these four genera, the genus Brachymeles is the least well known, with recent studies indicating the recognized diversity of the group is vastly underestimated (Siler et al., 2009a, 2010a,b, 2011; in press a,b,c,d; Siler and Brown, 2010, 2011). Within the genus, all but two of the 36 recognized species are endemic to the Philippines (Brown, 1956; Brown and Rabor, 1967; Brown and Alcala, 1980; Siler et al., 2009a, 2010a,b, 2011; in press a,b,c,d; Siler and Brown, 2010, 2011); the exceptions are B. apus from northern Borneo (Hikida, 1982) and B. miriamae from Thailand (Siler et al., 2011). Eighteen species are pentadactyl (B. anim, B. bicolor, B. boholensis, B. boulengeri, B. gracilis, B. kadwa, B. makusog, B. mindorensis, B. orientalis, B. pito, B. schadenbergi, B. sampu, B. syam, B. talinis, B. taylori, B. tungaoi, B. vindumi, and B. walo), thirteen are non-pentadactyl, with incompletely developed limbs and reduced numbers of digits (B. apat, B. bonitae, B. cebuensis, B. elerae, B. dalawa, B. isa, B. lima, B. muntingkamay, B. pathfinderi, B. samarensis, B. tatlo, B. tridactylus, and B. wrighti), and five are entirely limbless (B. apus, B. minimus, B. miriamae, B. lukbani, and B. vermis). Within the non-pentadactyl species, there exist a wide range of limb- and digit-reduced states. Some species have minute limbs that lack full digits (B. apat, B. bonitae, B. cebuensis, B. dalawa, B. isa, B. lima, B. muntingkamay, B. samarensis, B. tatlo, B. tridactylus; Duméril and Bibron, 1839; Brown, 1956; Brown and Rabor, 1967; Siler et al., 2009a, 2010a,b, 2011; in press a,b,c,d; Siler and Brown, 2010, 2011). Other non-pentadactyl species have moderately developed limbs with four digits on the hands and feet (B. elerae, B. wright; Siler et al., in press b), or four digits on the feet and five digits on the hands (B. pathfinderi: Taylor, 1917, 1925; Siler et al., in press a). 2 All species are semi-fossorial and typically found in dry, rotting material inside decaying logs or in loose soil, forest floor detritus, and leaf litter. The genus Brachymeles was first described by Duméril and Bibron (1839) for the small, limb-reduced species Brachymeles bonitae. As species diversity accumulated, various authors have noted morphological variation among island populations of many of the polytypic and widespread species (Taylor, 1922; Brown, 1956; Brown and Rabor, 1967; Brown and Alcala, 1980). Historically, the shared body plans and similar external morphological features among populations of Brachymeles, and the absence of dense population sampling across the Philippines, proved problematic for diagnosing species (Brown, 1956; Brown and Rabor, 1967; Brown and Alcala, 1980). Although long considered to be a small clade of Southeast Asian lizards (the last revision enumerated only 15 species; Brown and Alcala, 1980), recent studies have significantly increased the known species diversity and expanded the range of variation in body form (Siler et al., 2009a, 2010a,b, 2011; in press a,b,c,d; Siler and Brown, 2010, 2011). Additionally, several rare, mid-to-high elevation species long represented by only a few specimens, in some cases without knowledge of their exact type locality (e.g., Brachymeles bicolor, B. elerae, B. wrighti, B. pathfinderi), have recently been rediscovered (Siler, 2010; Siler et al., in press a,b). These studies, coupled with increased sampling throughout the Philippines, have provided a comprehensive dataset with which to begin evaluating the taxonomic stability of polytypic and widespread species across the Philippines, and address questions concerning the evolution of limb reduction and loss. The availability of tissue samples for all but two known species of Brachymeles now allows for robust estimates of phylogenetic relationships among recognized widespread and polytypic species, and evaluation of species boundaries. 3 In Chapter One (Siler et al., 2011) I investigate the biogeography of Brachymeles from a phylogenetic perspective, providing the first estimate of phylogenetic relationships for this unique radiation of Southeast Asian lizards. I strove to estimate the phylogenetic position of Brachymeles among scincid lizards in order to provide insight into patterns of body form evolution and polarity of character change and provide the first statistical tests of several hypotheses. I also employ a Bayesian ancestral area reconstruction to gain insight into the biogeographical history of the genus. Finally, I test the following taxonomic hypotheses: (1) Brachymeles is monophyletic; (2) All recognized and formerly recognized polytypic species are monophyletic; and (3) All recognized widespread species are monophyletic. My data reveal patterns inconsistent with all of the above predictions and at odds with currently recognized taxonomy; I conclude that species diversity within the genus is vastly underestimated and that cryptic patterns of lineage diversification prevail in this poorly known group of Southeast Asian lizards. In Chapter Two (Siler and Brown, 2011), I focus on testing hypotheses of body form evolution among squamate reptiles by investigating patterns of body form change in skinks of the genus Brachymeles using a phylogenetic comparative approach, derived from morphological data. I explore the data for evidence of threshold values of morphological features after which changes in body form occur. Additionally, I test for patterns of correlated evolution of morphological characters, and provide the first exploration of the impact of various methodological choices used in previous studies of body form evolution, including the impact of choice of morphometric variable as a measurement of body size for non-phylogenetic and phylogenetic size-correction as well as the overall method for multivariate principal component analyses. Finally, using my robust estimate of phylogenetic relationships, I explore the 4 prevalence and directionality of evolutionary changes in limb, digit, and ear character states, and the impact of outgroup sampling and ancestral outgroup character states on ancestral state reconstructions. The goals of Chapters Three (Siler and Brown, 2010), Four (Siler et al., in press c), and Five (Siler et al., in press d) are to revise the taxonomy of the B. gracilis, B. orientalis, B. samarensis, B. schadenbergi, and B. talinis species complexes such that individual units (species) represent independently evolving, cohesive lineage segments (sensu Simpson, 1961; Wiley 1978; Frost and Hillis, 1990; de Queiroz, 1998, 1999). Comprehensive examination of all recently collected specimens from throughout the known range of these species, and historically collected specimens available in museum collections, results in the complete reorganization of species diversity within the genus, increasing the recognized diversity by more than 125%. I provide a phylogenetic analysis and the first illustrations of many of these taxa, fully describe each species, and clarify taxonomic boundaries. I also provide information on each species’ natural history, ecology, and geographic distribution and comment on additional, presently unrecognized putative new species. 5 CHAPTER 1 Phylogeny of Philippine slender skinks (Scincidae: Brachymeles) reveal underestimated species diversity, complex biogeographical relationships, and cryptic patterns of lineage diversification Only four genera of scincid lizards are known to possess both fully limbed and limbless species (Brachymeles, Chalcides, Lerista, and Scelotes; Lande, 1978; Wiens and Slingluff, 2001; Brandley et al., 2008). Of these four genera, the genus Brachymeles is the least well known, with recent studies indicating the recognized diversity of the group is vastly underestimated (Siler, 2010; Siler and Brown, 2010; Siler et al., 2009a, 2010a,b; Siler et al., in press a,b,c,d). Within the genus, all but one of the 25 recognized species are endemic to the Philippines (Brown, 1956; Brown and Rabor, 1967; Brown and Alcala, 1980; Siler et al., 2009a, 2010a,b; Siler and Brown, 2010); the exception is B. apus from northern Borneo (Hikida, 1982). Thirteen species are pentadactyl (bicolor, boholensis, boulengeri, gracilis, sp. A [Masbate Island; Siler and Brown, 2010], makusog, mindorensis, orientalis, schadenbergi, talinis, taylori, sp. B [Luzon + Babuyan islands; Siler and Brown, 2010], and sp. C [Jolo Island; Siler and Brown, 2010]), eight are non-pentadactyl, with incompletely developed limbs and reduced numbers of digits (bonitae, cebuensis, elerae, muntingkamay, pathfinderi, samarensis, tridactylus, and wrighti), and four are entirely limbless (apus, minimus, lukbani, and vermis). Within the non-pentadactyl species, there exist a wide range of limb- and digit-reduced states. Some species have minute limbs that lack full digits (bonitae, cebuensis, muntingkamay, samarensis, tridactylus; Duméril and Bibron, 1839; Brown, 1956; Brown and Rabor, 1967; Siler et al., 2009a). Other non-pentadactyl species have moderately developed limbs with four digits on the hands and feet (elerae, wrighti), or four 6 digits on the feet and five digits on the hands (pathfinderi: Taylor, 1917, 1925). All species are semi-fossorial and typically found in dry, rotting material inside decaying logs or in loose soil, forest floor detritus, and leaf litter. The genus Brachymeles was first described by Dumeril and Bibron (1839) for the small, limb-reduced species Brachymeles bonitae. As species diversity accumulated, various authors have noted morphological variation among island populations of many of the polytypic and widespread species (Taylor, 1922; Brown, 1956; Brown and Rabor, 1967; Brown and Alcala, 1980). In Brachymeles, several species (B. Bonitae, B. samarensis, B. tridactylus) currently span recognized faunal regions within the Philippines, or Pleistocene Aggregate Island Complexes (PAICs; Brown and Guttman, 2002; Brown and Diesmos, 2002, 2009; Fig. 1.1, and defy biogeographic boundaries as traditionally conceived (Brown and Diesmos, 2009). Among skinks and other Philippine land vertebrates, multiple lineages have similar widespread distributions, spanning multiple PAICs. These widespread distributions have been the focus of many recent studies, which have revealed that few endemic Philippine reptiles actually possess broad distributions spanning regional faunistic boundaries (Brown et al., 2000, 2009; Brown and Diesmos, 2002, 2009; Siler et al., 2010a,b; Siler and Brown, 2010; Welton et al., 2009, 2010a,b). Although these recent efforts have shed light on cryptic diversity among Philippine vertebrates, the continued recognition of many widespread species may still compromise our understanding of patterns of regional diversity. Presently, the incredible diversity of endemic vertebrate species in the Philippines is recognized to be distributed among: (1) Pleistocene Aggregate Island Complexes (PAICs; Inger, 1954; Heaney, 1985; Voris, 2000; Brown and Diesmos, 2002), (2) individual islands within PAICs, and (3) upland subcenters of diversity within individual landmasses (review: Brown and Diesmos, 2009). 7 Figure 1.1. Map of the Philippines showing the five recognized major Pleistocene Aggregate Island Complexes (PAICs) and additional deep-water islands. Current islands in the Philippines are shown in medium grey; light gray areas enclosed in black 120 m bathymetric contours indicate the hypothesized maximum extent of land during the mid- to late Pleistocene. 8 9 Historically, the shared body plans and similar external morphological features among populations of Brachymeles, and the absence of dense population sampling across the Philippines, proved problematic for diagnosing species (Brown, 1956; Brown and Rabor, 1967; Brown and Alcala, 1980). Although long considered to be a small clade of Southeast Asian lizards (the last revision enumerated only 15 species; Brown and Alcala, 1980), recent studies have significantly increased the known species diversity and expanded the range of variation in body form (Siler et al., 2009a, 2010a,b; Siler and Brown, 2010). Additionally, several rare, mid-to-high elevation species long represented by only a few specimens, in some cases without knowledge of their exact type locality (e.g., Brachymeles bicolor, B. elerae, B. wrighti, B. pathfinderi), have recently been rediscovered (Siler, 2010; Siler et al., in press a,b; Siler and Brown, 2010). These studies, coupled with increased sampling throughout the Philippines, have provided a comprehensive dataset with which to begin evaluating the taxonomic stability of polytypic and widespread species across the Philippines. Additionally, the availability of tissue samples for all but two known species of Brachymeles now allows for robust estimates of phylogenetic relationships among recognized widespread and polytypic species, and evaluation of species boundaries. For example, Siler and Brown (2010) recently revised two polytypic species (B. boulengeri and B. schadenbergi) and one widespread species (B. talinis); this work resulted in the recognition of ten genetically and morphologically distinct species. Several other species including B. samarensis and B. bonitae (Brown, 1956; Brown and Rabor, 1967; Brown and Alcala, 1980) are still recognized as having widespread distributions that span multiple historically recognized biogeographic provinces in the Philippines (Dickerson et al., 1925; Kloss, 1929; Inger, 1954; Brown and Diesmos, 2002). 10 In this study we investigate the biogeography of Brachymeles from a phylogenetic perspective, providing the first estimate of phylogenetic relationships for this unique radiation of Southeast Asian lizards. We strove to estimate the phylogenetic position of Brachymeles among scincid lizards in order to provide insight into patterns of body form evolution and polarity of character change and provide the first statistical tests of several hypotheses. We provide the first glimpse into the major body form transitions in Brachymeles, particularly with respect to miniaturization, limb reduction, and digit loss. We also employ a Bayesian ancestral area reconstruction to gain insight into the biogeographical history of the genus. Finally we test the following taxonomic hypotheses: (1) Brachymeles is monophyletic; (2) All recognized and formerly recognized polytypic species are monophyletic; and (3) All recognized widespread species are monophyletic. Our data reveal patterns inconsistent with all of the above predictions and at odds with currently recognized taxonomy; we conclude that species diversity within the genus is vastly underestimated and that cryptic patterns of lineage diversification prevail in this poorly known group of Southeast Asian lizards. Methods Taxon sampling and data collection Ingroup sampling included 90 individuals collected from 43 localities, with 23 of the 25 currently recognized species of Brachymeles represented (Fig. 1.2; Appendix I; Siler and Brown, 2010). The two missing species in our analyses are Brachymeles vermis and B. wrighti. Brachymeles wrighti is known from two damaged specimens from northern Luzon Island, and B. vermis occurs in the Sulu archipelago (where biologists are not permitted to work due to logistical and security obstacles). No tissues have ever been collected for either of these species. 11 To assess the monophyly of the genus as well as investigate appropriate outgroup taxa, a broad sampling of scincid species from the subfamilies Lygosominae and Scincinae were included, as well as a single outgroup sample from the family Lacertidae (Appendix I). For all 108 samples, complete or partial sequences were collected for mitochondrial NADH Dehydrogenase Subunit 1 (ND1), NADH Dehydrogenase Subunit 2 (ND2), ATPase 8 (ATP8), and ATPase 6 (ATP6) genes (Table 1.1). Additionally, three nuclear loci, Brain-derived Neurotrophic Factor (BDNF), R35, and PTGER4, were completely sequenced for nearly all ingroup samples and many of the outgroup samples (Table 1.1, Appendix I). All sequences were deposited in GenBank (Appendix II). Genomic DNA was extracted from liver tissues stored in 95–100% ethanol following a guanidine thiocyanate protocol (Esselstyn et al., 2008). We used a combination of published and newly developed primers, as well as a variety of thermal profiles (Table 1.1). Amplified products were visualized on 1.5% agarose gels. PCR products were purified with 1 µL of a 20% dilution of ExoSAP-IT (US78201, Amersham Biosciences, Piscataway, NJ) on the following thermal profile: 31 min at 37º, followed by 15 min at 80º. Cycle sequencing reactions were run using ABI Prism BigDye Terminator chemistry (Ver. 3.1; Applied Biosystems, Foster City, CA), and purified with Sephadex (NC9406038, Amersham Biosciences, Piscataway, NJ) in Centri-Sep 96 spin plates (CS-961, Princeton Separations, Princeton, NJ). Purified products were analyzed with an ABI Prism 3130xl Genetic Analyzer (Applied Biosystems). Continuous gene sequences were assembled and edited using Sequencher 4.8 (Gene Codes Corp., Ann Arbor, MI). 12 Figure 1.2. Distribution of pentadactyl and non-pentadactyl Brachymeles samples from the Philippines (see species keys within each map). Current islands in the Philippines are shown in medium grey; light gray areas enclosed in black 120 m bathymetric contours indicate the hypothesized maximum extent of land during the mid- to late Pleistocene. 13 14 Table 1.1. Summary of primers and annealing temperatures employed in this study. Locus Primer Name Sequence Annealing Temperatures Primer Source NADH 1 16dr 5'–CTACGTGATCTGAGTTCAGACCGGAG–3' 52–53º Brandley et al., 2005 tMet 5'–TCGGGGTATGGGCCCRARAGCTT–3' 52–53º Brandley et al., 2005 NADH 2 ND2.Brach.F1 5'–TTATCGCAACAAAACACCACCC–3' 52–53º This study ND2.Brach.R1 5'–AGCYCAGAGGTGATTCACGC–3' 52–53º This study ND2.Brach.R2 5'–CCGCTGGATTGGGTGTTTAGC–3' 52–53º This study ATP8,6 ATP.F 5'–CTCAGARATCTGCGGGYCAAATCACA–3' 58º M. Brandley, unpublished data ATP.R 5'–GTGCYTTCTCGRRTAATRTCYCGTCAT–3' 58º M. Brandley, unpublished data BDNF BDNF.F 5'–CCCCAATGAAAGAAGTGASCCTC–3' 55º Crottini et al., 2009 BDNF.R 5'–TGGGTAGTTCGGCACTGAGAATTCC–3' 55º Crottini et al., 2009 PTGER4 PTGER4.F1 5'–GACCATCCCGGCCGTMATGTTCATCTT–3' 55º Townsend et al., 2008 PTGER4.R5 5'–AGGAAGGARCTGAAGCCCGCATACA–3' 55º Townsend et al., 2008 R35 R35.F 5'–GACTGTGGAYGAYCTGATCAGTGTGG–3' 55º Fry et al., 2006 R35.R 5'–GCCAAAATGAGSGAGAARCGCTTCTG–3' 55º Fry et al., 2006 15 Sequence alignment and phylogenetic analyses Initial alignments were produced in Muscle (Edgar, 2004), and manual adjustments made in MacClade 4.08 (Maddison and Maddison, 2005). To assess phylogenetic congruence between the mitochondrial and nuclear data, we inferred the phylogeny for each gene independently using likelihood and Bayesian analyses, and performed pairwise partition homogeneity tests in PAUP 4.0b 10 (Swofford, 2002) with 100 replicates for each pairwise comparison to assess set congruence. Following the observation of no statistically significant incongruence between datasets, we felt justified in using the combined, concatenated, data for subsequent analyses. Exploratory analyses of the combined dataset of 108 individuals (including outgroup taxa with missing data for several genes) and a reduced dataset of individuals with no missing data exhibited identical relationships; we therefore chose to include all available data (108 individuals) for subsequent analyses of the concatenated dataset. Alignments and resulting topologies were deposited in TreeBase (SN11187). Parsimony analyses were conducted in PAUP* 4.0b 10 (Swofford, 2002), with gaps treated as missing data and all characters weighted equally. Most parsimonious trees were estimated using heuristic searches with 1000 random addition-sequence replicates and tree bisection and reconnection (TBR) branch swapping. To assess clade support, nonparametric bootstrapping was conducted using 1000 bootstrap replicates, each with 100 random addition-sequence replicates and TBR branch swapping. Partitioned Bayesian analyses were conducted in MrBayes v3.1.2 (Ronquist and Huelsenbeck, 2003). The mitochondrial dataset was partitioned by codon position for the protein-coding region of ND1 and ND2 and by gene region for the short gene regions ATP8 and ATP6. The Akaike Information Criterion (AIC), as implemented in jModeltest v0.1.1 (Guindon 16 and Gascuel, 2003; Posada, 2008), was used to select the best model of nucleotide substitution for each partition (Table 1.2). The best-fit model for each data partition was implemented in subsequent Bayesian analyses. A rate multiplier model was used to allow substitution rates to vary among subsets, and default priors were used for all model parameters. We ran four independent Metropolis-coupled MCMC analyses, each with four chains and an incremental heating temperature of 0.05. All analyses were run for 18 million generations, sampling every 5000 generations. To assess stationarity, all sampled parameter values and log-likelihood scores from the cold Markov chain were plotted against generation time and compared among independent runs using Tracer v1.4 (Rambaut and Drummond, 2007). Finally, we plotted the cumulative and non-overlapping split frequencies of the 20 most variable nodes, and compared split frequencies among independent runs using Are We There Yet? [AWTY (Wilgenbusch et al., 2004)]. Although all samples showed patterns consistent with stationarity after 2.5 million generations (i.e., the first 12.5%), we conservatively discarded the first 20% of samples as burn-in. In preliminary Bayesian analyses of the combined dataset, the independent runs failed to converge. We tried (1) lowering the incremental heating temperature to 0.02, (2) using an unconstrained branch length prior with an exponential distribution of 25 (Siler et al. 2010c; Marshall 2006, 2010), and (3) removing outgroup taxa with large amounts of missing data. Although some of the trials of individual permutations of parameters resulted in a failure to converge, the incorporation of the above, plus an unconstrained branch length prior with an exponential distribution and a mean of 25 resulted in convergence. Once complete convergence was achieved, we proceeded with final analyses, presented here. 17 Table 1.2. Models of evolution selected by AIC and applied for partitioned, phylogenetic analyses. Partition AIC Model Number of Characters NADH 1, 1st codon position GTR + Γ 322 NADH 1, 2nd codon position GTR + Γ 322 NADH 1, 3rd codon position GTR + Γ 322 NADH 2, 1st codon position GTR + Γ 287 NADH 2, 2nd codon position GTR + Γ 287 NADH 2, 3rd codon position GTR + Γ 287 ATP8 HKY + Γ 157 ATP6 GTR + Γ 682 BDNF GTR + Γ 715 PTGER4 HKY + Γ 490 R35 GTR + Γ 689 18 Partitioned maximum likelihood (ML) analyses were conducted in RAxMLHPC v7.0 (Stamatakis, 2006) on the concatenated dataset the same partitioning strategy as for Bayesian analysis. The more complex model (GTR + Γ) was used for all subsets (Table 1.2), and 100 replicate ML inferences were performed for each analysis. Each inference was initiated with a random starting tree, and employed the rapid hill-climbing algorithm (Stamatakis, 2007). Clade confidence was assessed with 100 bootstrap pseudoreplicates employing the rapid hill climbing algorithm (Stamatakis et al., 2008). Topology tests We tested taxonomy- and phylogeography-based hypotheses to address questions concerning the patterns of Brachymeles diversification (Fig. 1.3): (1) Is the genus Brachymeles monophyletic? (2) Are the currently and formerly recognized polytypic species (B. boulengeri, B. gracilis, B. schadenebergi) monophyletic? (3) Are the two “widespread” species (B. bonitae, B. samarensis) monophyletic? (4) Does the PAIC model of diversification explain the patterns of genetic diversity found in widespread species of Philippine Brachymeles? And, (5) Are the patterns of genetic diversity in widespread species of Philippine Brachymeles similar to those noted in other lineages (Siler et al., 2010c; Jones & Kennedy, 2008; McGuire & Kiew, 2001; Steppan et al., 2003; Alfaro et al., 2004)? We evaluated each question using Bayesian methods, and the approximately unbiased (AU) test (Shimodaira and Hasegawa, 2001; Shimodaira, 2002) as implemented in Siler et al. (2010c). The topological constraints for these questions are illustrated in Figure 1.3, with hypotheses 1–6 derived from taxonomic questions, and hypotheses 7 and 8 derived from the PAIC predictions; the remaining hypotheses (9–11) have been observed in other taxa and are, in part, derived from 19 Figure 1.3. Six taxonomy-based hypotheses tested in the study. Each hypothesis is illustrated by constraint trees used in AU and Bayesian tests. The highest P-values recovered from each AU test (AU), and the posterior probabilities (PP) of the constraint topology, are shown. 20 21 expectations based on geological history and/or island proximity. Using the full, combined dataset, and the same settings as the RAxML analyses described above, 100 ML searches were performed under each of the 13 constraints. All 1,200 trees produced by RAxML (100 from the unconstrained analysis and 100 from each of the 11 constrained analyses), were filtered in PAUP to remove identical topologies. A modified version of RAxML (provided by Alexandros Stamatakis) allowed the per-site likelihoods to be estimated for each of the 116 unique topologies under a partitioned model. An AU test was then performed on the per-site likelihoods from all 116 using CONSEL v0.1i (Shimodaira and Hasegawa, 2001). The p-value reported for a given hypothesis is the largest p-value of all the trees inferred under that constraint. To automate various steps in the process, perl and python scripts were written by J. Oaks and CDS (available by request). For the Bayesian approach, we took the percentage of 11520 post burn-in trees consistent with each hypothesis to represent the posterior probability that the hypothesis is true. Relative time analyses To test the combined dataset for deviations from a molecular clock, we optimized likelihood scores in PAUP* 4.0b10 with a molecular clock enforced and not enforced on the maximum-likelihood topology. A likelihood ratio test ([LRT] Arbogast et al., 2002; Felsenstein, 2004) significantly rejected a molecular clock (p ≤ 0.00), and subsequent analyses were conducted within a relaxed clock framework. The chronogram used for ancestral state reconstructions in this study was inferred in a Bayesian framework using BEAST v1.5.3 (Drummond and Rambaut, 2007). A starting tree was designated for each run by manually adjusting the xml BEAUti v1.5.2 (Drummond and Rambaut 2007) output file. The consensus tree file from Bayesian analyses was 22 imported into R (R Development Team, 2008), and using the ape (Paradis et al., 2004), the phylogeny was paired down into individual lineages per species or morphologically distinct, non-monophyletic populations (B. bonitae and B. samarensis). The 47-taxon phylogeny was then converted to a chronogram using the nonparametric rate smoothing method of Sanderson (1997) implemented in the ape (Paradis et al. 2004) package of R, and was exported in Newick format for use as the starting tree for BEAST analyses. Four independent BEAST runs of 50 million generations were completed under the same partitioning strategy as for Bayesian analyses, imposing an uncorrelated lognormal relaxed clock prior on substitution rate (Drummond et al., 2006) and Yule speciation prior. Parameters were sampled every 5000 generations and the initial 50% of each run was discarded as burn-in, leaving a combined 20,000 trees in the posterior distribution. To evaluate convergence among MCMC analyses, trends and distributions of parameters, including the likelihood score, were examined in Tracer (Rambaut and Drummond 2007). Biogeographical reconstructions To explore whether there is statistical support for historical biogeographic patterns within Philippine species of the genus Brachymeles, we compared empirically observed (extant) species distributions to estimates of ancestral distributions using the program BayesTraits version 1.0 (Pagel, 1994; Pagel and Lutzoni, 2002). For all analyses we examined a model of character evolution that assumed equal rates of distributional transitions. For all analyses we seeded the mean and variance of the gamma prior from uniform distributions on the interval 0 to 20 by enforcing the “Hyperpriorall” command of BayesTraits. The LogCombiner v1.5.4 program of the BEAST v1.5.3 (Drummond and Rambaut 2007) package was used to combine trees from the 23 posterior distributions of the four independent Beast runs, producing a file with 2,000 trees from the posterior distribution. All 2,000 chronograms were then used in analyses of distribution data in BayesTraits in an effort to account for phylogenetic uncertainty. In the program BayesTraits, we ran MCMC chains for 25 million generations, sampling every 5000th generation, and discarded the first 50% of samples as burn-in. The remaining 2,500 samples were used to summarize the posterior probabilities of ancestral character states for all nodes of the tree. The “AddNode” command of BayesTraits was used to specify all nodes in the chronograms for visualization of the posterior probabilities of character states at each node. We ran a series of additional analyses on nodes with ambiguous estimated ancestral character states. The “fossil” command of BayesTraits was used to sequentially enforce the character states making up 95% of the posterior probability at a single node, prioritizing character states with the highest posterior probability. Bayes factors were again applied, and the state supported at each ambiguous node was summarized with the Bayes factors measure of support for that ancestral state (Kass and Raftery 1995; Nylander et al. 2004). We enforced the ancestral states for all nodes sister to Philippine Brachymeles to be considered non-Philippine in distribution. Results Taxon sampling, data collection, and sequence alignment The complete, aligned matrix contains 82 samples of Brachymeles, representing 23 of the 25 recognized taxa, for the mitochondrial genes and nuclear loci. Seventeen additional samples are included as outgroups, consisting of representatives from the subfamilies Lygosominae and Scincinae within the family Scincidae as well as a single representative from the lizard family Lacertidae. Following initial unrooted analyses, and the results of recent squamate evolution 24 studies (Whiting et al., 2003; Townsend et al., 2004; Wiens et al., 2006; Brandley et al., 2005; Brandley et al., 2008), we rooted the tree using samples of Takydromus sexilineatus from China. Within each gene, variable and parsimony-informative characters are observed as follows: 118 and 107 out of 158 (ATP8); 357 and 339 out of 683 (ATP6); 504 and 464 out of 966 (ND1); 575 and 531 out of 861 (ND2); 115 and 69 out of 715 (BDNF); 127 and 95 out of 490 (PTGER); 304 and 220 out of 689 (R35). The number of most parsimonious trees and consistency indices resulting from MP analyses of the combined dataset is 78 trees/CI = 0.318. Phylogenetic analyses Analyses of the combined data (ND1, ND2, ATP8, ATP6, BDNF, PTGER4, R35) result in topologies with high Maximum Likelihood bootstrap support and posterior probabilities (Fig. 1.4). Topologies are congruent across these analyses (Fig. 1.4). All analyses support three clades of outgroup scincid taxa (Fig. 1.4). Outgroup samples from the subfamily Lygosominae are never recovered as part of a single clade (Fig. 1.4); however, given the possibility that the chosen root for analyses and the outgroup sampling strategy likely influence outgroup relationships, additional taxa should be obtained for a more exhaustive analysis of scincid relationships before definitive conclusions may be drawn. The genera Eumeces and Plestiodon are recovered as a single, strongly supported clade in all analyses (Fig. 1.4, Clade 1). Although this clade is often supported as the closest group of outgroup species to Brachymeles + Davewakeum (ML; Fig. 1.4), support for its placement was always low, and in Bayesian analyses, the clade is regularly recovered as part of a three clade polytomy of outgroup samples (results not shown). The species Davewakeum miriamae is 25 always recovered nested within Brachymeles samples, between the clade B. apus + B. cf. apus from Borneo and all Philippine Brachymeles (Fig. 1.4). Although the genus Brachymeles (as currently recognized) is never recovered as a monophyletic group, all analyses strongly support the monophyly of Brachymeles + Davewakeum (Fig. 1.4, Clade 2). The two limbless species Brachymeles apus (Borneo) and Davewakeum miriamae (Thailand) are always recovered as the two lineages most closely related to all Philippine Brachymeles (Fig. 1.4). Within the Philippines, all limbless species and the majority of limb-reduced species are recovered as part of two reciprocally monophyletic sub-clades, and together are sister to all pentadactyl species and the remaining non-pentadactyl taxa (Fig. 1.4, Clade 3). Sampled populations of the currently recognized widespread, limb-reduced species Brachymeles bonitae and B. samarensis are never recovered as monophyletic (Fig. 1.4, Clade 3). Brachymeles cebuensis, one of only two species of Brachymeles with unequal numbers of fingers and toes (three fingers/two toes) is recovered as sister to B. samarensis from Leyte Island (Fig. 1.4, Clade 3). Within Clade 1, all analyses recover a population of Brachymeles bonitae with one fore-limb digit and one hind limb digit as sister to the tridactyl species B. tridactylus, and the five other populations of B. bonitae (Fig. 1.4). Additionally, a morphologically distinct population of B. cf. bonitae with limbs but no digits is supported to be the sister species to B. tridactylus (Fig. 1.4, Clade 3). All pentadactyl species and three non-pentadactyl species of Brachymeles are always recovered as part of a clade, sister to Clade 3 (Fig. 1.4, Clade 4). Although the two species formerly part of the Brachymeles schadenbergi species complex (B. orientalis and B. schadenbergi) are always recovered as reciprocally monophyletic lineages (Fig. 1.4, Clade 8), the polytypic species B. gracilis, and the four species formerly part of the B. boulengeri species 26 Figure 1.4. Hypothesized relationships of Brachymeles, illustrated by ML estimates (-ln L 54137.110363). Nodes supported by ≥95% Bayesian PP and ML bootstrap support were considered significantly supported and are indicated by black circles. Terminals are labeled with abbreviated taxonomic names, followed by general geographic distribution (Appendix I). The placement of the genus Davewakeum is indicated by red braches. Colored boxes highlight hypothesized monophyletic groups. Colored clade bars highlight general body plans observed for species within designated clades. Alpha and numerical labels correspond to clades referred to in the Results and Discussion. For interpretation of the references to color in this figure legend, the reader is referred to the web version of this article. 27 28 complex, are strongly supported to be paraphyletic (Fig. 1.4, Clades 5, 6, 8). All analyses recover four well-supported clades within Clade 4 (Fig. 1.4). Although Bayesian analyses provided high support for the relationships between these clades, likelihood analyses provide less support (Fig. 1.4, Clade 4). Three non-pentadactyl species are recovered as part of Clade 4 in all analyses (Fig. 1.4). The tetradactyl species Brachymeles elerae and the tridactyl species B. muntingkamay are always recovered as sister taxa (Fig. 1.4, Clade 7); however, the relationship of Clade 7 to the other major clades in Clade 4 is less well supported. Brachymeles pathfinderi, the only other species with unequal digit numbers (five fingers/four toes), is recovered with strong support to be nested within the polytypic species B. gracilis (Fig. 1.4, Clade 6). Brachymeles bicolor, the longest species, is recovered as sister to a subclade of three medium-sized species (B. boulengeri + B. mindorensis + B. taylori) and three large species (B. talinis + two undescribed species [Siler and Brown, 2010]). Brachymeles boholensis, formerly recognized as a subspecies of the B. boulengeri species complex, is consistently supported as part of Clade 8, sister to B. orientalis, B. schadenbergi, and B. makusog (Fig. 1.4). Topology tests Results from the Bayesian methods and the approximately unbiased (AU) test were highly consistent. Among the taxonomy-based hypotheses, both methods rejected hypotheses of monophyly for the genus Brachymeles, the widespread species B. bonitae, B. gracilis, and B. samarensis, and the former polytypic species B. boulengeri (Fig. 1.3). Additionally, both methods failed to reject the monophyly of the former polytypic species B. schadenbergi, now recognized as two distinct sister species (Siler and Brown, 2010; Fig. 1.3). All biogeography- 29 based hypotheses were rejected by both methods (Fig. 1.3). Body form evolution Our simplified mapping of major body plan variation onto the preferred phylogenetic tree (Fig. 1.4) makes it clear that the evolutionary history of Brachymeles involves multiple instances of evolutionary shifts in body size, limb reduction, and digit loss. Although a full understanding of these trends will require a comprehensive analysis of both external (body size, limb proportions, digital states) and internal (vertebral numbers and elongation) morphology, preliminary trends can be ascertained on the basis of results presented here. If it is assumed, for example, that the ancestors of Brachymeles possessed similar body plans as the genus’ putative closest relatives (Eumeces, Plestiodon, Lygosoma, Emoia Dasia and Eutropis), then limb reduction and loss may have occurred along the lineages leading to B. apus and B. cf. apus, in the lineage leading to Davewakeium miriamae, in the lineage leading to the B. bonitae and B. samarensis complexes, and independently in the lineages leading to B. pathfinderi and B. muntingkamay + B. elerae. It is interesting to note that the known diversity of pentadactyl species in the genus is endemic to the Philippine. Historical biogeography Although the placement of Brachymeles within the family Scincidae remains somewhat ambiguous, the impact of ancestral range for all Brachymeles does not appear to heavily impact ancestral reconstructions within the genus (not shown). The results of analyses of ancestral areas are never significantly impacted by placing restrictions on the ancestral character states among outgroup taxa and the node giving rise to all Brachymeles (not shown). Without a priori 30 Figure 1.5. Maximum clade credibility chronograms and estimated ancestral states of geographic range in Brachymeles skinks. Ancestral area reconstructions are indicated at each node. Triangles indicate unambiguous reconstructions of an ancestral area (posterior probability ≥ 0.95), colored according to the hypothesized state. Circles represent ambiguous character reconstructions, with colors representing the preferred area. Colored blocks at each ambiguous node represent alternate states supported in analyses. Bayes factors are provided as an indication of the strength of support for preferred states at ambiguous nodes receiving moderate to strong statistical. For interpretation of the references to color in this figure legend, the reader is referred to the web version of this article. 31 32 knowledge of the true patterns of diversification within the Philippines, we conservatively chose a model allowing for equal rates of transition among major faunal regions of the Philippines. Ancestral state reconstruction analyses resulted in many nodes where the reconstructed ancestral range is ambiguous (Fig. 1.5). The Luzon PAIC is the preferred ancestral range in most cases with varying degrees of support (Fig. 1.5). Importantly, all analyses resulted in unambiguous support for ancestral ranges at eleven nodes in the phylogeny, supporting the Luzon, Negros-Panay, and Mindanao PAICs as the ancestral ranges for several clades of Philippine Brachymeles (Fig. 1.5A–C). Given strong statistical support for ancestral areas at eleven nodes, we are confident in hypothesizing five dispersal events (Fig. 1.5), including clear dispersal from Luzon to Mindoro, Luzon to the central Visayan islands, dispersal from the Visayas to Mindoro and Luzon, and a clear instance of dispersal from the Mindanao island group to southern Luzon. Considering the moderate to strong statistical support for a specific reconstruction at seven ambiguous nodes (indicated by Bayes factors of 4.13–9.10; Kass and Raftery 1995; Nylander et al. 2004), we infer the possibility of five additional dispersal events (Fig. 1.5). Discussion Taxon sampling Our widespread sampling of individuals across the range of most Philippines Brachymeles species allows for fine-scale resolution of phylogenetic relationships and an unprecedented and comprehensive taxonomic review (Siler, 2010; Siler et al., 2009a, 2010a,b; Siler and Brown, 2010; Siler et al., in press c,d). The two species missing in our analyses are Brachymeles wrighti from northern Luzon Island and B. vermis from the Sulu Archipelago in the southern Philippines. Both species are represented by only a few museum specimens worldwide, and no genetic 33 samples have ever been collected. Previous studies that have included samples of Brachymeles have not been able to confidently place the genus Brachymeles within the family Scincidae (Brandley et al., 2005, 2008). Although our attempt to sample widely from outgroup taxa results in some well-supported relationships, the most closely related species to the genus Brachymeles remains unclear (see also Brandley et al., 2005). We are unable to collect full sequence data for all included outgroup taxa (Appendix I), and missing data may have contributed to weaker support for outgroup relationships. It is anticipated that additional outgroup and gene sampling will aid resolution of these relationships. Phylogeny and cryptic genetic diversity Cryptic diversity has been documented as a global phenomenon (Pfenninger and Schwenk, 2007; Bickford et al., 2007), and we now suspect the phenomenon to also characterize Philippine slender skinks (Siler et al., 2009a, 2010a,b; Siler and Brown, 2010; Siler et al., in press c,d). Although we focus on diversity of skinks of the genus Brachymeles, our results support the taxonomic issues identified in numerous studies for the family Scincidae (e.g., the non-monophyly of Lygosominae), and phylogenetic studies across the family are needed to provide sweeping taxonomic revisions. Although we did not expect to find that Davewakeum miriamae is nested within the genus Brachymeles, this result, in retrospect, is not surprising when comparing morphology of this genus to species of Brachymeles. Davewakeum shares several unique morphological features with B. apus, B. bonitae, and B. samarensis, including the fusion of the mental and first infralabial scales, the presence of a moderate-sized interparietal scale, nasal scales, two loreal scales, a frontal scale, frontoparietal scales, the presence of a single scale 34 row on the lower eyelid (Siler et al., 2010b; Siler, pers. obs.), and a general elongated, limb-reduced body plan. With the results of this study, and the fact that the genus Brachymeles (Duméril and Bibron, 1839) was described well before Davewakeum (Heyer, 1972), we consider Davewakeum to be a junior synonym of Brachymeles and, consequently, Brachymeles miriamae, new combination, to be the fifth limbless species of Brachymeles. We note that at least one additional known limbless species (B. cf. apus, from Kalimantan, south Borneo) awaits description (Iskandar and Bickford, unpublished data). The conservative body plans within the genus Brachymeles have led to confusion over species boundaries, the long accepted recognition of polytypic species, and the recognition of “widespread” species with distributions across accepted faunal boundaries (Brown, 1956; Brown and Rabor, 1967; Brown and Alcala, 1980). With the exception of Brachymeles schadenbergi, the results of this study do not support the monophyly of the currently and previously recognized polytypic species in the genus (Fig. 1.3, 1.4). Furthermore, all currently recognized subspecies within the genus are both strongly supported divergent lineages in the phylogeny and represent unique morphologies, most likely worthy of specific rank (Fig. 1.4; Siler and Brown, 2010; Siler et al., in press d). The degree to which convergent morphology has led to the underestimation of diversity within the genus can further be exemplified by examining the “widespread” species densely sampled in this study. Populations of the previously-recognized widespread pentadactyl species, B. talinis, have recently been revised to represent five unique pentadactyl species in the genus, each with non-overlapping geographic distributions (Fig. 1.4): B. makusog (Siler et al., 2010a), B. talinis, B. sp. A (Siler and Brown, 2010), B. sp. B (Siler and Brown, 2010), and B. sp. C (Siler 35 and Brown, 2010). Additionally, populations of the two former polytypic species, B. boulengeri and B. schadenbergi, have recently been revised, with all subspecies being elevated to full, morphologically distinct species (Siler and Brown, 2010; Fig. 1.4, Clade 5, 8). Currently, Brachymeles bonitae and B. samarensis are recognized to have atypical distributions that span multiple PAICs (Fig. 1.4, Clade 3). Brachymeles samarensis is known to occur on two islands in the Greater Luzon PAIC (Catanduanes, Luzon), as well as two islands and one small island group in the Mindanao PAIC (Leyte, Samar, Lapinig Island Group; Fig. 1.1, 1.2). In comparison, B. bonitae has the widest recognized distribution of any species in the genus. Populations referable to this species occur in three distinct PAICs (Greater Luzon, Greater Mindoro, Greater Negros-Panay) and two small deep-water island groups (Babuyan, Romblon). However, our results indicate that both B. bonitae and B. samarensis are complexes of numerous, morphologically similar species (Fig. 1.4, Clade 3). Although populations within both species complexes share similar body plans, unique sets of characters do exist, including differences in the numbers of fore- and hind limb digits (Siler et al., in press c; Siler, unpublished data). These inter-population differences have historically been recognized as morphological variation within widespread species (Brown, 1956; Brown and Rabor, 1967; Brown and Alcala, 1980); however, upon our observation that character differences coincide with deep genetic divergences and biogeographic breaks in lineage distributions, we suspect that many inter-populational variants in B. samarensis and B. bonitae will prove to be full species in accordance with any modern lineage-based species concept (see Siler et al., in press c), as they have in the B. boulengeri and B. shadenbergi complexes (Siler and Brown, 2010). Recent studies have revealed numerous other “widespread” Philippine endemic reptiles to actually represent complexes of cryptic diversity, with few species actually possessing 36 distributions that span recognized faunistic boundaries (Brown et al., 2000; Brown and Diesmos, 2002, 2009; Siler et al., 2010a,b; Siler and Brown, 2010; Welton et al., 2009, 2010a,b). Exceptions do exist (Brown and Alcala, 1970), but many of these have turned out to represent invasive species with suspected histories of human mediated introductions (Diesmos et al., 2006; Brown et al., 2010). It is clear that the diversity of Brachymeles is vastly underestimated, and detailed morphological comparisons are needed to revise the taxonomy within the genus. Finally, the phylogeny supports dispersal events into the Southeast Asian mainland (Thailand) from Borneo and subsequent dispersal into the Philippines, some level of uncertainty remains in the species diversity of Brachymeles outside of the Philippines (Fig. 1.4). The apparent disjunct distribution of Brachymeles in Southeast Asia may be an artifact of high levels of extinction outside of the Philippines or an absence of discovery. The phylogeny suggests at least one genetically distinct, undescribed limbless species in the southern regions of Borneo (Kalimantan, Indonesia; Fig. 1.4), and it is highly probable that other undescribed species will eventually be discovered in other regions of Asia. It is remarkable to note that the entire diversity of limbed, pentadactyl, reduced limbed, and limbless body forms are found in the Philippines (Fig. 1.4); we take this pattern as a testament to the richness of processes of diversification found within this small but remarkable island archipelago (Brown and Diesmos, 2009). Diversification and body form evolution within a semi-fossorial genus Previous surveys of body plan diversity within Brachymeles have focused solely on morphological variation (Brown and Rabor, 1967; Brown and Alcala, 1980; Brown and Alcala, 1995), mentioning the potential for undocumented cryptic diversity within the genus as an 37 ancillary possibility, not an expectation, much less a predominant phenomenon. However, a number of studies have shown that the evolution of a burrowing lifestyle is correlated with decreasing dispersal abilities (Selander et al., 1974; Patton and Yang, 1977; Patton and Feder, 1978) as well as changes in body form (see Crottini et al., 2009 for review). Several lineages of Brachymeles have experienced a reduction in limb size and digit numbers (Fig. 1.4), which may further reduce their vagility (Daniels et al., 2005; Mulvaney et al., 2005). Over time, reduced dispersal abilities may lead to an increasingly patchy distribution, reduction in gene flow among populations, and the accumulation of inter-population genetic differences (Nevo, 1979). This process also could be amplified within an island archipelago or a geographically complex island such as Luzon or Mindanao. We expect that this process has contributed to cryptic lineage diversification in this unique southeast Asian radiation. The results of phylogenetic analyses provide evidence for three losses of external limb elements, and three distinct instances of changes in digit states. Although five species of Brachymeles are externally limbless (B. apus, B. minimus, B. miriamae, B. lukbani, B. vermis), it is currently unknown whether internal girdle elements are present in any of the five species, an indication that the species have retained some vestigial limb elements. Additionally, there is evidence for up to four independent losses of auricular openings, with the openings being completely covered by scales in B. apus, B. cf. apus, B. miriamae, all species of Brachymeles in Clade 3 of Figure 1.4, and B. muntingkamay. It is also interesting to note that all species and populations with unequal digit numbers in the fore- and hind limbs have fewer toes than fingers in Brachymeles (B. bonitae, B. cebuensis, B. pathfinderi, B. samarensis), in contrast to many previous studies which have shown that reductions in digit number are more common in the fore-limbs of scincid lizards (Brandley et al. 2008; Skinner and Lee, 2010). 38 Biogeographic patterns Although numerous previous studies have observed phylogenetic patterns consistent with PAIC-based models of diversification (e.g., Heaney et al., 1998; Kennedy et al., 2000; Brown & Diesmos, 2002; Brown & Guttman, 2002; Evans et al., 2003; Esselstyn et al., 2004), we rejected all topologies predicted from a PAIC-based model (Fig. 1.3). Additionally, we rejected all hypotheses derived from patterns observed in other taxa (Alfaro et al., 2004; McGuire & Kiew, 2001; Siler et al., 2010c). Phylogenetic analyses and ancestral state reconstructions provide support for multiple dispersal events in Brachymeles leading to complex and biogeographically convoluted distribution patterns observed today. Ancestral range reconstructions unambiguously estimate the ancestral range for 11 nodes in the chronogram, supporting a minimum of five geographic range shifts between major faunal regions in the Philippines (Fig. 1.3). Of these hypothesized inter-PAIC transitions, with the exception of a dispersal out of the Mindanao PAIC, all geographic transitions are hypothesized to have originated in the Luzon or central Visayan PAICs (Fig. 1.3A–C). Additionally we note that although only five inter-PAIC dispersal events are unambiguously reconstructed (Fig. 1.5A–C), an additional 5 instances of between-PAIC dispersal can be inferred with strong statistical support (Bayes factors 6–10; Kass and Raftery 1995; Nylander et al. 2004). Given that the major PAIC platforms of the archipelago have never been connected by dry land (Kloss, 1929, Inger, 1985; Heaney, 1985, Voris, 2000, Yumul et al., 2003, 2008), suggesting that faunal exchange among PAICs necessitates over-water dispersal (review: Brown and Diesmos, 2009), we find it reasonable to conclude that much of the historical dispersion of Brachymeles throughout the archipelago has been through the process of 39 waif dispersal over water. Clearly the evolutionary and biogeographic history of semi-fossorial slender lizards has been heavily impacted by over water faunal exchange throughout the archipelago. This may appear at odds with the general assumption of low vagility assumed for reduced-limbed lizards with a burrowing lifestyle, but we find it conceivable, and even plausible, that dispersal between islands is mediated by frequent rafting of mats of vegetation, topsoil, and logs; these possible vectors have frequently observed washing out of the mouths of rivers following heavy storms (CDS and RMB, personal observations). Conclusion Our data represent a comprehensive, phylogenetic study for a closely related group of lizards. We have included samples from nearly all recognized species within the genus Brachymeles, and our intraspecific sampling has uncovered cryptic genetic diversity within many species (e.g., Brachymeles bonitae and B. samarensis). This study provides the foundation for a robust model system with which to address patterns of body form evolution, processes of diversification, and species delineation. With the exception of the recently published Lerista dataset (Skinner et al., 2008; Skinner, 2010; Skinner and Lee, 2010), our estimates of phylogeny represent the most comprehensive dataset for fine-scale studies of limb-reduction and loss in squamate reptiles. It is clear that the current recognized diversity of Brachymeles skinks is vastly underestimated, and that numerous taxonomic revisions will be necessary to fully appreciate the processes of diversification within this nearly endemic Philippine radiation. New species await description (e.g., the new limbless species in southern Borneo; Fig. 4), and likely await discovery, and future survey work should focus on regions outside of the Philippines (e.g., Borneo, Malay Peninsula, Indochina). This study has revealed another case of extensive cryptic diversity in a 40 once recognized assemblage of “widespread” Philippine species (Fig. 1.4). Together with numerous recent studies (Brown et al., 2009; Esselstyn et al., 2009; Esselstyn and Brown, 2009; Oliveros and Moyle, 2010; Siler et al., 2010c; Linkem et al., 2010) this effort has resulted in wholesale discovery of numerous new species and cryptic evolutionary lineages of endemic Philippine vertebrates. Once considered a small radiation of Asian skinks, the recognized species diversity of the genus Brachymeles will likely increase by more than 300% over the next five years (Siler et al., unpublished data). We rejected all PAIC-based models of diversification (e.g., Heaney et al., 1998; Kennedy et al., 2000; Brown & Diesmos, 2002; Brown & Guttman, 2002; Evans et al., 2003; Esselstyn et al., 2004), as well as all patterns observed in other studies (Alfaro et al., 2004; McGuire & Kiew, 2001; Siler et al., 2010c; Fig. 1.3). However, the results of this study provide evidence for five major dispersal events across faunal zone boundaries that have given rise to the major clades of Brachymeles species diversity in the Philippines (Fig. 1.5). Surprisingly, all but one of these dispersal events are hypothesized to have originated in the Luzon or central Visayan PAICs (Fig. 1.3A–C). The results of this study, coupled with our knowledge of the geologic history of the region (Kloss, 1929, Inger, 1985; Heaney, 1985, Voris, 2000, Yumul et al., 2003, 2008), suggests that much of the historical faunal exchange of Brachymeles throughout the archipelago has been through the process of over-water (waif) dispersal. Without time-calibrated phylogenies, and the absence of closely related fossil calibrations, it is difficult to say when the hypothesized dispersal events occurred, leading to the complex distribution patterns observed today. The transition from quadrapedal to limbless body plans has occurred repeatedly in independent lineages of squamate reptiles (i.e., snakes, lizards, amphisbaenians; Wiens and 41 Slingluff, 2001; Greer, 1991; Pough et al., 2004). It is clear that these transitions also occur repeatedly within single radiations of closely related species (Fig. 1.4). The results of this study provide the first evidence of repeated limb, digit, and auricular opening loss in the genus Brachymeles. Given our results, and those of other studies that explicitly test morphological patterns of body form change within squamate reptiles (for review, see Wiens and Slingluff, 2001; Brandley et al., 2008), we are left with many unanswered questions. Given the apparent evidence for repeated body form change in Brachymeles, can we estimate the number of times characters have been lost (or potentially gained) in Brachymeles? Do the patterns of morphological changes observed within this unique radiation of Southeast Asian lizards support previous hypotheses of correlated morphological evolution associated with limb-reduction and loss in squamate reptiles (for review, see Wiens and Slingluff, 2001; Brandley et al., 2008)? Is there evidence for a gradual, evolutionary sequence involved in the process towards limb loss? What inferences can we make from statistical reconstructions (estimates) of ancestral morphology and character state change on the phylogeny? These and other broad-scale evolutionary questions that address the processes of body form evolution must be assessed within a comparative framework, and require the addition of robust morphological datasets. 42 CHAPTER 2 Evidence for repeated acquisition and loss of complex body form characters in an insular clade of Southeast Asian semi-fossorial skinks The unidirectional loss of complex characters has been a major theme in the development of theories of evolutionary change of morphology and body plan evolution (Dollo, 1893, 1922; Muller, 1939; Simpson, 1953; Gould, 1970). Dollo’s law, or the irreversible loss of complex characters (Dollo, 1893, 1905, 1922; Simpson, 1953; Gould, 1970), has been the subject of many recent empirical studies (for review, see Galis et al., 2010). Although re-acquisition of complex characters historically was believed to be improbable following significant genetic differentiation (Muller, 1939; Simpson, 1953; Marshall et al., 1994; Zufall and Rausher, 2004), Dollo’s Law has come into question recently with the advent of phylogenetic methods and new tools for ancestral character state reconstruction (for review, see: Kohlsdorf and Wagner, 2006; Collin and Miglietta, 2008; Goldberg and Igic, 2008; Lynch and Wagner, 2009; Wiens, 2011). For example, in a recent reviews by Galis et al. (2010) and Wiens (2011), numerous examples of studies supporting the re-acquisition of complex traits were discussed, including the re-acquisition of teeth and nipples in mammals (Kurtén, 1964; Gilbert, 1986; Sherman et al., 1999; Lihoreau et al., 2006), teeth in frogs (Wiens, 2011), wings in insects (Whiting et al., 2003), coiling in snails (Collin and Cipriano, 2003; Pagel, 2004), sexuality in orobatid mites (Domes et al., 2007), complex life cycles in marsupial frogs (Wiens et al., 2007), and phalanges and digits in squamate reptiles (Greer, 1992; Kohlsdorf and Wagner, 2006; Brandley et al., 2008). Nevertheless, statistical phylogenetic tests of Dollo’s Law have led to questions concerning potential pitfalls and methodological weaknesses (Trueman et al., 2004; Urdy and Chirat, 2005; Goldberg and 43 Igic, 2008; Galis et al., 2010; but see Kohlsdorf et al., 2010). Although these potential methodological limitations have been presented, studies continue to find evidence for the re-acquisition of complex traits. In addition to the studies on the polarity of character change, evolutionary patterns of limb-reduction and loss have provided biologists with a rich suite of hypotheses for tests in a phylogenetic framework (for review, see Brandley et al., 2008). Recent advances in the field of phylogenetics and the availability of molecular data have resulted in a resurgence of interest in the patterns and processes of body form evolution among squamate reptiles (Wiens and Slingluff 2001; Whiting et al. 2003; Kearney and Stuart 2004; Sanger and Brown 2004; Wiens 2004; Schmitz et al. 2005; Kohlsdorf and Wagner 2006; Wiens et al. 2006; Brandley et al. 2008; Skinner et al. 2008; Skinner and Lee 2009, 2010; Skinner 2010; Galis et al. 2010; Kohlsdorf et al. 2010). From studies of development (Shubin and Alberch 1986; Cohn and Tickle 1999; Shapiro 2002) to studies of locomotion (for review, see Bergmann and Irschick 2010), researchers have attempted to address questions concerning the repeated transition from quadrupedal to limbless body plans in independent lineages of squamate reptiles (Greer 1991; Pough et al. 2004; Wiens et al. 2006). Long believed to be an irreversible evolutionary process, recent studies have provided evidence for digit reacquisition (Kohlsdorf and Wagner 2006; Brandley et al. 2008; Kohlsdorf et al. 2010). To date, fine-scale studies of squamate body form evolution have been limited by a paucity of model systems to test the irreversibility of character change (but see Kohlsdorf and Wagner 2006; Skinner et al. 2008; Skinner 2010). Previous studies of squamate body form evolution have focused most often on broad- scale patterns of limb reduction and loss, and a suite of morphological changes have been identified as associated with this evolutionary transition. These include body elongation, reduction in limb 44 size, loss of digits, miniaturization, increase in the number of presacral vertebrae, loss of external ear openings, and loss of associated limb girdles (for review, see Brandley et al. 2008). Changes in the number of digits have been shown to likely occur through an ordered evolutionary sequence (Alberch and Gale 1985; Shubin and Alberch 1986; Shapiro 2002). Historically, these were assumed to occur through the irreversible loss of the limb and digit character (Brandley et al. 2008). This assumption of irreversibility has had a marked influence on the interpretation of recent findings concerning the re-evolution of multiple digits and limbs from limb-reduced ancestors (Whiting et al. 2003: Kearney and Stuart 2004; Collin and Miglietti 2008). Recent studies focusing on ancestral state reconstructions have highlighted several potential methodological pitfalls by demonstrating well supported but misleading reconstructions of character change; this discussion has focused on extent of outgroup sampling and character states at the root of the phylogeny (Goldberg and Igic 2008; Galis et al. 2010). Finally, the assumption of ordered sequential change has had a significant impact on studies of ancestral squamate digit states (Kohlsdorf and Wagner 2006; Brandley et al. 2008; Skinner et al. 2008; Skinner et al. 2010; Skinner 2010). However, recent findings indicate that an ordered model of digit evolution does not always provide the best-fit model of the evolution of digit change in scincid lizards (Skinner and Lee 2010; Skinner 2010). There are few genera of scincid lizards that possess both fully limbed and limbless species (Brachymeles, Chalcides, Lerista, and Scelotes; Lande 1978; Wiens and Slingluff 2001), providing rare model systems for fine-scale studies of body form evolution. Most studies of these genera have included only morphological data (e.g., Lande 1978; Choquenot and Greer 1987; Greer 1987, 1990, 1991; Caputo et al. 1995; Greer et al. 1998) or limited taxonomic sampling (Scelotes: Whiting et al. 2003; Chalcides: Brown and Pestano 1998; Pestano and Brown 1999). However, recent studies of Lerista addressed patterns of body form evolution 45 Figure 2.1. Hypothesized relationships of Brachymeles from Siler et al. (2011), illustrated by ML estimates (-ln L 60687.493127). Nodes supported by ≥95% Bayesian PP and ML bootstrap support were considered significantly supported and are indicated by black circles. Terminals are labeled with abbreviated taxonomic names, followed by general geographic distribution. Limb and digit states, numbers of presacral vertebrae, and proportionally-drawn body form cartoons are shown for reference. Externally limbless, non-pentadactyl, and pentadactyl species are highlighted by red, blue and black braches, respectively. Alpha and numerical labels correspond to clades referred to in the Results and Discussion. 46 47 using a molecular and morphological dataset and robust taxonomic sampling (Skinner et al. 2008; Skinner and Lee, 2009, 2010; Skinner 2010). Limb reduction and loss has been shown to occur frequently in Lerista, a genus of 94 species, with rates of change suggested to be much higher than previously estimated (Skinner et al. 2008; but see Wiens 2009). In contrast to some recent evidence for digit, and possibly limb, re-evolution (Kohlsdorf and Wager 2006; Brandley et al. 2008; Kohlsdor et al. 2010), studies of Lerista support unidirectional loss of digits only (Skinner et al. 2008; Skinner and Lee 2009, 2010; Skinner 2010). Of these four known squamate systems, the genus Brachymeles remains the least studied, and to date, patterns of body form evolution among species of this enigmatic lizard radiation have received little attention (but see Siler et al. 2011). Morphological diversity within the Southeast Asian lizard genus Brachymeles has only recently been brought to light by a series of systematic studies (Siler et al. 2009a, 2010a,b; Siler and Brown 2010; Siler et al. 2011, in press c,d). Within this genus, all but two of the 26 recognized species are endemic to the Philippines (Brown and Alcala 1980; Siler et al. 2009a, 2010a,b; Siler and Brown 2010; Siler et al. 2011, in press c,d); the exceptions are B. apus from northern Borneo (Hikida 1982) and B. miriamae (Heyer 1972) from Thailand (formerly Davewakeum miriamae; Siler et al. 2011). Thirteen species are pentadactyl (bicolor, boholensis, boulengeri, gracilis, kadwa, makusog, mindorensis, orientalis, schadenbergi, talinis, taylori, tungaoi, and vindumi), and the remaining thirteen species exhibit limbless or intermediate states, including incompletely developed limbs and reduced numbers of digits (bonitae, cebuensis, elerae, muntingkamay, pathfinderi, samarensis, tridactylus, and wrighti). Five of the non-pentadactyl species are completely limbless (apus, minimus, miriamae, lukbani, and vermis). Within the non-pentadactyl species there exists a wide range of limb- and digit-reduced states, 48 from minute limbs that lack full digits (bonitae, cebuensis, muntingkamay, samarensis, tridactylus), to moderately developed limbs with four to five digits on the hands and feet (elerae, pathfinderi, wrighti). Because of the body form variation in this clade, and the fact that its many closely related species differ by the presence or absence of digits and characters of the limbs, this group provides an ideal system for testing Dollo’s Law and the prediction of unidirectional limb reduction and loss. Siler et al. (2011) provided the first estimate of phylogenetic relationships among species in the genus Brachymeles. The seven-gene dataset included representatives for all but two of the currently known species in the genus as well as broad outgroup sampling (Siler et al. 2011). Results of this study indicated that multiple instances of limb-reduction and loss have occurred in this radiation of burrowing skinks. Additionally, several widespread limb-reduced species (e.g., B. bonitae, B. samarensis) were not found to be monophyletic, and were shown to be species complexes with unique digit numbers and morphologies (Siler et al. 2011). However, no morphological data were presented, and the focus remained solely on the phylogenetic relationships, taxonomic stability, and biogeographic patterns. Here we add additional molecular sequence data to the datasets of Siler et al. (2011), and a large, newly acquired, comprehensive morphological dataset, to assess patterns of body form evolution within this unique clade of species. Our combined molecular and morphological datasets represent one the most fine-scaled systems for studying body form evolution in a group of closely related squamates to date. In order to test hypotheses of body form evolution among squamate reptiles, we investigate patterns of body form change in skinks of the genus Brachymeles using a phylogenetic comparative approach, derived from morphological data. We explore the data for evidence of threshold values of morphological features after which changes in body form occur. 49 Additionally, we test for patterns of correlated evolution of morphological characters. We provide the first exploration of the impact of various methodological choices used in previous studies of body form evolution, including the impact of choice of morphometric variable as a measurement of body size for non-phylogenetic and phylogenetic size-correction as well as the overall method for multivariate principal component analyses. Finally, using our robust estimate of phylogenetic relationships, we explore the prevalence and directionality of evolutionary changes in limb, digit, and ear character states, and the impact of outgroup sampling and ancestral outgroup character states on ancestral state reconstructions. Our results demonstrate one of the best-documented cases of limb reduction, loss, and evolutionary reacquisition of these complex characters in a closely related clade of lizards. We identify the first known case of loss and reacquisition of external ear openings (another trait lost in association with burrowing lifestyles) and highlight the occurrence of taxa occupying two new classes of morphospace: species with minute limbs but with multiple digits and species lacking digits but with longer limbs than congeners with multiple digits. Additionally, our comparative analyses incorporating an historical context via phylogeny revealed significant statistical support for otherwise undetectable patterns of character correlation. Together, our findings provide yet another violation of Dollo’s Law in a new, rich model system for future studies of the historical framework for patterns and processes of body form evolution. Methods Taxon sampling and data collection Phylogenetic analyses for this study took advantage of the datasets of Siler et al. (2011); however, we collected 1,323 bp of additional molecular data. Ingroup sampling included 90 50 individuals collected from 43 localities, with 24 of the 26 currently recognized species of Brachymeles represented (Fig. 2.1; Siler et al. 2011). The study incorporated a broad sampling of outgroup scincid species from the subfamilies Lygosominae and “Scincinae”, as well as a single outgroup sample from the family Lacertidae (Fig. 2.1; Siler et al. 2011). The phylogeny of Siler et al. (2011) was based on a sequence data for seven-genes: (mitochondrial) NADH Dehydrogenase Subunit 1 (ND1), NADH Dehydrogenase Subunit 2 (ND2), ATPase 8 (ATP8), ATPase 6 (ATP6); (nuclear) Brain-derived Neurotrophic Factor (BDNF), R35, Prostaglandin E receptor 4 (PTGER4). For this study, additional complete or partial sequences were collected for the mitochondrial Cytochrome Oxidase Subunit II (COXII) and Cytochrome Oxidase subunit III (COXIII) genes, and components of seven flanking transfer RNA genes (tRNAlys, tRNAleu, tRNAlle, tRNAgln, tRNAtrp, tRNAala, tRNAasn) using the primers of Siler et al. (2011). In addition, the two nuclear loci, Glyceraldehyde-3-phosphate Dehydrogenase (GapD) and α-enolase, were completely sequenced for nearly all ingroup samples and many of the outgroup samples using the primers and protocols of Friesen (1997). All newly collected sequences were deposited in GenBank (accession #’s HQ906962–907136). Sequence alignment and phylogenetic analyses Initial alignments were produced in Muscle (Edgar, 2004), and manual adjustments made in MacClade 4.08 (Maddison and Maddison, 2005). To assess phylogenetic congruence between the mitochondrial and nuclear data, we inferred the phylogeny for each gene independently using likelihood and Bayesian analyses, and performed pairwise partition homogeneity tests in PAUP 4.0b 10 (Swofford, 2002) with 100 replicates for each pairwise comparison to assess set congruence. Following the observation of no statistically significant incongruence between datasets, we felt justified in using the combined, concatenated, data for subsequent analyses. 51 Exploratory analyses of the combined dataset of 108 individuals (including outgroup taxa with missing data for several genes) and a reduced dataset of individuals with no missing data exhibited identical relationships; we therefore chose to include all available data (108 individuals) for subsequent analyses of the concatenated dataset. Alignments and resulting topologies were deposited in TreeBase (SN 11274). Partitioned Bayesian analyses were conducted in MrBayes v3.1.2 (Ronquist and Huelsenbeck, 2003). The mitochondrial dataset was partitioned by codon position for the protein-coding region of ND1 and ND2 and by gene region for the short gene regions ATP8 and ATP6. The Akaike Information Criterion (AIC), as implemented in jModeltest v0.1.1 (Guindon and Gascuel, 2003; Posada, 2008), was used to select the best model of nucleotide substitution for each partition (Table 1.2). The best-fit model for each data partition was implemented in subsequent Bayesian analyses. A rate multiplier model was used to allow substitution rates to vary among subsets, and default priors were used for all model parameters. We ran four independent Metropolis-coupled MCMC analyses, each with four chains and an incremental heating temperature of 0.05. All analyses were run for 18 million generations, sampling every 5000 generations. To assess stationarity, all sampled parameter values and log-likelihood scores from the cold Markov chain were plotted against generation time and compared among independent runs using Tracer v1.4 (Rambaut and Drummond, 2007). Finally, we plotted the cumulative and non-overlapping split frequencies of the 20 most variable nodes, and compared split frequencies among independent runs using Are We There Yet? [AWTY (Wilgenbusch et al., 2004)]. Although all samples showed patterns consistent with stationarity after 2.5 million generations (i.e., the first 12.5%), we conservatively discarded the first 20% of samples as burn-in. 52 Table 2.1. Summary of numbers of specimens examined per species, and adult specimens per species included in this study. The number of x-rays examined per species are provided for reference. Species or Morphologically Unique Lineage Specimens Examined Adult Specimens Included in Analyses X-rays Examined Brachymeles apus 1 1 1 Brachymeles bicolor 28 9 5 Brachymeles boholensis 39 18 7 Brachymeles bonitae (central Luzon Island) 11 11 11 Brachymeles cf. bonitae (northern Luzon Island population) 2 1 2 Brachymeles cf. bonitae (Masbate Island population) 10 6 2 Brachymeles cf. bonitae (Mindoro Island population) 23 17 3 Brachymeles cf. bonitae (Camiguin Norte Island population) 8 7 4 Brachymeles cf. bonitae (Lubang Island population) 6 4 6 Brachymeles boulengeri 26 13 6 Brachymeles cebuensis 9 7 5 Brachymeles elerae 4 3 2 Brachymeles gracilis hilong 20 15 9 Brachymeles gracilis gracilis 62 15 13 Brachymeles lukbani 11 10 6 Brachymeles makusog 14 9 8 Brachymeles mindorensis 35 12 5 Brachymeles minimus 6 4 6 Brachymeles miriamae 2 2 2 Brachymeles muntingkamay 12 10 10 Brachymeles orientalis 53 20 6 Brachymeles pathfinderi 39 29 6 Brachymeles samarensis (Samar Island) 6 6 6 Brachymeles cf. samarensis (Leyte Island population) 14 14 7 Brachymeles cf. samarensis (Catanduanes Island population) 9 9 9 Brachymeles schadenbergi 49 12 6 Brachymeles talinis 31 14 6 Brachymeles taylori 35 17 6 Brachymeles tridactylus 22 14 10 Brachymeles sp. A 12 5 2 Brachymeles sp. B 33 17 9 53 In preliminary Bayesian analyses of the combined dataset, the independent runs failed to converge. We tried (1) lowering the incremental heating temperature to 0.02, (2) using an unconstrained branch length prior with an exponential distribution of 25 (Siler et al. 2010c, 2011; Marshall 2006, 2010), and (3) removing outgroup taxa with large amounts of missing data. Although some of the trials of individual permutations of parameters resulted in a failure to converge, the incorporation of the above, plus an unconstrained branch length prior with an exponential distribution and a mean of 25 resulted in convergence. Once complete convergence was achieved, we proceeded with final analyses, presented here. Partitioned maximum likelihood (ML) analyses were conducted in RAxMLHPC v7.0 (Stamatakis, 2006) on the concatenated dataset the same partitioning strategy as for Bayesian analysis. The more complex model (GTR + Γ) was used for all subsets, and 100 replicate ML inferences were performed for each analysis. Each inference was initiated with a random starting tree, and employed the rapid hill-climbing algorithm (Stamatakis, 2007). Clade confidence was assessed with 100 bootstrap pseudoreplicates employing the rapid hill climbing algorithm (Stamatakis et al., 2008). Relative time analyses To test the combined dataset for deviations from a molecular clock, we optimized likelihood scores in PAUP* 4.0b10 with a molecular clock enforced and not enforced on the maximum-likelihood topology. A likelihood ratio test ([LRT] Arbogast et al. 2002; Felsenstein 2004) significantly rejected a molecular clock (p = 0.00), and subsequent analyses were conducted within a relaxed clock framework. The relative rate chronogram used for morphological analyses in this study was inferred in a Bayesian framework using BEAST v1.5.3 (Drummond 54 and Rambaut 2007). The dataset was paired down into individual lineages per species or morphologically distinct, non-monophyletic populations (B. bonitae and B. samarensis; Siler et al. 2011). Four independent BEAST runs of 50 million generations were completed under the same partitioning strategy as for Bayesian analyses, imposing an uncorrelated lognormal relaxed clock prior on substitution rate (Drummond et al. 2006) and Yule speciation prior. Parameters were sampled every 5000 generations and the initial 50% of each run was discarded as burn-in, leaving a combined 20,000 trees in the posterior distribution. To evaluate convergence among MCMC analyses, trends and distributions of parameters, including the likelihood score, were examined in Tracer (Rambaut and Drummond 2007) and Are We There Yet? [AWTY (Wilgenbusch et al., 2004)]. Testing morphological hypotheses We test morphology-based hypotheses to address questions concerning the patterns of Brachymeles diversity (Fig. 2.2): 1) Did limb reduction occur once? 2) Did the complete loss of external limb elements occur once? 3) Did ear loss occur once? 4) Is there support for a gradual transition from pentadactyl to limbless body forms? In an attempt to thoroughly evaluate each, we conducted analyses within Bayesian and maximum likelihood (ML) frameworks. The topological constraints for these questions are outlined in Figure 2.2. The ML approach consisted of conducting an approximately unbiased (AU) test (Shimodaira and Hasegawa 2001; Shimodaira 2002), as implemented in Siler et al. (2010c). Using the full, combined dataset, partitioned maximum likelihood (ML) analyses were conducted in RAxMLHPC v7.0 (Stamatakis 2006), under the same partitioning strategy used for phylogenetic analyses. A complex model (GTR + Γ) was used for all subsets, and 100 ML 55 searches were performed under each of the 4 constraints. All 500 trees produced by RAxML (100 from the unconstrained analysis and 100 from each of the 4 constrained analyses), were filtered in PAUP to remove identical topologies. A modified version of RAxML (provided by Alexandros Stamatakis) allowed the per-site likelihoods to be estimated for each of the 54 unique topologies under a partitioned model. An AU test was then performed on the per-site likelihoods from all 54 using CONSEL v0.1i (Shimodaira and Hasegawa 2001). The p-value reported for a given hypothesis is the largest p-value of all the trees inferred under that constraint. To automate various steps in the process, Perl and Python scripts were written by J. Oaks and CDS (available by request). For the Bayesian approach, we took the percentage of 11520 post-burnin trees consistent with each hypothesis to represent the posterior probability that the hypothesis is true. Testing hypotheses of correlated character evolution We tested the morphological data for phylogenetic signal of morphometric data using Pagel’s lambda (Freckelton et al. 2002) and Blomberg’s K (Blomberg et al. 2003). Both raw and natural-log transformed morphometric variables were analyzed. The topology and branch lengths from the chronogram estimated in BEAST analyses were imported into R (R Development Team 2008), and the geiger (Harmon et al. 2008) and Picante (Kembel et al. 2010) packages were used to conduct transformations to test for phylogenetic signal. Following the observation of significant phylogenetic signal in all morphometric characters (Fig. 2.3), independent contrasts were used to explore the impact of phylogeny on subsequent analyses of morphology. Bivariate and multivariate analyses were performed on raw morphometric data as well as independent contrasts of the morphometric variables to explore both raw morphological patterns 56 observed in Brachymeles and those observed in a phylogenetic context. Morphometric data were measured for ten characters for twenty-seven lineages of Brachymeles (including B. miriamae). These lineages corresponded to the species, subspecies, and morphologically unique populations (i.e., Brachymeles bonitae, B. samarensis) sampled in phylogenetic analyses (Fig. 2.1). Meristic and mensural characters are based on Siler et al. (2009a, 2010a,b), and include: snout–vent length (SVL), head length (HL), tail length (TL), total length (TotL; SVL + TL), fore- and hind limb length (FLL and HLL), midbody width (MBW), and numbers of presacral vertebrae (PSV), fore-limb digits (Fldig), and hind limb digits (Hldig). Species, subspecies, or morphologically distinct populations of Brachymeles possess limbs with as few as one recognizable digit or up to as many as five recognizable digits. Following the methods of Brandley et al. (2008), we coded limbless species as well as species or populations with limbs consisting of only a small stump and no recognizable digits as having zero digits. We measured the ten morphological characters used in this study from 632 specimens of Brachymeles, with an average of 20 specimens per species, subspecies, or morphologically distinct population (Table 2.1). Measurements of juvenile and sub-adult specimens were excluded from analyses (Table 2.1). Additionally, we recorded presacral vertebrae numbers from x-rays for an average of 6 specimens per species, subspecies, or morphologically distinct population (Table 2.1). Minor differences in body size characters between sexes and populations may exist in nature or simply as an artifact of sample size, and we attempted to account for this by combining data from broad geographic sampling for both sexes whenever possible. Following the methods of Wiens and Slingluff (2001) and Brandley et al. (2008), the value of 1 was added to all variable measurements (some taxa have values of zero for digit numbers), and each measurement was natural log-transformed. Independent contrasts (Felsenstein 1985) were 57 then calculated for each natural log-transformed variable using the Phylogenetic Diversity Analysis Programs (PDAP; Midford et al. 2005) module in Mesquite version 1.06 (Maddison and Maddison 2005). The topology and branch lengths from the chronogram estimated in BEAST analyses were used to calculate contrasts. To check that independent contrasts were adequately standardized, the slopes of the regression lines between the absolute values of the contrasts against the square root of the sum of the corrected branch lengths (or their standard deviations) were inspected (Garland et al. 1992). No significant relationships were observed and the independent contrasts subsequently were considered to be appropriately standardized. Previous studies corrected for size in body and limb measurements by regressing independent contrasts for each measurement on the contrasts for head length (Wiens and Slingluff 2001; Brandley et al. 2008), based on the observation that relative limb and body lengths vary greatly in lizards compared to the conservative shape of the skull (Stokely 1947). In Brachymeles, most species possess what appears to be a conservative body plan, with relatively small limbs even observed in pentadactyl species. We explored whether head length is an appropriate measure with which to standardize morphometric variables, and in doing so account for body size allometry (methodology provided in Appendix III Materials & Methods). To test for a relationship between body and limb size, as well as body size and presacral vertebrae number, we regressed relative body size measurements against relative limb size and presacral vertebrae number for each of the three sets of size-corrected morphometric variables. Additionally, we regressed digit and presacral vertebrae number against the three sets of relative limb length measurements as well as the raw non-size-corrected limb lengths to test for relationships between limb size and digit number and number of presacral vertebrae. All regressions were made through the origin (Garland et al. 1992). 58 We used principal components analysis (PCA) on a correlation matrix of raw size-corrected variables following the methods of Wiens and Slingluff (2001) to determine whether any body-form groupings can be recovered without a priori designation of groups. All analyses were performed using the seven morphometric variables only, the seven morphometric variables and digit numbers (for the hand and foot), and the seven morphometric variables, digit numbers, and number of presacral vertabrae. Methods for simultaneously correcting for body size allometry and conducting PCAs, while taking the phylogeny into account have recently been developed (Revell 2009). To explore differences between methodologies, we repeated all bivariate analyses using phylogenetic size-corrected (PSC) data calculated in R using the phyl_resid function provided in Revell (2009), as well as independent contrasts of the PSC data. Additionally, PCAs of raw, size-corrected variables were compared to results of phylogenetic principal component analyses (Revell 2009). Exploring morphological thresholds Previous studies of squamate reptiles have reported thresholds of raw morphometric body proportions that appear to mark a demarcation between long, fully pentadactyl limbs and shortened limbs and reduced digit states (Lande 1978; Brandley et al. 2008). To determine whether these hypothesized thresholds occur across the diversity of Brachymeles, we created bivariate and overlaid scatterplots of raw digit numbers and presacral vertebrae number against ratios of limb, snout–vent, and total lengths to head length as well as midbody width to head length following the methods of Lande (1978) and Brandley et al. (2008). The plots were subsequently inspected for trends in body form change. As in Brandley et al. (2008), raw data were used for more easily interpretable results and comparison with previous studies. 59 Testing for evidence of character re-evolution To explore whether there is evidence of the re-evolution of limbs, digits, or ear openings in Brachymeles, we compared empirically observed (extant) character states to estimates of ancestral states using the program BayesTraits version 1.0 (Pagel 1994; Pagel and Lutzoni 2002). For analyses involving the estimation of ancestral external limb and ear states we examined two models of character evolution: 1) assuming equal rates of character acquisition and loss, 2) assuming independent rates of character acquisition and loss. Following the methods of Skinner and Lee (2010), we examined five disparate models of digit evolution to evaluate which models best fit the data (Table 2.5). For all analyses we seeded the mean and variance of the gamma prior from uniform distributions on the interval 0 to 20 by enforcing the “Hyperpriorall” command of BayesTraits. These analyses were then repeated and compared to runs with uniform priors with upper and lower bounds of 0 and 100 (Skinner and Lee 2010). The LogCombiner v1.5.4 program of BayesTraits was used to combine trees from the posterior distributions of the four independent Beast runs. Of the 20,000 trees in the posterior distribution, we discarded the first 97.5%, producing a file with 2,000 trees from the posterior distribution. All 2,000 chronograms were then used in analyses of morphological data in BayesTraits in an effort to account for phylogenetic uncertainty. We ran MCMC chains for 25 million generations, sampling every 5000th generation, and discarded the first 50% of samples as burn-in. The ratedev parameter was adjusted for each analysis to maintain acceptance rates of 20–40%. The remaining 2,500 samples were used to summarize the posterior probabilities of ancestral character states for all nodes of the tree. Bayes factors comparing the best fit model to all other models of character evolution were applied, accepting more parameterized models when the 60 Bayes factor shows strong to very strong support (Kass and Raftery 1995; Nylander et al. 2004). The “AddNode” command of BayesTraits was used to specify all nodes in the chronograms for visualization of the posterior probabilities of character states at each node. We ran a series of additional analyses on nodes with ambiguous estimated ancestral character states. The “fossil” command of BayesTraits was used to sequentially enforce the character states making up 95% of the posterior probability at a single node, prioritizing character states with the highest posterior probability. Bayes factors were again applied, and the state supported at each ambiguous node was summarized with the Bayes factors measure of support for that ancestral state (Figs. 6, 7). To explore the impact of the ancestral character states among outgroup taxa on reconstructions within Brachymeles (Goldberg and Igic 2008), additional analyses were conducted in which we assumed the ancestral states for all nodes sister to Brachymeles was a limbed, pentadactyl species with external ear openings. Results Phylogeny of Brachymeles Our complete, aligned matrix contain 82 samples of Brachymeles, representing 24 of the 26 recognized taxa, and containing both mitochondrial genes and nuclear loci. Seventeen additional outgroup samples included representatives from the subfamilies Lygosominae and “Scincinae” within the family Scincidae as well as a single representative from the lizard family Lacertidae. Following the study of Siler et al. (2011), we rooted the tree using samples of Takydromus sexilineatus from China. All analyses strongly supported five distinct instances of limb reduction in the genus Brachymeles (including B. miriamae; Fig. 2.1). Complete limb loss is strongly supported to have 61 occurred three separate times (Fig. 2.1). Interestingly, the two non-Philippine species (B. apus [Borneo], B. miriamae [Thailand]) are always recovered as the two lineages sister to all Philippine Brachymeles (Fig. 2.1). Within the Philippines, all limbless species and the majority of limb-reduced species are recovered as part of two reciprocally monophyletic groups, and together are sister to all pentadactyl species and the remaining non-pentadactyl taxa (Fig. 2.1). The widespread limb-reduced species, Brachymeles bonitae and B. samarensis, are not recovered as monophyletic groups (Fig. 2.1). Furthermore, with strong statistical support, Siler et al. (2011) rejected the hypothesized monophyly of both of these species complexes. Not only are all of the lineages within these complexes well supported and genetically distinct, but they differ morphologically as well (Fig. 2.1, 2.4). Populations within both species complexes differ in body size, limb and digit characters, and scale counts (Brown and Alcala 1980; Siler et al. 2011), and even the number of digits and presacral vertebrae. Morphological hypothesis tests Results from the Bayesian methods and the approximately unbiased (AU) test were highly consistent. Both methods rejected all morphology-based hypotheses (Fig. 2.2). Although we treat the former monotypic genus Davewakeum miriamae as the fifth limbless species of Brachymeles following Siler et al. (2011), each hypothesis was re-evaluated with both the Bayesian method and by conducting AU tests with B. miriamae samples incorporated into excluded from constraint trees. No differences were observed in the resulting support for each of the four hypotheses. Additionally, hypothesis #4 was tested using three topological constraints: 1) A single transition across all Brachymeles (with and without B. miriamae), 2) Two transitions for Clades 1 and 2, respectively, and 3) A single transition for Clade 1. All three versions of 62 hypothesis #4 were rejected by both analyses (Fig. 2.2). Analyses of Correlated Character Evolution Tests for the presence of phylogenetic signal resulted in λ values estimated at 1.0 and K values that were significantly different from 0 (SVL K = 0.8452; MBW K = 1.5540; TL K = 0.8877; HL K = 1.3734; HLL K = 2.4268; FLL K = 2.6651; TotL K = 0.7828; Fig. 2.3). Regression analyses show highly consistent results regardless of the variable used for size-correction. Additionally, analyses of size-corrected data based on either residuals from bivariate regressions of phylogenetically independent contrasts (RSC-IC; Lande 1978; Wiens and Slingluff 2001; Brandley et al. 2008), or phylogenetically independent contrasts of phylogenetically size-corrected data (PSC-IC; Revell 2009), show largely similar results (Table 2.2). Multivariate correlation analyses revealed head length to be most correlated to all other variables, an indication that it would be the most appropriate variable for use in size-correction. Although bivariate regression analyses of raw size-corrected data show highly significant relationships between relative SVL (rSVL), tail length (rTL), total length (rTotal), relative midbody width (rMBW), changes in relative fore- (rFLL) and hind limb (rHLL) lengths, several of these significant relationships disappear when phylogeny is taken into account (Table 2.2). However, the opposite is true of the relationship between several of these characters (rSVL, rTL, rTotal, and rMBW) and raw digit numbers and presacral vertebrae numbers, where regression analyses of all three methods of size-correction result in highly significant relationships only when phylogeny is taken into account (Table 2.2). Finally, regression analyses of raw, non-size-corrected measurements of limb length, digit numbers, and presacral vertebrae numbers show highly significant relationships regardless of whether phylogeny is taken into account (Table 2.3). 63 Table 2.2. Bivariate regression analyses of meristic and mensural variables associated with the transition from pentadactyl to limbless body plans in squamates. Each regression analysis was performed using relative size measurements (rSVL, rTL, rTotal, rMBW, rFLL, rHLL) calculated from raw data (Raw), raw data that has been phylogenetically size-corrected (Raw PSC), regression residual-based size-corrected independent contrasts (RSC-IC), and phylogenetic size-corrected independent contrasts (PSC-IC). All phylogenetic size-corrections were conducted in R following the methods of Revell (2009). Significant P-values at α ≤ 0.05 are shown in bold, with P-values significant after a table-wide Benjamini and Hochberg (1995) correction marked with an asterisk. 64 R aw R aw P SC R SC -I C PS C -I C df = 3 1 df = 3 1 df = 3 0 df = 3 0 In de pe nd en t va ria bl e D ep en de nt va ria bl e R2 P R2 P R2 P R2 P rS V L PS V 0. 03 8 0. 28 4 0. 11 4 0. 05 9 0. 44 7 < 0. 00 1* 0. 24 0 0 .0 05 * rS V L rF LL 0. 76 9 < 0. 00 1* 0. 53 0 < 0. 00 1* 0. 25 2 0 .0 04 * 0. 27 7 0 .0 02 * rS V L rH LL 0. 70 8 < 0. 00 1* 0. 56 2 < 0. 00 1* 0. 22 0 0 .0 08 * 0. 31 1 0 .0 01 * rT L PS V 0. 03 4 0. 31 1 0. 03 0 0. 34 5 0. 08 4 0. 11 3 0. 10 2 0. 08 0 rT L rF LL 0. 55 1 < 0. 00 1* 0. 00 0 0. 93 9 0. 00 1 0. 84 8 0. 00 4 0. 73 2 rT L rH LL 0. 49 7 <0 .0 01 * 0. 00 0 0. 96 9 0. 00 2 0. 80 9 0. 00 0 0. 96 0 rT ot al PS V 0. 03 8 0. 28 5 0. 00 4 0. 74 2 0. 22 3 0 .0 07 * 0. 16 4 0 .0 24 * rT ot al rF LL 0. 69 6 < 0. 00 1* 0. 16 6 0 .0 21 * 0. 05 9 0. 19 0 0. 04 3 0. 26 1 rT ot al rH LL 0. 63 2 < 0. 00 1* 0. 19 1 0 .0 12 * 0. 03 0 0. 34 9 0. 07 4 0. 14 0 rM B W PS V 0. 03 0 0. 34 0 0. 01 5 0. 50 5 0. 19 6 0 .0 13 * 0. 19 4 0 .0 13 * rM B W rF LL 0. 63 6 < 0. 00 1* 0. 07 1 0. 14 1 0. 19 7 0 .0 12 * 0. 17 3 0 .0 20 * rM B W rH LL 0. 58 3 < 0. 00 1* 0. 06 3 0. 16 6 0. 19 9 0 .0 12 * 0. 16 8 0 .0 22 * rF LL Fi ng er s 0. 12 3 0. 04 9 0. 60 6 < 0. 00 1* 0. 39 6 < 0. 00 1* 0. 26 0 0 .0 03 * rH LL To es 0. 15 4 0 .0 26 * 0. 56 8 < 0. 00 1* 0. 40 6 < 0. 00 1* 0. 22 0 0 .0 08 * rF LL PS V 0. 02 9 0. 34 9 0. 29 7 0 .0 01 * 0. 42 9 < 0. 00 1* 0. 18 0 0 .0 17 * rH LL PS V 0. 02 6 0. 37 4 0. 28 1 0 .0 02 * 0. 39 7 < 0. 00 1* 0. 14 8 0. 03 3 PC 1 Fi ng er s 0. 17 3 0 .0 18 * 0. 43 1 < 0. 00 1* 0. 10 8 0. 07 6 0. 06 2 0. 18 5 PC 1 To es 0. 21 3 0 .0 08 * 0. 46 2 < 0. 00 1* 0. 26 1 0 .0 04 * 0. 15 3 0. 03 2 PC 1 PS V 0. 00 3 0. 77 0 0. 14 1 0 .0 34 0. 56 5 < 0. 00 1* 0. 32 4 0 .0 01 * ! 65 Table 2.3. Bivariate regression analyses of non-size-corrected meristic and mensural variables associated with the transition from pentadactyl to limbless body plans in squamates for raw values and independent contrasts. Significant P-values at α ≤ 0.05 are shown in bold, with P-values significant after a table-wide Benjamini and Hochberg (1995) correction marked with an asterisk. Raw Independent Contrasts df = 31 df = 30 Independent variable Dependent variable R 2 P R2 P FLL Fingers 0.936 < 0.001* 0.346 < 0.001* HLL Toes 0.948 < 0.001* 0.461 < 0.001* Fingers Toes 0.978 < 0.001* 0.686 < 0.001* FLL PSV 0.673 < 0.001* 0.642 < 0.001* HLL PSV 0.697 < 0.001* 0.661 < 0.001* 66 Figure 2.2. Four morphology-based hypotheses tested in the study, derived from hypothesized patterns of body form evolution in squamate reptiles. Each hypothesis is illustrated by constraint trees used in AU and Bayesian tests. The highest P-values recovered from each AU test (AU), and the posterior probabilities (PP) of the constraint topology, are shown. aAnalyses conducted on constraint topologies with and without the inclusion of Brachymeles miriamae. bAnalyses repeated for individual clades within Philippine Brachymeles as well as for the entire genus. 67 68 Correlation analyses of pairs of variables shown to have significant relationships in bivariate linear regressions revealed positive and negative correlations with changes in body and limb size and changes in limb lengths and numbers of digits and presacral vertebrae. Multivariate analyses (PCA) of all three sets of data gave highly consistent results, showing strong separation between qualitatively defined (above) body forms of Brachymeles (Fig. 2.4, Appendix III). When all ten variables were included in a PCA, the first principal component explains 85.6% of the variation in the non-phylogenetic data. Size-corrected measures of body width and limb lengths, as well as digit numbers show positive loadings on the first principal component, with size-corrected measures of body length and presacral vertebrae numbers loading negatively (Fig. 2.4). The second principal component explains significantly less variation in the data (8.7 %), and shows moderately strong positive loadings for size-corrected body and limb lengths and digit numbers, with size-corrected measures of body width loading negatively (Fig. 2.4). Additional principal components were not retained because cumulative totals of the first two components reached nearly 95%, and subsequent components were associated with low eigenvalues (often well below 1.0), and low levels of explained variance (≤ 2.5%). All non-phylogenetic multivariate analyses support a relationship of body elongation and increased number of presacral vertebrae with decreased body width, limb lengths, and digit numbers (Appendix III). When phylogeny is taken into account, the same general pattern is observed, with the exception of the placement of Brachymeles bicolor and B. pathfinderi in morphospace. Both of these species are outliers in the observed patterns in Brachymeles (Fig. 2.4). 69 Table 2.4. Correlation analyses of pairs of morphological variables showing significant relationships from bivariate regression analyses. Relative measures of body size are based on regression residual, size-corrected independent contrasts. Values represent the Pearson product-moment correlation coefficients. Variable 1 Variable 2 PMCC rSVL PSV 0.6587 rSVL rFLL -0.4770 rSVL rHLL -0.5211 rTotal PSV 0.4643 rMBW PSV -0.4592 rMBW rFLL 0.4459 rMBW rHLL 0.4426 rFLL Fingers 0.6346 rHLL Toes 0.6354 rFLL PSV -0.6684 rHLL PSV -0.6559 PC1 Toes -0.3290 PC1 PSV 0.7520 FLL Fingers 0.6076 HLL Toes 0.6885 Fingers Toes 0.8254 FLL PSV -0.8153 HLL PSV -0.8107 70 Morphological thresholds Threshold plots revealed a general trend of increased body length associated with decreased limb lengths and numbers of digits (Fig. 2.5); however, no obvious threshold values exist for which all digits are lost or all external fore- and hind limb elements are lost (Fig. 2.5). There appears to be a general threshold of relative SVL and MBW after which relative limb lengths are greatly reduced and digits are lost. With the exception of Brachymeles bicolor and B. pathfinderi, species with a SVL > ~ 12 times its head length, and a MBW ≤ ~ 1.3 times its head length, have considerably smaller, non-pentadactyl limbs (Fig. 2.5). Digit loss was also associated with changes in relative limb lengths as well as raw limb lengths, and general threshold values are observed (Fig. 2.5). Again, with the exception of B. pathfinderi, loss of fore-limb digits appears to be initiated in species with fore-limb lengths ≈ head length, and raw fore-limb lengths < ~ 5.8 mm. Loss of hind limb digits appears to be initiated with hind limb lengths ≤ ~ 1.75 times head length, and raw hind limb lengths < ~ 12.2 mm. Additionally, the increase in number of presacral vertebrae is associated with both a loss of digits as well as a decrease in relative limb lengths (Fig. 2.5). No species with greater than 41 presacral vertebrae possessed five fingers, and when we exclude the apparent outlier (B. bicolor), fore-limb digit loss appears to be initiated in species with greater than 34 presacral vertebrae. With the exception of B. pathfinderi, hind limb digit loss follows an identical pattern. Relative fore-limb and hind limb lengths were observed to decrease by > ~ 40% and > ~ 47% respectively, in species with greater than 41 presacral vertebrae (Fig. 2.5). With few exceptions, threshold plots revealed numerous cases in which different areas of morphospace were occupied by either pentadactyl or non-pentadactyl species, with little to no overlap. 71 Figure 2.3. Graphical representation of phylogenetic signal observed for morphometric variables measured for this study. The mean species’ values for each measured variable, and body forms for each species of Brachymeles, are mapped onto the chronogram for reference. 72 73 Figure 2.4. Multivariate plots of morphometric and meristic data showing variable loadings for the first and second components for a phylogenetic PCA. Colored spheres indicate body form groups among Brachymeles, with shapes referring to labeled phylogenetic clades in Figure 2.1. 74 75 Figure 2.5. Bivariate scatter plots exploring hypothesized thresholds of relative body and limb lengths, relative body width, raw limb lengths, and numbers of presacral vertebrae at which changes in digit number and limb length occur (Brandley et al. 2008). Body proportions are derived from previous studies and were obtained by dividing raw measures of snout–vent length (SVL), fore-limb length (FLL), hind limb length (HLL), and midbody width (MBW) by head length (HL). Hypothesized morphological thresholds indicated by gray boxes, with proposed outliers labeled for reference. 76 77 Evidence of evolutionary re-acquisition of complex characters Although the placement of Brachymeles within the family Scincidae remains somewhat ambiguous (Brandley et al. 2005, 2008; Siler et al. 2011; Fig. 2.1), the impact of ancestral body form for all Brachymeles does not appear to heavily impact ancestral reconstructions within the genus (not shown). The results of analyses of limb, digit, and ear opening states are never significantly impacted by placing restrictions on the ancestral character states among outgroup taxa and the node giving rise to all Brachymeles (not shown). Exploration of the assumed ancestral character states among outgroup taxa always resulted in highly consistent reconstructions for ingroup nodes. Additionally, our inclusion of a large, diverse group of outgroup taxa aided in avoiding some of the pitfalls of ancestral state reconstructions highlighted by other researchers (Goldberg and Igic 2008). Ancestral state reconstructions for limbs and ear openings resulted in support for models with equal rates of character gain and loss. The likelihood scores were nearly identical between analyses of a two-rate model versus an equal rates model, with the Bayes factor (limbs, 0.562; ear openings, 0.706) providing non-significant support for the more parameterized models. We therefore used equal rates models for all subsequent analyses. Ancestral limb state reconstruction analyses resulted in four nodes where the reconstructed ancestral state is ambiguous, with the limbed state preferred in all cases with varying degrees of support (Fig. 2.6). These results weakly support the hypothesis of limbed ancestors in Brachymeles (Fig. 2.6). The ancestral reconstructions of ear openings supported a minimum of three state changes to have occurred (Fig. 2.6). Unlike the support observed for unidirectional limb loss within Brachymeles, we consistently observe strong support for the re-acquisition of ear openings within the Philippine clade, with one or two subsequent losses of the character (Fig. 2.6). 78 Exploratory analyses of digit evolution resulted in unequivocally strong support for the same two-rate unordered model of character evolution that best explained the data for the hand and foot (Table 2.5). Not only were the resulting likelihood values significantly better than those from analyses of other models, but Bayes factors of pairwise comparisons to the preferred model, with the exception of the unordered model A for toe evolution (Bayes factors = 8.339), were all greater than 10 (Table 2.5). Significantly, both unordered models (those allowing for different rates of character loss and acquisition) provide better fit to the data than ordered or unidirectional models (Table 2.5). Evidence of digit re-acquisition is observed for both the hand and foot, with strong support for the re-evolution of a pentadactyl hand from a digit-reduced ancestor (Fig. 2.7; Table 2.6). Within the Philippine species, there is moderate to strong evidence for six instances of digit re-acquisition on the hand and five instances on the foot (Fig. 2.7; Table 2.6). Although all analyses provide unequivocal support for several instances of digit re-acquisition, many additional nodes receive ambiguous ancestral state reconstructions, indicating that the potential number of times digits have re-evolved in Brachymeles may be higher or lower than the number we currently observe (Fig. 2.7; Table 2.6). As noted in previous studies (Brandley et al. 2008), the results of ordered analyses (not shown) provide highly similar to identical ancestral reconstructions, but at times these reconstructions are more ambiguous. Regardless of the model, all analyses result in strong support for the re-evolution of a fully pentadactyl body form from an ancestor with reduced numbers of digits, with ordered models providing even less support for a pentadactyl ancestor (Fig. 2.7). Digit re-acquisition in Brachymeles appears to be equally common on the hand and foot, with evidence for the re- acquisition of 1–5 digits (Fig. 2.7; Table 2.6). 79 Table 2.5. BayesTraits models of digit evolution explored in ancestral state reconstructions, and subsequent results. Transition descriptions and the number of parameters are shown for reference. Table entries include the mean likelihood for each model followed by the standard deviation, the harmonic mean likelihood value, and the Bayes factors from bivariate comparisons with the model that best explains the data. Preferred model in bold for emphasis. 80 M od el St at e tra ns iti on s Pa ra m et er -L i -H M L i 2 ln B F M an us A U no rd er ed (a ll tra ns iti on s be tw ee n di gi t s ta te s oc cu r a t e qu al ra te s) q0 1 = q1 0 -5 7. 38 62 2 ± 0. 90 6 -5 8. 09 15 3 12 .9 03 B O rd er ed (s in gl e st at e tra ns iti on s al lo w ed o nl y) q0 1 = q1 0 -6 2. 62 20 1 ± 1. 07 6 -6 3. 57 49 8 23 .8 70 C U no rd er ed (a ll st at e tr an si ti on s al lo w ed ) q0 1 ! q 10 -5 0. 63 11 8 ± 1. 00 9 -5 1. 63 98 3 0 D O rd er ed (s in gl e st at e tra ns iti on s al lo w ed o nl y) q0 1 ! q 10 -5 7. 46 33 1 ± 1. 60 8 -6 0. 10 42 8 16 .9 29 E U ni di re ct io na l ( di gi t g ai n pr oh ib ite d) q1 0 -6 3. 40 82 5 ± 1. 10 4 -6 4. 62 09 5 25 .9 62 Pe s A U no rd er ed (a ll tra ns iti on s be tw ee n di gi t s ta te s oc cu r a t e qu al ra te s) q0 1 = q1 0 -5 8. 07 33 8 ± 0. 84 6 -5 8. 95 08 1 8. 33 9 B O rd er ed (s in gl e st at e tra ns iti on s al lo w ed o nl y) q0 1 = q1 0 -6 2. 37 96 9 ± 1. 03 3 -6 3. 91 87 1 18 .2 75 C U no rd er ed (a ll st at e tr an si ti on s al lo w ed ) q0 1 ! q 10 -5 3. 83 90 6 ± 0. 99 8 -5 4. 78 14 1 0 D O rd er ed (s in gl e st at e tra ns iti on s al lo w ed o nl y) q0 1 ! q 10 -5 7. 04 62 2 ± 1. 36 2 -6 0. 12 49 3 10 .6 87 E U ni di re ct io na l ( di gi t g ai n pr oh ib ite d) q1 0 -6 9. 38 82 4 ± 1. 27 4 -7 0. 72 88 7 31 .8 95 ! 81 Table 2.6. Statistical support for re-acquisition of digits and ears in Brachymeles. Data are only presented for species where moderate to high evidence exists for the re-acquisition of digits or external ear openings. Ancestral character states making up ≥ 0.95 of the posterior probability are listed, with Bayes factors indicating the preferred state in cases of ambiguous state reconstruction. The posterior probability of the preferred ancestral state is provided for reference, with probabilities above 0.95 bolded for emphasis. Clade references refer to those labeled in Figure 2.7. 82 Li ne ag e A nc es tra l s ta te Ext an t st at e Pr efe rr ed a nc es tra l st at e (2 ln B F) Po st er io r p ro ba bi lit y of pr efe rr ed a nc es tra l s ta te Fi ng er s A ll Br ac hy m el es 0, 1, 2, or 3 0– 5 0 (8 .5 4– 9. 04 ) 0 (0 .8 90 ) Ph ili pp in e Br ac hy m el es + B. m ir ia m ae 0, 1, 2, or 3 0– 5 0 (7 .7 7– 12 .9 0) 0 (0 .8 79 ) Cla de A 0 0, 1, 2, or 3 – 0 (0 .9 64 ) Cla de B 0 0, 1, 2, or 3 – 0 (0 .9 69 ) Cla de C 0 0, 2, or 3 – 0 (0 .9 98 ) Cla de D 0 0 or 2 – 0 (0 .9 60 ) B. c f. bo ni ta e (L uzo n) 0 1 – 0 (0 .9 79 ) B. c f. bo ni ta e (L ub an g) 0 or 2 2 0 (1 2. 18 ) 0 (0 .8 92 ) B. tr id ac ty lu s 0 or 3 3 0 (1 2. 43 ) 0 (0 .8 84 ) B. s am ar en si s ( Sa m ar ) 0 or 2 2 0 (5 .2 9) 0 (0 .5 50 ) B. c f. sa m ar en si s ( Cat an du an es ) 0 or 2 2 0 (7 .2 3) 0 (0 .9 13 ) B. e le ra e 3 or 4 4 3 (5 .4 1) 3 (0 .8 24 ) Toe s Cla de E 0 0, 1, 2, or 3 – 0 (0 .9 57 ) Cla de F 0 0, 1, 2, or 3 – 0 (0 .9 99 ) Cla de G 0 0, 1, or 2 – 0 (0 .9 98 ) B. b on ita e (L uzo n) 0 or 2 1 or 2 0 (1 3. 70 ) 0 (0 .8 27 ) B. c f. bo ni ta e (L uzo n) 0 1 – 0 (0 .9 67 ) B. tr id ac ty lu s 0 or 3 3 0 (1 2. 14 ) 0 (0 .8 26 ) B. c f. sa m ar en si s ( Le yt e) 1, 2, or 3 2 or 3 2 (5 .0 8– 5. 44 ) 2 (0 .7 36 ) B. e le ra e 3 or 4 4 3 (4 .0 4) 3 (0 .7 79 ) Ea rs A ll Br ac hy m el es A bs en t A bs en t, p re se nt – A bs en t ( 0. 96 6) Ph ili pp in e Br ac hy m el es A bs en t, p re se nt A bs en t, p re se nt A bs en t ( 5. 09 ) A bs en t ( 0. 61 9) B. e le ra e A bs en t Pr es en t – A bs en t ( 0. 99 9) ! 83 Discussion Patterns of limb reduction and loss Topology tests rejected single origins of digit reduction, limb loss, and ear loss, and rejected the hypothesis of a gradual transition from pentadactyl to limbless body plans within Brachymeles, regardless of the inclusion of B. miriamae (Fig. 2.2). Phylogenetic analyses and ancestral state reconstructions provide support for multiple origins of body form changes within Brachymeles. We find evidence for three losses of external limb elements, and three distinct instances of changes in digit states. Although five species of Brachymeles are externally limbless (B. apus, B. minimus, B. miriamae, B. lukbani, B. vermis), internal pectoral and pelvic girdle elements are visible in x-rays of all five species (CDS, pers. obs.), indicating that the species have retained some vestigial elements of limbs. Previous studies have shown that reductions in digit number are more common in the fore-limbs of scincid lizards, with only four genera possessing species with the opposite pattern (Bipes [Bipedidae], Bachia [Gymnopthalmidae], Anomolopus [Scincidae], and Teius [Teiidae]; Brandley et al. 2008; Skinner and Lee 2010); however, in contrast all species and populations with unequal digit numbers in the fore- and hind limbs have fewer toes than fingers in Brachymeles (B. bonitae, B. cebuensis, B. pathfinderi, B. samarensis). The results of regression and correlation analyses are for the most part consistent with the results of previous studies (Tables 2.2–2.4), with many of the general patterns observed across squamates also observed for Brachymeles. We find a strong relationship between limb reduction, body elongation, and digit loss (Tables 2.2–2.4). Additionally, body width and vertebral changes are also strongly associated with body and limb length changes and digit loss (Tables 2.2–2.4). Relative measures of tail and total lengths either are not correlated with limb reduction, vertebral changes, and digit loss, or only are correlated with changes in the number of presacral vertebrae 84 (Table 2.2). This result is consistent with our knowledge of the ecology of Brachymeles (Brown and Alcala 1980; Siler 2010; Siler et al. 2009a, 2010a,b; Siler and Brown 2010; Siler et al. 2011, in press a,b,c,d); in this genus, all species are fossorial or semi-fossorial and elongation of the body results predominately from increasing SVL, not TL (Tables 2.2, 2.4). Multivariate analyses further support the patterns of body form change highlighted in bivariate analyses (Tables 2.2, 2.4; Fig. 2.4, Appendix III). Changes in body shape are moderately correlated with hind limb digit loss and strongly correlated with changes in presacral vertebrae number (Tables 2.2, 2.4). In general, limb reduction and subsequent loss and digit loss are associated with longer, narrower bodies and increased numbers of presacral vertebrae (Fig. 2.4, Appendix III). We explored patterns of morphological evolution from two points of view: 1) patterns that can be directly observed and empirically quantified, and 2) those that hold regardless of phylogenetic relationships. It is commonly the case that significant relationships and correlations between characters become weaker or non-significant when a phylogenetic context is employed (Cronquist 1981; Kelly and Purvis 1993; Kelly 1995; Kelly and Beerling 1995; Ackerly and Reich 1999; Hutcheon et al. 2002)—a pattern observed in this study. However, our analyses also revealed the opposite pattern to occur as well: numerous significant relationships between morphological characters appeared only after taking phylogeny into account, suggesting that the use of an historical context for comparative analyses incorporated via phylogeny can reveal novel and significant statistical support for otherwise undetectable patterns of character correlation. Our exploration of morphological thresholds in Brachymeles reveals several interesting and unexpected patterns. Brandley et al.’s (2008) study of squamate body form evolution revealed 85 two regions of morphospace to be unoccupied: species with short limbs and multiple digits, and species with long limbs and no digits. For example, no species with limb lengths less than half their HL have been shown to have multiple digits. However, the results of this study provide evidence for both of these morphologies to be occupied by species of Brachymeles (Fig. 2.5). For example, with the exception of B. elerae, all species with 1–3 fingers have fore-limb lengths less than half their HL, and a population of B. bonitae with two toes has a HLL less than half its HL. Additionally, the observed relationships between raw limb lengths and digit loss also do not directly follow previous studies (Brandley et al. 2008). Seven species with fore-limb lengths less than 2 mm possess more than one finger, and six species with hind limb lengths less than 3.1 mm possess more than one toe (Fig. 2.5). Another previously undocumented extreme is also exhibited in Brachymeles. To the best of our knowledge, this study is the first to provide evidence for species lacking digits to have longer limb lengths than species with multiple digits (Fig. 2.5). This indicates that even within this relatively small radiation of skinks, there are exceptions to general, previously documented, and widely accepted (see Brandley et al. 2008, for review) patterns of body form change. These findings have general implications, and potentially suggest that whatever functional, mechanical or developmental constraints have shaped morphological evolution among other lizards (except Bipes) may have been lost in Brachymeles. In all threshold plots, two outliers were consistently recovered (B. bicolor and B. pathfinderi; Fig. 2.5). Both of these species represent unique morphologies within the genus, with B. bicolor representing by far the longest species of Brachymeles, and B. pathfinderi being the only digit reduced species to be nested within a clade of pentadactyl species (Fig. 2.1). Despite these outlier species, we observe general patterns of body form change. Loss of fingers appears to occur when relative and raw FLL ≤ 1.0 and 5.8 mm, respectively, and loss of toes occurs when 86 relative and raw HLL ≤ 1.75 times HL and 12.2 mm, respectively (Fig. 2.5). Excluding B. bicolor and B. pathfinderi, body plan shifts towards limb reduction and digit loss are clearly visible along the spectrum of observed midbody widths and numbers of presacral vertebrae (Fig. 2.5). We compared two common methods for size correction while exploring whether head length is an appropriate measure with which to correct for size. The results of analyses using size-corrected data from the phylogenetic size-correction method of Revell (2009), or the commonly used size-correction method based on residuals from linear regression analyses of independent contrasts (Garland 1992), were highly consistent (Table 2.2). Although using alternative characters for size correction (SVL, MBW) in regression, correlation, and multivariate analyses showed highly consistent results (not shown), multivariate correlation analyses indicated that, for Brachymeles, head length is the most appropriate variable for size correction. Comparisons of principal component analyses with raw, size-corrected data, and phylogenetic PCAs (Revell 2009), showed highly consistent results in the values, loadings, and scores of the analyses, as well as in the partitioning of species in morphospace (Fig. 2.4, Appendix III). Complex character "re-evolution" and Dollo’s Law Most previous studies of squamate limb and digit evolution have worked within the framework of unidirectional character loss (see Brandley et al. 2008, for review). Although several recent studies have provided numerous lines of evidence for the re-evolution of digits among squamate reptiles (Kohlsdorf and Wagner 2006; Brandley et al. 2008; Kohlsdorf et al. 2010; but see Galis et al. 2010), the hypothesis of digit evolution occurring in an ordered sequence (e.g., Alberch and Gale 1985; Shubin and Alberch 1986; Shapiro 2002) has led to little exploration of disparate models of character evolution. Recently, Skinner and Lee (2010) and 87 Skinner (2010) showed that unordered models of character evolution provided the best fit data on fore- and hind limb digits in Lerista (one of the four genera to possess species with fully limbed, intermediate, and limbless body forms). However, Bayes factors we inferred in this study showed weak positive support for their best-fit model (Kass and Raftery 1995; Nylander et al. 2004). Surprisingly, the studies of Lerista did not find evidence for digit re-acquisition (Skinner et al. 2008; Skinner and Lee 2009, 2010; Skinner 2010) whereas in this study, we found one of the first documented cases of high statistical support for complex character re-acquisition in a clade of closely related species. We considered applying a model that takes into account state-specific rates of speciation and extinction (BiSSE, Maddison et al. 2007). The assumptions of the BiSSE model’s original implementation included analyzing trait-dependent diversification for: (1) binary characters only, (2) completely resolved, known phylogenies (= no missing taxa), and (3) large phylogenies. FitzJohn et al. (2009) relaxed one of these assumptions (complete taxon sampling); however, our dataset violates three (original), and both (current), assumptions of the model and preclude its implementation in this study. Evaluations of this model’s limitations for smaller datasets are needed in which only a few changes in character states have taken place. Considering our robust datasets, phylogeny, and best-fit models of character evolution, the phylogenetic results of this study unambiguously support five instances of digit re-acquisition in the hand and four instances of digit re-acquisition in the foot (Fig. 2.7; Table 2.6). Additionally, Bayes factors comparing preferred states for eleven ambiguously reconstructed nodes moderately to highly support an ancestral state with fewer digits than that observed in extant species (Fig. 2.7; Table 2.6). In contrast, the data also support independent instances of complete loss of external limb elements (Fig. 2.7). 88 Figure 2.6. Maximum clade credibility chronograms and estimated ancestral states of limb and ear opening presence or absence in Brachymeles skinks. Ancestral state reconstructions are indicated at each node. Triangles indicate unambiguous reconstructions of a character state (posterior probability ≥ 0.95), colored according to the hypothesized state. Circles represent ambiguous character reconstructions, with colors representing the preferred state and values showing the Bayes factor as an indication of the strength of support for that state. Colored blocks at each ambiguous node represent alternate states supported in analyses. 89 90 Figure 2.7. Maximum clade credibility chronograms and estimated ancestral states of limb and ear opening presence or absence in Brachymeles skinks. Ancestral state reconstructions are indicated at each node. Triangles indicate unambiguous reconstructions of a character state (posterior probability ≥ 0.95), colored according to the hypothesized state. Circles represent ambiguous character reconstructions, with colors representing the preferred state and values showing the Bayes factor as an indication of the strength of support for that state. Colored blocks at each ambiguous node represent alternate states supported in analyses. The posterior probabilities of a 5-digit fore- and hind limb ancestral state to all Brachymeles, B. miriamae + Philippine Brachymeles, and Philippine Brachymeles resulting from the ordered model of Brandley et al. (2008) and the best fit, unordered model shown for reference. 91 92 One of our most striking findings involve support for the re-evolution of a pentadactyl body form from a digitless or digit-reduced ancestor (Fig. 2.7; Table 2.6). In exploring the impact of the model on this result, we repeated all ancestral state reconstructions with the suite of models compared in Skinner and Lee (2010). Similar to the findings of Brandley et al. (2008), ancestral reconstructions with ordered models of evolution instead of the best-fit undordered models were more ambiguous. However, regardless of the model of character evolution, all analyses preferred digitless or digit-reduced ancestral states for the nodes giving rise to all Philippines species of Brachymeles with ≥ 95% of the combined posterior probabilities of digitless and digit-reduced states for each node (Fig. 2.7). The Philippine radiation of Brachymeles includes the known diversity of pentadactyl species in the genus, which are supported to have evolved from digitless or at least digit-reduced ancestors (Fig. 2.7; Table 2.6). Although this finding stands in contrast to expectations derived from Dollo’s Law (Dollo 1893, 1905, 1922; Simpson 1953; Gould 1970), preliminary data on the phalangeal formula of species of Brachymeles supports the findings of previous studies concerning evidence for digit re-acquisition. Kolsdorf and Wagner (2006) and Brandley et al. (2008) noted several species in which digit re-evolution was reconstructed unambiguously, and phalangeal formulas are uniform among digits when compared with the primitive phalangeal formula among squamates (fore-limb: 2-3-4-5-3; hind limb: 2-3-4-5-4). Among these strongly supported instances of digit, and possibly limb, re-evolution, examples of phalangeal uniformity include Bachia (fore-limb, 0-2-2-2-2; hind limb, 2-2-2-2-0; Kolsdorf and Wagner 2006), Bipes (fore-limb, 3-3-3-3-3; Zangerl 1945), and Scelotes (fore-limb, 2-3-3-3-2; hind limb, 2-3-4-4-2; Brandley et al. 2008). Surprisingly, the phalangeal formulas of all pentadactyl species of Brachymeles show striking similarities to those observed in Scelotes (fore-limb, 2-3-3-3-2; hind 93 limb, 2-3-4-4-3; C. D. Siler, pers. obs.). Given that pentadactyl species have not lost all digit identity, it remains plausible that the observed phalangeal formulas among extant taxa is simply due to loss of phalangeal elements in the common ancestor. However, the fact that this phalangeal formula has been maintained over significant evolutionary time suggests that there may be a developmental constraint on digit morphology. Regardless of how the pentadactyl state has evolved in Brachymeles, this strange, shared phalangeal formula among all pentadactyl members of the genus may be evidence that digits have been re-acquired via a novel evolutionary pathway, unique among pentadactyl lizards. In addition to the possible re-acquisition of digits and limbs, the results of this study provide unambiguous phylogenetic support for two instances of external ear re-acquisition in Brachymeles (Fig. 2.6; Table 2.6). Although the absence of ear openings is common among small, burrowing, or semi-fossorial skinks, external ear openings invariably have been hypothesized to be lost in a unidirectional manner (i.e., present-to-absent), without reversals or re-evolution of exposed tympannae (Greer 2002). Not only do we demonstrate strong evidence for the re-acquisition of external ear openings in Brachymeles, but at least one subsequent, additional or secondary, loss of this character is strongly inferred to have taken place leading to the extant character state observed in B. muntingkamay (Fig. 2.6). These findings are the first of their kind, and suggest that the previous assumption about the unidirectionality of changes in this character may be incorrect. Presently, it is not clear whether the loss of external ear openings in Brachymeles involves a re-structuring of bone or simply a re-structuring of skin, the former process presumably being more complex of a morphological change. If all species with external ear openings possess an atypical inner ear morphology, the finding would lend additional support to members of the genus having re-evolved complex characters via a novel evolutionary pathway. 94 Conclusions Our data represent one of the most comprehensive, fine-scaled, studies of body-form evolution to date for a closely related group of lizards. Not only have we sampled nearly every recognized species within the genus Brachymeles, but also we have sufficient sampling to investigate intraspecific variation within many species (e.g., Brachymeles bonitae and B. samarensis). Coupled with this nearly complete taxonomic sampling, our robust morphological and molecular dataset provide a rich system with which to address questions concerning body form evolution within one of the few genera to possess the full suite of body forms extremes, including representatives inhabiting previously undocumented portions of body form morphospace. Although within the genus, general external morphologies appear conservative, on the whole, Brachymeles appears to occupy previously undocumented regions of morphospace (Fig. 2.4, 2.5, Appendix III). Examples of this include species with relatively tiny limbs and multiple digits and species with relatively longer limbs and no digits (Fig. 2.5). Multivariate analyses of morphological data indicate species with similar body forms have evolved into similar regions of morphospace (Fig. 2.4, Appendix III). Ancestral character state reconstructions are limited in that they provide only a statistical framework with which to investigate data in the context of a reduced tree with branch lengths and a single character per terminus. With that in mind, there are two perspectives to consider when interpreting the results of this study: (1) what do our data, phylogeny, and best-fit models of character evolution tell us about the prevalence and directionality of body form evolution in Brachymeles? And (2) what are the limitations of our data and analyses for making these 95 inferences? Although alternative explanations are possible, we believe that the strong statistical support uncovered here for the reversibility of complex characters in a closely related group of lizards is some of the most compelling recent examples of clear exceptions to Dollo’s Law. Regardless of the perspective, it is clear that multiple instances of digit and ear state changes have occurred during the evolutionary history of Brachymeles. Considering the comprehensive and fine-scale approach to this study, the results of ancestral state reconstructions support the re-acquisition of both digits and external ear openings. Furthermore, all analyses support the re-acquisition of a pentadactyl body form from a digitless or digit-reduced ancestor, regardless of the model enforced. Although these results are novel, it is important to consider the limitations of our data and methods of inference. Due to disproportional diversification in the archipelago, undiscovered mainland diversity, and/or massive extinction outside the archipelago, nearly all of the known diversity within Brachymeles is endemic to the Philippines. The only three non-Philippine species (Brachymeles apus, Brachymeles cf. apus, and B. miriamae) are all limbless and sister to the Philippine radiation (Fig. 2.1). Even with a near complete range of body forms within the genus, the majority of the variation occurs within two major clades (Fig. 2.1, Clade 1, 2), with all pentadactyl species part in Clade 2. With this in mind, it is conceivable that there have been multiple independent losses of limbs, digits, and external ear openings giving rise to the Philippine radiation. If this were plausible, such a scenario would suggest that many of the pentadactyl species with external ear openings gave rise to the currently recognized diversity of Brachymeles and have either gone extinct or have yet to be discovered. However, we consider the above scenario unlikely due to the fact that the mainland Southeast Asian herpetofauna has become very well known as a result of extremely active field work in the region (e.g., Van Dijk 96 et al. 1998; Chanard et al. 1999; Malkmus et al. 2002; Pauwels et al. 2003; Grismer et al. 2006a,b; Das 2007, 2010; Manthey and Grossmann 1997; Sang et al. 2009), and no fossil evidence has come to light suggesting otherwise. With the comprehensive nature of this and previous studies, we are likely approaching a methodological limit to our ability to understand the processes behind body form change in Brachymeles. The phylogenetic evidence at hand unambiguously supports the evolution of unique body morphologies and the re-acquisition of complex characters. However, support for the directionality of character change will remain debatable until these patterns are investigated with new approaches, including developmental, ecological, and behavioral studies. Regardless, our results provide new, detailed, insight into heretofore incompletely understood range of diversity in this widespread and conceptually intriguing process of body form evolution among squamate reptiles. 97 CHAPTER 3 Phylogeny-based species delimitation in Philippine slender skinks (Reptilia: Squamata: Scincidae: Brachymeles): taxonomic revision of pentadactyl species groups and description of three new species There are only four genera of scincid lizards possessing both fully limbed and limbless species (Brachymeles, Chalcides, Lerista, and Scelotes; Lande, 1978; Wiens and Slingluff, 2001; Brandley et al., 2008). Within the genus Brachymeles, all but one of the 18 recognized species are endemic to the Philippines. The exception is B. apus from northern Borneo (Brown and Alcala, 1980; Hikida, 1982; Siler et al., 2009a, 2010a,b). Six species are pentadactyl (B. bicolor, B. boulengeri, B. gracilis, B. makusog, B. schadenbergi, and B. talinis), eight are non-pentadactyl, with reduced limbs and numbers of digits (B. bonitae, B. cebuensis, B. elerae, B. muntingkamay, B. pathfinderi, B. samarensis, B. tridactylus, and B. wrighti), and four are entirely limbless (B. apus, B. minimus, B. lukbani, and B. vermis). Within the non-pentadactyl species (Duméril and Bibron, 1839; Brown, 1956; Brown and Rabor, 1967; Taylor, 1917, 1925, 1918) exist a wide range of limb- and digit-reduced states, from minute limbs that lack full digits (B. bonitae, B. cebuensis, B. muntingkamay, B. samarensis, B. tridactylus), to moderately developed limbs with four to five digits on the hands and feet (B. elerae, B. pathfinderi, B. wrighti: Brown and Alcala, 1980; Hikida, 1982; Siler et al., 2009a, 2010b). All species are semi-fossorial and typically found in dry, rotting material inside decaying logs or in loose soil and leaf litter. Shared body plans and similar external morphological features among populations of Brachymeles has proven problematic for diagnosing species (Brown and Alcala, 1980; Siler et al., 98 2009a, 2010a,b). Additionally, several rare, mid-to-high elevation species have long been represented by only a few specimens, in some cases without knowledge of their exact type locality (e.g., Brachymeles bicolor, B. elerae, B. wrighti, B. pathfinderi). Three species are polytypic: B. boulengeri contains four subspecies and B. gracilis and B. schadenbergi each contain two (Brown, 1956; Brown and Rabor, 1967; Brown and Alcala, 1980). Several other species are recognized as having widespread distributions that span historical faunal demarcations in the Philippines (Heaney, 1985, 1986; Brown and Guttman, 2002; Brown and Diesmos, 2002), including B. talinis, B. samarensis, and B. bonitae (Brown, 1956; Brown and Rabor, 1967; Brown and Alcala, 1980). Taxonomic History The genus Brachymeles was first described by Duméril and Bibron (1839) for the small, limb-reduced species Brachymeles bonitae. Three additional species (Senira bicolor [Gray, 1845], Eumeces (Riopa) gracilis [Fischer, 1885], E. (R.) schadenbergi [Fischer, 1885]) were transferred to the genus by Boettger (1886) and Boulenger (1887). These four species represented the known diversity in the genus for thirty years, until Taylor published a series of herpetofaunal descriptions in the early 1900s. In Taylor’s (1917) review of the genus, he revised B. gracilis to not only include populations in the Mindanao Faunal Region, but also populations on Negros and Mindoro islands (Fig. 3.1). A few years later, Taylor (1922c) described B. boulengeri, based on material from Polillo Island, and included populations from Luzon, Mindoro, and Negros islands as representatives of the species (Fig. 3.1). Thirty years later, Brown (1956) described B. gracilis taylori, and included B. boulengeri as one of three subspecies of the polytypic species B. gracilis. Brown and Rabor’s (1967) description of B. gracilis boholensis and B. g. mindorensis brought the number of subspecies within B. gracilis to five. It was not 99 Figure 3.1. Map of the Philippine islands, with island labels provided for islands with representative samples used for this study. The five recognized major Pleistocene Aggregate Island Complexes (PAICs), major island groups, and additional deep-water islands are labeled for reference. Islands of the Romblon Island Group are designated by the first letter of the island name (T, Tablas Island; R, Romblon Island; S, Sibuyan Island). Current islands in the Philippines are shown in medium grey; light gray areas enclosed in black 120 m bathymetric contours indicate the hypothesized maximum extent of land during the mid- to late Pleistocene. 100 101 until 1980 that Brown and Alcala (1980) resurrected the polytypic species B. boulengeri, and included four subspecies (B. b. boulengeri, B. b. boholensis, B. b. mindorensis, B. b. taylori), all believed to be distinct from B. gracilis. This view characterized the taxonomy of B. boulengeri for the next 30 years. Numerous authors have mentioned the morphological variation among island populations of B. boulengeri and other species (Taylor, 1922b; Brown, 1956; Brown and Rabor, 1967; Brown and Alcala, 1980), but all refrained from elevating these subspecies to full species. Brachymeles boulengeri boulengeri and B. b. taylori have larger geographic distributions across multiple islands within a single faunal region (Taylor, 1922b; Brown and Rabor, 1967; Brown and Alcala, 1980), whereas B. b. boholensis and B. b. mindorensis are single island endemics (Brown, 1956; Brown and Rabor, 1967; Brown and Alcala, 1980). Although Brachymeles talinis was described originally as B. schadenbergi talinis (Brown, 1956), and considered it part of the widespread B. schadenbergi complex from the Sulu Islands and the Mindanao, Visayan, and Luzon Pleistocene Aggregate Island Complexes (PAICs; Brown and Guttman, 2002; Brown and Diesmos, 2002), the subspecies was described on the basis of material from Negros Island (Brown, 1956). Brown (1956) referred to series of specimens from Jolo and Luzon islands as likely exemplars of B. schadenbergi talinis, and hypothesized three explanations for the unusual distribution of B. schadenbergi in the Philippines: (1) chance colonization across ocean barriers into distinct faunal regions by two subspecies; (2) morphological convergence within a polytypic species; and (3) prolonged maintenance of two morphologically similar, disjunct distributions of sibling species within the Philippines. At the time, Brown (1956) supported the first hypothesis with reservations; however, in Brown and Rabor’s (1967) review of Brachymeles, newly available material supported the third hypothesis, and led to the recognition of B. talinis from Jolo, Negros, and Luzon islands as a distinct “sibling 102 species” of B. schadenbergi populations from Basilan, Mindanao, Bohol, and Leyte islands. When Brown and Alcala (1980) revised the genus, they restricted the geographic distribution of B. talinis to the central and northern Philippine islands, and postponed the assignment of the two specimens from Jolo until the morphological variability of that island population was better understood. Although samples from throughout the central and northern range of B. talinis have been available, the recognition of this widespread species has continued for more than 40 years (Brown and Alcala, 1980; Siler et al., 2009a, 2010a,b). Following the separation of Brachymeles talinis from the B. schadenbergi complex, Brown and Rabor (1967) recognized two subspecies of B. schadenbergi, one from western and south-central Mindanao Island and Basilan Island (B. s. schadenbergi), and the other from eastern Mindanao, Camiguin Sur, Bohol, and Leyte islands (B. s. orientalis). Fischer (1885) had previously designated the type locality for B. schadenbergi as southern Mindanao Island, and specimens from south-central Mindanao Island have thus been identified as B. schadenbergi schadenbergi (Brown and Rabor, 1967; Brown and Alcala, 1980). In addition to its already broad geographic distribution, Brown and Alcala (1980) predicted that B. s. orientalis would also be observed on Samar Island. Both Brachymeles boulengeri and B. talinis are distributed across several distinct PAICs, including the Luzon, Mindanao, Mindoro, and Visayan island complexes (Fig. 3.1). Because many recent studies have revealed that few endemic Philippine reptiles actually possess broad distributions spanning these regional faunistic boundaries (Brown et al., 2000a; Brown and Diesmos, 2002, 2009; Siler et al., 2010a; Welton et al., 2009, 2010a,b), we have begun to reevaluate the known polytypic and widespread species in the genus Brachymeles. Our goal is to revise the taxonomy such that individual units (species) represent independently evolving, 103 cohesive lineage segments (sensu Simpson, 1961; Wiley 1978; Frost and Hillis, 1990; de Queiroz, 1998, 1999). Careful examination of numerous recently collected specimens from throughout the known ranges of B. boulengeri, B. schadenbergi, and B. talinis, as well as all relevant name-bearing type material, results in the reorganization of B. boulengeri, B. schadenbergi, and B. talinis into ten distinct species. In this paper we provide a phylogenetic analysis of most of these taxa, fully describe each evolutionary lineage, clarify species boundaries, and provide the first illustrations of most these taxa. We also provide information on each species’ natural history, ecology, and geographic distribution. Materials and Methods Field work, sample collection, and specimen preservation Fieldwork was conducted on Bohol, Calayan, Camiguin Norte, Camiguin Sur, Catanduanes, Dinagat, Leyte, Luzon, Masbate, Mindanao, Mindoro, Negros, Panay, Polillo, Romblon, Samar, Sibuyan, and Tablas islands, all in the Philippines (Fig. 3.1) between 1992 and 2009. Specimens were collected between 900 and 1600 hr, euthanized with aqueous chloretone, dissected for genetic samples (liver preserved in 95% ethanol or flash frozen in liquid nitrogen), fixed in 10% buffered-formalin and eventually (< 2 mo) transferred to 70% ethanol. Newly sequenced voucher specimens are deposited in U.S. and Philippine museum collections (Acknowledgments and Specimens Examined); if available, voucher information corresponding to data from GenBank sequences is included in Table 3.1. Taxon sampling and outgroup selection for phylogenetic analyses Because our primary goal was to estimate phylogenetic relationships among the subspecies and island populations of Brachymeles boulengeri, B. schadenbergi, and B. talinis, we sequenced 104 only 1–2 exemplars per species; however, in the case of a species occurring on multiple islands within a single PAIC, or across a large island such as Mindanao, we sampled multiple populations to provide greater geographic resolution. We chose two scincid taxa (Plestiodon egregius and Lygosoma bowringii) based on relationships presented in a recent phylogenetic analysis of scincid lizards (Brandley et al., 2005) as outgroups. A total of 39 ingroup samples were used to construct phylogenetic inferences. There are no tissue samples of the population of B. talinis from Jolo Island, and this population is therefore not included in the phylogenetic analyses. DNA extraction, purification, and amplification We extracted total genomic DNA from tissues (Table 3.1) using the modified guanidine thiocyanate extraction method of Esselstyn et al. (2008). The mitochondrial ATPase 8 (ATP8) and ATPase 6 (ATP6) protein coding genes were amplified using standard PCR methods with the primers ATPf (5'-CTCAGARATCTGCGGGYCAAATCACA-3') and ATPr (5'- GTGCYTTCTCGRRTAATRTCYCGTCAT-3'; M. Brandley, unpublished data). PCR products were visualized on 1.0% agarose gels, then purified them with ExoSAP-IT (US78201, Amersham Biosciences, Piscataway, NJ). Purified templates were sequenced with the same primers and the ABI Prism BigDye Terminator chemistry (Ver. 3.1; Applied Biosystems, Foster City, CA). Cycle-sequencing products were purified with Sephadex Medium (NC9406038, Amersham Biosciences, Piscataway, NJ) in Centri-Sep 96 spin plates (CS-961, Princeton Separations, Princeton, NJ). Sequencing products were run on an ABI Prism 3130xl Genetic Analyzer (Applied Biosystems). Gene sequences were assembled with Sequencher 4.8 (Gene Codes Corp., Ann Arbor, MI). 105 Table 3.1. Summary of specimens corresponding to genetic samples included in the study, general locality, and GenBank accession number. PNM/CMNH = deposited in the Cincinnati Museum of Natural History; LSUHC = La Sierra University Herpetological Collections; * = currently uncataloged specimen, deposited in the National Museum of the Philippines. 106 Sp ec ie s V ou ch er Lo ca lit y G en ba nk A cc es sio n N um be rs A TP as e 8, 6 Ly go so m a bo wr in gi LS U H C 69 70 W es t M al ay sia H Q 23 93 66 Pl es tio do n eg re gi us M V Z 11 01 3 N ot A va ila bl e N C0 00 88 8 Br ac hy m el es ta yl or i A CD 8 62 * Ph ili pp in es , C eb u Is la nd H Q 23 93 68 Br ac hy m el es ta yl or i K U 3 07 73 8 Ph ili pp in es , N eg ro s I sla nd , M un ic ip al ity o f V al en ci a, M t. Ta lin is H Q 23 93 69 Br ac hy m el es ta yl or i RM B 32 26 * Ph ili pp in es , N eg ro s I sla nd , M un ic ip al ity o f V al en ci a, M t. Ta lin is H Q 23 93 70 Br ac hy m el es m in do re ns is K U 3 07 73 9 Ph ili pp in es , M in do ro Is la nd , M un ic ip al ity o f B on ga bo ng H Q 23 93 71 Br ac hy m el es m in do re ns is K U 3 07 74 0 Ph ili pp in es , M in do ro Is la nd , M un ic ip al ity o f B on ga bo ng H Q 23 93 72 Br ac hy m el e bo ho le ns is RM B 28 66 * Ph ili pp in es , B oh ol Is la nd , M un ic ip al ity o f B ila r H Q 23 93 73 Br ac hy m el e bo ho le ns is RM B 28 75 * Ph ili pp in es , B oh ol Is la nd , M un ic ip al ity o f B ila r H Q 23 93 74 Br ac hy m el es b ou le ng er i K U 3 07 75 3 Ph ili pp in es , P ol ill o Is la nd , M un ic ip al ity o f P ol ill o H Q 23 93 75 Br ac hy m el es b ou le ng er i K U 3 07 75 4 Ph ili pp in es , P ol ill o Is la nd , M un ic ip al ity o f P ol ill o H Q 23 93 76 Br ac hy m el es b ou le ng er i K U 3 13 83 1 Ph ili pp in es , L uz on Is la nd , M un ic ip al ity o f L ab o, M t. La bo H Q 23 93 77 Br ac hy m el es b ou le ng er i K U 3 13 82 9 Ph ili pp in es , L uz on Is la nd , M un ic ip al ity o f L ab o, M t. La bo H Q 23 93 78 Br ac hy m el es b ou le ng er i K U 3 20 05 8 Ph ili pp in es , L uz on Is la nd , M un ic ip al ity o f L ag un a, M t. M ak ili ng H Q 23 93 79 Br ac hy m el es b ou le ng er i K U 3 20 05 9 Ph ili pp in es , L uz on Is la nd , M un ic ip al ity o f L ag un a, M t. M ak ili ng H Q 23 93 80 Br ac hy m el es k ad wa A CD 3 29 0* Ph ili pp in es , L uz on Is la nd H Q 23 93 81 Br ac hy m el es k ad wa RM B 40 40 * Ph ili pp in es , L uz on Is la nd , M un ic ip al ity o f I ro sin , M t. Bu lu sa n H Q 23 93 82 Br ac hy m el es k ad wa K U 3 07 96 5 Ph ili pp in es , C am ig ui n N or te Is la nd , M un ic ip al ity o f C al ay an H Q 23 93 83 Br ac hy m el es k ad wa K U 3 07 98 5 Ph ili pp in es , C am ig ui n N or te Is la nd , M un ic ip al ity o f C al ay an H Q 23 93 84 Br ac hy m el es k ad wa K U 3 04 90 6 Ph ili pp in es , C al ay an Is la nd , M un ic ip al ity o f C al ay an H Q 23 93 85 Br ac hy m el es k ad wa K U 3 04 87 5 Ph ili pp in es , C al ay an Is la nd , M un ic ip al ity o f C al ay an H Q 23 93 86 Br ac hy m el es ta lin is RM B 33 05 * Ph ili pp in es , N eg ro s I sla nd , M un ic ip al ity o f V al en ci a, M t. Ta lin is H Q 23 93 87 Br ac hy m el es ta lin is K U 3 03 99 0 Ph ili pp in es , S ib uy an Is la nd , M un ic ip al ity o f M ag di w an g H Q 23 93 88 Br ac hy m el es ta lin is K U 3 06 78 6 Ph ili pp in es , P an ay Is la nd , M un ic ip al ity o f S ib al om H Q 23 93 89 Br ac hy m el es ta lin is K U 3 06 78 1 Ph ili pp in es , P an ay Is la nd , M un ic ip al ity o f S ib al om H Q 23 93 90 Br ac hy m el es ta lin is K U 3 15 35 8 Ph ili pp in es , T ab la s I sla nd , M un ic ip al ity o f C al at ra va H Q 23 93 91 Br ac hy m el es ta lin is K U 3 15 35 9 Ph ili pp in es , T ab la s I sla nd , M un ic ip al ity o f C al at ra va H Q 23 93 92 Br ac hy m el es tu ng ao i K U 3 23 93 5 Ph ili pp in es , M as ba te Is la nd , M un ic ip al ity o f M ob o H Q 23 93 93 Br ac hy m el es tu ng ao i K U 3 23 93 6 Ph ili pp in es , M as ba te Is la nd , M un ic ip al ity o f M ob o H Q 23 93 94 Br ac hy m el es tu ng ao i K U 3 23 93 3 Ph ili pp in es , M as ba te Is la nd , M un ic ip al ity o f M ob o H Q 23 93 95 Br ac hy m el es tu ng ao i K U 3 23 93 4 Ph ili pp in es , M as ba te Is la nd , M un ic ip al ity o f M ob o H Q 23 93 96 Br ac hy m el es sc ha de nb er gi PN M /C M N H H 14 57 Ph ili pp in es , M in da na o Is la nd , M un ic ip al ity o f K ia m ba , M t. Bu sa H Q 23 93 97 Br ac hy m el es sc ha de nb er gi K U 3 14 98 0 Ph ili pp in es , M in da na o Is la nd , M un ic ip al ity o f Z am bo an ga C ity H Q 23 93 98 107 T ab le 3 .1 C on tin ue d Sp ec ie s V ou ch er Lo ca lit y G en ba nk A cc es si on N um be rs A TP as e 8, 6 Br ac hy m el es sc ha de nb er gi K U 3 14 98 1 Ph ili pp in es , M in da na o Is la nd , M un ic ip al ity o f Z am bo an ga C ity H Q 23 93 99 Br ac hy m el es o ri en ta lis K U 3 14 09 2 Ph ili pp in es , M in da na o Is la nd , M un ic ip al ity o f S an F ra nc is co H Q 23 94 00 Br ac hy m el es o ri en ta lis K U 3 11 23 9 Ph ili pp in es , L ey te Is la nd , M un ic ip al ity o f B ay ba y H Q 23 94 01 Br ac hy m el es o ri en ta lis K U 3 11 23 0 Ph ili pp in es , L ey te Is la nd , M un ic ip al ity o f B ay ba y H Q 23 94 02 Br ac hy m el es o ri en ta lis K U 3 10 94 5 Ph ili pp in es , S am ar Is la nd , M un ic ip al ity o f T af t H Q 23 94 03 Br ac hy m el es o ri en ta lis K U 3 10 35 7 Ph ili pp in es , C am ig ui n Su r I sl an d, M un ic ip al ity o f M am ba ja o H Q 23 94 04 Br ac hy m el es o ri en ta lis K U 3 05 46 9 Ph ili pp in es , D in ag at Is la nd , M un ic ip al ity o f L or et o H Q 23 94 05 Br ac hy m el es o ri en ta lis K U 3 24 02 8 Ph ili pp in es , B oh ol Is la nd , M un ic ip al ity o f B ila r H Q 23 94 06 108 Table 3.2. Models of evolution selected by AIC and applied for partitioned, Bayesian phylogenetic analyses1. Partition AIC Model Number of Characters ATP8, 1st codon position HKY + G 53 ATP8, 2nd codon position HKY + I + G 53 ATP8, 3rd codon position GTR + G 53 ATP6, 1st codon position GTR + I 227 ATP6, 2nd codon position GTR + I + G 227 ATP6, 3rd codon position GTR + G 227 1The model GTR + I + G was used for partitioned RAxMLHPC analyses. 109 Figure 3.2. Maximum clade credibility tree from a phylognetic analyis of mitochondrial data (ATP 6 and 8; -lnL 5249.903214). Nodes shown with numerical values corresponding to MLBP, and Bayesian PP support values respectively. Terminals are labeled with taxonomic names, and sampling localities. 110 111 Alignment and phylogenetic analysis An initial alignment was produced in Muscle v3.7 (Edgar, 2004), and visual inspections were made in MacClade 4.08 (Maddison and Maddison, 2005). No instances of insertions or deletions, or ambiguously aligned regions, were observed in the data, and all data were used for analyses. The final alignment consisted of 838 aligned nucleotides. Phylogenetic analyses were conducted using parsimony, likelihood, and Bayesian optimality criteria. Parsimony (MP) analyses were conducted in PAUP* 4.0 (Swofford, 2002) with all characters weighted equally. Most-parsimonious trees were estimated using heuristic searches with 1000 random addition-sequence replicates and tree bisection and reconnection (TBR) branch swapping. To assess heuristic support, nonparametric bootstrapping was conducted using 1000 replicates, each with 100 random addition-sequence replicates and TBR branch swapping. Partitioned maximum likelihood (ML) analyses were conducted in RAxMLHPC v7.04 (Stamatakis, 2006). The alignment was partitioned into six regions consisting of the codon positions of ATP8 and ATP6. Analyses that partition protein-coding genes by codon position have been shown to improve resulting inferences (Brandley et al., 2005). The partitions were run under the same model (GTR + I + Γ) with 100 replicate best-tree inferences. Each inference was performed with a random starting tree, and relied on the rapid hill-climbing algorithm (Stamatakis 2006). Clade support was assessed with 1000 bootstrap pseudoreplicates. We considered branches receiving ≥70% bootstrap support to be well-supported (Hillis and Bull, 1993; see also Wilcox et al., 2002). The Akaike Information Criterion (AIC), as implemented in MrModelTest 2.2 (Nylander, 2004), was used to find appropriate models of sequence evolution. The best-fit model for each of the six partitions (Table 3.2) was used for Bayesian analyses performed in MrBayes 3.1 (Ronquist and Huelsenbeck, 2003). The same partitioning strategy 112 used for maximum likelihood analyses was used for Bayesian inferences. Searches over tree space were conducted with four runs, each with four chains, and were run for 2 × 107 generations. Trees were sampled every 1000 generations, with 4000 samples discarded as burn-in; this left 16001 post-burn-in trees from each run included in the summary. Visual inspection for chain stationarity and high ESS values was conducted within the program Tracer v1.4 (Rambaut and Drummond, 2007). Additionally, correlations of split frequencies and cumulative split frequencies were examined using the program AWTY (Nylander et al., 2008). We considered topologies with posterior probabilities ≥0.95 to be well-supported (Wilcox et al., 2002). Morphological data We examined fluid-preserved specimens (Appendix IV) for variation in qualitative and mensural characters. Sex was determined by gonadal inspection, and measurements were taken to the nearest 0.1 mm with digital calipers by CDS. Museum abbreviations for specimens examined follow Leviton et al. (1985). Meristic and mensural characters were chosen based on Siler et al. (2009a, 2010a,b): characters evaluated were snout–vent length (SVL), axilla–groin distance (AGD), total length (TotL), midbody width (MBW), midbody height (MBH), tail length (TL), tail width (TW), tail height (TH), head length (HL), head width (HW), head height (HH), snout–forearm length (SnFa), eye diameter (ED), eye–narial distance (END), snout length (SNL), internarial distance (IND), forelimb length (FLL), hind limb length (HLL), midbody scale-row count (MBSR), paravertebral scale-row count (PVSR), axilla–groin scale-row count (AGSR), Finger-III lamellae count (FinIIIlam), Toe-IV lamellae count (ToeIVlam), supralabial count (SL), infralabial count 113 (IFL), supraciliary count (SC), and supraocular count (SO). In the description, ranges are followed by mean ± standard deviation in parentheses. Species concept We follow the General Lineage Concept of species (de Queiroz, 1998, 1999) as a logical extension of the Evolutionary Species Concept (Simpson, 1961; Wiley, 1978; Frost and Hillis, 1990). We consider as distinct lineages those populations that are morphologically, and genetically distinct. Lineage-based species concepts have been successfully employed in the recognition of Philippine biodiversity (Brown et al., 2000b, 2002, 2008, 2009; Brown and Guttman, 2002; Gaulke et al., 2007; Welton et al., 2009, 2010) due to the highly partitioned nature of the archipelago (Brown and Diesmos, 2009), and because the geological history of the islands has been so well documented (Hall, 2002; Yumul, 2009). In this study we use an estimate of phylogenetic relationships as a guide for delimiting species but restrict our diagnoses of new species to those populations diagnosed by non-overlapping morphological character states. Results Phylogeny Of 838 aligned mitochondrial nucleotide positions, 392 and 306 were variable and parsimony-informative, respectively. Just considering the alignment for Brachymeles sequence data, 310 and 279 were variable and parsimony-informative, respectively. The ML analysis resulted in a single optimal tree (–lnL = 5249.903). The resulting topology from the Bayesian 114 analysis is very similar to the ML tree. Trees estimated from ML, MP, and Bayesian analyses are consistent with respect to support for nine unique species of Brachymeles. No inferences support the monophyly of B. boulengeri. All analyses recover B. b. boholensis as part of a clade with B. s. orientalis and B. s. schadenbergi with high support (Fig. 3.2). The ML and Bayesian analyses support a close relationship among B. b. boulengeri, B. b. mindorensis, and B. b. taylori, but not their monophyly (Fig. 3.2). Results of both analyses (ML and Bayesian) show a a polytomy with four lineages including B. b. mindorensis, B. b. taylori, B. b. boulengeri, and a clade consisting of the remaining species (Fig. 3.2). All analyses support a clade of B. b. boholensis, B. s. schadenbergi, and B. s. orientalis as sister to a clade of three distinct lineages of B. talinis samples, while MP analyses consistently supported the clade of B. talinis as sister to a clade of B. b. mindorensis, B. b. taylori, and B. b. boulengeri. With the inclusion of two short mitochondrial genes for only three of the 18 recognized species in the genus, it is likely that differences in topologies among ML and Bayesian analyses reflect limited taxon and character sampling. Nevertheless, all analyses result in the strong support of nine genetically distinct lineages of Brachymeles (Fig. 3.2). Additionally, samples of B. talinis cluster into three major clades, each of which is strongly supported in all analyses (Fig. 3.2). Uncorrected pairwise sequence divergences are low within named taxa and relatively high between these lineages (Table 3.3). Levels of sequence divergence show that the nine mtDNA lineages discovered by our phylogenetic analyses (B. b. boholensis, B. b. boulengeri, B. sp. nov. (Masbate Island), B. sp. nov. (Calayan, Camiguin Norte, and Luzon islands), B. b. mindorensis, B. talinis, B. b. taylori, B. s. orientalis, B. s. schadenbergi) are distinguished from congeners by levels of genetic divergence equal to, or greater than, those between previously defined species—viz., B. boulengeri, B. talinis, B. schadenbergi (Table 3.3; Fig. 3.2). The two most 115 genetically similar lineages (B. sp. nov. [Masbate Island] and B. sp. nov. [northern Philippines]) are separated by 3.8–5.2% sequence divergence, and sequence divergences among all subspecies of B. boulengeri, and among both subspecies of B. schadenbergi, are greater than 7.3% (Table 3.3; Fig. 3.2). The three lineages with the greatest range of sequence divergence across populations are the presently defined subspecific taxa that occur across multiple islands within a single PAIC (B. b. boulengeri, B. b. taylori, B. talinis; Table 3.3; Fig. 3.2, 3.3, 3.5). Sequence divergence among populations in the lineage of northern populations of B. talinis, and among populations of B. schadenbergi orientalis, are much lower than those of other lineages known to be distributed across multiple islands (Table 3.3; Fig. 3.3, 3.4, 3.5). Morphology Variation in morphological characters (Tables 3.4–3.6) mirrors the results observed in phylogenetic analyses, and supports the recognition of nine Brachymeles lineages. Additionally, comparison of meristic and mensural morphological characters identified a tenth unique lineage from Jolo Island, previously recognized as a population of B. talinis. Characters differing among these ten lineages include: body size, degree of limb development, finger and toe lamellae counts, head and body scale counts and patterns, and pigmentation patterns (Tables 3.4–3.6; species accounts below). We observed no mensural or meristic differences between the sexes of any of the 10 species. Superficially, subspecies of both B. boulengeri and B. schadenbergi, and island populations of B. talinis, appear morphologically similar, especially in overall body size; however, numerous non-overlapping differences were detected in meristic, mensural, and color pattern characters for each complex member, readily defining ten distinct lineages between the three complexes (Tables 3.4–3.6). 116 Table 3.3. Uncorrected pairwise sequence divergence (%) for mitochondrial data for Brachymeles boholensis, B. boulengeri, B. mindorensis, B. taylori, B. talinis, B. kadwa, B. tungaoi, B. orientalis, and B. schadenbergi (Fig. 3.3). Percentages on the diagonal represent intraspecific genetic diversity (bolded for emphasis). 117 bo ho le ns is bo ul en ge ri m in do re ns is ta yl or i ta li ni s ka dw a tu ng ao i or ie nt al is sc ha de nb er gi bo ho le ns is 0. 6 bo ul en ge ri 15 .3 –1 5. 9 0. 0– 4. 7 m in do re ns is 16 .1 –1 6. 7 10 .6 –1 1. 5 0. 6 ta yl or i 15 .6 –1 6. 0 10 .2 –1 1. 6 11 .0 –1 1. 2 0. 3– 4. 8 ta li ni s 13 .0 –1 4. 6 10 .4 –1 1. 8 11 .8 –1 2. 4 10 .3 –1 2. 4 0. 1– 4. 5 ka dw a 12 .7 –1 3. 6 10 .4 –1 1. 7 11 .5 –1 2. 1 9. 3– 10 .3 6. 9– 8. 6 0. 1– 2. 2 tu ng ao i 13 .2 –1 3. 9 10 .5 –1 2. 1 10 .7 –1 1. 6 9. 7– 10 .1 7. 2– 8. 3 3. 8– 5. 2 0. 0– 1. 5 or ie nt al is 13 .4 –1 4. 7 14 .7 –1 6. 5 15 .6 –1 6. 7 15 .5 –1 6. 9 14 .3 –1 5. 8 15 .2 –1 6. 2 15 .3 –1 6. 1 0. 6– 2. 1 sc ha de nb er gi 12 .6 –1 3. 8 14 .5 –1 6. 0 16 .0 –1 7. 3 15 .2 –1 6. 3 13 .8 –1 5. 4 15 .2 –1 6. 5 15 .2 –1 6. 2 7. 3– 8. 5 0. 1– 2. 6 118 Figure 3.3. Hypothesized distributions of Brachymeles boholensis, B. boulengeri, B. mindorensis, and B. taylori in the Philippines. The sampling localities are indicated by black shapes, and the hypothesized geographic range of each species indicated by shaded islands, with shapes and shades of islands corresponding to the map’s key. 119 120 Figure 3.4. Hypothesized distributions of Brachymeles orientalis, B. schadenbergi, and B. vindumi in the Philippines. The sampling localities are indicated by black shapes, and the hypothesized geographic range of each species indicated by shaded islands, with shapes and shades of islands corresponding to the map’s key. Unknown Mindanao Island range boundaries indicated by dashed lines. 121 122 Figure 3.5. Hypothesized distributions of Brachymeles tungaoi, B. kadwa, and B. talinis in the Philippines. The sampling localities are indicated by black shapes, and the hypothesized geographic range of each species indicated by shaded islands, with shapes and shades of islands corresponding to the map’s key. Islands of the Romblon Island Group are designated by the first letter of the island name (T, Tablas Island; R, Romblon Island; S, Sibuyan Island). 123 124 In summary, each lineage possesses unique and non-overlapping suites of diagnostic character states of morphology, perfectly corresponding to nine of the clades defined in phylogenetic analyses of DNA sequence data (tissues unavailable for B. cf. talinis from Jolo Island). Combined with biogeographic evidence, and clearly separate geographical ranges, our data suggest the presence of ten evolutionary lineages, worthy of taxonomic recognition. Taxonomic conclusions Our inferred phylogeny (Fig. 3.2), biogeographically separate ranges of island endemic species; diagnostic, non overlapping morphological character states; and genetic divergences between the taxa (Table 3.3) indicate the distinctiveness of a new species from Luzon, Calayan, and Camiguin Norte islands, a new species from Masbate Island, and a new species from Jolo Island. Additionally, the molecular and morphological data strongly support the elevation of all subspecies of Brachymeles boulengeri and B. schadenbergi to full species (Table 3.3; Fig. 3.2). Each of the ten species is morphologically distinct from each other and all other known species in the genus, and each of the nine species included in phylogenetic analyses are also genetically distinct. With the exception of B. talinis, each lineage is endemic to one of four isolated PAICs, thereby providing additional support for the distinctiveness of each lineage’s evolutionary history and integrity. Accordingly, we recognize all four subspecies of the former polytypic species B. boulengeri, and both subspecies of the former polytypic species B. schadenbergi, as full species. TAXONOMIC ACCOUNTS 125 Brachymeles boulengeri Taylor 1922b: 246 Figs. 3.3, 3.6, 3.11A Brachymeles boulengeri (part), Taylor, 1922b, Type locality: Polillo Island, Philippines (holotype presumed lost). Brachymeles gracilis Boulenger (part), Brown, 1956; Brown and Rabor, 1967. Brachymeles gracilis (part), Brown and Alcala, 1970. Brachymeles boulengeri boulengeri (part), Brown and Alcala, 1980. Designation of a neotype for Brachymeles boulengeri.—Taylor’s holotype for B. boulengeri (Philippine Bureau of Science Publication No. 17:246, collected 15 July 1920) was destroyed in the destruction of the Philippine Bureau of Science in WWII, with no mention of a repository for the holotype. In the absence of an existing holotype and in accordance with article No. 75 of the International Code of Zoological Nomenclature (ICZN, 1979), we designate a neotype for this species. Accordingly, we choose an adult male specimen from the type locality of Polillo Island. Preserved adult specimens from Taylor’s (1915) type locality (Polillo Island) have been examined in the collections at CAS; unfortunately these original specimens are either poorly preserved, incomplete or not sexually mature. However, recent collections from Polillo Island (Fig. 3.1) have resulted in well preserved adult individuals that clearly exhibit the diagnostic characters for the species. From these collections we have chosen a male neotype collected as part of a series that contains adults of both sexes and agrees with Taylor’s (1922a) holotype description. Neotype.—PNM 9720 (RMB Field No. 5647, formerly KU 307756), adult male, collected from a fallen, rotting log in secondary growth forest (10:00–12:30 hr) in Barangay Pinaglubayan, 126 Municipality of Polillo, Quezon Province, Polillo Island, Philippines (14°45'09" N, 121°58'06" E; WGS-84), by RMB, J. Fernandez, Y. Vicente, and M. Vicente. Diagnosis.—Brachymeles boulengeri can be distinguished from congeners by the following combination of characters: (1) body size moderate (SVL 60.5–93.1 mm); (2) pentadactyl; (3) Finger-III lamellae five or six; (4) Toe-IV lamellae nine or ten; (5) moderate limb length; (6) supralabials six or seven; (7) infralabials seven; (8) pineal eye spot present; (9) supranasals not contacting on midline; (10) prefrontals not contacting on midline; (11) midline contact of first pair of chin shields; (12) enlarged chin shields in two pairs; (13) nuchal scales undifferentiated; (14) fourth and fifth supralabial below eye; (15) auricular opening present; (16) continuous, light dorsolateral stripes present; and (17) mid-dorsal stripes absent (Tables 3.4, 3.5). Comparisons.—Characters distinguishing Brachymeles boulengeri from all pentadactyl species of Brachymeles are summarized in Tables 3.4 and 3.5. Brachymeles boulengeri most closely resembles B. boholensis, B. mindorensis, and B. taylori, but differs from these three taxa by having six or seven supralabials and five or six supraciliaries, and by the absence of continuous, dark mid-dorsal stripes (Tables 3.4, 3.5). Brachymeles boulengeri further differs from B. boholensis by having a relatively longer tail, five or six Finger-III lamellae, the fourth and fifth supralabial below the eye, midline contact between the first pair of enlarged chin shields, and by lacking a third pair of enlarged chin shields (Tables 3.4, 3.5); from B. mindorensis it is differentiated by its smaller body size, shorter hind limbs, and possession of nine or 10 Toe-IV lamellae, seven infralabials, and by having the fourth and fifth supralabial below the eye (Tables 3.4, 3.5); and from B. taylori by the midline contact between the first pair of enlarged chin shields, and the presence of continuous, light dorsolateral stripes (Tables 3.4, 3.5). 127 From all non-pentadactyl species of Brachymeles (B. apus, B. bonitae, B. cebuensis, B. elerae, B. lukbani, B. minimus, B. muntingkamay, B. pathfinderi, B. samarensis, B. tridactylus, B. vermis, and B. wrighti), B. boulengeri differs by having a pentadactyl body form (vs. non-pentadactyl), greater forelimb lengths (> 8.2 mm vs. < 6.9 mm), greater hind-limb lengths (> 14.3 mm vs. < 12.9 mm), Toe-IV lamellae nine or 10 (vs. eight or fewer), a midbody scale row count of 26 or 27 (vs. < 24 in all non-pentadactyl species except for 28 in B. wrighti [Taylor, 1925]), and by the presence of a postnasal scale (vs. absence). With the exception of B. pathfinderi, B. boulengeri differs further from all non-pentadactyl species by the absence of a third pair of enlarged chin shields (vs. presence) and the presence of auricular openings (vs. absence). From all non-pentadactyl species except for B. pathfinderi, B. boulengeri differs by having a paravertebral scale count of 63–66 (vs. > 84). From B. apus, B. lukbani, B. minimus, and B. vermis, B. boulengeri is distinguished by the presence (vs. absence) of limbs. Description of neotype.—(Fig. 3.6) Adult male, hemipenes everted; SVL 93.1 mm; body moderate relative to other Brachymeles; head weakly differentiated from neck, nearly as wide as body, HW 10.3% SVL, 109.0% HL; HL 36.5% SnFa; SnFa 9.4% SVL; snout moderately long, rounded in dorsal and lateral profile, SNL 52.2% HL; auricular opening present, moderate; eyes moderate, ED 2.2% SVL, 23.5% HL, 72.0% END, pupil subcircular; body slightly depressed, MBW 141.8% MBH; body scales smooth, glossy, imbricate; longitudinal scale rows at midbody 26; paravertebral scale rows 64; axilla–groin scale rows 43; limbs well developed, pentadactyl, digits small; FinIIIlam 5; ToeIVlam 9; FLL 19.2% AGD, 12.5% SVL; HLL 28.7% AGD, 18.7% SVL; order of digits from shortest to longest for hand: V = I < IV = II < III, for foot: I < V < II < III < IV; tail original, not as wide as body, sharply tapered towards end, TW 70.1% MBW, TL 84.6% SVL. 128 Rostral projecting dorsoposteriorly to point in line with anterior edge of nasal scale, broader than high, forming a narrow suture with frontonasal; frontonasal wider than long; nostril ovoid, centered in a single rectangular nasal; nasals well separated; supranasals present, large, moderately separated by frontonasal; postnasals present; prefrontals narrowly separated by frontal; frontal suboctagonal, anterior margin in moderate contact with frontonasal and first two anterior supraoculars, 5× wider than anteriormost supraocular; supraoculars five; frontoparietals moderate, in broad medial contact, contact 2–4 supraoculars; interparietal diamond-shaped, slightly wider than long, nearly one half frontal length; parietal eyespot present in posterior one third of scale; parietals separated by interparietal; nuchals non-enlarged, undifferentiated from dorsal scales; loreals two, decreasing in size from anterior to posterior; anterior loreal approximately as long as and slightly higher than posterior loreal, in contact with prefrontal, postnasal, supranasal, second supralabial; posterior loreal and frontonasal; preocular single, nearly two-thirds height of posterior loreal; presubocular single; supraciliaries six, most anterior contacting prefrontal and separating posterior loreal from first supraocular, most posterior extending to midline of last supraocular; subocular row complete; lower eyelid with one row of scales, lacking an enlarged oval window, largely transparent; supralabials seven, fourth and fifth below the eye, infralabials seven. Mental wider than long, in contact with first infralabials; postmental single, wider than mental, followed by two pairs of enlarged chin shields; first pair in broad medial contact, second pair slightly wider than first, separated by a single medial scale. Scales on limbs smaller than body scales; scales on dorsal surfaces of digits large, wrapping around lateral edges of digits; lamellae undivided; palmar surfaces of hands and plantar surfaces 129 of feet covered by small, irregular scales, each with raised anterior edges; scales on dorsal surface of hands and feet smaller than limb scales, lacking raised edges. Coloration of neotype in preservative.—Ground color of body medium brown; lateral and ventral surfaces of body lacking dark pigment; dorsum, from posterior edge of supranasals to tail tip, uniformly dark brown, with color spanning six full and two half rows of scales at midbody and narrowing to cover four rows of scales posterior to parietals; darker pigmentation covers entire surface of dorsal scales, with exception of pigmentation on half rows of scales; head scales uniform brown; lateral half of supraoculars lacking dark pigmentation; rostral, nasal, postnasal, supranasal, and first supralabial dark gray with light brown blotches; pineal eyespot charcoal, surrounded by cream border. Faint, indistinct light dorsolateral stripes, formed by the absence of dark pigmentation, extending from level of anterior edge of eye to base of tail, spanning one full and two half rows of scales; small blotch of dark brown pigment dorsal to auricular opening. Limbs mottled light and medium brown dorsally, yellowish brown ventrally; dorsal and ventral surface of digits dark brown. Coloration in life.—(Fig. 3.11A). Dorsal ground color homogeneous medium-brown to yellowish-brown; gradual lateral dorsolateral demarcation between dorsal (dark) and ventral (light) coloration; lateral and ventral surfaces of body homogeneous medium-brown to yellowish-brown; dark-brown spots and longitudinal lines of spots absent from lateral surfaces. Measurements of neotype in mm.—SVL 93.1; AGD 60.7; TotL 171.9; MBW 14.7; MBH 10.4; TL 78.8; TW 10.3; TH 8.3; HL 8.8; HW 9.6; HH 7.2; SnFa 24.0; ED 2.1; END 2.9; SNL 4.6; IND 3.1; FLL 11.7; HLL 17.5; MBSR 26; PVSR 64; AGSR 43; FinIIIlam 5; ToeIVlam 9; SL 7; IFL 7; SC 6; SO 5. 130 Variation.—Variation in mensural characters is summarized in Table 3.6. Among the 19 specimens examined for the degree of contact between parietal scales, nine specimens possessed parietals separated by the interparietal (KU 307750, 307758, 320060, 322315–20) and 10 possessed parietals in moderate to broad medial contact (KU 307438–9, 307751–4, 307757, 320058–9, 322314) behind the interparietal. Scale counts were observed to vary among the measured series. With the exception of a single specimen with five supraciliaries (KU 307752), all specimens examined had six supraciliaries. The number of supralabials varied between six (CAS 61297, 62272–3, 62276–7, KU 307438–9, 307752–4, 307757–8) and seven (CAS 61096, KU 307751). Specimens were observed to have midbody scale row counts of 26 (CAS 61096, 31297, 62273, 62276–7, KU 307439, 307751–4, 307758) and 27 (CAS 62272, KU 307750, 307757); axilla–groin scale row counts of 42 (KU 307439, 307758), 43 (KU 307750–4, 307757), 44 (CAS 61096, 62272–3, 62276–7), and 46 (CAS 61297); and paravertebral scale row counts of 63 (KU 307439, 307750, 307752, 307754, 307757–8), 64 (CAS 61096, 62272–3, 62277, KU 307751, 307753), 65 (CAS 62276), and 66 (CAS 61297). We also observed lamellae counts to vary among the measured series. With the exception of a single specimen with six Finger-III lamellae (KU 307750), all specimens examined had five. Two specimens examined had ten Toe-IV lamellae (KU 307750, 307757), while the remaining specimens examined had nine. Distribution.—Brachymeles boulengeri occurs in central and southern Luzon, and on Marinduque and Polillo islands (Fig. 3.3). The species has been collected in the Camarines Norte Province of the Bicol Peninsula, and may eventually be found to occur further south on the Bicol Peninsula and even on Catanduanes Island. 131 Ecology and natural history.—Brachymeles boulengeri occurs in disturbed and secondary-growth forest. Little or no original, low elevation forest remains throughout the range of B. boulengeri, but we assume the species once also occurred in first growth forest when this forest type extended into low elevation areas. Individuals have been observed under piles of rotting coconut husks, in the humus material within rotting logs, and in loose soil and leaf litter surrounding the root networks of trees. This species is quite common at the type locality, which has been virtually completely converted to coconut plantations. When disturbed, individuals immediately move in a rapid serpentine manner, attempting to burrow into loose soil or humus. Sympatric lizard species observed on Luzon, Polillo, and Marinduque islands include: (Agamidae) Bronchocela cristatella, Draco spilopterus, Gonocephalus sophiae, Hydrosaurus pustulatus; (Gekkonidae) Cyrtodactylus philippinicus, Gehyra mutilata, Gekko gecko, Gekko mindorensis, Hemidactylus frenatus, H. garnoti, H. luzonensis, H. platyurus, Pseudogekko compressicorpus, P. smaragdina; (Scincidae) Brachymeles bonitae, B. bicolor, B. elerae, B. lukbani, B. makusog, B. muntingkamay, B. samarensis, B. kadwa, B. wrighti, Emoia atrocostata, Eutropis bontocensis, E. multicarinata, E. multifasciata, Lamprolepis smaragdina, Lipinia pulchella, Sphenomorphus cumingi, S. decipiens, S. jagori, S. leucospilos, S. luzonensis, S. steerei, S. stejnegeri, Tropidophorus grayi; (Varanidae) Varanus marmoratus, and Varanus olivaceus. Brachymeles boholensis Brown and Rabor 1967 Figs. 3.3, 3.6, 3.11C Brachymeles gracilis boholensis, Brown and Rabor, 1967, Type locality: 6 km southeast of Sierra Bullones, Teacher’s Park, Bohol Island, Philippines, 400–433 m elevation, 132 9°47'32.53" N, 124°18'14.4" E (holotype: CAS-SU24528). Brachymeles gracilis (part), Brown and Alcala, 1970. Brachymeles boulengeri boholensis (part), Brown and Alcala, 1980. Diagnosis.—Brachymeles boholensis can be distinguished from congeners by the following combination of characters: (1) body size moderate (SVL 83.8–93.6 mm); (2) limbs pentadactyl; (3) Finger-III lamellae six; (4) Toe-IV lamellae nine or ten; (5) limb length moderate; (6) supralabials seven; (7) infralabials seven; (8) pineal eye spot present; (9) supranasals not contacting on midline; (10) prefrontals not contacting on midline; (11) enlarged chin shields in three pairs; (12) nuchal scales undifferentiated; (13) fifth and sixth supralabial below eye; (14) auricular opening present; (15) continuous, light, dorsolateral stripes present; and (16) continuous, dark mid-dorsal stripes present (Tables 3.4, 3.5). Comparisons.—Characters distinguishing Brachymeles boholensis from all pentadactyl species of Brachymeles are summarized in Tables 3.4 and 3.5. Brachymeles boholensis most closely resembles B. boulengeri, B. mindorensis, and B. taylori, but differs from them by having six lamellae on Finger-III and by the presence of three pairs of enlarged chin shields (Tables 3.4, 3.5). Brachymeles boholensis differs further from B. boulengeri by having seven supralabials, six supraciliaries, and the fifth and sixth supralabial below the eye, and by the presence of continuous, dark mid-dorsal stripes (Tables 3.4, 3.5); from B. mindorensis by having a smaller body size, shorter hind limbs, nine or 10 Toe-IV lamellae, seven infralabials, and by the absence of contact between supranasals, and the absence of contact between prefrontals (Tables 3.4, 3.5); and from B. taylori by having seven supralabials, the fifth and sixth supralabial below the eye, and the presence of continuous, light dorsolateral stripes (Tables 3.4, 3.5). 133 From all non-pentadactyl species of Brachymeles (B. apus, B. bonitae, B. cebuensis, B. elerae, B. lukbani, B. minimus, B. muntingkamay, B. pathfinderi, B. samarensis, B. tridactylus, B. vermis, and B. wrighti), B. boholensis differs by having pentadactyl (vs. non-pentadactyl) limbs, greater forelimb lengths (greater than 9.0 mm vs. less than 6.9 mm), greater hind limb lengths (greater than 15.4 mm vs. less than 12.9 mm), Toe-IV lamellae nine or 10 (vs. eight or fewer), fifth and sixth supralabial below the eye (vs. fourth and fifth), and by presence of a postnasal scale (vs. absence). Additionally, Brachymeles boholensis differs from all non-pentadactyl species except B. wrighti by having 26–28 midbody scale rows (vs. fewer than 24); from all non-pentadactyl species except B. pathfinderi by having 63–66 paravertebrals (vs. greater than 84) and by the presence of auricular openings (vs. absence); and from B. apus, B. lukbani, B. minimus, and B. vermis by the presence of limbs (vs. absence). Description (based on holotype and 38 referred specimens, including 12 paratypes at CAS).—Details of the head scalation of an adult female are shown in Figure 3.6. Measurements of the holotype are provided below in brackets. Body moderate relative to other Brachymeles; maximum SVL 93.6 mm for males, 94.0 mm for females [89.5, female] (Tables 3.4, 3.5); head weakly differentiated from neck, nearly as wide as body, HW 10.0–12.4% (11.3 ± 0.7) SVL [11.8], 104.2–131.9% (112.6 ± 6.7) HL [110.7]; HL 35.2–43.6% (38.9 ± 2.3) SnFa [39.3]; SnFa 24.1–28.0% (26.0 ± 1.0) SVL [27.0]; snout moderately long, broadly rounded in dorsal profile, rounded in lateral profile, SNL 54.6–64.6% (59.3 ± 2.8) HL [57.4]; auricular opening present, moderate; eyes small, ED 1.8–2.2% (2.0 ± 0.1) SVL [2.1], 17.6–23.9% (20.3 ± 1.6) HL [19.5], 45.1–61.8% (52.5 ± 3.7) END [52.9], pupil subcircular; body slightly depressed, MBW 98.1–136.2% (113.0 ± 10.3) MBH [131.0]; scales smooth, glossy, imbricate; longitudinal scale rows at midbody 26–28 [28]; paravertebral scale rows 63–66 [64]; axilla–groin scale rows 42–46 [44]; 134 limbs well developed, pentadactyl, digits small; FinIIIlam 6 [6]; ToeIVlam 7–10 [7]; FLL 15.6–20.5% (17.6 ± 1.4) AGD [20.5], 10.2–12.9% (11.4 ± 0.8) SVL [12.4]; HLL 27.6–34.6% (30.0 ± 2.3) AGD [32.9], 17.8–21.5% (19.4 ± 1.2) SVL [20.0]; order of digits from shortest to longest for hand: I = V < II = III = IV, for foot: V < I < II < III = IV; tail not as wide as body, sharply tapered towards end, TW 61.6–78.4% (70.3 ± 5.0) MBW [63.5], TL 52.7–90.0% (75.7 ± 13.0) SVL [86.8]. Rostral projecting dorsoposteriorly to point in line with center of nasal;, broader than high, in contact with frontonasal; frontonasal wider than long; nostril ovoid, centered in a single rectangular nasal; nasals well separated; supranasals present, large, moderately separated by frontonasal; postnasals present; prefrontals broadly separated by frontal; frontal nearly diamond shaped, in moderate contact with frontonasal, first two anterior supraoculars, 4× wider than anterior supraocular; supraoculars five; frontoparietals moderate in size, in contact, each frontoparietal in contact with posterior three or four supraoculars; interparietal moderate in size, quadrilaterally shaped, longer than wide, its length slightly greater than midline length of frontoparietals; parietal eyespot present in posterior half of scale; parietals separated by interparietal; nuchals undifferentiated; loreals two, antreior loreal largest, in contact with prefrontal, postnasal, supranasal, second supralabial, posterior loreal and frontonasal; preocular single, nearly two thirds as high as posterior loreal; supraciliaries six, anterior supraciliary contacting prefrontal and separating posterior loreal from first supraocular; subocular row complete; lower eyelid with one row of scales, lacking an enlarged oval window, largely transparent; supralabials seven, fifth and sixth beneath center of eye; infralabials seven. Mental wider than long, in contact with first infralabials; postmental single, enlarged, slightly wider than mental, followed by three pairs of enlarged chin shields, first pair in broad medial 135 contact, second pair equal in width to first pair, broadly separated by single medial scale, third pair separated by three medial scales. Scales on limbs smaller than body scales; scales on dorsal surfaces of digits large, wrapping around lateral edges of digits; lamellae undivided; palmar surfaces of hands and plantar surfaces of feet covered by small, variably shaped scales, each bearing variably raised anterior edges; scales on dorsal surface of hands and feet smaller than limb scales, lacking raised edges. Coloration in preservative.—Ground color of body medium brown, lateral surface lacking dark pigment, dorsal surface bearing continuous, longitudinal rows of olive-green to brown pigment, spanning six full and two half rows of scales at midbody, narrowing to four full and two half rows of scales posterior to parietals, extending from posterior edge of parietals to tail tip; dark pigmentation covering one half to three fourths of dorsal scales; lateral surface of body with six continuous to discontinuous longitudinal rows of olive-green to brown stripes, extending from posterior edge of eye to base of tail; dorsolateral stripes present, lacking dark pigmentation, spanning two half rows of scales, extending from posterior edge of supraoculars to base of tail. Ventral scales with or without dark spots. Head scales uniform medium brown, darker brown than ventral scales; rostral, nasal, postnasal, supranasal, first supralabial, mental, and first infralabial dark gray; pineal eyespot poorly defined, small, and light to dark brown. Limbs mottled light and medium brown dorsally, yellowish brown ventrally; dorsal and ventral surfaces of digits dark brown. Coloration in life.—(Fig. 11C). Ground color of body medium brown to tan; longitudinal rows of darker brown pigmentation; dorsolateral stripes light-brown to tan; limbs bearing dark-brown mottling dorsally. 136 Variation.—Morphometric variation is summarized in Table 3.6. We observed variation among the 20 specimens examined for the degree of contact between head scales. Six specimens were observed to have parietals separated by the interparietal (KU 323944, 323949, 323953, 323962, 323975–6) and 14 specimens possessed parietals in moderate to broad medial contact (KU 323948, 323952, 323954–6, 323960, 323963, 323966, 323970, 323972, 323981, 323982, 323990, 324001) behind the interparietal. Additionally seven specimens do not have the first pair of enlarged chin shields in medial contact (KU 323954–5, 323970, 323975, 323981–2, 324001) and 13 specimens with the first pair of enlarged chin shields in moderate to broad medial contact (KU 323944, 323948–9, 323952–3, 323956, 323960, 323962–3, 323966, 323972, 323976, 323990). Scale counts were observed to vary among the measured series. Specimens were observed to have midbody scale row counts of 26 (CAS-SU 18709, 18717, 24502, 24523–5, 24541, 24543, 25443–4), 27 (CAS-SU 24503–4, 24522, 24867), and 28 (CAS-SU 24518, 24520–21, 24528, 25447); axilla–groin scale row counts of 42 (CAS-SU 18717, 24502, 24520, 24524), 43 (CAS-SU 24523, 24541, 24543), 44 (CAS-SU 24504, 24518, 24525, 24528, 24867, 25447), 45 (CAS-SU 24503, 24521, 25443), and 46 (CAS-SU 18709, 24522, 25444); and paravertebral scale row counts of 63 (CAS-SU 18717, 24502, 24520, 24524, 24541, 24543), 64 (CAS-SU 24504, 24523, 24525, 24528, 24867, 25447), 65 (CAS-SU 24518), and 66 (CAS-SU 18709, 24503, 24521–2, 25443–4). We also observed Toe-IV lamellae counts to vary among the measured series. With the exception of a single specimen with seven Two-IV lamellae (CAS-SU 24528, holotype), all specimens examined had either nine (CAS-SU 18709, 24504, 24523–4, 24867, 25444) or ten (CAS-SU 18717, 24502–3, 24518, 24520–2, 24525, 24541, 24543, 25443, 25447). We observed 137 the holotype to have malformed digits, which we believe resulted in fewer Toe-IV lamellae than are observed for all other individuals of this species. Distribution.—Brachymeles boholensis is known only from Bohol Island (Fig. 3.3). Ecology and natural history.—Brachymeles boholensis occurs in agricultural habitats, as well as in disturbed and secondary-growth forests. No original, low elevation forest remains on Bohol Island, but we assume the species once also occurred in primary forest at low elevations. Individuals have been observed under piles of rotting coconut husks, in the humus material within rotting logs, and in loose soil and leaf litter surrounding the root networks of trees. Interestingly, this species seems to be a ubiquitous habitat generalist on Bohol, whereas its congener, B. orientalis, seems to be restricted to fallen and rotting logs in secondary-growth forest on the same island (CDS personal observations). As is typical for species in the genus, individuals immediately attempt to evade capture by moving to quickly burrow into loose soil or humus. Although only two species of Brachymeles have been confirmed to occur on Bohol Island (B. boholensis and B. orientalis), populations of B. samarensis are known to occur on Lapinig Grande and Lapinig Chico islands just off the northeast coast of Bohol Island (Brown and Alcala, 1980). No individuals of this species lacking fully formed digits occur on Bohol; however, given proximity of these small islands to mainland Bohol, it seems likely that this neighboring, limb-reduced species of Brachymeles eventually may be discovered on Bohol. Sympatric lizard species observed on Bohol Island include: (Agamidae) Bronchocela cristatella, Draco bimaculatus, D. ornatus, D. reticulates, Gonocephalus semperi, Hydrosaurus pustulatus; (Gekkonidae) Cyrtodactylus annulatus, Gehyra mutilata, Gekko gecko, Hemidactylus frenatus, H. platyurus, Hemiphyllodactylus typus, Lepidodactylus aureolineatus, L. planicaudus, 138 Pseudogekko compressicorpus, P. brevipes; (Scincidae) Brachymeles schadenbergi orientalis, Emoia atrocostata, Eutropis multicarinata, E. multifasciata, Lamprolepis smaragdina, Lipinia pulchella, L. quadrivittata, Sphenomorphus acutus, S. cumingi, S. fasciatus, S. jagori, S. minanensis, S. steerei, S. variegatus; (Varanidae) Varanus cumingi. Also, Brachymeles samarensis (Scincidae) is known to occur on Lipinig Grande and Lipinig Chico islands just off the northeast coast of Bohol Island (Brown and Alcala, 1980). Brachymeles mindorensis Brown and Rabor 1967 Figs. 3.3, 3.7 Brachymeles gracilis mindorensis, Brown and Rabor, 1967, Type locality: Bank of Tarogin River, 30 km southeast of Calapan, Mindoro Oriental Province, Mindoro Island, Philippines, 0–33 m elevation, 13°11'25.44" N, 121°8'52.8" E (holotype: CAS-SU 24487). Brachymeles gracilis (part), Brown and Alcala, 1970. Brachymeles boulengeri mindorensis (part), Brown and Alcala, 1980. Diagnosis.—Brachymeles mindorensis can be distinguished from congeners by the following combination of characters: (1) body size moderate (SVL 90.0–104.2 mm); (2) pentadactyl; (3) Finger-III lamellae five or six; (4) Toe-IV lamellae eight or nine; (5) moderate limb length; (6) supralabials seven; (7) infralabials six; (8) pineal eye spot present; (9) enlarged chin shields in two pairs; (10) nuchal scales undifferentiated; (11) fifth and sixth supralabial below eye; (12) auricular opening present; (13) continuous, light, dorsolateral stripes present; and (14) continuous, dark mid-dorsal stripes present (Tables 3.4, 3.5). Comparisons.—Characters distinguishing Brachymeles mindorensis from all pentadactyl species of Brachymeles are summarized in Tables 3.4 and 3.5. Brachymeles mindorensis most 139 closely resembles B. boholensis, B. boulengeri, and B. taylori, but differs from these three taxa by having a larger body size, longer hind limbs, eight or nine Toe-IV lamellae, and six infralabials (Tables 3.4, 3.5). Brachymeles mindorensis further differs from B. boholensis by having five or six Finger-III lamellae and by the absence of a third pair of enlarged chin shields (Tables 3.4, 3.5); from B. boulengeri by having seven supralabials, six supraciliaries, and the fifth and sixth supralabial below the eye, and by the presence of continuous, dark mid-dorsal stripes (Tables 3.4, 3.5); and from B. taylori by having seven supralabials and the fifth and sixth supralabial below the eye, and by the presence of continuous, light dorsolateral stripes (Tables 3.4, 3.5). From all non-pentadactyl species of Brachymeles (B. apus, B. bonitae, B. cebuensis, B. elerae, B. lukbani, B. minimus, B. muntingkamay, B. pathfinderi, B. samarensis, B. tridactylus, B. vermis, and B. wrighti), B. mindorensis differs by having a pentadactyl body form (vs. non-pentadactyl), longer forelimb lengths (greater than 10.0 mm vs. less than 6.9 mm), greater hind limb lengths (greater than 18.8 mm vs. less than 12.9 mm), and the fifth supralabial below the eye (vs. fourth), and by the presence of a postnasal scale (vs. absence). Additionally, Brachymeles mindorensis differs from all non-pentadactyl species except B. wrighti by having a midbody scale row count 26–28 (vs. fewer than 24); from all non-pentadactyl species except B. pathfinderi by having a paravertebral count 63–65 (vs. greater than 84) and by the presence of auricular openings (vs. absence); and from B. apus, B. lukbani, B. minimus, and B. vermis by the presence of limbs (vs. absence). Description (based on holotype and 33 referred paratypes at CAS).—Details of the head scalation of an adult male are shown in Figure 3.7. Measurements of the holotype are included below in brackets. Body moderate relative to other Brachymeles, elongate with respect to other 140 lizards; maximum SVL 104.2 mm for males, 106.8 mm for females [106.8, female] (Tables 3.4, 3.5); head weakly differentiated from neck, nearly as wide as body, HW 10.5–12.9% (11.4 ± 0.7) SVL [10.9], 104.2–130.1% (116.1 ± 6.0) HL [114.6]; HL 31.6–42.9% (37.3 ± 3.1) SnFa [39.2]; SnFa 24.1–29.9% (26.5 ± 1.3) SVL [24.1]; snout moderately long, rounded in dorsal and lateral profile, SNL 50.6–68.2% (57.3 ± 4.9) HL [52.2]; auricular opening present, small; eyes moderate, ED 2.0–2.6% (2.2 ± 0.2) SVL [2.0], 19.4–27.4% (22.7 ± 2.0) HL [21.1], 51.8–72.2% (60.7 ± 5.1) END [58.5], pupil nearly round; body slightly depressed, MBW 105.4–156.0% (120.2 ± 14.0) MBH [125.0]; scales smooth, glossy, imbricate; longitudinal scale rows at midbody 26–28 [26]; paravertebral scale rows 63–65 [65]; axilla–groin scale rows 42–45 [45]; limbs well developed, pentadactyl, digits small; FinIIIlam 5–6 [5]; ToeIVlam 8–9 [9]; FLL 14.5–21.3% (17.8 ± 1.9) AGD [15.5], 10.1–13.1% (11.5 ± 0.9) SVL [10.9]; HLL 16.7–37.9% (31.5 ± 5.0) AGD [25.1], 10.5–24.0% (20.3 ± 2.9) SVL [17.6]; order of digits from shortest to longest for hand: I = V < II = IV < III, for foot: I < V < II < III = IV; tail not as wide as body, sharply tapered towards end, TW 54.4–80.1% (69.1 ± 8.1) MBW [54.4], TL 60.4–99.3% (84.6 ± 11.5) SVL [93.5]. Rostral projecting dorsoposteriorly to point in line with anterior edge of nasal, broader than high, in narrow contact with frontonasal; frontonasal wider than long; nostril ovoid, centered in a single rectangular nasal; nasals well separated; supranasals present, large, narrowly separated by frontonasal; postnasals present; prefrontals narrowly separated by frontal; frontal octagonal, narrowly contacting frontonasal and first two supraoculars anteriorly, 4× wider than anteriormost supraocular; supraoculars five; frontoparietals moderate, in broad medial contact, each frontoparietal in contact with supraoculars 2–4; interparietal large, quadrilaterally shaped, slightly longer than wide, its length slightly greater than midline length of frontoparietal; parietal 141 eyespot present in posterior one half of scale; parietals moderately separated behind interparietal; nuchals undifferentiated from adjacent dorsal scales; loreals two, anterior loreal in contact with prefrontal, postnasal, supranasal, second supralabial, posterior loreal and frontonasal; preocular, single, nearly one third as high as posterior loreal; presubocular single; supraciliaries six, the anteriormost contacting prefrontal and separating posterior loreal from first supraocular; subocular row complete; lower eyelid with one row of scales, lacking an enlarged oval window, largely transparent; supralabials seven, fifth and sixth below eye; infralabials six. Mental wider than long, in contact with first infralabials; single enlarged postmental, equal in width to mental followed by two pairs of enlarged chin shields; first pair in moderate contact, second pair wider than first, moderately separated by single medial scale. Scales on limbs smaller than body scales; scales on dorsal surfaces of digits large, wrapping around lateral edges of digits; lamellae undivided; palmar surfaces of hands and plantar surfaces of feet covered by small, variably shaped scales, each with variably raised anterior edges; scales on dorsal surface of hands and feet smaller than limb scales, lacking raised edges. Coloration in preservative.—Ground color of body medium brown; dorsal surface of body with eight longitudinal rows of dark-brown stripes, six continuous medial rows, two discontinuous lateral rows, spanning eight full rows of scales at midbody, narrowing to six full rows of scales posterior to parietals, extending from posterior edge of parietals to tail tip; pigmentation covering middle one third of dorsal scales; dorsolateral stripes present, lacking dark pigmentation, spanning one whole and two half rows of scales, extending from posterior edge of supraoculars to base of tail. Lateral surface of body light brown ground color with three or four rows of nearly continuous spots of dark-brown pigmentation, extending from auricular opening to tail tip. Tail striped with longitudinal rows of dark pigmentation. Ventral scales 142 lacking dark spots. Head scales uniform medium brown, darker brown than ventral scales; posteriormost supraocular lacking pigmentation; dark pigmentation surrounding auricular opening, connected to dark pigmentation on head scales; rostral, nasal, postnasal, supranasal, and first supralabial dark gray; pineal eyespot poorly defined, small and light cream. Limbs mottled dark brown dorsally, yellowish brown ventrally; dorsal and ventral surface of digits dark brown. Coloration in life.—Ground color of body dark- to medium-brown; continuous, dark mid-dorsal stripes dark brown to black; dorsolateral stripes light-brown to tan, gradually become predominately tan on tail; limbs dark-brown dorsally. Variation.—Morphometric variation of the series is summarized in Table 3.6. We observed variation among the 16 specimens examined for the degree of contact between head scales. Five specimens were have parietals separated by the interparietal (KU 304352, 304354, 304488, 308447–8) and 11 specimens have parietals in moderate to broad medial contact (KU 304351, 304353, 304355, 304412–3, 307739–42, 308404, 308534) behind the interparietal; four specimens have supranasals narrowly separated by the frontonasal (KU 307740–1, 308404, 308448), six specimens have supranasals in medial point contact (KU 304351–4, 307742, 308447), and six specimens have supranasals in moderate medial contact (KU 304355, 304412–3, 304488, 307739, 308534); 13 specimens have prefrontals moderately separated by the frontal (KU 304351–4, 304412–3, 304488, 307739–41, 308447–8, 308534), one specimen has prefrontals narrowly separated by the frontal ( KU 308404), and two specimens have prefrontals in medial point contact (KU 304355, 307742). Scale counts were observed to vary among the measured series. Specimens were observed to have midbody scale row counts of 26 (CAS-SU 24487, 24551, 24561, 24566, 24574, 24577, 24579), 27 (CAS-SU 24549, 24573), and 28 (CAS-SU 24550, 24552–4, 24562, 24564, 24568, 143 24570, 24578); axilla–groin scale row counts of 42 (CAS-SU 24564), 43 (CAS-SU 24573), 44 (CAS-SU 24553–4, 24561–2, 24568, 24570, 24578), and 45 (CAS-SU 24487, 24549–52, 24566, 24574, 24577, 24579); and paravertebral scale row counts of 63 (CAS-SU 24564, 24573), 64 (CAS-SU 24561–2, 24568), and 65 (CAS-SU 24487, 24549–54, 24566, 24570, 24574, 24577–9). We also observed lamellae counts to vary among the series. With the exception of two specimens with six Finger-III lamellae (CAS-SU 24561, 24574), all specimens examined had five. Specimens were observed to have Toe-IV lamellae counts of eight (CAS-SU 24549–54, 24561–2, 24564, 24566, 24570, 24573, 24577–8) or nine (CAS-SU 24487, 24568, 24574, 24579). Distribution.—Brachymeles mindorensis is known only from Mindoro Island (Fig. 3.3). Ecology and natural history.—Brachymeles mindorensis occurs in disturbed and secondary-growth forest. Individuals have been observed under piles of rotting coconut husks, in the humus material within rotting logs, and in loose soil and leaf litter surrounding the root networks of trees. The species has been observed to be quite common in certain habitats on Mindoro Island (CDS, RMB personal observations). Brachymeles mindorensis occurs sympatrically with B. bonitae (Brown, 1956; Brown and Rabor, 1967; Brown and Alcala, 1980), and is the largest species of the B. boulengeri complex. When individuals were disturbed, they attempted to quickly burrow back into loose soil or humus. Sympatric lizard species observed on Mindoro Island include: (Agamidae) Bronchocela marmoratus, Draco quadrasi, Gonocephalus interruptus, Hydrosaurus pustulatus; (Gekkonidae) Cyrtodactylus philippinicus, Gehyra mutilata, Gekko gecko, G. mindorensis, Hemidactylus frenatus, H. garnoti, H. platyurus, Hemiphyllodactylus typus, Lepidodactylus naujanensis; (Scincidae) Brachymeles bonitae, Dasia olivaceum, Emoia atrocostata, Eutropis multicarinata, 144 E. multifasciata, Lamprolepis smaragdina, Lipinia auriculatum, Sphenomorphus cumingi, S. jagori, S. steerei; (Varanidae) Varanus marmoratus. Brachymeles taylori Brown 1956 Figs. 3, 7, 11B Brachymeles gracilis taylori, Brown, 1956, Type-locality: Sitio Lunga, 13 km West Dumaguete, 3 km West Valencia, on low ridge on the north side of the Maite River, Negros Oriental Province, Negros Island, Philippines, 600 m elevation, 9°17'32.96" N, 123°14'2.4" E (holotype: CAS-SU 24487). Brachymeles gracilis (part), Brown and Alcala, 1970. Brachymeles boulengeri taylori (part), Brown and Alcala, 1980. Diagnosis.—Brachymeles taylori can be distinguished from congeners by the following combination of characters: (1) body size moderate (SVL 65.8–99.2 mm); (2) pentadactyl; (3) Finger-III lamellae five or six; (4) Toe-IV lamellae nine or ten; (5) moderate limb length; (6) supralabials six; (7) infralabials seven; (8) pineal eye spot present; (9) supranasals not contacting on midline; (10) prefrontals not contacting on midline; (11) enlarged chin shields in two pairs; (12) nuchal scales undifferentiated; (13) fourth and fifth supralabial below eye; (14) auricular opening present; (15) dorsolateral stripes absent; and (16) continuous, dark mid-dorsal stripes present (Tables 3.4, 3.5). Comparisons.—Characters distinguishing Brachymeles taylori from all pentadactyl species of Brachymeles are summarized in Tables 3.4 and 3.5. Brachymeles taylori most closely resembles B. boholensis, B. boulengeri, and B. mindorensis, but differs from these three taxa by the absence of continuous, light dorsolateral stripes (Tables 3.4, 3.5). Brachymeles taylori can 145 further be distinguished from B. boholensis by having five or six Finger-III lamellae, six supralabials, and the fourth and fifth supralabial below the eye, and by the absence of a third pair of enlarged chin shields (Tables 3.4, 3.5); from B. boulengeri by having six supralabials and six supraciliaries, and the presence of continuous, dark mid-dorsal stripes (Tables 3.4, 3.5); and from B. mindorensis by having a smaller body size, shorter hind limbs, nine or ten Toe-IV lamellae, six supralabials, seven infralabials, the fourth and fifth supralabial below the eye, and no contact between supranasals and prefrontals (Tables 3.4, 3.5). From all non-pentadactyl species of Brachymeles (B. apus, B. bonitae, B. cebuensis, B. elerae, B. lukbani, B. minimus, B. muntingkamay, B. pathfinderi, B. samarensis, B. tridactylus, B. vermis, and B. wrighti), B. taylori differs by having pentadactyl limbs (vs. non-pentadactyl), longer forelimbs (greater than 9.0 mm vs. less than 6.9 mm), longer hind limbs (greater than 15.6 mm vs. less than 12.9 mm), and Toe-IV lamellae nine or ten (vs. eight or fewer), and by the presence of a postnasal scale (vs. absence). Additionally, Brachymeles taylori differs from all non-pentadactyl species except B. wrighti by having a midbody scale row count 26–28 (vs. fewer than 24); from all non-pentadactyl species except B. pathfinderi by having a paravertebral count 62–69 (vs. greater than 84) and by the presence of auricular openings (vs. absence); and from B. apus, B. lukbani, B. minimus, and B. vermis by the presence of limbs (vs. absence). Description (based on holotype and 33 referred specimens, including 5 paratypes at CAS).—Details of the head scalation of an adult female are shown in Figure 3.7. Measurements of the holotype are provided below in brackets. Body moderate relative to other Brachymeles, elongate with respect to other lizards; maximum SVL 99.2 mm for males, 93.2 mm for females [65.8, female] (Tables 3.4, 3.5); head weakly differentiated from neck, nearly as wide as body, HW 11.3–15.3% (12.3 ± 1.0) SVL [15.3], 104.4–139.5% (120.5 ± 10.2) HL [132.8]; HL 34.8–44.6% 146 (39.2 ± 2.5) SnFa [36.4]; SnFa 23.4–31.7% (26.2 ± 1.7) SVL [31.7]; snout moderately long, broadly rounded in dorsal profile, depressed in lateral profile, SNL 44.1–62.5% (52.2 ± 4.6) HL [62.5]; auricular opening present, moderate; eyes moderate, ED 1.6–2.8% (2.1 ± 0.2) SVL [2.8], 15.9–24.4% (20.8 ± 2.4) HL [24.4], 48.8–69.5% (59.6 ± 6.1) END [62.7], pupil nearly round; body slightly depressed, MBW 89.1–148.4% (115.1 ± 14.7) MBH [112.9]; scales smooth, glossy, imbricate; longitudinal scale rows at midbody 26–28 [27]; paravertebral scale rows 62–69 [64]; axilla–groin scale rows 42–47 [43]; limbs well developed, pentadactyl, digits small; FinIIIlam 5–6 [6]; ToeIVlam 8–10 [9]; FLL 15.7–20.4% (17.8 ± 1.2) AGD [19.9], 10.4–14.1% (11.5 ± 0.9) SVL [14.1]; HLL 26.7–36.8% (31.1 ± 2.5) AGD [35.6], 17.8–25.2% (20.1 ± 1.7) SVL [25.2]; order of digits from shortest to longest for hand: I = V < IV < II = III, for foot: I < V < II < III = IV; tail not as wide as body, sharply tapered posteriorly, TW 54.0–80.3% (68.9 ± 6.7) MBW [75.0], TL 69.2–103.1% (83.3 ± 10.4) SVL [98.2]. Rostral projecting dorsoposteriorly to point in line with anterior edge of nasal, broader than high, in moderate contact with frontonasal; frontonasal wider than long; nostril ovoid, in center of single rectangular nasal; nasals well separated; supranasals present, large, narrowly separated by frontonasal; postnasals present; prefrontals moderately separated by frontal; frontal nearly octagonal, its anterior margin in moderate contact with frontonasal, in contact with first two anterior supraoculars, 4.5 × wider than anteriormost supraocular; supraoculars five; frontoparietals moderate, in broad medial contact, each frontoparietal in contact with supraoculars two–four; interparietal moderate, quadrilaterally shaped, longer than wide, its length nearly equal to midline length of frontoparietal; parietal eyespot present in posterior one half of scale; parietals in moderate contact behind interparietal or narrowly separated; nuchals undifferentiated; loreals two, decreasing in size from anterior to posterior, subequal, anterior 147 loreal in contact with prefrontal, postnasal, supranasal, second supralabial, posterior loreal and frontonasal; preocular single, nearly two thirds as high as posterior loreal; single presubocular; supraciliaries six, the anteriormost contacting prefrontal and separating posterior loreal from first supraocular; subocular row complete; lower eyelid with one row of scales, lacking an enlarged oval window, largely transparent; supralabials six, fourth and fifth below the eye; infralabials seven. Mental wider than long, in contact with first infralabial; postmental single, enlarged, slightly wider than mental, followed by two pairs of enlarged chin shields, scales of first pair separated or in moderate contact, second pair slightly wider than first, broadly separated by a single medial scale. Scales on limbs smaller than body scales; scales on dorsal surfaces of digits large, wrapping around lateral edges of digits; lamellae undivided; palmar surfaces of hands and plantar surfaces of feet covered by small, irregular scales, each with irregular raised anterior edges; scales on dorsal surface of hands and feet smaller than limb scales, lacking raised edges. Coloration in preservative.—Ground color of body medium olive-brown; dorsal pigmentation nearly all dark brown, gradually fading into olive-brown lateral surface and yellowish-brown ventral surface of body, ventral surface without dark pigmentation; dark dorsal pigmentation in nearly continuous block across dorsal surface or at times forming ten continuous longitudinal rows of dark-brown pigment, spanning six full rows of scales across dorsal surface, extending from posterior edge of parietals to tail tip, additional three to four scale rows on each lateral surface with dark coloration, covering one half to two thirds of dorsal and lateral scales; dorsolateral stripes absent. Tail coloration matches body coloration. Head scales uniform dark brown, darker brown than ventral scales; rostral, nasal, postnasal, supranasal, and first 148 supralabial dark gray; pineal eyespot poorly defined, small and light cream. Limbs mottled medium brown dorsally, yellowish brown ventrally; dorsal and ventral surface of digits dark brown. Coloration in life.—(Fig. 3.11B). Ground color of body light to medium-brown; medium to dark brown dorsal pigmentation gradually fading into medium brown lateral pigmentation; limbs mottled medium to dark brown dorsally. Variation.—Morphometric variation of the series is summarized in Table 3.6. We observed variation among the 14 specimens examined for the degree of contact between head scales. Six specimens have parietals moderately separated by the interparietal (KU 324048, 324050, 324052–5), one specimen has parietals narrowly separated by the interparietal (KU 324051), and seven specimens have parietals in moderate medial contact (KU 306651, 324044–7, 324049, 324056) behind the interparietal; eight specimens do not have the first pair of enlarged chin shields in medial contact (KU 324045, 324048–50, 324053–6), one specimen has the first pair of enlarged chin shields in point medial contact (KU 324046), and five specimens have the first pair of enlarged chin shields in moderate medial contact (KU 306651, 324044, 324047, 324051–2). Scale counts were observed to vary among the measured series. Specimens were observed to have midbody scale row counts of 26 (CAS-SU 18641, 18656–7, 18748, 21873, 21877, 21880, 21884, 22355, CAS 154971, 154673, 154680–2, 154686), 27 (CAS-SU 18615, 22356, CAS 154679), and 28 (CAS-SU 18649, 21883, CAS 154678); axilla–groin scale row counts of 42 (CAS 154680, 154686), 43 (CAS-SU 18615, 18656, CAS 154682), 44 (CAS-SU 18641, 18748, 21873, 21877, 21880, 22356, CAS 154678, 154679, 154681), 45 (CAS-SU 21884, 22355, CAS 154671), 46 (CAS-SU 18649, 21883, CAS 154673) and 47 (CAS-SU 18657); and paravertebral scale row counts of 62 (CAS 154680, 154686), 64 (CAS-SU 18615, 18656, CAS 154682), 66 149 (CAS-SU 18641, 18748, 21873, 21877, 21880, 21884, 22356, CAS 154678–9, 154681), 67 (CAS-SU 18649, CAS 154671, 154673), 68 (CAS-SU 21883, 22355), and 69 (CAS-SU 18657). We also observed lamellae counts to vary among the measured series. Specimens were observed to have Finger-III lamellae counts of five (CAS-SU 18641, 18649, 18656, 18748, 21883–4, 22356, CAS 154671, 154673, 154678–80) or six (CAS-SU 18615, 18657, 21873, 21877, 21880, 22355, CAS 154681–2, 154686); Toe-IV lamellae counts of eight (CAS 154678), nine (CAS-SU 18615, 18649, 18656, 21880, 22356, CAS 154671, 154673, 154682, 154686), and ten (CAS-SU 18641, 18657, 18748, 21873, 21877, 21883–4, 22355, CAS 15479–81). There is some color variation in the examined series, with the degree and definition of continuous, dark mid-dorsal stripes. All specimens have continuous, dark lines running down the mid-dorsal surface of the body; however, the continuous lines in some specimens are present without a dark, mid-dorsal background coloration (KU 324045–6, 324049–51, 324053–4). The dark lines in other specimens overlay a dark, mid-dorsal region covered by a long streak of dark background pigmentation (KU 324044, 324047–8, 324052, 324055–6). Distribution.—Brachymeles taylori is known from Negros, Cebu, Inampulugan, Pan de Azucar, Danjugan, Ponson, and Poro Islands (Fig. 3.3). Ecology and natural history.—Brachymeles taylori occurs in agricultural areas as well as disturbed and secondary-growth forest. Little or no original, low elevation forest remains in the Visayas, but we assume the species once also occurred in primary forest. Individuals have been observed under piles of rotting coconut husks, in the humus material within rotting logs, and in loose soil and leaf litter surrounding the root networks of trees. The species is quite common throughout its range (CDS personal observations), and occurs sympatrically with three other species of Brachymeles (B. cebuensis, B. talinis, and B. tridactylus [Brown, 1956; Brown and 150 Rabor, 1967; Brown and Alcala, 1980]). Similar to B. boulengeri, B. taylori appears to have a wider geographic distribution that spans multiple Philippine islands. This is in contrast to the island endemic species, B. boholensis and B. mindorensis, which are known from just Bohol and Mindoro Islands respectively. As with all members of the genus, when disturbed, individuals move rapidly attempting to burrow into the loose soil or humus. Sympatric lizard species observed within the range of Brachymeles taylori include: (Agamidae) Bronchocela marmoratus, Draco spilopterus, Gonocephalus sophiae, Hydrosaurus pustulatus; (Dibamidae) Dibamus argenteus; (Gekkonidae) Cyrtodactylus philippinicus, Gehyra mutilata, Gekko gecko, G. mindorensis, G. enrstkelleri, Luperosaurus corfieldi, Pseudogekko brevipes, Hemidactylus frenatus, H. platyurus, Hemiphyllodactylus typus, Lepidodactylus christiani, L. herrei, L. lugubris; (Scincidae) Brachymeles cebuensis, B. talinis, B. cebuensis, Emoia atrocostata, Eutropis multicarinata, E. multifasciata, Lamprolepis smaragdina, Lipinia auriculata, L. pulchella, L. quadrivittata, L. rabori, Sphenomorphus arborens, S. coxi, S. jagori, S. steerei, Tropidophorus grayi; (Varanidae) Varanus nuchalis. Brachymeles orientalis Brown and Rabor 1967 Figs. 4, 8, 11F,G Brachymeles schadenbergi orientalis, Brown and Rabor, 1967, Type-locality: Bario Dusita, 11 km southeast of Sierra Bullones, Bohol Province, Bohol Island, Philippines, 533 m elevation, 9°46'57.5" N, 124°18'10.8" E (holotype: CAS-SU 24436). Brachymeles schadenbergi (part), Brown and Alcala, 1970. Brachymeles schadenbergi (part), Brown and Alcala, 1980. 151 Diagnosis.—Brachymeles orientalis can be distinguished from congeners by the following combination of characters: (1) body large (SVL 97.6–112.3 mm); (2) pentadactyl; (3) Finger-III lamellae six or seven; (4) Toe-IV lamellae eight to ten; (5) limbs relatively long; (6) supralabials six or seven; (7) infralabials six or seven; (8) pineal eye spot present; (9) supranasal contact absent; (10) prefrontals not contacting on midline; (11) enlarged chin shields in two pairs; (12) nuchal scales undifferentiated; (13) fourth and fifth supralabial below eye; (14) auricular opening present; (15) dorsolateral stripes absent; and (16) mid-dorsal stripes absent (Tables 3.4, 3.5). Comparisons.—Characters distinguishing Brachymeles orientalis from all pentadactyl species of Brachymeles are summarized in Tables 3.4 and 3.5. Brachymeles orientalis most closely resembles B. makusog and B. schadenbergi, but differs from both taxa by having six or seven Finger-III lamellae, eight to ten Toe-IV lamellae, and the fourth and fifth supralabial below the eye (Tables 3.4, 3.5), and by the presence (vs. absence) of reddish-orange to salmon-colored scales on the lateral surfaces of the body. Brachymeles orientalis can further be distinguished from B. makusog by having a greater maximum axilla–groin scale row count and a greater maximum paravertebral scale row count (Table 3.5), and from B. schadenbergi by having no contact between supranasals, and by the absence of continuous, dark mid-dorsal stripes and dark lateral stripes (Table 3.5). From all non-pentadactyl species of Brachymeles (B. apus, B. bonitae, B. cebuensis, B. elerae, B. lukbani, B. minimus, B. muntingkamay, B. pathfinderi, B. samarensis, B. tridactylus, B. vermis, and B. wrighti), B. orientalis differs by having pentadactyl limbs (vs. non-pentadactyl), longer forelimb lengths (greater than 10.4 mm vs. less than 6.9 mm), greater hind limb lengths (greater than 18.6 mm vs. less than 12.9 mm), and by the presence (vs. absence) of a postnasal scale. Additionally, B. orientalis differs from all non-pentadactyl species except B. pathfinderi 152 by having Toe-IV lamellae eight to ten (vs. 4 or fewer), a paravertebral scale row count 69–72 (vs. greater than 84), and by the presence (vs. absence) of auricular openings; from all non-pentadactyl species except B. wrighti by having a midbody scale row count 26–28 (vs. fewer than 24); and from B. apus, B. lukbani, B. minimus, and B. vermis by the presence of limbs (vs. absence). Description (based on holotype and 52 referred specimens, including 13 paratypes from CAS).—Details of the head scalation of an adult male are shown in Figure 3.8. Measurements of the holotype are provided below in brackets. Body large relative to other Brachymeles, elongate with respect to other lizards; maximum SVL 112.3 mm for males, 115.2 mm for females [99.9, female] (Tables 3.4, 3.5); head weakly differentiated from neck, nearly as wide as body, HW 10.2–12.7% (11.2 ± 0.7) SVL [11.9], 87.5–120.0% (108.4 ± 7.3) HL [120.0]; HL 33.7–45.0% (37.6 ± 2.6) SnFa [38.0]; SnFa 25.3–30.2% (27.6 ± 1.1) SVL [26.1]; snout long, rounded in dorsal and lateral profile, SNL 46.6–65.2% (57.5 ± 4.2) HL [62.5]; auricular opening present, moderate; eyes moderate, ED 1.5–2.3% (1.8 ± 0.2) SVL [1.8], 14.8–19.6% (17.3 ± 1.3) HL [18.2], 38.2–56.7% (44.8 ± 3.7) END [45.9], pupil subcircular; body slightly depressed, MBW 93.1–138.2% (114.5 ± 11.4) MBH [124.9]; scales smooth, glossy, imbricate; longitudinal scale rows at midbody 26–30 [28]; paravertebral scale rows 69–73 [72]; axilla–groin scale rows 46–49 [48]; limbs well developed, pentadactyl, digits small; FinIIIlam 6–7 [6]; ToeIVlam 8–10 [8]; FLL 17.0–24.8% (20.7 ± 2.0) AGD [18.8], 10.7–15.4% (13.1 ± 1.1) SVL [12.3]; HLL 27.6–42.7% (34.2 ± 3.4) AGD [32.2], 18.4–24.2% (21.6 ± 1.7) SVL [21.2]; order of digits from shortest to longest for hand: I < V < II = IV < III, for foot: I < V < II < III = IV; tail nearly as wide as body, sharply tapered towards end, TW 55.6–86.9% (69.7 ± 6.4) MBW [70.9], TL 62.2–106.0% (85.2 ± 11.6) SVL [106.0]. 153 Table 3.4. Summary of meristic and mensural characters in all known pentadactyl species of Brachymeles. Sample size, body length and total length among males and females, and general geographical distribution (PAIC = Pleistocene Aggregate Island Complexes, sensu Brown and Diesmos, 2002) are included for reference (SVL, TotL, MBW, FLL, and HLL given as range over mean ± standard deviation; all body proportions given as percentage over mean ± standard deviation). In cases of scale count variation within species, numbers of individuals showing specific counts are given in parentheses. 154 bo ho le ns is (5 m , 1 4 f) bo ule ng er i (7 m , 8 f) m in do re ns is (6 m , 1 2 f) ta yl or i (8 m , 1 3 f) gr ac il is g ra ci li s (7 m , 1 1 f) gr ac il is h il on g (8 m , 1 2 f) bi co lo r (7 m , 6 f) R an ge B oh ol Is la nd L uzo n P A IC M in do ro Is la nd N eg ro s & C eb u Isl an d M in da na o P A IC M in da na o P A IC L uzo n Isl an d S VL (f) S VL (m ) 83 .8 –9 4. 0 (88 .4 ± 3 .1 ) 84 .1 –9 3. 6 (89 .1 ± 4 .1 ) 60 .5 –9 5. 5 (84 .0 ± 1 1. 2) 72. 3 –9 3. 1 (82 .5 ± 6 .7) 90 .0 –1 06 .8 (98 .8 ± 5 .3 ) 93 .9 –1 04 .2 (10 0. 2 ± 4 .1 ) 65 .8 –9 3. 2 (83 .9 ± 7.4 ) 83 .1 –9 9. 2 (87. 0 ± 5 .2 ) 62 .8 –75 .8 (67. 6 ± 3 .7) 60 .1 –8 2. 3 (67. 5 ± 7.6 ) 59 .9 –8 1. 5 (71. 8 ± 7.0 ) 61 .5 –78 .5 (70. 5 ± 5 .1 ) 12 5. 9– 15 3. 3 (13 9. 4 ± 1 0. 1) 12 0. 4– 14 0. 3 (13 4. 0 ± 7.6 ) T ot L (f) T ot L (m ) 12 9. 6– 174 .8 (15 4. 1 ± 1 4. 7) 15 4. 5– 16 6. 2 (16 0 .7 ± 5 .9 ) 12 9. 7– 16 7.4 (15 9. 3 ± 1 3. 1) 12 4. 3– 173 .1 (15 1. 4 ± 1 9. 4) 16 2. 5– 20 6. 7 (18 0. 2 ± 1 4. 2) 16 5. 3– 19 7.0 (18 4. 9 ± 1 1. 5) 13 0. 3– 16 8. 5 (14 9. 9 ± 1 3. 0) 14 9. 6– 176 .7 (16 4. 3 ± 1 1. 3) 11 6. 4– 13 4. 4 (12 6. 3 ± 5 .5 ) 11 3. 9– 13 3. 7 (12 3. 2 ± 8 .8 ) 94 .3 –1 59 .2 (12 6. 4 ± 1 7.1 ) 11 6. 7– 13 9. 4 (12 7.4 ± 7. 8) 22 5. 3– 29 0. 7 (26 0. 7 ± 3 0. 7) 23 3. 4– 30 1. 4 (28 0. 1 ± 2 4. 9) M B W 11 .9 –1 5. 0 (13 .4 ± 1 .0 ) 9. 9– 14 .7 (12 .4 ± 1 .7) 12 .8 –2 0. 8 (16 .0 ± 1 .8 ) 11 .0 –1 6. 8 (13 .8 ± 1 .7) 8. 1– 11 .6 (9. 5 ± 0 .9 ) 7.9 –1 2. 1 (10 .1 ± 1 .2 ) 13 .6 –1 5. 3 (14 .4 ± 0 .6 ) T L /S VL 53 –9 0 (76 ± 1 3) 67 –1 14 (89 ± 1 6) 60 –9 9 (85 ± 1 1) 69 –1 03 (83 ± 1 0) 69 –1 00 (88 ± 1 0) 57 –9 8 (78 ± 1 4) 62 –1 16 (97 ± 2 2) T W/M B W 62 –78 (70 ± 5 ) 60 –8 1 (70 ± 6 ) 54 –8 0 (69 ± 8 ) 54 –8 0 (69 ± 7) 57 –79 (67 ± 6 ) 57 –8 1 (69 ± 7) 69 –8 4 (76 ± 6 ) F L L 9. 0– 11 .2 (10 .1 ± 0 .7) 8. 2– 11 .7 (1 0. 5 ± 0 .8 ) 10 .0 –1 3. 0 (11 .4 ± 0 .8 ) 9. 0– 10 .4 (9. 8 ± 0 .4 ) 5. 9– 7.9 (6. 9 ± 0 .6 ) 7.1 –9 .3 (8. 3 ± 0 .6 ) 9. 0– 12 .0 (10 .5 ± 1 .1 ) F L L /S VL 10 –1 3 (11 ± 1 ) 12 –1 4 (13 ± 1 ) 10 –1 3 (11 ± 1 ) 10 –1 4 (12 ± 1 ) 9– 12 (10 ± 1 ) 10 –1 4 (12 ± 1 ) 6. 6– 8. 8 (7.7 ± 0. 7) H L L 15 .4 –1 8. 7 (17. 2 ± 1 .0 ) 14 .3 –1 8. 7 (17. 2 ± 1 .1 ) 18 .8 –2 3. 1 (20 .6 ± 1 .2 ) 15 .6 –1 8. 7 (17. 0 ± 1 .0 ) 10 .3 –1 3. 6 (12 .0 ± 0 .7) 12 .2 –1 6. 0 (14 .3 ± 1 .0 ) 16 .1 –2 0. 5 (17. 6 ± 1 .3 ) H L L /S VL 18 –2 2 (19 ± 1 ) 18 –2 4 (21 ± 2 ) 18 –2 4 (21 ± 2 ) 18 –2 5 (20 ± 2 ) 15 –2 0 (18 ± 1 ) 17 –2 3 (20 ± 1 ) 11 .3 –1 4. 9 (1 3. 0 ± 1 .1 ) F in IIIla m 6 (19 ) 5 (14 ) 6 (1) 5 (16 ) 6 (2) 5 (12 ) 6 (9) 4 (8) 5 (10 ) 5 (20 ) 4 (8) 5 (5) T oe IVla m 9 (7) 10 (1 2) 9 (13 ) 10 (2 ) 8 (14 ) 9 (4) 9 (10 ) 10 (1 1) 7 (4 ) 8 (14 ) 8 (13 ) 9 (7) 6 (2) 7 (1 1) 155 T A B L E 4 .— C on ti n u ed . ta li ni s (1 1 m , 1 0 f) ka dw a (1 2 m , 1 5 f) tu ng ao i (2 m , 6 f ) m ak us og (7 m , 4 f ) or ie nt al is (2 1 m , 1 9 f) sc ha de nb er gi (1 4 m , 1 0 f) vin du m i (1 m , 1 f ) R an ge V is ay an P A IC L uz on , B ab uy an C la ro , C al ay an I sl an ds M as ba te I sl an d L uz on P A IC M in da na o P A IC M in da na o P A IC Jo lo I sl an d S V L ( f) S V L ( m ) 10 3. 8– 12 6. 7 (1 16 .5 ± 6 .8 ) 10 3. 1– 12 3. 1 (1 13 .6 ± 7 .1 ) 90 .6 –1 35 .7 (1 09 .7 ± 1 1. 7) 97 .0 –1 28 .2 (1 09 .3 ± 9 .1 ) 78 .2 –1 06 .2 (9 5. 6 ± 1 0. 7) 89 .9 , 1 04 .8 98 .6 –1 18 .0 (1 08 .8 ± 8 .0 ) 82 .5 –1 23 .5 (1 10 .9 ± 1 3. 7) 97 .6 –1 15 .2 (1 04 .6 ± 5 .9 ) 84 .7 –1 12 .3 (9 9. 0 ± 8 .4 ) 93 .1 –1 13 .5 (1 04 .8 ± 6 .7 ) 94 .4 –1 15 .8 (1 04 .5 ± 6 .1 ) 10 4. 9 11 3. 6 T ot L ( f) T ot L ( m ) 18 7. 5– 23 6. 2 (2 09 .4 ± 1 8. 0) 19 1. 7– 23 8. 4 (2 09 .0 ± 1 2. 4) 17 0. 4– 22 1. 0 (1 96 .3 ± 1 8. 7) 18 1. 9– 25 5. 2 (2 08 .3 ± 2 0. 3) 16 8. 9– 20 6. 5 (1 87 .2 ± 1 5. 9) 17 8. 3, 2 03 .1 18 3. 8– 21 7. 3 (2 01 .5 ± 1 7. 7) 16 2. 3– 24 1. 3 (2 01 .5 ± 2 5. 1) 15 9. 7– 21 3. 0 (1 94 .3 ± 1 7. 1) 15 4. 6– 22 1. 1 (1 84 .8 ± 2 2. 3) 18 0. 8– 21 7. 4 (2 02 .4 ± 1 7. 6) 17 9. 2– 21 9. 7 (2 03 .0 ± 1 4. 4) – – M B W 15 .9 –2 0. 9 (1 8. 5 ± 1 .5 ) 14 .3 –2 1. 0 (1 6. 9 ± 1 .8 ) 11 .9 –1 7. 0 (1 4. 4 ± 1 .6 ) 13 .0 –1 9. 9 (1 7. 5 ± 2 .1 ) 11 .0 –1 8. 9 (1 5. 1 ± 1 .8 ) 13 .5 –1 9. 1 (1 5. 2 ± 1 .7 ) 14 .2 , 1 4. 8 T L /S V L 61 –1 07 (8 4 ± 1 2) 68 –1 06 (8 7 ± 1 2) 82 –1 16 (9 7 ± 1 1) 61 –1 17 (8 4 ± 1 6) 62 –1 06 (8 5 ± 1 2) 65 –1 03 (9 2 ± 1 1) – T W /M B W 63 –9 4 (7 5 ± 6 ) 66 –8 4 (7 5 ± 5 ) 62 –8 0 (7 0 ± 6 ) 69 –8 3 (7 5 ± 4 ) 56 –8 7 (7 0 ± 6 ) 57 –7 7 (6 8 ± 6 ) 83 , 7 9 F L L 11 .3 –1 7. 7 (1 4. 2 ± 1 .4 ) 10 .7 –1 5. 0 (1 3. 0 ± 1 .2 ) 11 .0 –1 3. 8 (1 2. 2 ± 0 .9 ) 12 .8 –1 7. 0 (1 4. 5 ± 1 .1 ) 10 .4 –1 5. 6 (1 3. 4 ± 1 .5 ) 11 .1 –1 3. 5 (1 2. 5 ± 0 .8 ) 13 .2 , 1 3. 3 F L L /S V L 10 –1 5 (1 2 ± 1 ) 10 –1 6 (1 2 ± 1 ) 11 –1 4 (1 3 ± 1 ) 12 –1 7 (1 3 ± 1 ) 11 –1 5 (1 3 ± 1 ) 10 –1 4 (1 2 ± 1 ) 12 , 1 3 H L L 20 .5 –2 7. 9 (2 3. 7 ± 2 .2 ) 17 .9 –2 4. 1 (2 1. 8 ± 1 .6 ) 17 .0 –2 2. 4 (2 0. 0 ± 1 .8 ) 19 .4 –2 5. 3 (2 2. 1 ± 1 .9 ) 18 .6 –2 5. 3 (2 2. 1 ± 2 .2 ) 18 .5 –2 1. 9 (2 0. 6 ± 1 .2 ) 22 .7 , 2 2. 7 H L L /S V L 18 –2 5 (2 1 ± 2 ) 17 –2 6 (2 0 ± 2 ) 20 –2 3 (2 1 ± 1 ) 18 –2 5 (2 0 ± 2 ) 18 –2 4 (2 2 ± 2 ) 17 –2 2 (2 0 ± 1 ) 20 , 2 2 F in II Il am 5 (1 9) 6 (2 ) 5 (2 5) 6 (2 ) 5 (5 ) 6 (3 ) 5 (6 ) 6 (5 ) 6 (3 6) 7 (4 ) 5 (1 3) 6 (1 1) 6 (2 ) T oe IV la m 8 (2 ) 9 (1 2) 10 ( 7) 7 (1 ) 8 (1 4) 9 (1 1) 10 ( 1) 9 (5 ) 10 ( 3) 9 (6 ) 10 ( 5) 8 (4 ) 9 (2 9) 10 ( 7) 8 (1 4) 9 (1 0) 9 (1 ) 10 ( 1) 156 Table 3.5. Summary of qualitative diagnostic characters (present, absent) in all known pentadactyl species of Brachymeles. The pairs of enlarged scales posterior to the postmental scale are abbreviated as chin shield pairs with reference to the 1st, 2nd, and 3rd pairs (when present). 157 bo ho le ns is (5 m , 1 4 f) bo ule ng er i (7 m , 8 f ) m in do re ns is (6 m , 1 2 f) ta yl or i (8 m , 1 3 f) gr ac il is g ra ci li s (7 m , 1 1 f) gr ac il is h il on g (8 m , 1 2 f) bi co lo r (7 m , 6 f ) M B SR 26 –2 8 26 –2 7 26 –2 8 26 –2 8 24 –2 6 27 –3 0 27 –2 9 A G SR 42 –4 6 42 –4 6 42 –4 5 42 –4 7 46 –4 9 44 –5 0 64 –7 2 PV SR 63 –6 6 63 –6 6 63 –6 5 62 –6 9 67 –7 0 66 –7 3 88 –9 2 SL 7 (1 9) 6 (1 2) 7 (3 ) 7 (1 8) 6 (2 1) 6 (1 8) 6 (2 0) 6 (1 3) IF L 7 (1 9) 7 (1 5) 6 (1 8) 7 (2 1) 7 (1 8) 6 (2 0) 6 (1 3) SC 6 (1 9) 5 (1 ) 6 (1 4) 6 (1 8) 6 (2 1) 6 (1 8) 6 (2 0) 6 (1 3) SO 5( 19 ) 5 (1 5) 5 (1 8) 5 (2 1) 5 (1 8) 5 (2 0) 5 (1 3) Pi ne al e ye sp ot + + + + – + + Su pr an as al c on ta ct – – – or + – – – + Pr ef ro nt al c on ta ct – – – or + – + – – Fr on to pa ri et al c on ta ct + + + + + – or + + Pa ri et al s co nt ac t – or + – or + – or + – or + + + + 1s t c hi n sh ie ld p ai r co nt ac t – or + + + – or + – – or + + E nl ar ge d ch in s hi el d pa ir s 3 2 2 2 3 3 2 C hi n sh ie ld p ai r si ze 3 < 1 < 2 1 < 2 1 < 2 1 < 2 3 < 1 < 2 3 < 1 < 2 2 < 1 C hi n sh ie ld p ai r se pa ra tio n1 1( 0/ 1) ; 2 (1 ); 3 (3 ) 1( 0/ 1) ; 2 (1 ) 1( 0) ; 2 (1 ) 1( 0) ; 2 (1 ) 1( 1) ; 2 (1 ); 3 (3 ) 1( 0/ 1) ; 2 (1 ); 3 (3 /5 ) 1( 0) ; 2 (3 ) Su bo cu la r su pr al ab ia l 5t h an d 6t h 4t h an d 5t h 5t h an d 6t h 4t h an d 5t h 4t h an d 5t h 4t h an d 5t h 4t h an d 5t h D if fe re nt ia te d nu ch al s – – – – – – + U ni fo rm b od y co lo r – – – – + + – C on tin uo us , l ig ht do rs ol at er al s tr ip es + + + – + + – C on tin uo us d ar k m id -d or sa l st ri pe s2 + – + + + – or + – D ar k la te ra l s tr ip es 2 + + + + + + – D ar k ve nt ra l p ig m en ta tio n + – – – + + – 1 P ar en th es es s ho w th e nu m be r of s m al l v en tr al s ca le r ow s se pa ra tin g ea ch e nl ar ge d pa ir o f ch in s hi el ds . 2 C ha ra ct er r ef er s to lo ng itu di na l r ow s of d ar k sc al e pi gm en ta tio n, o ft en in th e fo rm o f sp ot s, a lig ne d in to r ow s. 158 T A B L E 5 .— C on ti nu ed . ta lin is (1 1 m , 1 0 f) ka dw a (1 2 m , 1 5 f) tu ng ao i (2 m , 6 f) m ak us og (7 m , 4 f) or ie nt al is (2 1 m , 1 9 f) sc ha de nb er gi (1 4 m , 1 0 f) vin du m i (1 m , 1 f) M B SR 26 –3 0 26 –2 8 26 –2 8 25 –2 8 26 –2 8 26 –2 8 30 , 3 1 A G SR 43 –4 8 47 –4 9 46 –4 9 42 –4 7 46 –4 9 45 –5 0 49 , 4 9 PV SR 67 –7 2 68 –7 0 66 –6 8 60 –6 9 69 –7 2 67 –7 2 74 , 7 4 SL 7 (2 0) 7 (2 7) 7 (4 ) 6 (7 ) 7 (4 ) 6 (3 1) 7 (9 ) 6 (2 ) 7 (2 2) 7 (2 ) IF L 7 (2 1) 6 (2 7) 6 (4 ) 6 (1 0) 7 (1 ) 6 (7 ) 7 (3 3) 6 (1 0) 7 (1 4) 6 (2 ) SC 6 (2 1) 6 (2 7) 6 (4 ) 6 (1 1) 6 (4 0) 6 (2 4) 6 (2 ) SO 5 (2 1) 5 (2 7) 5 (4 ) 5 (1 1) 5 (4 0) 5 (2 4) 5 (2 ) Pi ne al e ye sp ot + + + + + + + Su pr an as al c on ta ct + + + – – + + Pr ef ro nt al c on ta ct – – – – – – – Fr on to pa ri et al c on ta ct + – or + + + + + + Pa ri et al s co nt ac t – or + – or + – or + – – or + – or + + 1s t c hi n sh ie ld p ai r c on ta ct – or + – or + + – or + – or + – or + – E nl ar ge d ch in s hi el d pa ir s 2 2 2 2 2 2 2 C hi n sh ie ld p ai r s iz e 2 < 1 1 < 2 1 = 2 2 < 1 2 < 1 2 < 1 2 < 1 C hi n sh ie ld p ai r s ep ar at io n1 1( 0/ 1) ; 2 (3 ) 1( 0/ 1) ; 2 (1 ) 1( 0) ; 2 (1 ) 1( 1) ; 2 (3 ) 1( 0/ 1) ; 2 (3 ) 1( 0) ; 2 (3 ) 1( 1) ; 2 (1 ) Su bo cu la r s up ra la bi al 5t h a nd 6 th 5t h a nd 6 th 5t h a nd 6 th 4t h an d 5t h o r 5 th a nd 6 th 4t h an d 5t h 5t h a nd 6 th 5t h a nd 6 th D if fe re nt ia te d nu ch al s – – – – – – – U ni fo rm b od y co lo r – – – – – – – C on tin uo us , l ig ht do rs ol at er al s tr ip es – or + +, p oo rl y de fi ne d +, p oo rl y de fi ne d – – – + C on tin uo us d ar k m id -d or sa l st ri pe s2 – or + + + – – – or + – D ar k la te ra l s tr ip es 2 + + + – – – or + + D ar k ve nt ra l p ig m en ta tio n – + – – – – + 1 P ar en th es es s ho w th e nu m be r o f s m al l v en tr al s ca le ro w s se pa ra tin g ea ch e nl ar ge d pa ir o f c hi n sh ie ld s. 2 C ha ra ct er re fe rs to lo ng itu di na l r ow s of d ar k sc al e pi gm en ta tio n, o ft en in th e fo rm o f s po ts , a lig ne d in to ro w s. 159 Table 3.6. Summary of univariate morphological variation among mensural characters in series of Brachymeles boholensis, B. boulengeri, B. mindorensis, B. taylori, B. talinis, B. kadwa, B. tungaoi, B. orientalis, B. schadenbergi and B. vindumi. 160 boholensis (5 m; 14 f) boulengeri (7 m; 8 f) mindorensis (6 m; 12 f) taylori (8 m; 13 f) talinis (11 m; 10 f) SVL (m) 84.1–93.6 (89.1 ± 4.1) 72.3–93.1 (82.5 ± 6.7) 93.9–104.2 (100.2 ± 4.1) 83.1–99.2 (87.0 ± 5.2) 103.1–123.1 (113.6 ± 7.1) SVL (f) 83.8–94.0 (88.4 ± 3.1) 60.5–95.5 (84.0 ± 11.2) 90.0–106.8 (98.8 ± 5.3) 65.8–93.2 (83.9 ± 7.4) 103.8–126.7 (116.5 ± 6.8) AGD (m) 54.7–61.9 (58.1 ± 2.8) 46.3–60.7 (53.0 ± 5.0) 59.5–67.6 (63.3 ± 3.3) 52.8–66.0 (55.9 ± 4.2) 64.2–90.3 (74.6 ± 7.5) AGD (f) 53.0–61.2 (57.0 ± 2.7) 36.2–61.3 (54.3 ± 8.3) 56.3–74.9 (64.8 ± 5.5) 46.6–60.6 (54.7 ± 4.6) 66.5–81.4 (74.7 ± 4.9) TotL (m) 154.5–166.2 (160.7 ± 5.9) 124.3–173.1 (151.4 ± 19.4) 165.3–197.0 (184.9 ± 11.5) 149.6–176.7 (164.3 ± 11.3) 191.7–238.4 (209.0 161 ± 12.4) TotL (f) 129.6–174.8 (154.1 ± 14.7) 129.7–167.4 (159.3 ± 13.1) 162.5–206.7 (180.2 ± 14.2) 130.3–168.5 (149.9 ± 13.0) 187.5–236.2 (209.4 ± 18.0) MBW (m) 12.2–13.9 (13.0 ± 0.7) 10.1–14.7 (12.1 ± 1.9) 12.8–16.0 (14.7 ± 1.1) 11.6–16.8 (13.3 ± 1.7) 15.9–20.1 (17.7 ± 1.3) MBW (f) 11.9–15.0 (13.6 ± 1.1) 9.9–14.6 (12.7 ± 1.7) 14.5–20.8 (16.7 ± 1.8) 11.0–16.6 (14.0 ± 1.8) 17.3–20.9 (19.3 ± 1.1) MBH (m) 11.7–12.5 (12.1 ± 0.4) 7.9–10.4 (9.0 ± 1.0) 10.2–12.9 (12.0 ± 1.0) 9.4–14.6 (11.8 ± 1.7) 10.4–15.9 (13.5 ± 1.7) MBH (f) 10.4–14.2 (11.8 ± 1.0) 6.2–10.2 (8.9 ± 1.3) 11.4–16.6 (14.2 ± 1.8) 10.4–15.2 (12.2 ± 1.5) 12.7–18.6 (16.2 ± 2.1) 162 TL (m) 70.4–74.8 (72.9 ± 2.3) 52.0–88.6 (69.2 ± 14.7) 62.2–94.2 (84.6 ± 12.0) 63.0–85.7 (76.4 ± 9.2) 86.8–115.3 (96.1 ± 8.5) TL (f) 45.3–82.3 (65.6 ± 13.0) 69.0–86.3 (76.0 ± 6.7) 65.5–99.9 (82.6 ± 11.6) 55.4–76.1 (67.0 ± 7.3) 70.7–115.2 (94.2 ± 17.6) TW (m) 8.5–10.0 (9.4 ± 0.5) 7.2–10.3 (8.7 ± 1.0) 10.2–11.9 (10.9 ± 0.6) 7.4–12.2 (9.5 ± 1.4) 11.8–15.9 (13.5 ± 1.2) TW (f) 8.4–10.4 (9.4 ± 0.5) 7.0–9.9 (8.6 ± 1.2) 10.0–12.5 (11.0 ± 0.7) 7.4–12.1 (9.4 ± 1.3) 12.9–15.6 (14.2 ± 0.9) TH (m) 7.6–8.1 (7.8 ± 0.2) 5.4–8.3 (6.8 ± 0.9) 8.0–9.5 (8.5 ± 0.6) 6.3–10.0 (8.0 ± 1.0) 9.7–11.4 (10.7 ± 0.6) TH (f) 6.9–8.5 (7.6 ± 0.5) 5.1–8.0 (6.5 ± 0.9) 7.3–10.0 (8.5 ± 0.7) 6.9–10.3 (8.0 ± 1.0) 10.6–13.2 163 (11.7 ± 0.9) HL (m) 8.3–9.0 (8.7 ± 0.4) 7.3–8.9 (8.3 ± 0.7) 8.6–10.5 (9.6 ± 0.7) 8.4–9.0 (8.7 ± 0.2) 9.2–12.2 (10.7 ± 0.9) HL (f) 8.6–9.8 (9.0 ± 0.4) 7.9–9.2 (8.3 ± 0.5) 8.9–10.9 (9.9 ± 0.7) 7.6–9.9 (8.7 ± 0.8) 9.9–12.6 (11.3 ± 0.9) HW (m) 9.3–10.9 (10.2 ± 0.6) 9.1–10.3 (9.5 ± 0.5) 10.3–12.1 (11.2 ± 0.6) 9.6–11.6 (10.4 ± 0.8) 11.9–14.5 (13.2 ± 0.8) HW (f) 9.3–10.5 (10.0 ± 0.4) 7.5–9.9 (9.1 ± 0.8) 10.7–12.4 (11.4 ± 0.5) 9.3–12.0 (10.5 ± 0.9) 12.8–15.8 (14.0 ± 0.9) HH (m) 7.2–7.9 (7.7 ± 0.3) 6.2–7.5 (6.9 ± 0.4) 8.2–10.1 (9.0 ± 0.6) 7.3–8.8 (7.9 ± 0.5) 8.8–12.7 (9.9 ± 1.1) HH 7.2–8.0 5.7–7.2 8.1–9.9 7.3–9.7 9.3– 164 (f) (7.5 ± 0.3) (6.6 ± 0.5) (8.9 ± 0.5) (8.1 ± 0.7) 12.5 (10.7 ± 1.0) SnFa (m) 22.9–25.1 (23.7 ± 1.0) 19.1–24.0 (22.4 ± 1.7) 25.9–28.1 (27.0 ± 0.7) 20.7–23.3 (22.1 ± 1.0) 26.2–34.1 (30.6 ± 2.3) SnFa (f) 21.3–24.2 (22.7 ± 0.8) 17.9–24.4 (22.7 ± 2.1) 24.3–27.5 (25.9 ± 1.0) 20.8–25.1 (22.2 ± 1.1) 29.1–34.7 (31.4 ± 1.9) ED (m) 1.7–2.1 (1.8 ± 0.2) 1.8–2.3 (2.0 ± 0.2) 2.0–2.5 (2.2 ± 0.2) 1.4–2.0 (1.8 ± 0.2) 2.0–2.3 (2.2 ± 0.1) ED (f) 1.6–2.0 (1.8 ± 0.1) 1.5–2.3 (1.9 ± 0.3) 2.0–2.6 (2.2 ± 0.2) 1.5–2.1 (1.8 ± 0.2) 2.0–2.5 (2.2 ± 0.1) END (m) 2.4–2.6 (3.5 ± 0.1) 2.7–3.0 (2.8 ± 0.1) 2.5–2.9 (2.7 ± 0.2) 2.8–3.4 (3.1 ± 0.2) 3.7–5.1 (4.3 ± 0.4) 165 END (f) 3.0–3.7 (3.4 ± 0.2) 2.1–3.0 (2.8 ± 0.3) 3.4–4.2 (3.6 ± 0.2) 2.7–3.5 (3.0 ± 0.2) 3.7–5.3 (4.5 ± 0.4) SNL (m) 5.0–5.3 (5.2 ± 0.1) 4.2–4.6 (4.4 ± 0.1) 5.4–6.0 (5.7 ± 0.2) 4.1–4.8 (4.4 ± 0.3) 5.7–7.5 (6.4 ± 0.6) SNL (f) 4.8–5.6 (5.3 ± 0.2) 3.4–4.8 (4.2 ± 0.4) 5.0–6.4 (5.5 ± 0.4) 4.1–5.0 (4.6 ± 0.3) 5.5–7.5 (6.6 ± 0.5) IND (m) 3.0–3.2 (3.1 ± 0.1) 2.8–3.1 (2.9 ± 0.1) 3.2–3.6 (3.4 ± 0.1) 2.7–3.2 (2.9 ± 0.2) 3.3–4.3 (3.9 ± 0.3) IND (f) 3.0–3.3 (3.1 ± 0.1) 2.3–3.2 (2.8 ± 0.3) 3.1–3.8 (3.4 ± 0.2) 2.7–3.2 (2.9 ± 0.2) 3.6–4.4 (3.9 ± 0.2) FLL (m) 9.6–11.1 (10.5 ± 0.7) 10.0–11.7 (10.5 ± 0.6) 10.7–12.8 (11.4 ± 0.7) 9.3–10.4 (9.9 ± 0.4) 11.3–17.7 (13.9 166 ± 1.8) FLL (f) 9.0–11.2 (9.9 ± 0.7) 8.2–11.3 (10.4 ± 1.0) 10.0–13.0 (11.4 ± 0.9) 9.0–10.3 (9.7 ± 0.4) 13.5–18.9 (14.6 ± 0.9) HLL (m) 16.2–17.5 (16.8 ± 0.5) 16.6–18.5 (17.4 ± 0.6) 20.1–22.6 (20.8 ± 0.9) 16.1–17.9 (16.9 ± 0.7) 20.5–27.9 (23.0 ± 2.4) HLL (f) 15.4–18.7 (17.3–1.2) 14.3–18.7 (17.0 ± 1.4) 18.8–23.1 (20.6 ± 1.3) 15.6–18.7 (17.1 ± 1.1) 20.5–26.1 (24.4 ± 1.7) 167 Rostral projecting dorsoposteriorly to point in line with anterior edge of nasal, broader than high, in narrow contact with frontonasal; frontonasal wider than long; nostril ovoid, centered in a single rectangular nasal; supranasals present, large, narrowly separated by frontonasal; postnasals present; prefrontals moderately separated by frontal; frontal nearly diamond shaped, its anterior margin in moderate contact with frontonasal, in contact with first two anterior supraoculars, 4× wider than anteriormost supraocular; supraoculars five; frontoparietals moderate, in broad medial contact, each frontoparietal in contact with supraoculars two–four; interparietal moderate, quadrilaterally shaped, longer than wide, its length slightly greater than midline length of frontoparietal; parietal eyespot present in posterior half of scale; parietals in narrow contact or separated behind interparietal; nuchals non-enlarged, undifferentiated; loreals two, decreasing in size from anterior to posterior, anterior loreal about as long as and 1.8× higher than posterior loreal, in contact with prefrontal, postnasal, supranasal, second supralabial, posterior loreal and frontonasal, and occasionally with first supralabial; preocular single, nearly two thirds as high as posterior loreal; presubocular single; supraciliaries six, the anteriormost contacting prefrontal and separating posterior loreal from first supraocular; subocular row complete; lower eyelid with one row of scales, lacking an enlarged oval window, largely transparent; supralabials six or seven [6], first 2× size of other supralabials, fourth and fifth below the eye; infralabials six or seven [7]. Mental wider than long, in contact with first infralabial; single enlarged postmental, wider than mental; followed by two pairs of enlarged chin shields, first pair narrowly separated by single row of undifferentiated scales or in moderate medial contact, scales of second pair narrower than first, broadly separated by three medial scales. 168 Scales on limbs smaller than body scales; scales on dorsal surfaces of digits large, wrapping around lateral edges of digits; lamellae undivided; palmar surfaces of hands and plantar surfaces of feet covered by small, irregular scales, each with irregular raised anterior edges; scales on dorsal surface of hands and feet smaller than limb scales, lacking raised edges. Coloration in preservative.—Ground color of body cream; lateral and ventral surfaces of body lacking dark pigment; dorsum of body, from posterior edge of supranasals to tail tip, uniformly dark brown with dark pigmentation spanning six and two half rows of scales at midbody and narrowing to cover four and two half rows of scales posterior to parietals; body dark brown dorsally abruptly changing to cream laterally and ventrally; head scales uniform dark brown; rostral, nasal, postnasal, supranasal, and first supralabial light gray; pineal eyespot charcoal; small dark brown blotch dorsal to auricular openings. Limbs mottled light and medium brown dorsally, cream colored ventrally; dorsal and ventral surface of digits light brown. Coloration in life.—(Fig. 3.11F,G). Dorsal ground color homogeneous medium-brown; sharp lateral demarcation between dorsal and lateral and ventral coloration; lateral and ventral surfaces of body bright burnt orange, orange-brown, or salmon colored; dark-brown spots and longitudinal lines of spots absent from lateral surfaces. Limbs medium-brown dorsally, burnt orange to orange-brown ventrally. Dorsal head scales uniform medium-brown. Variation.—Morphometric variation of the series is summarized in Table 3.6. We observed variation among the 19 specimens examined for the degree of contact between head scales. Twelve specimens were observed to have parietals moderately separated by the interparietal (KU 305470, 310734–6, 310942, 310944, 310949, 310951, 311232–5), one specimen has parietals in point medial contact (KU 311231), and six specimens have parietals in moderate medial contact (KU 310739, 310943, 310945–6, 310955, 311241) behind the interparietal; nine specimens do 169 not have the first pair of enlarged chin shields in medial contact (KU 210736, 310942, 310945–6, 310949, 310951, 311231, 311234–5) and ten specimens have the first pair of enlarged chin shields in moderate medial contact (KU 305470, 310734–5, 310739, 310943–4, 310955, 311232–3, 311241). Scale counts were observed to vary among the measured series. The number of supralabials varied between six (CAS-SU 18702, 24428, 24434, 24436–7, 24442, 24446–9, 24451, 24458, 25452, 25460, 28332, CAS 102404, 110978–81, 133301, 133616, 133749, 133752, 133754, KU 310734, 310736, 310942, 311231–2, 311234) and seven (CAS-SU 24450, 28320–1, 28338, 28370, CAS 110976–7, 110982–3); infralabials varied between six (CAS-SU 24446, KU 310734, 310736, 310942, 311231–2, 311234) and seven (CAS-SU 18702, 24428, 24434, 24436–7, 24442, 24447–51, 24458, 25452, 25460, 28320–1, 28332, 28338, 28370, CAS 102404, 110976–83, 133301, 133616, 133749, 133752, 133754). Specimens were observed to have midbody scale row counts of 26 (CAS-SU 24428, 24446), 27 (CAS-SU 24458, 25460), 28 (CAS-SU 18702, 24434, 24436–7, 24442, 24447–52, CAS 102404, 133301, 133752, 133754), 29 (CAS-SU 28320, 28338, CAS 110976, 110981, 133616, 133749), and 30 (CAS-SU 28231–2, 28370, CAS 110977–80, 110982–3); axilla–groin scale row counts of 46 (CAS-SU 25452, CAS 110983, 133616), 47 (CAS-SU 24450, 24458, 25460, CAS 110979–81, 133301), 48 (CAS-SU 18702, 24428, 24436, 24442, 24446, 24449, 28332, 28338, CAS 110976, 110978, 110982, 133749), and 49 (CAS-SU 24434, 24437, 24447–8, 24451, 28320–1, 28370, CAS 102404, 110977, 133752, 133754); and paravertebral scale row counts of 69 (CAS-SU 25452, CAS 133616), 70 (CAS-SU 24450, 24458, 25460, CAS 133301), 71 (CAS-SU 18702, 24428, 24442, 24446, 24449, 28332, 28338, CAS 110980, 110983, 133749), 72 (CAS-SU 24434, 24436–7, 24447–8, 24451, 28320–1, CAS 102404, 110976–9, 110981–2, 133752, 133754), and 73 (CAS-SU 28370). 170 We also observed lamellae counts to vary among the measured series. Specimens were observed to have Finger-III lamellae counts of six (CAS-SU 18702, 24428, 24434, 24436–7, 24442, 24446–7, 24449–51, 24458, 25460, 28320–1, 28332, 28338, 28370, CAS 102404, 110976–83, 133301, 133616, 133749, 133754, KU 310734, 311231–2, 311234) or seven (CAS-SU 24448, CAS 133752, KU 310736, 310942); Toe-IV lamellae counts of eight (CAS-SU 24436, 25452, 28320, CAS 102404), nine (CAS-SU 18702, 24428, 24434, 24437, 24442, 24446–51, 24458, 25460, 28321, 28332, 28370, CAS 110976–7, 110979, 110981–3, 133301, 133616, 133754, KU 310734, 310942, 311232, 311234), or ten (CAS-SU 28338, CAS 110978, 110980, 133749, 133752, KU 310736, 311231). Distribution.—Brachymeles orientalis is known from Bohol, Samar, Leyte, Dinagat, Camiguin Sur islands, and the eastern and central portions of Mindanao Island (Fig. 3.4). Ecology and natural history.—Brachymeles orientalis occurs in agricultural areas as well as disturbed and secondary growth forest. On Samar, Leyte, Mindanao, and Camiguin Sur islands, we have collected this species in primary forest, and on Bohol Island it is present in mature secondary growth. Individuals have been observed under piles of rotting coconut husks, in the humus material within rotting logs, and in loose soil and leaf litter surrounding the root networks of trees. The species is quite common throughout its range with the exception of Bohol Island (CDS personal observation), and occurs sympatrically with four other species of Brachymeles in different parts of its range (Brown, 1956; Brown and Rabor, 1967; Brown and Alcala, 1980). Brachymeles orientalis occurs sympatrically with B. boholensis on Bohol Island, B. gracilis hilong and B. samarensis on Samar and Leyte islands, B. gracilis hilong on Mindanao Island, and B. cf. gracilis hilong on Camiguin Sur Island (CDS pers. observ.). Similar to B. boulengeri, B. orientalis appears to have a wider geographic distribution that spans multiple Philippine 171 islands. This is in contrast to the pentadactyl, island endemic species, B. boholensis, B. tungaoi, and B. mindorensis, which are known from just Bohol, Masbate, and Mindoro islands respectively. As do all members of the genus, disturbed individuals move in a rapid serpentine manner and always attempt to burrow back into loose soil or humus. Sympatric lizard species observed within the range of Brachymeles orientalis include: (Agamidae) Bronchocela cristatella, Draco bimactulatus, D. cyanopterus, D. mindanensis, D. ornatus, Gonocephalus interruptus, G. semperi, Hydrosaurus pustulatus; (Gekkonidae) Cyrtodactylus agusanensis, C. annulatus, C. jambangan, Gehyra mutilata, Gekko gecko, Gekko mindorensis, Hemidactylus frenatus, H. platyurus, Pseudogekko compressicorpus; (Scincidae) Brachymeles gracilis hilong, Brachymeles cf. gracilis gracilis, Brachymeles samarensis, Eutropis indeprensa, E. multifasciata, Lamprolepis smaragdina, L. pulchella, L. quadrivittata, Sphenomorphus abdictus abdictus, S. acutus, S. cumingi, S. cf. mindanensis, S. coxi, S. fasciatus, S. jagori, S. llanosi, S. steerei, S. variegatus, Tropidophorus misaminus; and (Varanidae) Varanus cumingi. Brachymeles schadenbergi (Fischer 1885) Figs. 3.4, 3.8, 3.11E Senira bicolor (part), Gray, 1845. Eumeces (Riopa) schadenbergi, Fisher, 1885, Type-locality: “Southern Mindanao Island, Philippines” (Reported by Fischer [1885] as No. 845 housed in the Dresden Museum). Brachymeles schadenbergi (part), Boettger, 1886; Boulengeri, 1887; Boettger, 1893; Taylor, 1917, 1922b,c; Brown and Alcala, 1970. Brachymeles schadenbergi schadenbergi (part), Brown, 1956; Brown and Rabor, 1967. 172 Diagnosis.—Brachymeles schadenbergi can be distinguished from congeners by the following combination of characters: (1) body large (SVL 93.1–115.8 mm); (2) pentadactyl; (3) Finger-III lamellae five or six; (4) Toe-IV lamellae eight or nine; (5) limbs relatively long; (6) supralabials six or seven; (7) infralabials six or seven; (8) pineal eye spot present; (9) supranasals in contact; (10) prefrontals not contacting on midline; (11) enlarged chin shields in two pairs; (12) nuchal scales undifferentiated; (13) fifth and sixth supralabial below eye; (14) auricular opening present; and (15) continuous, light dorsolateral stripes absent (Tables 3.4, 3.5). Comparisons.—Characters distinguishing Brachymeles schadenbergi from all pentadactyl species of Brachymeles are summarized in Tables 3.4 and 3.5. Brachymeles schadenbergi most closely resembles B. makusog and B. orientalis, but differs from both taxa by having eight or nine Toe-IV lamellae, and the fifth and sixth supralabial below the eye, and by contact between supranasals (Tables 3.4, 3.5). Brachymeles schadenbergi can further be distinguished from B. makusog by having a greater maximum axilla–groin scale row count and a greater maximum paravertebral scale row count (Table 3.5), and from B. orientalis by the absence (vs. presence) of reddish-orange to salmon-colored scales on the lateral surfaces of the body. From all non-pentadactyl species of Brachymeles (B. apus, B. bonitae, B. cebuensis, B. elerae, B. lukbani, B. minimus, B. muntingkamay, B. pathfinderi, B. samarensis, B. tridactylus, B. vermis, and B. wrighti), B. schadenbergi differs by having a pentadactyl body form (vs. non-pentadactyl), longer forelimb lengths (greater than 11.1 mm vs. less than 6.9 mm), greater hind limb lengths (greater than 18.5 mm vs. less than 12.9 mm), and by the presence of a postnasal scale (vs. absence). Additionally, B. schadenbergi differs from all non-pentadactyl species except B. pathfinderi by having Toe-IV lamellae eight or nine (vs. 4 or fewer), 67–72 paravertebrals (vs. greater than 84), and by the presence (vs. absence) of auricular openings; 173 from all non-pentadactyl species except B. wrighti by having a midbody scale row count 26–28 (vs. fewer than 24); and from B. apus, B. lukbani, B. minimus, and B. vermis by the presence (vs. absence) of limbs. Description (based on holotype description and 34 referred specimens).—Details of the head scalation of an adult male are shown in Figure 3.8. The holotype was not examined by authors; however, measurements of the holotype taken from the original description are provided below in brackets. Body large relative to other Brachymeles, elongate with respect to other lizards; maximum SVL 115.8 mm for males, 113.5 mm for females [85] (Tables 3.4, 3.5); head weakly differentiated from neck, nearly as wide as body, HW 10.2–11.7% (11.2 ± 0.5) SVL, 102.0–116.8% (108.7 ± 4.2) HL; HL 37.0–40.2% (38.4 ± 0.9) SnFa; SnFa 25.7–27.4% (26.8 ± 0.5) SVL; snout moderately long, rounded in dorsal and lateral profile, SNL 48.8–58.8% (54.3 ± 2.9) HL; auricular opening present, moderate; eyes moderate, ED 1.8–2.2% (2.1 ± 0.1) SVL, 18.4–21.8% (20.0 ± 1.0) HL, 44.7–57.5% (52.3 ± 4.3) END, pupil nearly round; body slightly depressed, MBW 94.8–135.4% (115.8 ± 13.0) MBH; scales smooth, glossy, imbricate; longitudinal scale rows at midbody 26–28 [28 fide Fisher, 1885]; paravertebral scale rows 67–72; axilla–groin scale rows 45–50 [46 fide Fisher, 1885]; limbs well developed, pentadactyl, digits small; FinIIIlam 5–6; ToeIVlam 8–9; FLL 12.5–21.6% (18.0 ± 2.4) AGD, 10.3–13.7% (12.0 ± 0.9) SVL [12.9 fide Fisher, 1885]; HLL 20.1–24.4% (29.7 ± 3.9) AGD, 17.4–22.0% (19.8 ± 1.4) SVL [22.4 fide Fisher, 1885]; order of digits from shortest to longest for hand: V = I < II = IV < III, for foot: I < V < II < III < IV; tail not as wide as body, gradually tapered towards end, TW 57.4–76.8% (68.5 ± 5.7) MBW, TL 64.6–102.6% (91.6 ± 10.8) SVL. Rostral projecting dorsoposteriorly to point in line with anterior edge of nasal, broader than high, separated from frontonasal; frontonasal wider than long; nostril ovoid, centered in a single 174 rectangular nasal; supranasals present, large, in broad medial contact; postnasals present; prefrontals moderately separated by frontal; frontal nearly diamond shaped, its anterior margin in moderate contact with frontonasal, in contact with first two anterior supraoculars, 5× wider than anteriormost supraocular; supraoculars five; frontoparietals moderate, broad contact medially, each frontoparietal in contact with supraoculars two–four; interparietal moderate, quadrilaterally shaped, longer than wide, its length greater than midline length of frontoparietal; parietal eyespot present in posterior half of scale; parietals in moderate to broad contact behind interparietal or moderately separated; nuchals undifferentiated; loreals two, decreasing in size from anterior to posterior, subequal, in contact with prefrontal, postnasal, supranasal, second supralabial, posterior loreal and frontonasal; preocular single, nearly two thirds as high as posterior loreal; presubocular single; supraciliaries six, the anteriormost contacting prefrontal and separating posterior loreal from first supraocular; subocular row complete; lower eyelid with one row of scales, lacking an enlarged oval window, largely transparent; supralabials six or seven, fifth and sixth beneath center of eye; infralabials six or seven. Mental wider than long, in contact with first infralabials; single enlarged postmental, wider than mental, followed by two pairs of enlarged chin shields; first pair in slight contact or narrowly separated by single undifferentiated scale, second pair narrower than first, broadly separated by undifferentiated scales. Scales on limbs smaller than body scales; scales on dorsal surfaces of digits large, wrapping around lateral edges of digits; lamellae undivided; palmar surfaces of hands and plantar surfaces of feet covered by small, irregular scales, each with irregular raised anterior edges; scales on dorsal surface of hands and feet smaller than limb scales, lacking raised edges. 175 Coloration in preservative.—Ground color of body medium-brown; dorsal surfaces nearly all dark brown, gradually fading into medium-brown lateral and ventral surfaces of body; dark dorsal pigmentation in nearly continuous block across dorsal surface, spanning six full and two half rows of scales at midbody and narrowing to cover four full and two half rows of scales posterior to parietals; lateral surfaces with 1–2 irregular dark-brown lines on posterior half of axilla–groin region; head scales uniform dark-brown; rostral, nasal, postnasal, supranasal, first supralabial, mental, and first infralabial dark-gray; pineal eyespot poorly defined, surrounded by light-cream border. Tail coloration matches body coloration. Limbs mottled dark-brown dorsally, medium-brown ventrally; dorsal and ventral surface of digits dark brown. Coloration in life.—(Fig. 3.11E). Dorsal ground color homogeneous dark-brown; blotched, irregular, lateral demarcation between dorsal and lighter lateral and ventral coloration; lateral and ventral surfaces of body medium-brown; lateral surfaces with irregularly shaped rows of dark-brown spots. Limbs dark-brown dorsally, medium-brown ventrally. Dorsal head scales blotched dark and medium-brown. Variation.—Morphometric variation of the series is summarized in Table 3.6. We observed variation among the 36 specimens examined for the degree of contact between head scales. Twenty-one specimens were observed to have parietals moderately separated by the interparietal (KU 314969, 314976, 314984–5, 314988–9, 314992, 314997; MCZ 26552–3, 26556–8, 26561, 26563, 26566, 26568, 26571–2, 26574), one specimen has parietals narrowly separated by the interparietal (KU 314996), and 14 specimens have parietals in moderate medial contact (KU 314967, 314970–5, 314977–8, 314980, 314990–1, 314994; MCZ 26555) behind the interparietal; seven specimens do not have the first pair of enlarged chin shields in medial contact (KU 314971, 314973, 314976, 314990, 314992, 314994; MCZ 26552, 26554, 26563), 176 one specimen has the first pair of enlarged chin shields in point medial contact (KU 314997), and 26 specimens have the first pair of enlarged chin shields in moderate medial contact (KU 314967, 314969, 314970, 314972, 314974–5, 314977–8, 314980, 314984–5, 314988–9, 314991, 314996; MCZ 26553, 26555–8, 26561, 26566, 26568, 26571–2, 26574). Scale counts were observed to vary among the measured series. The number of supralabials varied between six (CAS 23495, KU 314991) and seven (CAS 23468–9, 23471, 23479–81, 23484–5, 23494, 23496, 60493, KU 314967, 314969, 314974–5, 314977–8, 314980, 314984–5, 314994, 314996); infralabials varied between six (KU 314967, 314969, 314974–5, 314977, 314980, 314984–5, 314991, 314996) and seven (CAS 23468–9, 23471, 23479–81, 23484–5, 23494–6, 60493). Specimens were observed to have midbody scale row counts of 26 (CAS 23468, 23479–81, 23494–6, 60493), 27 (CAS 23469, 23484), and 28 (CAS 23471, 23485); axilla–groin scale row counts of 45 (CAS 23495), 46 (CAS 23469, 23494, 23496), 47 (CAS 23468, 23484), 48 (CAS 23485, 60493), 49 (CAS 23471, 23480), and 50 (CAS 23479, 23481); and paravertebral scale row counts of 67 (CAS 23495), 68 (CAS 23494, 23496), 70 (CAS 23484), 71 (CAS 23468–9, 23471, 23480, 23485, 60493), and 72 (CAS 23479, 23481). We also observed lamellae counts to vary among the measured series. Specimens were observed to have Finger-III lamellae counts of five (CAS 23469, 23495, 60493, KU 314967, 314969, 314974, 314977–8, 314984–5, 314991, 314994, 314996) or six (CAS 23468, 23471, 23479–81, 23484–5, 23494, 23496, KU 314975, 314980); Toe-IV lamellae counts of eight (CAS 23468, 23494–5, 60493, KU 314967, 314969, 314974–5, 314977, 314984–5, 314991, 314994, 314996), or nine (CAS 23469, 23471, 23479–81, 23484–5, 23496, KU 314978, 314980). There is a small degree of color variation in the examined series, with the degree and definition of continuous, dark mid-dorsal pigmentation. Most of the examined specimens show 177 patterns consistent with a continuous, dark streak of pigmentation covering the mid-dorsal region of the body (KU 314969, 314974–5, 314977–8, 314980, 314984–5, 314991, 314994, 314996). In several specimens, continuous, dark mid-dorsal stripes are evident overlaying the dark ground coloration (KU 314967). Distribution.—Brachymeles schadenbergi is known from Basilan and western Mindanao islands (Fig. 3.4). Ecology and natural history.—Brachymeles schadenbergi occurs in a variety of habitats from disturbed and secondary growth to primary forest and intact climax forest. Individuals have been observed in the humus material within rotting logs and in loose soil and leaf litter surrounding the root networks of trees. Individuals are moderately common in populations sampled (CDS, RMB personal observation), and occur sympatrically with B. gracilis gracilis in western Mindanao Island (Brown, 1956; Brown and Rabor, 1967; Brown and Alcala, 1980). We collected numerous specimens in pitfall traps, indicating some level of surface activity. Although B. schadenbergi occurs on multiple islands in the southern Philippines, the species appears to have a more restricted geographic distribution when compared with more widespread pentadactyl species, such as B. boulengeri, B. talinis, B. orientalis, and B. kadwa. As in other members of the genus, disturbed individuals move in a rapid serpentine manner and always attempt to burrow back into loose soil or humus. Sympatric lizard species observed within the range of Brachymeles schadenbergi include: (Agamidae) Bronchocela cristatella, Draco bimaculatus, D. cyanopterus, D. mindanensis, Gonocephalus interruptus, Hydrosaurus amboinensis; (Gekkonidae) Cyrtodactylus jambangan, Gehyra mutilata, Gekko gecko, Hemidactylus frenatus, H. platyurus, Hemiphyllodactylus typus, Lepidodactylus sp., L. quadrivittata, Luperosaurus joloensis, Pseudogekko compressicorpus; 178 (Scincidae) Brachymeles gracilis gracilis, Eutropis indeprensa, E. multicarinata, E. multifasciata, E. englei, Lamprolepis smaragdina, Sphenomorphus atrigularis, S. fasciatus, S. jagori, S. steerei, S. variegatus, Tropidophorus misaminus, T. partelloi; and (Varanidae) Varanus cumingi. Brachymeles talinis Brown 1956 Figs. 3.5, 3.9, 3.11H Brachymeles schadenbergi talinis, Brown, 1956, Type-locality: “On the low ridge north side of the Maite River, 5 to 6 km west of Valencia,” Negros Oriental Province, Negros Island, Philippines, 933 m elevation, 9°17'19.25" N, 123°11'56.4" E (holotype: CAS-SU 18358). Brachymeles talinis, Brown and Rabor, 1967. Brachymeles talinis, Brown and Alcala, 1980. Diagnosis.—Brachymeles talinis can be distinguished from congeners by the following combination of characters: (1) body size large (SVL 103.8–123.1 mm); (2) pentadactyl; (3) Finger-III lamellae five or six; (4) Toe-IV lamellae eight to ten; (5) limbs relatively long; (6) paravertebral scale rows 67–72; (7) supralabials seven; (8) infralabials seven; (9) pineal eye spot present; (10) supranasals in contact; (11) prefrontals not contacting on midline; (12) enlarged chin shields in two pairs; (13) nuchal scales undifferentiated; (14) fifth and sixth supralabial below eye; (15) auricular opening present; (16) dark lateral stripes present; (17) venter devoid of dark pigmentation (Tables 3.4, 3.5). Comparisons.—Characters distinguishing Brachymeles talinis from all pentadactyl species of Brachymeles are summarized in Tables 3.4 and 3.5. Brachymeles talinis most closely resembles B. kadwa, B. makusog, B. tungaoi, and B. vindumi, but differs from these four taxa by having the 179 range of paravertebral scale rows reaching greater than 70 but fewer than 74, and seven infralabials (Table 3.5). Brachymeles talinis can further be distinguished from B. kadwa by having eight to ten Toe-IV lamellae, the first enlarged chin shield wider than the second, frontoparietals in contact, and by the absence of dark ventral pigmentation (Tables 3.4, 3.5); from B. makusog by having seven supralabials the fifth and sixth supralabial below the eye, supranasals in contact, and by the presence of dark lateral stripes (Tables 3.4, 3.5); from B. tungaoi by having a larger body size, shorter relative tail length, eight to ten Toe-IV lamellae, and the first enlarged chin shield wider than the second (Tables 3.4, 3.5); and from B. vindumi by having fewer axilla–groin scale rows, fewer paravertebral scale rows, and by the absence of dark ventral pigmentation (Table 3.5). From all non-pentadactyl species of Brachymeles (B. apus, B. bonitae, B. cebuensis, B. elerae, B. lukbani, B. minimus, B. muntingkamay, B. pathfinderi, B. samarensis, B. tridactylus, B. vermis, and B. wrighti), B. talinis differs by having a pentadactyl body form (vs. non-pentadactyl), longer forelimb lengths (greater than 11.3 mm vs. less than 6.9 mm), and greater hind limb lengths (greater than 20.5 mm vs. less than 12.9 mm), and by the presence of a postnasal scale (vs. absence). Additionally, B. talinis differs from all non-pentadactyl species except B. wrighti by having a midbody scale row count 26–30 (vs. fewer than 24); from all non-pentadactyl species except B. pathfinderi by having a paravertebral scale row count 68–70 (vs. greater than 84), and by the presence of auricular openings (vs. absence); from all non-pentadactyl species except B. apus and B. wrighti by having a larger body size (SVL greater than 103.1 mm vs. less than 81.3 mm); and from B. apus, B. lukbani, B. minimus, and B. vermis by the presence (vs. absence) of limbs. 180 Description (based on holotype and 30 referred specimens, including 2 paratypes from CAS).—Details of the head scalation of an adult male are shown in Figure 3.9. Measurements of the holotype are provided below in brackets. Body large relative to other Brachymeles, elongate with respect to other lizards; maximum SVL 123.1 mm for males, 116.5 mm for females [118.7, male] (Tables 3.4, 3.5); head weakly differentiated from neck, nearly as wide as body, HW 10.6–13.2% (11.8 ± 0.5) SVL [12.1], 111.7–136.2% (124.1 ± 6.8) HL [130.3]; HL 30.6–40.7% (35.4 ± 2.7) SnFa [33.5]; SnFa 25.1–29.8% (27.0 ± 1.3) SVL [27.6]; snout moderately long, broadly rounded in dorsal and lateral profile, SNL 51.5–65.8% (58.9 ± 4.0) HL [65.8]; auricular opening present, moderate; eyes moderate, ED 1.7–2.2% (1.9 ± 0.1) SVL [1.7], 17.4–24.8% (20.0 ± 1.9) HL [18.2], 40.9–62.1% (50.3 ± 5.7) END [41.5], pupil nearly round; body slightly depressed, MBW 109.3–153.8% (126.7 ± 14.4) MBH [109.6]; scales smooth, glossy, imbricate; longitudinal scale rows at midbody 26–30 [29]; paravertebral scale rows 67–72 [72]; axilla–groin scale rows 43–48 [48]; limbs well developed, pentadactyl, digits moderate; FinIIIlam 5–6 [6]; ToeIVlam 8–10 [10]; FLL 15.1–23.9% (19.1 ± 1.8) AGD [19.6], 10.1–15.3% (12.4 ± 1.2) SVL [14.9]; HLL 26.8–38.9% (31.8 ± 3.0) AGD [30.9], 18.0–24.9% (20.6 ± 1.8) SVL [23.5]; order of digits from shortest to longest for hand: V < I < IV < II < III, for foot: I = V < II < III = IV; tail nearly as wide as body at base, sharply tapered towards end, TW 63.4–94.0% (75.1 ± 6.2) MBW [94.0], TL 60.6–107.2% (83.9 ± 12.0) SVL [73.2]. Rostral projecting dorsoposteriorly to point in line with anterior edge of nasal, broader than high, completely separated from frontonasal by broad supranasal contact; frontonasal wider than long; nostril ovoid, in center of single trapezoidal nasal; supranasals present, large, in broad medial contact; postnasals present; prefrontals moderately separated by frontal; frontal nearly octagonal shaped, its anterior margin in moderate contact with frontonasal, in contact with first 181 two anterior supraoculars, 4× wider than anteriormost supraocular; supraoculars five; frontoparietals moderate, in moderate medial contact, each frontoparietal in contact with supraoculars two–four; interparietal moderate, quadrilaterally shaped, width nearly equal to length, its length nearly equal to midline length of frontoparietal; parietal eyespot present in posterior one third of scale; parietals in point to moderate contact behind interparietal or narrowly separated; nuchals undifferentiated; loreals two, decreasing in size from anterior to posterior, subequal, in contact with prefrontal, postnasal, supranasal, second supralabial, posterior loreal and frontonasal; preocular single, nearly three fourths as high as posterior loreal; single presubocular; supraciliaries six, the anteriormost contacting prefrontal and separating posterior loreal from first supraocular; subocular row complete; lower eyelid with one row of scales, lacking an enlarged oval window, largely transparent; supralabials seven, fifth and sixth below the eye; infralabials seven. Mental wider than long, in contact with first infralabials; single enlarged postmental, wider than mental; followed by two pairs of enlarged chin shields; first pair in moderate contact or moderately separated by a single medial scale, wider than second pair; second pair separated by three undifferentiated scales. Scales on limbs smaller than body scales; scales on dorsal surfaces of digits large, wrapping around lateral edges of digits; lamellae undivided; palmar surfaces of hands and plantar surfaces of feet covered by small, irregular scales, each with irregular raised anterior edges; scales on dorsal surface of hands and feet smaller than limb scales, lacking raised edges. Coloration in preservative.—Ground color of body medium brown; longitudinal stripes on dorsal surface of body present or absent; when present a total of eight longitudinal dark-brown spot rows, extending from posterior edge of parietals to base of tail: six continuous medial rows 182 and two discontinuous posterolateral rows, together spanning eight full rows of scales at midbody, narrowing to six full rows of scales posterior to parietals; when dark spot rows are absent, pigmentation forms nearly continuous dark dorsal surface, covering one half to entire surface of dorsal scales; dorsolateral stripes present or absent, when present, well defined, continuous, lacking dark pigmentation, spanning two whole and two half row of scales from auricular opening to base of tail. Lateral and ventral surface of body medium-brown. Lateral surface with three to six discontinuous longitudinal rows of dark-brown spots, rows often extending to edge of ventral surface. Ventral surface without dark pigmentation. Tail coloration equal to body coloration, dorsal surface covered with dark brown blotches, ventral surface covered with scattered dark brown spots, fewer than dorsal surface. Head scales homogeneous dark brown; rostral, nasal, postnasal, supranasal, first supralabial, mental and first infralabial dark gray; pigment surrounding pineal eyespot reduced to indistinct, small and medium brown. Limbs mottled medium brown dorsally, yellowish brown ventrally; dorsal and ventral surface of digits dark brown. Coloration in life.—(Fig. 3.11H). Dorsal ground color medium-brown; when present, longitudinal rows of spots dark-brown to black; dorsolateral stripes light- to medium-brown, bordered mid-dorsally by rows of dark spots; lateral surface ground color light-brown to tan; ventral surfaces of body light-brown to tan. Dorsal surfaces of limbs dark- to medium-brown, ventral surfaces light-brown. Dorsal head scales blotched dark and medium-brown. Variation.—Morphometric variation of the series is summarized in Table 3.6. We observed variation among the 19 specimens examined for the degree of contact between head scales. Four specimens were observed to have parietals moderately separated by the interparietal (KU 306757, 306763, 306767, 306786), one specimen has parietals narrowly separated by the interparietal 183 (KU 306758), and 14 specimens have parietals in moderate medial contact (KU 306756, 306759–60, 306762, 306764–6, 306769–71, 306773–6) behind the interparietal; 13 specimens do not have the first pair of enlarged chin shields in medial contact (KU 304756–7, 306759–60, 306762, 306764–6, 306767, 306769–70, 306774–5) and six specimens have the first pair of enlarged chin shields in moderate medial contact (KU 306758, 306763, 306771, 306773, 306776, 306786). Scale counts were observed to vary among the measured series. Specimens were observed to have midbody scale row counts of 26 (KU 306766), 28 (CAS-SU 22311, 22317, 37996, KU 306765), 29 (CAS-SU 12225, 18358, 22323, 27972, 89813, CAS 133871, KU 306758, 306774) and 30 (CAS-SU 22312, 27997, KU 306756, 306760, 306769, 306772–3, 306786); axilla–groin scale row counts of 43 (KU 306786), 44 (CAS-SU 12225, 22311, 27996–7), 45 (CAS-SU 22323, KU 306756, 306758, 306760, 306765–6, 306772), 46 (CAS-SU 22312, 22317, 27972, 89813, CAS 133871, KU 306773), 47 (KU 306774), and 48 (CAS-SU 18358, KU 306769); and paravertebral scale row counts of 67 (KU 306786), 68 (CAS-SU 12225, 22311, 27996–7, KU 306756, 306758), 69 (CAS-SU 22312, 22323, KU 306760, 306765–6, 306772–3), 70 (CAS-SU 22317, 37972, 89813, CAS 133871, KU 306769), 71 (KU 306774), and 72 (CAS-SU 18358). We also observed lamellae counts to vary among the measured series. With the exception of two specimens observed to have six Finger-III lamellae (CAS-SU 18358, CAS 133871), all other examined specimens were observed to have five. We also observed Toe-IV lamellae counts of eight (KU 306769, 306786), nine (CAS-SU 22311, 22317, 89813, KU 306756, 306758, 306760, 306765–6, 306772–4), and ten (CAS-SU 12225, 18358, 22312, 22323, 27972, 27996–7, CAS 133871). 184 Color variation exists in the degree and definition of continuous, dark mid-dorsal stripes. Many specimens show patterns consistent with continuous, mid-dorsal dark lines (KU 306651, 306756–7, 306759, 30676,2 306765–7, 306769–72, 306776, 306786, 306763). The dark lines are obscured in some and irregular in others, where the mid-dorsal region is covered by a long streak of dark pigmentation, with little to moderate line definition (KU 306759–60, 306764, 306774). Distribution.—Brachymeles talinis is known from Negros, Panay, Romblon, Sibuyan, and Tablas islands (Fig. 3.5). It is also likely to occur on Guimaras Island. Ecology and natural history.—Brachymeles talinis occurs in a variety of habitats from agricultural areas, to disturbed and secondary growth forest. Little or no original, lowland forest remains in the Visayas, but we assume the species originally occurred in primary forest. Individuals have been observed under piles of rotting coconut husks, in the humus material within rotting logs, and in loose soil and leaf litter surrounding the root networks of trees. The species is moderately common throughout its range (CDS personal observation), and occurs sympatrically with three other species (B. bonitae, B. talinis, and B. tridactylus [Brown, 1956; Brown and Rabor, 1967; Brown and Alcala, 1980]). Individuals were often encountered in pitfall traps, indicating some level of activity outside of fossorial microhabitats. Similar to B. boulengeri, B. talinis appears to have a wider geographic distribution that spans multiple Philippine islands. This is in contrast to the island endemic species, B. boholensis, B. tungaoi, and B. mindorensis, which are known from just Bohol, Masbate, and Mindoro Islands respectively. As do all members of the genus, when disturbed, individuals attempt to escape by moving in a rapid serpentine manner and attempting to burrow back into loose soil or humus. 185 Sympatric lizard species observed within the range of Brachymeles talinis include: (Agamidae) Bronchocela marmoratus, Draco spilopterus, Hydrosaurus pustulatus; (Dibamidae) Dibamus argenteus; (Gekkonidae) Cyrtodactylus philippinicus, Gehyra mutilata, Gekko gecko, Gekko mindorensis, Gonocephalus sophiae, Hemidactylus frenatus, H. platyurus, Hemiphyllodactylus typus, Lepidodactylus christiani, L. herrei, L. lugubris, Luperosaurus corfieldi, Pseudogekko brevipes; (Scincidae) Brachymeles tridactylus, B. taylori, Emoia atrocostata, Eutropis multicarinata, E. multifasciata, Lamprolepis smaragdina, Lipinia auriculata, L. pulchella, L. quadrivittata, L. rabori, Sphenomorphus arborens, S. coxi, S. jagori, S. steerei, Tropidophorus grayi; and (Varanidae) Varanus nuchalis. Brachymeles kadwa sp. nov. Figs. 5, 9, 11D Holotype.—PNM 9721 (RMB Field No. 12466, formerly KU 323091), adult male, collected under rotting logs in secondary-growth forest (10:00–12:30 hr) on 4 June 2009, on the campus of Aurora State College of Technology, Barangay Zabali, Municipality of Baler, Aurora Province, Luzon Island, Philippines (15°44'31" N, 121°34'34" E; WGS-84), by CDS, RMB, J. Fernandez, L. Welton, J. Brown, J. Siler, Y. Vicente, and M. Vicente. Paratopotypes.—Three adult males (KU 323092, 323095, 323096) and four adult females (KU 323106, 323094, 323104, 323100), collected between 4 and 7 June 2009. Paratypes.—Four adult males (KU 304875, 304900, 304915, 304941) and six adult females (KU 304897, 304902–3, 304905–6, 304929) collected between 15 and 22 March 2006 (19°17'38" N, 121°24'32" E; WGS-84; 245 m above sea level) Barangay Magsidel, Municipality of Calayan, Cagayan Province, Calayan Island, Philippines, by RMB, C. Oliveros, and J. 186 Fernandez; four adult males (KU 304575, 307984, 307996, 307998) and five adult females (KU 304559, 304593, 304708, 304754, 308011), four adult males and five adult females collected between 3 and 11 March 2006 from 300 m elevation (18°55'45" N, 121°53'56" E; WGS-84) Barangay Balatubat, Municipality of Calayan, Cagayan Province, Camiguin Norte Island, Philippines, by RMB, C. Oliveros, and J. Fernandez. Referred specimens.—CALAYAN ISLAND: CAGAYAN PROVINCE: Municipality of Calayan: Barangay Magsidel: KU 304908, , 304899, 304907, 304909, 304921, 304941; CAMIGUIN NORTE ISLAND: CAGAYAN PROVINCE: Municipality of Calayan: Barangay Balatubat: KU 304558, 304562–65, 304569, 304571–74, 304627–30, 304643, 304647, 304696–99, 304704–07, 304709–12, 304714, 304753, 304755–59, 307965–66, 307985–86, 307997, 307999–8003, 308006–10, 308012–15, 308017–18; LUZON ISLAND: AURORA PROVINCE: Municipality of Baler: Barangay Zabali, ASCOT: KU 323090–91, 323093, 323097–99, 323101–03, 323105, 323107; Municipality of Casiguran, IDC property: KU 323108–48; Municipality of San Luis: Barangay Real, Sitio Minoli: KU 322320. Diagnosis.—Brachymeles kadwa can be distinguished from congeners by the following combination of characters: (1) body size large (SVL 90.6–128.2 mm); (2) pentadactyl; (3) Finger-III lamellae five or six; (4) Toe-IV lamellae seven to ten; (5) limbs relatively long; (6) paravertebrals 68–70; (7) supralabials seven; (8) infralabials six; (9) pineal eye spot present, small; (10) supranasals in contact; (11) prefrontals not contacting on midline; (12) enlarged chin shields in two pairs; (13) nuchal scales undifferentiated; (14) fifth and sixth supralabial below eye; (15) auricular opening present; (16) continuous, light dorsolateral stripes present, indistinct; (17) continuous, dark mid-dorsal stripes present; (18) dark lateral stripes present; and (19) dark ventral pigmentation present (Tables 3.4, 3.5). 187 Comparisons.—Characters distinguishing the new species from all pentadactyl species of Brachymeles are summarized in Tables 3.4 and 3.5. Brachymeles kadwa most closely resembles B. makusog, B. tungaoi, B. talinis, and B. vindumi, but differs from these four taxa by having seven to ten Toe-IV lamellae and the second enlarged chin shield wider than the first (Tables 3.4, 3.5). Brachymeles kadwa can further be distinguished from B. makusog by having seven supralabials, the fifth and sixth supralabial below the eye, six infralabials, the presence of supranasal contact, the presence of continuous, light dorsolateral stripes, continuous, dark mid-dorsal stripes, dark lateral stripes, and dark ventral pigmentation (Table 3.5); from B. tungaoi by having a greater midbody width, shorter relative tail length, paravertebrals 68–70, and the presence of dark ventral pigmentation (Tables 3.4, 3.5); from B. talinis by having 28 or fewer midbody scale rows, 70 or fewer paravertebrals, infralabials six, and by the presence dark ventral pigmentation (Table 3.5); and from B. vindumi by having five or six Finger-III lamellae, 26–28 midbody scale rows, paravertebrals 68–70, and by the presence of continuous, dark mid-dorsal stripes (Tables 3.4, 3.5). From all non-pentadactyl species of Brachymeles (B. apus, B. bonitae, B. cebuensis, B. elerae, B. lukbani, B. minimus, B. muntingkamay, B. pathfinderi, B. samarensis, B. tridactylus, B. vermis, and B. wrighti), B. kadwa differs by having a pentadactyl body form (vs. non-pentadactyl), longer forelimb lengths (greater than 10.7 mm vs. less than 6.9 mm), and greater hind limb lengths (greater than 17.9 mm vs. less than 12.9 mm), and by the presence of a postnasal scale (vs. absence). Additionally, B. kadwa differs from all non-pentadactyl species except B. wrighti by having 26–28 midbody scales (vs. fewer than 24); from all non-pentadactyl species except B. pathfinderi by having 68–70 paravertebrals (vs. greater than 84), and by the presence of auricular openings (vs. absence); from all non-pentadactyl species except B. apus 188 and B. wrighti by having a larger body size (SVL greater than 90.6 mm vs. less than 81.3 mm); and from B. apus, B. lukbani, B. minimus, and B. vermis by the presence of limbs (vs. absence). Description of Holotype.—(Fig. 3.10) Mature male, hemipenes everted; SVL 106.2 mm; body moderately large relative to other Brachymeles, elongate with respect to other lizards; head weakly differentiated from neck, nearly as wide as body, HW 11.0% SVL, 111.1% HL; HL 38.1% SnFa; SnFa 26.0% SVL; snout moderately long, rounded in dorsal and lateral profile, SNL 56.1% HL; auricular opening present, small; eyes moderate, ED 1.9% SVL, 19.6% HL, 54.8% END, pupil nearly round; body slightly depressed, MBW 157.3% MBH; body scales smooth, glossy, imbricate; longitudinal scale rows at midbody 28; paravertebral scale rows 68; axilla–groin scale rows 47; limbs well developed, pentadactyl, digits moderate; FinIIIlam 5; ToeIVlam 10; FLL 20.3% AGD, 13.0% SVL; HLL 32.0% AGD, 20.6% SVL; order of digits from shortest to longest for hand: I = V < II = IV < III, for foot: V < I < II < III = IV; tail nearly as wide as body at base, gradually tapered towards end, TW 73.5% MBW, TL 101.6% SVL. Rostral projecting dorsoposteriorly to point in line with anterior edge of nostril, broader than high, separated from frontonasal by moderate contact of supranasals; frontonasal wider than long; nostril ovoid, centered in a single rectangular nasal; supranasals large, in moderate medial contact; postnasals present; prefrontals moderately separated by frontal; frontal nearly diamond shaped, its anterior margin in moderate contact with frontonasal, in contact with first two anterior supraoculars, 4× wider than anteriormost supraocular; supraoculars five; frontoparietals moderate, point contact medially or moderately separated, each frontoparietal in contact with supraoculars two–four; interparietal moderate, quadrilaterally shaped, its length slightly greater than midline length of frontoparietal; parietal eyespot present in posterior one third of scale, indistinct; parietals in moderate contact behind interparietal; nuchals undifferentiated; loreals two, 189 decreasing in size from anterior to posterior, subequal, in contact with prefrontal, postnasal, supranasal, second supralabial, posterior loreal and frontonasal; preocular single, nearly two thirds as high as posterior loreal; single presubocular; supraciliaries six, the anteriormost contacting prefrontal and separating posterior loreal from first supraocular, posteriormost extending to midline of last supraocular; subocular row complete; lower eyelid with one row of scales, lacking an enlarged oval window, largely transparent; supralabials seven, fifth and sixth below the eye; infralabials six. Mental wider than long, in contact with first infralabials; single enlarged postmental, slightly wider than mental; followed by two pairs of enlarged chin shields, first pair in moderate medial contact, second pair slightly wider than first, separated by a single undifferentiated scale. Scales on limbs smaller than body scales; scales on dorsal surfaces of digits large, wrapping around lateral edges of digits; lamellae undivided; palmar surfaces of hands and plantar surfaces of feet covered by small, irregular scales, each with raised anterior edges; scales on dorsal surface of hands and feet smaller than limb scales, lacking raised edges. Coloration in preservative.—Ground color of body dark brown; dorsal surface of body with eight longitudinal rows of dark-brown spots spanning eight full rows of scales at midbody and extending from posterior edge of parietals to base of tail: six rows in mid-dorsal region, flanked by discontinuous dorsolateral rows; spot rows narrowing to six full rows of scales posterior to parietals; dark coloration covering middle three fourths of dorsal scales; dorsolateral stripes somewhat indistinct, discontinuous, spanning two half rows of scales from auricular opening point just posterior to forelimb insertion; dark dorsal coloration blends gradually into medium brown lateral and ventral surface of body. Lateral surface with six discontinuous, dark-brown spot rows, extending to edge of ventral surface. Ventral surface with scattered dark brown spots. 190 Tail coloration similar to body coloration, dorsal surface covered with dark brown blotches, ventral surface covered with few dark brown spots. Head scales homogeneous dark brown; rostral, nasal, postnasal, supranasal, first supralabial, mental, and first infralabial dark gray; pineal eyespot indistinct, small and light brown. Limbs mottled dark brown dorsally, yellowish brown ventrally; dorsal and ventral surface of digits dark brown. Coloration in life.—(Fig. 3.11D). Ground color of body light to medium-brown; dorsal surfaces of limbs medium-brown. Measurements of holotype in mm.—SVL 106.2; AGD 68.2; TotL 214.0; MBW 15.9; MBH 10.1; TL 107.9; TW 11.7; TH 9.2; HL 10.5; HW 11.7; HH 8.6; SnFa 27.6; ED 2.1; END 3.8; SNL 5.9; IND 3.7; FLL 13.8; HLL 21.8; MBSR 28; PVSR 68; AGSR 47; FinIIIlam 5; ToeIVlam 10; SL 7; IFL 6; SC 6; SO 5. Variation.—Morphometric variation of the series is summarized in Table 3.6. We observed variation among the 25 specimens examined for the degree of contact between head scales. Fourteen specimens were observed to have parietals moderately separated by the interparietal (KU 304559, 304574–5, 304593, 304630, 304708, 304754–5, 304759, 304906, 307984–5, 307996, 308007), one specimen has parietals in point medial contact (KU 308011), and 10 specimens have parietals in moderate medial contact (KU 304875, 304897, 304900, 304902–3, 304905, 304915, 304929, 304941, 307998) behind the interparietal; two specimens have frontoparietals moderately separated by the frontal (KU 304559, 307984), one specimen has frontoparietals narrowly separated by the frontal (KU 304574), and 22 specimens have frontoparietals in moderate medial contact (KU 304575, 304593, 304630, 304708, 304754–5, 304759, 304875, 304897, 304900, 304902–3, 304905–6, 304915, 304929, 304941, 307985, 307996, 307998, 308007, 308011). We observed the first pair of enlarged chin shields narrowly 191 separated in a single specimen (KU 307996), and in moderate contact for all other examined specimens. Scale counts were observed to vary among the measured series. Specimens were observed to have midbody scale row counts of 26 (KU 304559, 307996, 323104), 27 (KU 304593, 307984, 307998), and 28 (KU 304575, 304708, 304754, 304875, 304897, 304900, 304902–3, 304905–6, 304915, 304929, 304941, 308011, 323091, 323091–2, 323094–6, 323100, 323106); axilla–groin scale row counts of 47 (KU 304559, 304575, 304593, 304875, 304902, 304929, 307996, 307998, 308011, 323091, 323096), 48 (KU 304708, 304754, 304897, 304900, 304915, 304941, 307984, 323092, 323094–5, 323100, 323104, 323106), 49 (KU 304903, 304905–6); and paravertebral scale row counts of 68 (KU 304559, 304593, 304900, 307996, 323091, 323096), 69 (KU 304575, 304708, 304754, 304875, 304929, 304941, 307984, 307998, 308011, 323092, 323094–5, 323100, 323104, 323106), and 70 (KU 304897, 304902–3, 304905–6, 304915). We also observed lamellae counts to vary among the measured series. With the exception of two specimens observed to have six Finger-III lamellae (KU 304903, 304906), all other examined specimens were observed to have five. We also observed Toe-IV lamellae counts of seven (KU 304593), eight (KU 304559, 304575, 304708, 304754, 304875, 304897, 304900, 304915, 304929, 304941, 307984, 307996, 307998, 308011), nine (KU 304902–3, 304905–6, 323092, 323094–6, 323100, 323104, 323106), or ten (KU 323091). Distribution.—Brachymeles kadwa is known from numerous localities on Luzon Island as well as from Calayan and Camiguin Norte Islands of the Babuyan Island Group (Fig. 3.5). Ecology and natural history.—Brachymeles kadwa occurs in agricultural areas, disturbed secondary growth forest, and first growth forests of Luzon, Camiguin Norte, and Calayan. Individuals have been observed under piles of rotting coconut husks, in the humus material 192 within rotting logs, and in loose soil and leaf litter surrounding the root networks of trees. This species is quite common in all sampling localities, and we have taken large series in pitfall traps, indicating some level of surface activity. When disturbed, individuals immediately moved in a rapid serpentine manner and attempted to burrow back into loose soil or humus. Sympatric lizard species observed on Luzon, Camiguin Norte, and Calayan Islands include: (Agamidae) Bronchocela cristatella, Draco spilopterus, Gonocephalus sophiae, Hydrosaurus pustulatus; (Gekkonidae) Cyrtodactylus philippinicus, Gehyra mutilata, Gekko gecko, Gekko mindorensis, Hemidactylus frenatus, H. garnoti, H. luzonensis, H. platyurus, Luperosaurus cf. cumingi, L. kubli, Pseudogekko compressicorpus, P. smaragdina; (Scincidae) Brachymeles bonitae, B. bicolor, B. elerae, B. lukbani, B. makusog, B. muntingkamay, B. samarensis, B. cf. talinis, B. wrighti, Emoia atrocostata, Eutropis bontocensis, E. multicarinata, E. multifasciata, Lamprolepis smaragdina, Lipinia pulchella, Sphenomorphus cumingi, S. decipiens, S. jagori, S. leucospilos, S. luzonensis, S. steerei, S. stejnegeri, Tropidophorus grayi; and (Varanidae) Varanus marmoratus. Etymology.—CDS is pleased to name this new species for his loving wife Jessi M. Siler for her endless support that has made all of this research possible. The name of the new species is derived from one of the local dialects spoken in the Philippines. The word “kadwa” is the Ilonggo term for friend and companion. Suggested common name: Jessi’s Slender Skink. Brachymeles tungaoi sp. nov. Figs. 3.5, 3.10 Holotype.—PNM 9722 (CDS Field No. 5125, formerly KU 323933), adult male, collected in rotting stump in disturbed, residential habitat (10:00–12:30 hr) 4 September, 2009, at 61 m 193 elevation in Municipality of Masbate City, Masbate Province, Masbate Island, Philippines (12°21'01" N, 123°37'42" E; WGS-84), by CDS and J. Fernandez. Paratopotypes.—KU 323934–36, three adult females, collected between 3 and 7 September, 2009, from 61–99 m elevation by CDS and J. Fernandez. Paratypes.—One adult male (CAS 144313), three adult females (CAS 144229–30, 144341), and four juvenile specimens of unknown sex (CAS 144290, 144306–7, 144342), collected 2 June 1976 “in humus under rotting log,” in Barangay Tugbo, Municipality of Mobo, Masbate Province, Masbate Island, Philippines (12°20'11.04" N, 123°37'58.8" E; WGS-84; 400 m elevation) by A. Alcala. Diagnosis.—Brachymeles tungaoi can be distinguished from congeners by the following combination of characters: (1) body size moderate (SVL 78.2–106.2 mm); (2) relative tail length long; (3) pentadactyl; (3) Finger-III lamellae five or six; (4) Toe-IV lamellae nine or ten; (5) limb length moderate; (6) paravertebral scale rows 66–68; (7) supralabials seven; (8) infralabials six; (9) pineal eye spot present, large; (10) supranasals in contact; (11) prefrontals not contacting on midline; (12) contact between first pair of chin shields; (13) enlarged chin shields in two pairs; (14) nuchal scales undifferentiated; (15) fifth and sixth supralabial below eye; (16) auricular opening present; (17) continuous, light dorsolateral stripes present, indistinct; (18) continuous, dark mid-dorsal stripes present; (19) dark lateral stripes present; and (20) dark ventral pigmentation absent (Tables 3.4, 3.5). Comparisons.—Characters distinguishing the new species from all pentadactyl species of Brachymeles are summarized in Tables 3.4 and 3.5. Brachymeles tungaoi most closely resembles B. kadwa, B. makusog, B. talinis, and B. vindumi, but differs from these four taxa by having a smaller body size, smaller midbody width, greater relative tail length, the first and 194 second pairs of enlarged chin shields equal in width, and contact between the first pair of enlarged chin shields (Tables 3.4, 3.5). Brachymeles tungaoi can be further distinguished from B. kadwa by having nine or ten Toe-IV lamellae, paravertebral scale rows 66–68, frontoparietal in contact, and by the absence of dark ventral pigmentation (Tables 3.4, 3.5); from B. makusog by having seven supralabials, six infralabials, the fifth and sixth supralabial below the eye, supranasals in moderate contact, the presence of continuous, light dorsolateral stripes, continuous, dark mid-dorsal stripes, and dark lateral stripes (Table 3.5); from B. talinis by having nine or ten Toe-IV lamellae, 66–68 paravertebrals, infralabials six (Tables 3.4, 3.5); and from B. vindumi by having five or six Finger-III lamellae, 26–28 midbody scale rows, and 66–68 paravertebrals (Tables 3.4, 3.5). From all non-pentadactyl species of Brachymeles (B. apus, B. bonitae, B. cebuensis, B. elerae, B. lukbani, B. minimus, B. muntingkamay, B. pathfinderi, B. samarensis, B. tridactylus, B. vermis, and B. wrighti), B. tungaoi differs by having a pentadactyl body form (vs. non-pentadactyl), longer forelimb lengths (greater than 11.0 mm vs. less than 6.9 mm), and greater hind limb lengths (greater than 17.0 mm vs. less than 12.9 mm), and by the presence of a postnasal scale (vs. absence). Additionally, Brachymeles tungaoi differs from all non-pentadactyl species except B. wrighti by having a midbody scale row count 26–28 (vs. fewer than 24); from all non-pentadactyl species except B. pathfinderi by having a paravertebral scale row count 66 (vs. greater than 84), and by the presence of auricular openings (vs. absence); and from B. apus, B. lukbani, B. minimus, and B. vermis by the presence of limbs (vs. absence). Description of Holotype.—(Fig. 10) Mature male, hemipenes everted; SVL 89.2 mm; body moderate relative to other Brachymeles, elongate with respect to other lizards; head weakly differentiated from neck, nearly as wide as body, HW 11.3% SVL, 115.9% HL; HL 38.0% SnFa; 195 SnFa 25.6% SVL; snout moderately long, bluntly rounded in dorsal profile, sharply rounded in lateral profile, SNL 60.1% HL; auricular opening present, moderate; eyes small, ED 1.9% SVL, 19.2% HL, 50.0% END, pupil nearly round; body slightly depressed, MBW 162.0% MBH; body scales smooth, glossy, imbricate; longitudinal scale rows at midbody 28; paravertebral scale rows 66; axilla–groin scale rows 46; limbs well developed, pentadactyl, digits moderate; FinIIIlam 6; ToeIVlam 10; FLL 22.5% AGD, 14.4% SVL; HLL 35.4% AGD, 22.6% SVL; order of digits from shortest to longest for hand: I = V < II = IV < III, for foot: I < V < II < IV < III; tail not as wide as body, gradually tapered towards end, TW 63.7% MBW, TL 99.9% SVL. Rostral projecting dorsoposteriorly to point in line with anterior edge of nasal, broader than high, moderately separated from frontonasal; frontonasal wider than long; nostril ovoid, centered in a single rectangular nasal; supranasals present, large, in narrow medial contact; postnasals present; prefrontals broadly separated by frontal; frontal nearly octagonal, its anterior margin in broad contact with frontonasal, in contact with first two anterior supraoculars, 5× wider than anteriormost supraocular; supraoculars five; frontoparietals moderate, in broad contact medially, each frontoparietal in contact with supraoculars two–four; interparietal moderate, quadrilaterally shaped, its length nearly equal to midline length of frontoparietal; distinct parietal eyespot present, large, in posterior half of scale; parietals broadly separated by interparietal; nuchals undifferentiated; loreals two, decreasing in size from anterior to posterior, subequal, in contact with prefrontal, postnasal, supranasal, second supralabial, posterior loreal and frontonasal; preocular single, nearly one half as high as posterior loreal; single presubocular; supraciliaries six, the anteriormost contacting prefrontal and separating posterior loreal from first supraocular, posteriormost extending to midline of last supraocular; subocular row complete; lower eyelid 196 with one row of scales, lacking an enlarged oval window, largely transparent; supralabials seven, fifth and sixth below the eye; infralabials six. Mental wider than long, in contact with first infralabials; single enlarged postmental, wider than mental; followed by two pairs of enlarged chin shields; first pair in broad medial contact, second pair separated by single undifferentiated scale. Scales on limbs smaller than body scales; scales on dorsal surfaces of digits large, wrapping around lateral edges of digits; lamellae undivided; palmar surfaces of hands and plantar surfaces of feet covered by small, irregular scales, each with raised anterior edges; scales on dorsal surface of hands and feet smaller than limb scales, lacking raised edges. Coloration of holotype in preservative.—Ground color of body medium brown; dorsal surface of body with eight continuous, longitudinal rows of dark-brown spots, extending from posterior edge of parietals to base of tail; spot rows span six full and two half rows of scales at midbody, narrowing to four full and two half rows of scales posterior to parietals; pigmentation covering middle one third of dorsal scales; dorsolateral stripes indistinct, discontinuous, spanning one whole and two half row of scales from auricular opening to midbody. Lateral and ventral surface of body light-brown. Lateral surface with three discontinuous rows of dark-brown spots, spanning posterior two thirds of axilla–groin distance. Ventral surface without dark pigmentation. Tail with dark dorsal blotches and spots; dark pigment reduced ventrally. Head scales homogeneous dark brown; rostral, nasal, postnasal, supranasal, first supralabial, mental, and first infralabial light gray; pineal eyespot large distinct, light cream. Limbs mottled medium to dark brown dorsally, yellowish brown ventrally; dorsal and ventral surface of digits dark brown. 197 Coloration of holotype in life.—Coloration in life is unrecorded; however, because Brachymeles specimens do not change significantly during preservation (CDS, RMB personal observation), we suspect that the preserved coloration and patterns are much like those in life. Measurements of holotype in mm.—SVL 89.2; AGD 56.8; TotL 178.3; MBW 13.9; MBH 8.6; TL 89.1; TW 8.8; TH 8.0; HL 8.7; HW 10.1; HH 7.2; SnFa 22.8; ED 1.7; END 3.3; SNL 5.2; IND 3.0; FLL 12.8; HLL 20.1; MBSR 28; PVSR 66; AGSR 46; FinIIIlam 6; ToeIVlam 10; SL 7; IFL 6; SC 6; SO 5. Variation.—Morphometric variation of the series is summarized in Table 3.6. Specimens were observed to have parietals moderately separated by the interparietal (CAS 144229–30, 144341, KU 323933, 323935–6) or in point medial contact (CAS 144313, KU 323934). Scale counts were observed to vary among the measured series. Specimens were observed to have midbody scale row counts of 26 (KU 323935), 27 (CAS 144313), and 28 (CAS 144229–30, 144341, KU 323933–4, 323936); axilla–groin scale row counts of 46 (KU 323933, 323935–6), 47 (CAS 144229–30, 144341, KU 323934), and 49 (CAS 144313); and paravertebral scale row counts of 66 (KU 323933–6), 67 (CAS 144229), and 68 (CAS 144230, 144313, 144341). We also observed lamellae counts to vary among the measured series. Specimens were observed to have Finger-III lamellae counts of five (CAS 144229–30, 144341, KU 323934–5) or six (CAS 144313, KU 323933, 323936); Toe-IV lamellae counts of nine (CAS 144229, 144313, 144341, KU 323935–6) or ten (CAS 144230, KU 323933–4). Distribution.—Brachymeles tungaoi is known only from Masbate Island (Fig. 3.5). Ecology and natural history.—Brachymeles tungaoi occurs in agricultural areas as well as disturbed and secondary growth forest habitat. Little or no original, low elevation forest remains on Masbate Island, but we assume the species once also occurred in primary forest. Individuals 198 were collected in the humus material within the rotting stumps of trees. When disturbed, individuals immediately moved in a rapid serpentine manner and attempted to burrow back into loose soil or humus. Sympatric lizard species observed on Masbate Island include: (Agamidae) Bronchocela cristatella, Draco spilopterus, Gonocephalus sophiae; (Gekkonidae) Cyrtodactylus philippinicus, Gehyra mutilata, Gekko gecko, Hemidactylus frenatus, H. platyurus; (Scincidae) Brachymeles bonitae, Emoia atrocostata, E. multicarinata, E. multifasciata, Lamprolepis smaragdina, Lipinia pulchella, Sphenomorphus decipiens, S. jagori; and (Varanidae) Varanus marmoratus. Etymology.—We take pleasure in naming the new species after our friend and dedicated field collaborator Jason B. “Tungao” Fernandez, with thanks for years of hard work towards the research of semi-fossorial lizards. Suggested common name: Tungao’s Slender Skink. Brachymeles vindumi sp. nov. Figs. 3.4, 3.10 Holotype.—CAS 60724 (EHT Field No. 1718), adult male, collected between 25 October and 17 November, 1920, in Sulu Province, Jolo Island, Philippines, by Edward H. Taylor. Paratypes.—One adult female (CAS 60725), one juvenile female (MCZ 26577), and one juvenile of unknown sex (CAS 60723), collected over the same dates and in the same locality as holotype. Diagnosis.—Brachymeles vindumi can be distinguished from congeners by the following combination of characters: (1) body size moderate (SVL 104.9–113.6 mm); (2) pentadactyl; (3) Finger-III lamellae six; (4) Toe-IV lamellae nine or ten; (5) moderate limb length; (6) midbody scale rows 30 or 31; (7) axilla–groin scale rows 49; (8) paravertebral scale rows 74; (9) 199 supralabials seven; (10) infralabials six; (11) pineal eye spot present, indistinct; (12) supranasals in contact; (13) prefrontals separate; (14) parietal in contact; (15) enlarged chin shields in two pairs; (16) first pair of chin shields separated; (17) nuchals undifferentiated; (18) fifth and sixth supralabials below the eye; (19) auricular opening present; (20) continuous, light dorsolateral stripes present, distinct; (21) dark lateral stripes present; and (22) dark ventral pigmentation present (Tables 3.4, 3.5). Comparisons.—Characters distinguishing the new species from all pentadactyl species of Brachymeles are summarized in Tables 3.4 and 3.5. Brachymeles vindumi most closely resembles B. kadwa, B. talinis, and B. tungaoi, but differs from these three taxa by having six Finger-III lamellae, six supralabials, midbody scale rows 30 or 31, axilla–groin scale rows 49, paravertebral scale rows 74, the first pair of enlarged chin shields separated, and the presence of continuous, light dorsolateral stripes (Tables 3.4, 3.5). Brachymeles vindumi can further be distinguished from B. kadwa and B. talinis by having nine or ten Toe-IV lamellae (Tables 3.4, 3.5); from B. talinis by having six infralabials (Table 3.5); from B. kadwa by contact between frontoparietals (Table 3.5); and from B. kadwa and B. tungaoi by contact between parietals (Table 3.5). From all non-pentadactyl species of Brachymeles (B. apus, B. bonitae, B. cebuensis, B. elerae, B. lukbani, B. minimus, B. muntingkamay, B. pathfinderi, B. samarensis, B. tridactylus, B. vermis, and B. wrighti), B. vindumi differs by having a pentadactyl body form (vs. non-pentadactyl), longer forelimb lengths (greater than 13.2 mm vs. less than 6.9 mm), greater hind limb lengths (greater than 22.7 mm vs. less than 12.9 mm), and greater number of midbody scale rows (30 or 31 vs. less than 28), and by the presence of a postnasal scale (vs. absence). Additionally, B. vindumi differs from all non-pentadactyl species except B. pathfinderi by having 200 a paravertebral scale row count 74 (vs. greater than 84) and by the presence of auricular openings (vs. absence); and from B. apus, B. lukbani, B. minimus, and B. vermis by the presence of limbs (vs. absence). Description of Holotype.—(Fig. 3.9) Mature male, hemipenes not everted; SVL 113.6 mm; body moderate relative to other Brachymeles, elongate with respect to other lizards; head weakly differentiated from neck, nearly as wide as body, HW 9.5% SVL, 112.5% HL; HL 33.7% SnFa; SnFa 25.1% SVL; snout moderately long, rounded in dorsal and lateral profile, SNL 59.7% HL; auricular opening present, moderate; eyes small, ED 2.0% SVL, 23.5% HL, 58.0% END, pupil nearly round; body slightly depressed, MBW 122.9% MBH; body scales smooth, glossy, imbricate; longitudinal scale rows at midbody 31; paravertebral scale rows 74; axilla–groin scale rows 49; limbs well developed, pentadactyl, digits moderate; FinIIIlam 6; ToeIVlam 9; FLL 18.1% AGD, 11.6% SVL; HLL 31.2% AGD, 20.0% SVL; order of digits from shortest to longest for hand: I < V < II < IV < III, for foot: I = V < II = III < IV; tail regenerated, not as wide as body, sharply tapered towards end, TW 83.1% MBW. Rostral projecting dorsoposteriorly to point in line with anterior edge of nasal, broader than high, moderately separated from frontonasal by supranasal contact; frontonasal wider than long; nostril ovoid, centered in a single rectangular nasal; supranasals present, large, in moderate medial contact; postnasals present; prefrontals narrowly separated by frontal; frontal nearly octagonal, its anterior margin in narrow contact with frontonasal, in contact with first two anterior supraoculars, 4× wider than anteriormost supraocular; supraoculars five; frontoparietals moderate, in broad medial contact, each frontoparietal in contact with supraoculars two–four; interparietal small, diamond shaped, its length equal in size to midline length of frontoparietal; parietal eyespot absent; parietals in broad contact behind interparietal; nuchals undifferentiated; 201 loreals two, decreasing in size from anterior to posterior, subequal, in contact with prefrontal, postnasal, supranasal, second supralabial, posterior loreal and frontonasal; preocular single, nearly two thirds as high as posterior loreal; single presubocular; supraciliaries six, the anteriormost contacting prefrontal and separating posterior loreal from first supraocular, posteriormost extending to midline of last supraocular; single subocular row complete; lower eyelid with one row of scales, lacking an enlarged oval window, largely transparent; supralabials seven, fifth and sixth below the eye; infralabials six. Mental wider than long, in contact with first infralabials; single enlarged postmental, slightly wider than mental; followed by two pairs of enlarged chin shields, scales of first pair separated by a single undifferentiated scale, second pair separated by three undifferentiated scales. Scales on limbs smaller than body scales; scales on dorsal surfaces of digits large, wrapping around lateral edges of digits; lamellae undivided; palmar surfaces of hands and plantar surfaces of feet covered by small, irregular scales, each with raised anterior edges; scales on dorsal surface of hands and feet smaller than limb scales, lacking raised edges. Coloration of holotype in preservative.—Ground color of body medium to dark brown; mid-dorsal surface of body covered with dark pigmentation, extending from posterior edge of supranasals to base of tail, made of eight irregular, longitudinal mid-dorsal rows of dark-brown spots, spanning six full and two half rows of scales at midbody, narrowing to six full rows of scales posterior to parietals, pigmentation covering middle one third of dorsal scales; dorsolateral stripes present, clearly defined, continuous, lacking dark pigmentation, spanning one whole and one half row of scales from anterior-most supraocular to base of tail. Lateral and ventral surface of body medium to dark brown. Lateral surface with six to eight irregular dark spot rows, gradually becoming fainter on ventral surface. Ventral surface with irregular dark spots and 202 blotches. Tail with continuous dark blotches and spots dorsally, dark pigment reduced ventrally. Head scales homogeneous mottled medium and dark brown dorsally; rostral, nasal, postnasal, supranasal, first supralabial, mental, and first infralabial light brown to tan; pineal eyespot absent; dark brown blotch of pigmentation on lateral surfaces of head, spanning from posterior edge of eye to posterior edge of auricular openings. Limbs mottled medium to dark brown; dorsal surface of digits dark brown, ventral surface of digits medium brown. Coloration of holotype in life.—Coloration in life is unrecorded; however, because Brachymeles specimens do not change significantly during preservation (CDS, RMB personal observation), we suspect that the preserved coloration and patterns are much like those in life. Measurements of holotype in mm.—SVL 113.6; AGD 72.7; TotL N/A; MBW 14.2; MBH 11.6; TL N/A; TW 11.8; TH 8.4; HL 9.6; HW 10.8; HH 7.9; SnFa 28.5; ED 2.3; END 3.9; SNL 5.7; IND 3.4; FLL 13.2; HLL 22.7; MBSR 31; PVSR 74; AGSR 49; FinIIIlam 6; ToeIVlam 9; SL 7; IFL 6; SC 6; SO 5. Variation.—Morphometric variation of the series is summarized in Table 3.6. Specimens were observed to have midbody scale row counts of 30 (CAS 60725) or 31 (CAS 60724), and Toe-IV lamellae counts of nine (CAS 60724) or ten (CAS 60725). Distribution.—Brachymeles vindumi is known only from Jolo Island (Fig. 3.4). Ecology and natural history.—Brachymeles vindumi presumably occurs in disturbed habitat as well as secondary growth forest on Jolo Island. Due to security concerns, no recent surveys have been conducted on Jolo Island, and therefore, no information is available on the ecology of this species. Sympatric lizard species observed on Jolo Island include: (Agamidae) Draco guentheri; (Gekkonidae) Cyrtodactylus annulatus, Gehyra mutilata, Gekko gecko, G. mindorensis, 203 Hemidactylus frenatus, H. platyurus, Luperosaurus joloensis; (Scincidae) Brachymeles vermis, Eutropis multifasciata, E. rudis, Lamprolepis smaragdina, Lipinia quadrivittata, Lygosoma bowringi, Sphenomorphus biparietalis, S. variegatus; (Varanidae) Varanus cumingi. Etymology.—We take pleasure in naming the new species for our close friend and colleague, Jens Vindum. The specific epithet is a patronym in the genitive singular, chosen in thanks for the many years of support and assistance he as provided during our research on Philippine amphibians and reptiles. Suggested common name: Jens’ Slender Skink. DISCUSSION Phylogenetic analyses of the mitochondrial ATPase 8 (ATP8) and ATPase 6 (ATP6) genes resulted in strong support for nine lineages of Brachymeles (Fig. 3.2). The phylogeny, combined with morphological data, supports the elevation of all subspecies of the polytypic species B. boulengeri and B. schadenbergi to full species. However, the inferred relationships between several of the species sampled are weakly supported. This may be indicative of rapid diversification of Brachymeles or simply indicate a lack of character support at some internal nodes. Given the use of only mitochondrial data for our phylogenetic analyses, caution must be taken when interpreting inter-species relationships, as a single locus can be subject to random variation, deep coalescence, lineage sorting, and natural selection (Edwards and Beerli, 2002; Galtier et al., 2009; Brown et al., 2010). Regardless of the potential weaknesses of our single-locus approach, our results are strongly supported by an independent, comprehensive dataset of morphological characters. No analyses supported the monophyly of species formerly part of Brachymeles boulengeri (B. boholensis, B. boulengeri, B. mindorensis, B. taylori; Fig. 3.2). Another clade including B. 204 talinis, B. kadwa, and B. tungaoi was estimated with strong support (Fig. 3.2). As previously recognized B. talinis spanned two distinct, recognized faunal regions (Luzon and Visayas). Given this formerly wide geographical distribution, it is not surprising that the northern populations (Luzon and the Babuyan islands) constitute a genetically distinct lineage that we describe here as B. kadwa. We were surprised, however, to discover an additional genetically distinct lineage on Masbate Island (Fig. 3.2). The fauna of Masbate Island is recognized as part of the Visayan or central Philippine islands, and has been hypothesized to have shared land bridge connections with the central islands during periods of glacial maxima (Dickerson, 1928; Inger, 1954; Heaney, 1985; Voris, 2000). Although we expected Masbate populations to be more closely related to Visayan (Negros + Panay) populations, all analyses strongly supported the sister relationship between B. tunagoi (Masbate) and B. kadwa (Luzon), providing additional biogeographic support for the distinctiveness of B. tungaoi. We are unaware of phylogeographic or phylogenetic studies including other vertebrate taxa from Masbate. Comparison of the systematic affinities of other Masbate species may provide interesting exceptions to the prevailing PAIC-oriented perspective of Masbate as a faunistic extension of the central Visayas (Heaney, 1985). The species recognized in this paper increase the total number of known species of Brachymeles to 25, all but one of which are endemic to the Philippines. During the last two years, our knowledge of the species diversity in the genus has expanded rapidly as the result of large-scale sampling efforts across the Philippines and the detailed analyses of morphological variation among species and populations (Siler et al., 2009a, 2010a,b). Prior to this effort, estimates of Brachymeles species diversity remained nearly constant for more than 30 years (but see Brown and Alcala, 1995), which is a testament to the extent of morphological similarity 205 among species within the genus and a lack of systematic studies of the group. It comes as little surprise that allopatric populations of “B. boulengeri” from the Luzon, Mindanao, Mindoro, and Visayan Pleistocene Aggregate Island Complexes have proven to be morphologically diagnosable with increased sampling. To date, few studies have provided evidence of truly “widespread” reptile species that have geographic distributions spanning recognized zoogeographic boundaries in the Philippines (but see Siler et al., 2010c), and as is quite often the case, these species frequently turn out to constitute multiple evolutionary lineages (McGuire and Alcala, 2000; Brown et al., 2002, 2009; Gaulke et al, 2007; Welton et al., 2009, 2010). All species of Brachymeles have a semi-fossorial life style, specializing in dry rotting material within rotten logs. Many are habitat specialists found exclusively in rotting logs, loose soil, or leaf litter, whereas others are common beneath piles of rotting coconut husks in disturbed, agricultural habitat. The species now found in residential and agricultural areas were once native to forested habitats. Prior to recent, focused survey efforts, the relatively low numbers of specimens of Brachymeles in museum collections handicapped our efforts at delimiting species. The rarity of Brachymeles in collections was due to their secretive, semi-fossorial lifestyle. This is the first, species-level phylogenetic study of Brachymeles. To date, taxonomic reviews of Brachymeles have focused solely on morphological variation (Brown, 1956; Brown and Rabor, 1967; Brown and Alcala, 1980; Brown and Alcala, 1995; Hikida, 1982). It is apparent that species diversity in the genus has been considerably underestimated; accordingly, discovery of additional undocumented (possibly cryptic) diversity is anticipated in other species groups (e.g., Siler et al., 2009a, 2010a,b). A number of studies have shown that the evolution of a burrowing lifestyle is correlated with decreasing dispersal abilities (Selander et al., 1974; Patton and Yang, 1977; Patton and Feder, 1978; Nevo, 1979; Wiens et al., 2006). Many 206 Brachymeles lineages have experienced reduction or loss of limbs, which may further reduce vagility (Daniels et al., 2005; Mulvaney et al., 2005; Wiens et al., 2006). Through time, reduced dispersal abilities may lead to increasingly patchy distributions, reduced gene flow between populations, and the accumulation of inter-population differences (Nevo, 1979). However, the role that geological history and complex geography play on the dispersal abilities and diversification patterns of Brachymeles species remains unknown. Regardless of what processes produce species diversity, we expect that additional species await discovery. With several species represented by only a few vouchered specimens, and frequent morphological convergence, it is clear that a comprehensive phylogenetic analysis of the genus will be required to assess, with accuracy, the species diversity within Brachymeles. Following the recognition of Brachymeles boholensis, B. boulengeri, B. tungaoi, B. kadwa, B. mindorensis, B. orientalis, B. schadenbergi, B. taylori, and B. vindumi there are now 13 pentadactyl species of Brachymeles. Of these, eight are large-bodied (B. bicolor, B. tungaoi, B. kadwa, B. makusog, B. orientalis, B. schadenbergi, B. talinis, and B. vindumi) and five (B. boholensis, B. boulengeri, B. gracilis, B. mindorensis, and B. taylori) have moderately sized bodies. The distribution of pentadactyl species in the Philippines is relatively even across the major recognized faunal regions, with four species known to occur in the Luzon Faunal Region, five in the Mindanao Faunal Region, three in the Visayan Faunal Region, one in the Mindoro Faunal Region, and one in the Sulu archipelago (Brown and Alcala, 1980, Brown and Alcala, 1995; Brown and Diesmos, 2002; Siler et al., 2010a). In contrast, the distribution of total species diversity in the genus is less uniform, with 11 species known from the Luzon Faunal Region versus six in the Mindanao Faunal Region, six in the Visayan Faunal Region, and only one and two in the Sulu archipelago and Mindoro Faunal Region respectively (Brown and Alcala, 1980; 207 Brown and Alcala, 1995; Brown and Diesmos, 2002; Siler et al., 2009a, 2010a,b). New species discoveries on Luzon Island have occurred with consistency during the last two decades; given the island’s complex mountain ranges (Sierra Madres, Cordillera, Zambales, Bicol Peninsula volcanoes) and geographic complexity (Defant et al., 1989; Yumul et al., 2009), the increase in the region’s faunal diversity is likely to continue (Ross and Gonzales, 1992; Brown et. al. 1995a,b, 1999, 2000a,b, 2007; Siler et al., 2009a, 2010a,b). It is worth noting that efforts to survey Mindanao have been less extensive than efforts on Luzon; this may account for some of the differences in diversity between the regions—which may be artifacts of sampling biases. At present there remains one polytypic species (B. gracilis) and two “widespread” species (B. bonitae and B. samarensis), all with distributions spanning boundaries between recognized faunal regions (Brown and Alcala, 1980). Closer investigation of island populations within each of these species may result in the discovery of new diversity in the genus. As our understanding of the total diversity within Brachymeles increases, it is important that continued efforts be made to conduct surveys focused on rotting log and leaf litter microhabitats throughout the ranges of all species. Accurate data on the distributions of these species will allow for a complete assessment of the geographic ranges of the species and appropriate decision of conservation status and actions can be made. At present, all nine species are known or believed to be common throughout their ranges. Although these species currently inhabit highly disturbed, agricultural and residential areas, no studies on the long-term effect of deforestation on populations of Brachymeles exist. Therefore, according to the IUCN categories and classification structure, we consider the conservation status of these species as “Least Concern (LC),” pending the collection of additional information that might suggest otherwise. 208 Figure 3.6. Illustration of head of adult female Brachymeles boholensis (KU 323972) and adult male neotype of Brachymeles boulengeri (PNM 9720; formerly KU 307756) in dorsal, lateral, and ventral views. Taxonomically diagnostic head scales are labeled as follows: C, chin shield; F, frontal; FN, frontonasal; FP, frontoparietal; IL, infralabial; IP, interparietal; L, loreal; M, mental; N, nasal; P, parietal; PF, prefrontal; PM, postmental; PN, postnasal; PO, preocular; PSO, presubocular; R, rostral; SC, supraciliary; SL, supralabial; SN, supranasal; and SO, supraocular. Roman numerals indicate scales in the supraocular series, with Arabic numbers indicating scales in the supraciliary series. Illustrations by CDS. 209 210 Figure 3.7. Illustration of head of adult male Brachymeles mindorensis (KU 304343) and adult female Brachymeles taylori (KU 324049) in dorsal, lateral, and ventral views. Labels for taxonomically diagnostic head scales follow those shown in Figure 3.6. Illustrations by CDS. 211 212 Figure 3.8. Illustration of head of adult male Brachymeles orientalis (KU 311241) and adult male Brachymeles schadenbergi (KU 314992) in dorsal, lateral, and ventral views. Labels for taxonomically diagnostic head scales follow those shown in Figure 3.6. Illustrations by CDS. 213 214 Figure 3.9. Illustration of head of adult male Brachymeles talinis (KU 306769) and adult male holotype of Brachymeles kadwa (PNM 9721; formerly KU 323091) in dorsal, lateral, and ventral views. Labels for taxonomically diagnostic head scales follow those shown in Figure 3.6. Illustrations by CDS. 215 216 Figure 3.10. Illustration of head of adult male holotype of Brachymeles tungaoi (PNM 9722; formerly KU 323933) and adult male holotype of Brachymeles vindumi (CAS 60724) in dorsal, lateral, and ventral views. Labels for taxonomically diagnostic head scales follow those shown in Figure 3.6. Illustrations by CDS. 217 218 Figure 3.11. Photographs in life of (A) Brachymeles boulengeri (KU 307756), SVL = 98.0 mm, (B) Brachymeles taylori (RMB 3283, deposited at PNM), SVL = 81.0 mm, (C) Brachymeles boholensis (RMB 2877, deposited at PNM), female, SVL = 89.0 mm, (D) Brachymeles kadwa (KU 304593), SVL = 101.0 mm, (E) Brachymeles schadenbergi (KU 314973), female, SVL = 107.0 mm, (F) Brachymeles orientalis (KU 311240), juvenile, SVL = 51.0 mm, (G) Brachymeles orientalis (KU 324029), female, SVL = 91.0 mm, and (H) Brachymeles talinis (RMB 3305; deposited at PNM), SVL = 139.0 mm. Photographs by CDS and RMB. 219 220 CHAPTER 4 Phylogeny-based species delimitation in Philippine slender skinks (Reptilia: Squamata: Scincidae: Brachymeles) II: taxonomic revision of Brachymeles samarensis and description of five new species Few genera of scincid lizards are known to possess species representing a full spectrum of body forms, from fully limbed, pentadactyl species to limbless species (see Siler and Brown, 2010 for review). Within the genus Brachymeles, all but two of the 26 recognized species are endemic to the Philippines, with the exceptions being a single species (B. apus) from northern Borneo and another (B. miriamae) from Thailand (Brown and Alcala, 1980; Hikida, 1982; Siler, 2010; Siler and Brown, 2010, 2011; Siler et al., 2009a, 2010a,b, in press a,b,c,d). Thirteen species are pentadactyl (bicolor, boholensis, boulengeri, gracilis, kadwa, makusog, mindorensis, orientalis, schadenbergi, talinis, taylori, tungaoi, and vindumi), eight are non-pentadactyl, with incompletely developed limbs and reduced numbers of digits (bonitae, cebuensis, elerae, muntingkamay, pathfinderi, samarensis, tridactylus, and wrighti), and five are entirely limbless (apus, minimus, miriamae, lukbani, and vermis). Within the non-pentadactyl species there has been documented a wide range of limb- and digit-reduced states, from minute limbs that lack full digits (bonitae, cebuensis, muntingkamay, samarensis, tridactylus), to moderately developed limbs with four to five digits on the hands and feet (elerae, pathfinderi, wrighti: Duméril and Bibron, 1839; Brown, 1956; Brown and Rabor, 1967; Brown and Alcala, 1980; Taylor, 1917, 1918, 1925; Siler, 2010; Siler and Brown, 2010, 2011; Siler et al., 2009a, 2010a,b, in press a,b,c,d). All species are semi-fossorial and typically found in dry, rotting material inside or underneath decaying logs or in loose soil, forest floor detritus, and leaf litter. 221 Figure 4.1. Map of the Philippine islands, with island labels provided for islands with representative samples used for this study. The five recognized major Pleistocene Aggregate Island Complexes (PAICs), major island groups, and additional deep-water islands are labeled for reference. Islands of the Romblon Island Group are designated by the first letter of the island name (T, Tablas Island; R, Romblon Island; S, Sibuyan Island). Current islands in the Philippines are shown in medium grey; light gray areas enclosed in black 120 m bathymetric contours indicate the hypothesized maximum extent of land during the mid- to late Pleistocene. 222 223 Although the genus was named well over 150 years ago (Duméril and Bibron, 1839), the rate of Brachymeles species descriptions reached an apparent asymptotic maximum in 1980 (Brown and Alcala, 1980). The one exception is B. minimus, a legless species described in 1995 (Brown and Alcala, 1995). For more than a century, limited numbers of specimens in museum collections, combined with the similar body plans and external morphological features among species of Brachymeles limited assessments of species-level diversity (Taylor, 1917; Brown, 1956; Brown and Rabor, 1967; Brown and Alcala, 1980). Recent studies have revealed the species-level diversity of Brachymeles skinks to be drastically underestimated, and have identified numerous non-monophyletic species complexes within the Philippines (Siler, 2010; Siler and Brown, 2010, 2011; Siler et al., 2009a, 2010a,b, in press a,b,c,d). Additionally, several rare, mid-to-high elevation species long represented by only a few specimens (e.g., Brachymeles bicolor, B. elerae, B. wrighti, B. pathfinderi), have recently been rediscovered and redescribed as valid taxa (Siler, 2010; Siler et al., in press a,b). Together, these studies, coupled with increased sampling throughout the Philippines, and a new, robust molecular dataset allow us to begin evalutating variation across the isolated populations of widespread species in the Philippines. In recent studies Siler and Brown (in press) revised two polytypic species (B. boulengeri and B. schadenbergi) and one widespread species (B. talinis), and inferred the presence of ten genetically and morphologically distinct allopatric evolutionary lineages (species). Several other species are still recognized as having widespread distributions that span historical faunal demarcations in the Philippines (Heaney, 1985; Brown and Guttman, 2002; Brown and Diesmos, 2002, 2009), including B. samarensis and B. bonitae (Brown, 1956; Brown and Rabor, 1967; Brown and Alcala, 1980). One of these species (B. samarensis) is the focus of this study. TAXONOMIC HISTORY 224 The genus Brachymeles was first described by Dumeril and Bibron (1839) for the small, limb-reduced species Brachymeles bonitae. Three additional species (Senira bicolor [Gray, 1845], Eumeces (Riopa) gracilis [Fischer, 1885], E. (R.) schadenbergi [Fischer, 1885]) were transferred to the genus by Boettger (1886) and Boulenger (1887). These four species represented the known diversity in the genus for thirty years, until Taylor published a series of herpetofaunal descriptions in the early 1900s. It would be fifty years before Brown (1956) described Brachymeles samarensis from a single juvenile specimen (FMNH 44472) collected in Guiuan, Samar Island, Philippines in 1945. At the time of description, Brown (1956) hypothesized the species was most closely related to B. elerae due to similarities in the number of paravertebral scale rows. This single juvenile would remain the only vouchered, type specimen of this unique, bidactyl species for more than sixty years (Brown and Alcala, 1980). By the time Brown and Rabor (1967) revised the genus Brachymeles, samples of specimens morphologically similar to B. samarensis had been collected from the islands of Luzon and Leyte. Additionally, Brown and Rabor (1967) reported on a second specimen from Samar Island; however, no information on where the specimen was deposited or its museum catalog number were provided. Although Brown and Rabor (1967) treated B. samarensis as a single widespread species, they referred to the species as a “complex,” suggesting they suspected that it contained multiple species, and noted several distinct morphological differences island populations, including differences in fore- and hind limb digit number and head scale patterns. Additional island populations of B. samarensis were subsequently sampled by the time Brown and Alcala (1980) revised the genus, including the Lapinig Group islands off the northeast coast of Bohol Island (Fig. 4.3). Ross and Gonzales (1992) would later report on observations of B. samarensis from Catanduanes Island off the northeast coast of the Bicol 225 Peninsula (Fig. 4.3), and in 2001, RMB recorded B. samarensis on the southern tip of the Bicol Peninsula in the foothills of Mt. Bulusan (unpublished data); these extralimital range extentions of B. samarensis beyond the confines of the Mindanao PAIC (Brown and Diesmos, 2002, 2009) have been interpreted as resulting from recent dispersal events. To date, Brachymeles samarensis remains a widespread species spanning islands of the Luzon and Mindanao Pleistocene Aggregate Island Complexes (PAICs; Brown and Guttman, 2002; Brown and Diesmos, 2002; Fig. 4.1). Widespread distributions such as this have been the focus of many recent studies (Brown et al., 2000a; Siler et al., 2010a,b, 2011; Siler and Brown, 2010, 2011; Welton et al., 2009, 2010a,b), which have revealed that few endemic Philippine reptiles actually possess broad distributions spanning these regional faunistic boundaries (review: Brown and Diesmos, 2009). The goal of the present study is to revise the taxonomy of the B. samarensis complex such that individual units (species) represent independently evolving, cohesive lineage segments (sensu Simpson, 1961; Wiley 1978; Frost and Hillis, 1990; de Queiroz, 1998, 1999). Comprehensive examination of all recently collected specimens from throughout the known range of B. samarensis results in the reorganization of the species complex into six distinct evolutionary lineages (species). In this paper we provide a phylogenetic analysis of all of these taxa, fully describe each species, clarify taxonomic boundaries, and provide the first illustrations of all included species. We also provide information on each species’ natural history, ecology, and geographic distribution. Materials and Methods Field work, sample collection, and specimen preservation 226 Fieldwork was conducted on Catanduanes, Lapinig Grande, Leyte, Luzon, and Samar islands, all in the Philippines (Fig. 4.1) between 2001 and 2009. Specimens were collected between 900 and 1600 hr, euthenized in aqueous chloretone, dissected for genetic samples (liver preserved in 95% ethanol or flash frozen in liquid nitrogen), fixed in 10% formalin and eventually (< 2 mo) transferred to 70% ethanol. Newly sequenced specimens are deposited in U.S. and Philippine museum collections, the Univrsity of Kansas Natural History Museum (KU), and the Texas Natural History Collections (TNHC) of the Texas Memorial Museum of the University of Texas at Austin. (Acknowledgments and Specimens Examined); voucher information corresponding to data from GenBank sequences is included in Table 4.1. Taxon sampling and outgroup selection for phylogenetic analyses Because our primary goal was to estimate phylogenetic relationships among the various populations of Brachymeles samarensis we sequenced 2–4 exemplars per sampled population. We included samples of Lygosoma bowringi as an outgroup representative based on relationships presented in a recent phylogenetic analyses of the genus Brachymeles (Siler and Brown, 2011; Siler et al., 2011). Additionally, we included samples of Brachymeles apus, B. bonitae, B. minimus, B. lukbani, and B. cebuensis to explore the sister group relationships within the B. samarensis complex. A total of 28 ingroup samples were used in phylogenetic inferences. DNA extraction, purification, and amplification We extracted total genomic DNA from tissues (Table 4.1) using the modified guanidine thiocyanate extraction method of Esselstyn et al. (2008). The mitochondrial NADH Dehydrogenase Subunit 1 (ND1), NADH Dehydrogenase Subunit 2 (ND2), and the nuclear loci, α-enolase and PTGER4, were completely sequenced for nearly all samples using the primers and 227 protocols provided in Siler et al. (2011). We visualized amplified products on 1.0% agarose gels, then purified them with 1 µL of a 20% solution of ExoSAP-IT (US78201, Amersham Biosciences, Piscataway, NJ) on the following thermal cycler profile: 31 min at 37º, followed by 15 min at 80˚. Upon successful amplification of targeted fragments, cycle-sequencing reactions were completed with the same primers and ABI Prism BigDye Terminator chemistry (Ver. 3.1; Applied Biosystems, Foster City, CA). Cycle-sequencing products were purified with Sephadex Medium (NC9406038, Amersham Biosciences, Piscataway, NJ) in Centri-Sep 96 spin plates (CS-961, Princeton Separations, Princeton, NJ). We analyzed purified products using an ABI Prism 3130xl Genetic Analyzer (Applied Biosystems), and gene sequences were assembled with Sequencher 4.8 (Gene Codes Corp., Ann Arbor, MI). Alignment and phylogenetic analysis An initial alignment was produced in Muscle v3.7 (Edgar, 2004), and manual adjustments were made in MacClade 4.08 (Maddison and Maddison, 2005). No instances of insertions or deletions, or ambiguously aligned regions, were observed in the data, and all data were used for analyses. The final alignment thus consisted of 2,570 characters. Phylogenetic analyses were conducted using parsimony and likelihood optimality criteria, as well as Bayesian methods. Parsimony (MP) analyses were conducted in PAUP* 4.0 (Swofford, 2002) with all characters weighted equally. Most-parsimonious trees were estimated using heuristic searches with 1000 random addition-sequence replicates and tree bisection and reconnection (TBR) branch swapping. To assess heuristic support, nonparametric bootstrapping was conducted using 1000 replicates, each with 100 random addition-sequence replicates and TBR branch swapping. 228 Partitioned maximum likelihood (ML) analyses were conducted in RAxMLHPC v7.04 (Stamatakis, 2006). The alignment was partitioned into eight regions consisting of the codon positions of ND1 and ND2, and the two nuclear loci, α-enolase and PTGER4, following the methods of Siler et al. (in press a). Analyses that partition protein-coding genes by codon position have been shown to improve resulting inferences (Brandley et al., 2005). The partitions were run under the same model (GTR + I) with 100 replicate best-tree inferences. Each inference was performed with a random starting tree, and relied on the rapid hill-climbing algorithm (Stamatakis 2006). Clade support was assessed with 1000 bootstrap pseudoreplicates. We considered branches receiving ≥70% bootstrap support to be well-supported (Hillis and Bull, 1993; see also Wilcox et al., 2002). The Akaike Information Criterion (AIC), as implemented in jModeltest v0.1.1 (Guindon and Gascuel, 2003; Posada, 2008), was used to select the best model of nucleotide substitution for each partition (Table 4.2). The best-fit model for each of the eight partitions (Table 4.2) was used for Bayesian analyses performed in MrBayes 3.1 (Ronquist and Huelsenbeck, 2003). The same partitioning strategy used for maximum likelihood analyses was used for Bayesian inferences. Searches over tree space were conducted with four runs, each with four chains, and were run for 2 × 107 generations. Trees were sampled every 1000 generations, with 4000 samples discarded as burn-in; this left 16001 post-burn-in trees from each run included in the posterior distribution of topologies. Visual inspection for chain stationarity and high ESS values was conducted within the program Tracer v1.4 (Rambaut and Drummond, 2007). Additionally, correlations of split frequencies and cumulative split frequencies were examined using the program AWTY (Nylander et al., 2008). We considered topologies with posterior probabilities ≥0.95 to be well-supported (Wilcox et al., 2002; Leaché and Reeder, 2002). 229 Morphological data We examined fluid-preserved specimens (Appendix V) for variation in qualitative and mensural characters. Sex was determined by gonadal inspection, and measurements were taken to the nearest 0.1 mm with digital calipers by CDS. X-rays were taken with a company cabinet X-ray on Kodak paper exposed at 5 miliampheres and 30 volts for 1 minute 15 seconds. Museum abbreviations for specimens examined follow Leviton et al. (1985). Meristic and mensural characters were chosen based on Siler et al. (2009a, 2010a,b): snout–vent length (SVL), axilla–groin distance (AGD), total length (TotL), midbody width (MBW), midbody height (MBH), tail length (TL), tail width (TW), tail height (TH), head length (HL), head width (HW), head height (HH), snout–forearm length (SnFa), eye diameter (ED), eye–narial distance (END), snout length (SNL), internarial distance (IND), fore-limb length (FLL), hind limb length (HLL), midbody scale-row count (MBSR), paravertebral scale-row count (PVSR), axilla–groin scale-row count (AGSR), Finger-III lamellae count (FinIIIlam), Toe-IV lamellae count (ToeIVlam), supralabial count (SL), infralabial count (IFL), supraciliary count (SC), and supraocular count (SO). Additionally, we counted the number of presacral vertebrae (PSV) from x-ray images of specimens. In the description, ranges are followed by mean ± standard deviation in parentheses. Species concept We follow the General Lineage Concept of species (de Queiroz, 1998, 1999) as a logical extension of the Evolutionary Species Concept (Simpson, 1961; Wiley, 1978; Frost and Hillis, 1990). We consider as distinct lineages those populations that are morphologically, and genetically distinct, especially if allopatric. Lineage-based species concepts have been 230 successfully employed in the recognition of Philippine biodiversity (Brown et al., 2000a, 2002, 2008, 2009; Brown and Guttman, 2002; Gaulke et al., 2007; Welton et al., 2009, 2010a,b; Siler et al., 2011) due to the highly partitioned nature of the archipelago (Brown and Diesmos, 2009), and because the geological history of the islands has been so well documented (Voris, 2000; Hall, 2002; Yumul, 2009). In this study we use an estimate of Phylogenetic relationships as a guide for delimiting species but restrict our diagnoses of new species to those populations diagnosed by differences in non-overlapping morphological character states. Results Phylogeny Of 2,570 mitochondrial characters, 848 were parsimony-informative. The maximum parsimony analysis inferred ten most parsimonious trees (tree length = 2084) that are topologically identical (topology not shown; bootstrap support summarized in Fig. 4.2). The resulting 100 inferences from the partitioned RAxML maximum likelihood analysis show an average likelihood score of –ln L 12011.371112, with a single inference having the highest likelihood score of –ln L 12011.367644. Trees recovered from ML, MP, and Bayesian analyses are topologically identical. No inferences support the monophyly of Brachymeles samarensis. All analyses recover two reciprocally monophyletic clades that include distinct lineages of the B. samarensis complex (Fig. 4.2). The Leyte Island and Lapinig Group Islands populations were recovered as a clade, sister to B. cebuensis from Cebu Island (Fig. 4.2). True B. samarensis from Samar Island was recovered as sister to a clade of two limbless species of Brachymeles (B. minimus and B. lukbani) and the Luzon and Catanduanes island populations of B. samarensis 231 (Fig. 4.2). Two separate lineages are recovered from the Bicol Peninsula of Luzon Island, with no support for their monophyly (Fig. 4.2). All analyses of result in the strong support of six genetically distinct lineages within the Brachymeles samarensis species complex (Fig. 4.2). Uncorrected pairwise sequence divergences are low within the lineages defined here as species and high between these lineages (Table 4.3). Percent divergences for the combined mitochondrial and nuclear data, respectively, show that the monophyletic lineages defined by our phylogenetic analyses (B. samarensis, B. sp. nov. [Leyte Island], B. sp. nov. [Lapinig Group Islands], B. sp. nov. [Catanduanes Island], B. sp. nov. [Southern Bicol Peninsula, Luzon Island], B. sp. nov. (Central Bicol Peninsula, Luzon Island]) are distinguished from congeners by levels of genetic divergence equal to, or greater than, those between previously defined species—viz., B. bonitae, B. cebuensis, B. minimus, B. lukbani (Table 4.3; Fig. 4.2). The three most closely related lineages (B. sp. nov. [Catanduanes Island], B. sp. nov. [Southern Bicol Peninsula, Luzon Island], B. sp. nov. (Central Bicol Peninsula, Luzon Island]) are separated by 4.1–9.6% mitochondrial sequence divergence. Sequence divergences among the other three lineages within the B. samarensis species complex (B. samarensis [Samar Island], B. sp. nov. [Lapinig Group islands], B. sp. nov. (Leyte Island]) are greater than 9.2% (Table 4.3; Fig. 4.2). Intraspecific sequence divergences are low in comparison to divergences among monophyletic lineages. Additionally, moderate levels of sequence divergence are observed even when analyses are restricted to only nuclear sequence data (Table 4.3). 232 Figure 4.2. Maximum likelihood estimate of combined mitochondrial and nuclear data for samples of Brachymeles used for this study (preferred ML tree, -ln L 12011.367644; ND1, ND2, α-enolase, PTGER4). Nodes are shown with numerical values corresponding to MPBP, MLBP, and Bayesian PP support values respectively. Terminals are labeled with taxonomic names, fore- and hind limb digit states, and number of presacral vertebrae. 233 234 Figure 4.3. (Left) Map of the Philippine islands showing previously recognized distribution of Brachymeles samarensis (indicated by black shaded islands), and recognized distributions of other members of the B. samarensis Complex (indicated by dark gray shapes). (Right) Hypothesized distributions of B. lima, B. tatlo, B. apat, B. dalawa, B. isa, and B. samarensis in the eastern-central Philippines. The sampling localities are indicated by black or white shapes, and the hypothesized geographic range of each species indicated by shaded islands and dashed lines, with shapes and shades of islands corresponding to the map’s key. 235 236 Table 4.1. Summary of specimens corresponding to genetic samples included in the study, general locality, and GenBank accession number. SP = Sabah Parks Reference Collection; KU = University of Kansas Natural History Museum; LSUHC = La Sierra University Herpetological Collections; TNHC = Texas Natural History Collections of the Texas Memorial Museum of the University of Texas at Austin. 237 Sp ec ie s V ou ch er Lo ca lit y G en ba nk A cc es si on N um be rs N D 1 N D 2 ! -e no la se PT G ER 4 Ly go so m a bo w ri ng i LS U H C 6 97 0 W es t M al ay si a Ly go so m a bo w ri ng i LS U H C 6 99 8 W es t M al ay si a Br ac hy m el es a pus SP 0 69 15 M al ay si a, B or ne o, S ab ah , M t. K in ab al u N at io na l P ar k Br ac hy m el es b on ita e K U 3 07 74 7 Ph ili pp in es , P ol ill o Is la nd , M un ic ip al ity o f Q ue zo n Br ac hy m el es b on ita e K U 3 26 08 0 Ph ili pp in es , P ol ill o Is la nd , M un ic ip al ity o f Q ue zo n Br ac hy m el es m in im us K U 3 08 13 1 Ph ili pp in es , C at an du an es Is la nd , M un ic ip al ity o f G ig m ot o Br ac hy m el es m in im us K U 3 08 12 9 Ph ili pp in es , C at an du an es Is la nd , M un ic ip al ity o f G ig m ot o Br ac hy m el e lu kb an i K U 3 13 60 2 Ph ili pp in es , L uz on Is la nd , M un ic ip al ity o f L ab o Br ac hy m el e lu kb an i K U 3 13 59 6 Ph ili pp in es , L uz on Is la nd , M un ic ip al ity o f L ab o Br ac hy m el es c eb ue ns is K U 3 20 41 9 Ph ili pp in es , C eb u Is la nd , M un ic ip al ity o f C ar ca r Br ac hy m el es c eb ue ns is K U 3 20 42 1 Ph ili pp in es , C eb u Is la nd , M un ic ip al ity o f C ar ca r Br ac hy m el es d al aw a2 K U 3 20 43 0 Ph ili pp in es , L ap in ig G ra nd e Is la nd , M un ic ip al ity o f C ar lo s P . G ar ci a Br ac hy m el es d al aw a2 K U 3 20 45 8 Ph ili pp in es , L ap in ig G ra nd e Is la nd , M un ic ip al ity o f C ar lo s P . G ar ci a Br ac hy m el es d al aw a1 K U 3 20 46 6 Ph ili pp in es , L ap in ig G ra nd e Is la nd , M un ic ip al ity o f C ar lo s P . G ar ci a Br ac hy m el es d al aw a2 K U 3 20 44 5 Ph ili pp in es , L ap in ig G ra nd e Is la nd , M un ic ip al ity o f C ar lo s P . G ar ci a Br ac hy m el es li m a1 K U 3 24 00 3 Ph ili pp in es , L uz on Is la nd , M un ic ip al ity o f T ob ac o Br ac hy m el es li m a2 K U 3 24 01 6 Ph ili pp in es , L uz on Is la nd , M un ic ip al ity o f T ob ac o Br ac hy m el es li m a2 K U 3 24 01 0 Ph ili pp in es , L uz on Is la nd , M un ic ip al ity o f T ob ac o Br ac hy m el es li m a2 K U 3 24 00 3 Ph ili pp in es , L uz on Is la nd , M un ic ip al ity o f T ob ac o Br ac hy m el es ta tlo 3 TN H C 6 24 69 Ph ili pp in es , L uz on Is la nd , M un ic ip al ity o f S or so go n Br ac hy m el es ta tlo 1 K U 3 24 01 7 Ph ili pp in es , L uz on Is la nd , M un ic ip al ity o f S or so go n Br ac hy m el es a pat 2 K U 3 24 02 5 Ph ili pp in es , C at an du an es Is la nd , M un ic ip al ity o f S an M ig ue l Br ac hy m el es a pat 2 K U 3 24 02 0 Ph ili pp in es , C at an du an es Is la nd , M un ic ip al ity o f S an M ig ue l Br ac hy m el es a pat 2 K U 3 24 02 2 Ph ili pp in es , C at an du an es Is la nd , M un ic ip al ity o f S an M ig ue l Br ac hy m el es s am ar en si s K U 3 10 85 0 Ph ili pp in es , S am ar Is la nd , M un ic ip al ity o f T af t Br ac hy m el es s am ar en si s K U 3 10 85 1 Ph ili pp in es , S am ar Is la nd , M un ic ip al ity o f T af t Br ac hy m el es s am ar en si s K U 3 10 84 9 Ph ili pp in es , S am ar Is la nd , M un ic ip al ity o f T af t Br ac hy m el es is a2 K U 3 11 22 5 Ph ili pp in es , L ey te Is la nd , M un ic ip al ity o f B ay ba y Br ac hy m el es is a2 K U 3 11 22 6 Ph ili pp in es , L ey te Is la nd , M un ic ip al ity o f B ay ba y Br ac hy m el es is a2 K U 3 11 22 7 Ph ili pp in es , L ey te Is la nd , M un ic ip al ity o f B ay ba y 1 H ol ot yp e; 2 P ar at op ot yp e; 3 P ar at yp e 238 Table 4.2. Models of evolution selected by AIC and applied for partitioned, Bayesian phylogenetic analyses1. Partition AIC Model Model Applied Number of Characters ND1, 1st codon position GTR + I + G GTR + G 322 ND1, 2nd codon position GTR + I + G GTR + G 322 ND1, 3rd codon position GTR + I + G GTR + G 322 ND2, 1st codon position TVM + I + G GTR + G 287 ND2, 2nd codon position GTR + I + G GTR + G 287 ND2, 3rd codon position TVM + I + G GTR + G 287 α-enolase TVMef + G GTR + G 261 PTGER4 HKY + I + G HKY + G 490 1The model GTR + G was used for partitioned RAxMLHPC analyses. 239 Table 4.3. Uncorrected pairwise sequence divergence (%) for mitochondrial data (below diagonal) and nuclear data (above diagonal), for Brachymeles samarensis, B. isa, B. dalawa, B. lima, B. apat, B. tatlo, B. bonitae, B. cebuensis, B. lukbani, and B. minimus (Fig. 4.2). Percentages on the diagonal represent intraspecific genetic diversity (bolded for emphasis). 240 sa m ar en si s is a da la wa lim a apa t ta tlo bo ni ta e ce bu en si s lu kba ni m in im us sa m ar en si s 0. 0 2. 2 1. 8– 2. 8 1. 1– 1. 5 1. 6 1. 5 2. 4 1. 2 2. 7– 3. 1 3. 4 is a 14 .3 0. 0– 0. 7 0. 2– 2. 8 1. 8– 2. 2 2. 0 1. 6– 2. 0 2. 6 1. 3 3. 0 3. 3 la pin ig 14 .6 –1 5. 2 9. 2– 10 .5 0. 0– 0. 1 1. 4– 2. 8 1. 6– 3. 6 1. 2– 3. 3 2. 2– 4. 8 1. 4– 2. 8 3. 0– 3. 6 3. 2– 4. 4 lim a 14 .5 –1 4. 7 14 .1 –1 4. 5 14 .9 –1 5. 8 0. 4– 0. 7 0. 5– 0. 9 0. 4– 1. 1 2. 3– 2. 7 1. 1– 1. 6 2. 6– 3. 2 3. 2– 3. 6 apa t 14 .4 –1 4. 5 14 .4 –1 4. 6 14 .5 –1 4. 8 4. 1– 4. 7 0. 0– 0. 2 0. 7– 1. 2 2. 7 1. 5 2. 8– 3. 1 3. 5 ta tlo 14 .9 –1 5. 0 14 .6 –1 4. 9 14 .7 –1 5. 4 9. 4– 9. 6 9. 3– 9. 5 1. 9 2. 6– 2. 8 1. 4– 1. 6 2. 7– 3. 1 3. 4– 3. 5 bo ni ta e 16 .9 –1 7. 3 15 .0 –1 5. 6 15 .5 –1 6. 5 15 .8 –1 6. 5 15 .7 –1 6. 2 15 .7 –1 6. 3 1. 4 2. 2 2. 6– 3. 0 3. 2 ce bu en si s 16 .2 11 .6 –1 1. 7 12 .0 –1 2. 4 14 .6 –1 4. 8 14 .7 14 .8 –1 4. 9 16 .5 –1 6. 7 0. 0 2. 8– 3. 0 3. 2 lu kba ni 14 .1 14 .1 –1 4. 4 14 .8 –1 5. 3 11 .5 –1 1. 9 11 .2 11 .8 –1 1. 9 15 .0 –1 5. 1 13 .4 0. 1 0. 7– 0. 8 m in im us 14 .1 14 .0 –1 4. 2 13 .8 –1 4. 3 11 .6 –1 2. 0 11 .0 –1 1. 2 11 .6 15 .0 –1 5. 1 13 .7 4. 9– 5. 0 0. 0 241 Morphology Variation in morphological characters (Tables 4.4–4.6) mirrors the results observed in phylogenetic analyses, and supports the recognition of six Brachymeles samarensis group lineages. Characters differing among these six lineages include: digit number, presacral vertebrae number, degree of digit development, head and body scale counts and patterns, and pigmentation patterns (Tables 4.4–4.6; species accounts below), all of which are typical morphological diagnostic characters employed historically by taxonomists working with this genus (review: Brown and Alcala, 1980). We observed no intraspecific mensural or meristic differences between the sexes of any of the 6 species. Superficially, the six lineages within the B. samarensis complex appear morphologically similar, especially in overall body size; however, upon closer inspection, three distinct body forms are observed. Among the six lineages, two are observed to be tridactyl (B. sp. nov. [Leyte Island] and B. sp. nov. [Lapinig Group Islands]), three are observed to be bidactyl (B. samarensis, B. sp. nov. [Catanduanes Island] and B. sp. nov. [Central Bicol Peninsula, Luzon Island]), and one is observed to be bidactyl, but with small, highly-reduced, and near imperceptable claws (B. sp. nov. [Southern Bicol Peninsula, Luzon Island]). Additionally, numerous non-overlapping differences were detected in meristic, mensural, osteological, and color pattern characters for each complex member, readily defining six distinct lineages within the complex (Tables 4.4–4.6). In summary, each lineage (most of which are allopatric) possesses unique and non-overlapping suites of diagnostic character states of morphology, perfectly corresponding to the six clades defined in phylogenetic analyses of DNA sequence data. Combined with 242 biogeographic evidence, and clearly separate geographical ranges, our data suggest the presence of six evolutionary lineages, worthy of taxonomic recognition. Taxonomic conclusions Our estimate of phylogeny (Fig. 4.2), biogeographically separate ranges of island or region endemic species, diagnostic, non-overlapping morphological character states, and genetic distances between the taxa (Table 4.3) indicate the distinctiveness of a new species from Catanduanes Island, two new species from the Bicol Peninsula of Luzon Island, a new species from the Lapinig Group Islands, and a new species from Leyte Island (Table 4.3; Fig. 4.2). Each of the six species of the B. samarensis complex is morphologically distinct from each other and all other known species in the genus, and each of the eleven species of Brachymeles included in phylogenetic analyses also are genetically distinct. Each monophyletic lineage, with the exception of the two occurring on the Bicol Peninsula of Luzon Island, is endemic to single islands within two isolated PAICs, thereby providing additional support for the distinctiveness of each clade’s evolutionary history and lineage integrity. Accordingly, we recognize Brachymeles samarensis as a species that occurs only on Samar Island in the eastern Visayan (central) Philippine islands (e.g., Mindanao PAIC; Fig. 4.3), and hereby recognize the five additional lineages within the B. samarensis species complex each as new species. TAXONOMIC ACCOUNTS Brachymeles samarensis Brown 1956: 6 Figs. 4.3, 4. 4 Brachymeles samarensis, Brown, 1956, Type locality: Guinuan, Samar Island, Philippines 243 (FMNH 44472); Brown and Rabor, 1967; Brown and Alcala, 1970; Brown and Alcala, 1980. Diagnosis.—Brachymeles samarensis can be distinguished from congeners by the following combination of characters: (1) body size small (SVL 57.9–66.1 mm); (2) limbs bidactyl; (3) limb length small; (4) supralabials six; (5) infralabials six; (6) suparciliaries six; (7) supraoculars five; (8) midbody scale rows 19–22; (9) axilla–groin scale rows 66–69; (10) paravertebral scale rows 86–88; (11) pineal eye spot present; (12) prefrontals not contacting on midline; (13) frontoparietals contact; (14) mental/1st infralabial fusion absent; (15) postnasals absent; (16) enlarged chin shields in three pairs; (17) nuchal scales differentiated; (18) fourth and fifth supralabial below eye; (19) auricular opening absent; (20) presacral vertebrae 45; and (21) uniform body color (Tables 4.4, 4.5). Comparisons.—Characters distinguishing Brachymeles samarensis from all non-pentadactyl, limbed species of Brachymeles are summarized in Tables 4.4 and 4.5. Brachymeles samarensis most closely resembles B. lima, B. apat, B. tatlo, and populations of B. bonitae, the only other bidactyl species. However, B. samarensis differs from these four taxa by having midbody scale rows as few as 19 and axilla–groin scale rows as few as 66 (Table 4.5). Brachymeles samarensis further differs from B. lima by having fewer presacral vertebrae, six infralabials, the presence of contact between frontoparietals, and non-fusion of mental and first infralabials (Tables 4.4, 4.5); from B. apat by having a smaller maximum relative tail length (Table 4.4); from B. tatlo by having greater snout–vent lengths among males and females, fewer presacral vertebrae, and fewer paravertebral scale rows (Tables 4.4, 4.5); and from B. bonitae by having only bidactyl body forms, longer relative hind limb lengths, fewer presacral vertebrae, fewer paravertebral scale rows, six supralabials, six infralabials, six supraciliaries, five supraoculars, the presence of contact between frontoparietals, and non-fusion of mental and first infralabials (Tables 4.4, 4.5). 244 Brachymeles samarensis can be distinguished from all limbless species of Brachymeles (B. apus, B. lukbani, B. minimus, B. miriamae, B. vermis) by having limbs; and from all pentadactyl species of Brachymeles (B. boholensis, B. boulengeri, B. bicolor, B. gracilis, B. kadwa, B. makusog, B. mindorensis, B. orientalis, B. schadenbergi, B. talinis, B. taylori, B. tungaoi, B. vindumi) by having non-pentadactyl (vs. pentadactyl) limbs, shorter fore-limb lengths (less than 2.6 mm vs. greater than 5.9 mm), shorter hind limb lengths (less than 3.1 mm vs. greater than 10.3 mm), a narrower body (less than 6.4 mm vs. greater than 7.9 mm), and by the absence of a postnasal scale and auricular opening (vs. presence). Description (based on holotype description and six referred specimens).—Details of the head scalation of an adult female are shown in Figure 4.5. Measurements of the holotype are provided below in brackets. Body small, slender; maximum SVL 57.9 mm for males, 66.1 mm for females, [43.5, juvenile] (Tables 4.4, 4.5); head weakly differentiated from neck, nearly as wide as body, HW 7.3–9.2% (8.3 ± 0.7) SVL, 91.4–117.8% (102.7 ± 10.8) HL; HL 36.6–42.5% (38.8 ± 2.1) SnFa; SnFa 18.8–23.5% (20.9 ± 1.6) SVL; snout short, bluntly rounded in dorsal and lateral profile, SNL 50.9–55.3% (53.3 ± 1.8) HL; ear completely hidden by scales; eyes small, ED 1.3–1.6% (1.4 ± 0.1) SVL, 17.0–18.7% (17.6 ± 0.6) HL, 42.6–48.0% (45.8 ± 2.1) END, pupil subcircular; body slightly depressed, nearly uniform in thickness, MBW 109.1–150.6% (130.4 ± 14.9) MBH; scales smooth, glossy, imbricate; longitudinal scale rows at midbody 19–22 [22]; paravertebral scale rows 86–88 [86]; axilla–groin scale rows 66–69; limbs short, poorly developed, with digits reduced to two claws on both fore-limbs and hind limbs, finger and toe lamellae absent; FLL 2.4–5.7% (3.9 ± 1.3) AGD, 1.8–3.9% (2.9 ± 0.9) SVL; HLL 5.3–7.2% (6.2 ± 0.7) AGD, 4.0–5.0% (4.6 ± 0.4) SVL [6.9]; tail not as wide as body, gradually tapered towards end, TW 70.2–82.6% (76.7 ± 5.0) MBW, TL 56.5–80.6% (68.4 ± 11.6) SVL. 245 Rostral projecting onto dorsal snout to point in line with middle of nasal, broader than high, in contact with frontonasal; frontonasal wider than long; nostril ovoid, in center of single trapezoidal nasal, longer axis directed anteroventrally and posterodorsally; supranasals present, large, broadly separated; postnasals absent; prefrontals moderately separated; frontal octagonal-shaped, its anterior margin in moderate contact with frontonasal, in contact with first two anterior supraoculars, 3× wider than anterior supraocular; supraoculars five; frontoparietals moderate, in broad medial contact, each frontoparietal in contact with interior three supraoculars; interparietal moderate, its length roughly equal to midline length of frontoparietal, longer than wide, diamond-shaped, wider anteriorly; parietals broader than frontoparietals, in broad contact behind interparietal; nuchals enlarged; two loreals, decreasing in size from anterior to posterior, anterior loreal about as long as and slightly higher than posterior loreal; one preocular; one presubocular; supraciliaries six, the anteriormost contacting prefrontal and separating posterior loreal from first supraocular, posteriomost extending to posterior edge of fifth supraocular; single subocular scale row complete, in contact with supralabials; lower eyelid with one row of scales; supralabials six, first 2× size of other supralabials, fourth and fifth below eye; infralabials six (Fig. 4.4). Mental wider than long, in contact with first infralabials; postmental single, enlarged, its width equal to width of mental; followed by three pairs of enlarged chin shields, first pair in broad medial contact, second pair wider than first, broadly separated by single medial scale, third pair separated by three medial scales (Fig. 4.4). Scales on limbs smaller than body scales; scales on dorsal surfaces of digits wrapping around lateral edges of digits; lamellae absent; palmar surfaces of hands and plantar surfaces of feet with several small, irregular scales, each with irregular raised anterior edges; fore-limb digits equal in 246 size; hind limb digits unequal in size, middle digit greatest in length, first and third digits equal in length. Coloration in preservative.—The ground color of the body is medium brown, with each dorsal scale having a dark, auburn streak on the anterior two thirds to one half of the scale with light brown posterior. Streaks on each individual scale consist of four to seven longitudinal thin lines of auburn pigment with smudges of auburn between streaks. Posterior edge of all body scales transparent. The streaks are present around the entire body and more distinct on the ventrum. Ventral scales have auburn streak at the anterior end with cream color posterior. Caudals and subcaudals coloration matches ventral body coloration. Forelimb and hind limb scales are same color as their surrounding body scales. Precloacal scale coloration matches surrounding ventral scale coloration. Head scales have mottled light and dark brown coloration that match dorsal background coloration. Supraocular scales, rostral, nasal, supranasal, and supralabials are gray-cream color. The mental, infralabial, postmental, and chin shield scales are cream with slight brown mottling with lighter appearance compared to bordering ventral scales. Coloration in life.—Coloration in life closely matches the coloration in preservative with minor differences, including a dark brown body color and dark brown to black streaks of pigmentation. Variation.—Morphometric variation of the series is summarized in Table 4.6. We observed a single instance of digit variation, where one specimen (KU 310849) has no fore-limb digits and two hind limb digits. All examined specimens have two loreals with the exception of a single specimen (KU 310852), which has a single loreal on the right side of the body resulting from the fusion of the first and second loreals. Additionally, the first and second pairs of enlarged chin shields are equal in width among all examined specimens with the exception of a single 247 specimen (KU 310850), in which the width of the second pair of enlarged chin shield is greater than the width of the first pair. Distribution.—Brachymeles samarensis is known only from Samar Island (Fig. 4.3). Ecology and natural history.—Brachymeles samarensis occurs in primary- and secondary-growth forest habitats. In contrast to the other members of the B. samarensis complex, this species appears to be a forest obligate, and was only observed within rotting logs in secondary-growth forest. Three species of Brachymeles have been confirmed to occur on Samar Island (B. gracilis hilong, B. orientalis, and B. samarensis (Brown and Alcala, 1980; Siler and Brown, 2010; Siler et al., 2011, in press c,d). Other sympatric lizard species observed on Samar Island include: (Agamidae) Bronchocela cristatella, Draco bimaculatus, D. ornatus, D. reticulates, Gonocephalus semperi, Hydrosaurus pustulatus; (Gekkonidae) Cyrtodactylus annulatus, C. sumoroi, Gehyra mutilata, Gekko gecko, G. mindorensis, Hemidactylus frenatus, H. platyurus, Hemiphyllodactylus typus, Lepidodactylus aureolineatus, L. planicaudus, Pseudogekko compressicorpus; (Scincidae), Emoia atrocostata, Eutropis multicarinata, E. multifasciata, Lamprolepis smaragdina, Lipinia pulchella, L. quadrivittata, Sphenomorphus acutus, S. cumingi, S. fasciatus, S. jagori, S. cf. mindanensis, S. steerei, S. variagatus, Tropidophorus misaminus; (Varanidae) Varanus cumingi samarensis. Brachymeles isa sp. nov. Figs. 4.3, 4.6, 4.7 Holotype.—PNM 9746 (CDS Field No. 3418, formerly KU 311228), adult female, collected under rotting logs in secondary-growth forest (10:00–12:30 hr) on 8 November 2007, in the Sitio 248 San Vicente Tree Nursery, Barangay Pilim, Baybay City, Leyte Province, Leyte Island, Philippines (10°43'35" N, 124°49'05" E; WGS-84), by CDS and J. Fernandez. Paratopotypes.—One adult male (KU 311225), one adult female (KU 311229), and three juveniles (KU 311224, PNM 9747–48) collected between 29 October and 8 November 2007. Paratypes.—One adult male (CAS-SU 26120), four adult females (CAS-SU 26110, 26112, 26121–22), and two juveniles (CAS-SU 26115, 26123) collected between 1 May and 4 June 1964, in Barrio Tambis, Municipality of Burauen, Leyte Province, Leyte Island, Philippines (11°00'37" N, 124°52'19" E; WGS-84), by D. S. Rabor; one adult male (CAS-SU 26771), two adult females (CAS-SU 26770, 26772), and one juvenile (CAS-SU 26773), collected between 10 June and 17 July 1964, in the Municipality of Mahaplag, Leyte Province, Leyte Island, Philippines (10°35'42" N, 124°59'13" E; WGS-84), by D. S. Rabor. Diagnosis.—Brachymeles isa can be distinguished from congeners by the following combination of characters: (1) body size small (SVL 47.2–66.1 mm); (2) limbs tridactyl; (3) limb length small; (4) supralabials six; (5) infralabials five or six; (6) suparciliaries six; (7) supraoculars five; (8) midbody scale rows 21–22; (9) axilla–groin scale rows 71–74; (10) paravertebral scale rows 93–96; (11) pineal eye spot present; (12) prefrontals not contacting on midline; (13) frontoparietals contact; (14) enlarged chin shields in three pairs; (15) nuchals enlarged; (16) fourth and fifth supralabial below eye; (17) auricular opening absent; (18) presacral vertebrae 47; and (19) uniform body color (Tables 4.4, 4.5). Comparisons.—Characters distinguishing Brachymeles isa from all non-pentadactyl, limbed species of Brachymeles are summarized in Tables 4.4 and 4.5. Brachymeles isa most closely resembles B. dalawa, B. muntingkamay, and B. tridactylus, the only other tridactyl species, but differs from these three taxa by having five or six infralabials (Table 4.5). Brachymeles isa 249 further differs from B. dalawa by having longer body sizes among males, longer relative fore-limb lengths, a greater number of paravertebral scale rows, a uniform body color, and by the absence of contact between prefrontals (Tables 4.4, 4.5); from B. muntingkamay by having a shorter maximum body length, shorter fore-limb lengths, shorter hind limb lengths, a greater number of axilla–groin scale rows, a greater number of paravertebral scale rows, six supraciliaries, five supraoculars, the presence of a pineal eyespot, the absence of contact between prefrontals, the presence of contact between frontoparietals, the presence of differentiated nuchals, the presence of a continuous subocular scale row, and the absence of longitudinal rows of spots around the body (Tables 4.4, 4.5); and from B. tridactylus by having a shorter maximum body length, shorter relative tail length, shorter fore-limb length, a greater number of presacral vertebrae, six supralabials, six supraciliaries, five supraoculars, the presence of contact between frontoparietals, the presence of a continuous subocular scale row, and the absence of longitudinal rows of spots around the body (Tables 4.4, 4.5). Brachymeles isa can be distinguished from all limbless species of Brachymeles (B. apus, B. lukbani, B. minimus, B. miriamae, B. vermis) by having limbs; and from all pentadactyl species of Brachymeles (B. boholensis, B. boulengeri, B. bicolor, B. gracilis, B. kadwa, B. makusog, B. mindorensis, B. orientalis, B. schadenbergi, B. talinis, B. taylori, B. tungaoi, B. vindumi) by having non-pentadactyl (vs. pentadactyl) limbs, shorter fore-limb lengths (less than 1.7 mm vs. greater than 5.9 mm), shorter hind limb lengths (less than 3.0 mm vs. greater than 10.3 mm), a narrower body (less than 5.3 mm vs. greater than 7.9 mm), and by the absence of a postnasal scale and auricular opening (vs. presence). Description of holotype.—Details of the head scalation are shown in Figure 4.7. Adult female, body small, slender, SVL 59.1 mm; head weakly differentiated from neck, nearly as 250 wide as body, HW 6.5% SVL, 105.5% HL; HL 31.5% SnFa; SnFa 19.5% SVL; snout short, bluntly rounded in dorsal and lateral profile, SNL 71.2% HL; ear completely hidden by scales; eyes small, ED 1.7% SVL, 27.5% HL, 56.2% END, pupil subcircular; body slightly depressed, nearly uniform in thickness, MBW 126.7% MBH; scales smooth, glossy, imbricate; longitudinal scale rows at midbody 22; paravertebral scale rows 93; axilla–groin scale rows 71; limbs short, poorly developed, with digits reduced to three claws on both fore-limbs and hind limbs, finger and toe lamellae absent; FLL 2.7% AGD, 2.1% SVL; HLL 5.2% AGD, 4.1% SVL; tail not as wide as body, gradually tapered towards end, TW 73.7% MBW, TL 69.4% SVL. Rostral projecting onto dorsal snout to point in line with posterior edge of nasal, broader than high, in contact with frontonasal; frontonasal wider than long; nostril ovoid, in center of single trapezoidal nasal, longer axis directed anteroventrally and posterodorsally; supranasals present, large, broadly separated; postnasals absent; prefrontals broadly separated; frontal nearly diamond-shaped, its anterior margin in moderate contact with frontonasal, in contact with first two anterior supraoculars, 4× wider than anterior supraocular; supraoculars five; frontoparietals moderate, in narrow medial contact, each frontoparietal in contact with interior three supraoculars; interparietal moderate, its length roughly equal to midline length of frontoparietal, longer than wide, diamond-shaped, wider anteriorly; parietals as broad as frontoparietals, in broad contact behind interparietal; enlarged nuchals present; loreals two, decreasing in size from anterior to posterior, anterior loreal about as long as and slightly higher than posterior loreal; one preocular; one presubocular; supraciliaries six, the anteriormost contacting prefrontal and separating posterior loreal from first supraocular, posteriomost extending to middle of fifth supraocular; single subocular scale row complete, in contact with supralabials; lower eyelid with 251 one row of scales; supralabials six, first 2× size of other supralabials, third, fourth, and fifth below eye; infralabials six (Fig. 4.6). Mental wider than long, in contact with first infralabials; postmental single, enlarged, its width greater than width of mental; followed by three pairs of enlarged chin shields, first pair in broad medial contact, equal in width to third pair, second pair wider than first and third, broadly separated by single medial scale, third pair separated by three medial scales (Fig. 4.6). Scales on limbs smaller than body scales; scales on dorsal surfaces of digits wrapping around lateral edges of digits; lamellae absent; palmar surfaces of hands and plantar surfaces of feet with several small, irregular scales, each with irregular raised anterior edges; fore-limb digits equal in size; hind limb digits unequal in size, middle digit greatest in length, first and third digits equal in length. Coloration in preservative.—The ground color of the body is medium brown, with each dorsal scale having a dark, auburn streak on the anterior two thirds to one half of the scale with light brown posterior. Posterior edge of all body scales transparent. The streaks are present around the entire body. Ventral scales have smaller streaks restricted to the anterior one third to two-thirds of each scale with cream color posterior. Ventral caudal and subcaudal scales have less cream pigmentation, giving it a darker appearance. Streaks on each individual scale consist of four to six longitudinal thin stripes of auburn piugment with smudges of auburn between them. Forelimb and hind limb scales are darker shade of brown. Forelimb scales have weakly defined scale boundaries. Precloacal scales have slightly lighter coloration than surrounding ventral scales. Head scales have mottled light and dark brown coloration that match dorsal body scales. The rostral, nasal, supranasal, and first supralabial scales have cream coloration slightly lighter than supraocular scales. Supraocular scales and other supralabial scales possses a ligher 252 gray-umber coloration. Supralabial, infralabial, postmental, chin shields are beige with slight light brown mottling. Coloration in life.—(Fig. 4.7). Coloration in life closely matches the coloration in preservative with minor differences, including a dark brown body color and dark brown to black streaks of pigmentation. Variation.—Morphometric variation of the series is summarized in Table 4.6. We observed a single instance of digit variation, where one specimen (KU 311225) has two hind limb digits. The pineal eyespot was observed to be absent in a single specimen (CAS 26120), and present in all other examined specimens. The number of infralabials was observed to vary among examined specimens: more than half of the specimens possess six infralabials six (CAS-SU 26110, 26112, 26123, 26772, 26120, 26771, KU 311224–8), and five specimens possess five infralabials (CAS-SU 26121–2, 26770, 26773, KU 311229). Five specimens were observed with enlarged mental scales resulting from fusion with the 1st infralabial (CAS-SU 26121–2, 26770, 26773, KU 311229). Additionally, all specimens have two loreals with the exception of four specimens, which have single, enlarged loreals on both sides of the head (KU 311227) or on only the left side of the head (KU 311224–5, 311229). Distribution.—Brachymeles isa is known only from Leyte Island (Fig. 4.3). Ecology and natural history.—Brachymeles isa occurs in agricultural habitats, as well as in disturbed and secondary-growth forest. Little original, forest remains on Leyte Island, but we assume the species once also occurred in first growth forest at low elevations. Individuals have been observed in the rotting material within fallen logs, and leaf litter surrounding the root networks of trees. Similar to B. samarensis, this species is found in sympatry with B. orientalis and B. gracilis hilong. 253 Other lizard species observed in sympatry on Leyte Island include: (Agamidae) Bronchocela cristatella, Draco bimaculatus, D. ornatus, D. reticulates, Gonocephalus semperi, Hydrosaurus pustulatus; (Gekkonidae) Cyrtodactylus annulatus, C. gubaot, Gehyra mutilata, Gekko gecko, G. mindorensis, Hemidactylus frenatus, H. platyurus, Hemiphyllodactylus typus, Lepidodactylus aureolineatus, L. planicaudus, Pseudogekko compressicorpus; (Scincidae), Emoia atrocostata, Eutropis multicarinata, E. multifasciata, Lamprolepis smaragdina, Lipinia pulchella, L. quadrivittata, Sphenomorphus acutus, S. cumingi, S. fasciatus, S. jagori, S. cf. mindanensis, S. steerei, S. variagatus, Tropidophorus misaminus; (Varanidae) Varanus cumingi samarensis. Etymology.—CDS is pleased to name this new species in honor of the Philippine-American Education Foundation (PAEF), in honor of their continued support and contributions to this research. As the Fulbright Commission in the Philippines, PAEF is responsible for leading the advancement of international exchange programs between the United States and the Philippines, with the mission of promoting mutual understanding between citizens of both countries. Suggested common name: The PAEF Slender Skink. Brachymeles dalawa sp. nov. Figs. 4.3, 4.6, 4.8 Holotype.—PNM 9749 (CDS Field No. 3700, formerly KU 320466), adult male, collected under rotting coconut husks in secondary-growth forest (10:00–12:30 hr) on 21 March 2009, in Barangay Villa Milagrosa, Municipality of President Carlos P. Garcia, Bohol Province, Bohol Island, Philippines (10°07'16" N, 124°34'30" E; WGS-84), by CDS and J. Fernandez. Paratopotypes.—Nine adult males (KU 320435, 320444–6, 320451, 320462, 320466, PNM 9754–55), 21 adult females (KU 320428–30, 320438–40, 320442, 320447, 320449–50, 320452– 254 5, 320457–61, 320463, 320467), and 10 juveniles (KU 320436–7, 320441, 320443, 320448, 320456, PNM 9750–53) collected between 19 and 21 March 2009. Paratypes.—One adult male (CAS-SU 28453) collected on 11 April 1967, under rotting coconut tree, 0.5 km SW of Barrio Pitogo, in the Municipality of Ubay, Bohol Province, Lapinig Grande Island, Philippines (10°07'05" N, 124°33'04" E; WGS-84), by A. C. Alcala; one adult female (CAS-SU 27554) collected on 15 April 1967, under rotting log in secondary-growth forest, in the Municipality of Ubay, Bohol Province, Polong Dako Island, Philippines (10°04'11" N, 124°30'14" E; WGS-84), by A. C. Alcala; three adult females (CAS-SU 27556, 28454–5) collected on 20 April 1967, under rotting logs and leaves in a patch of secondary-growth trees, in the Municipality of Ubay, Bohol Province, Lapinig Chico Island, Philippines (10°05'22" N, 124°30'32" E; WGS-84), by A. C. Alcala. Diagnosis.—Brachymeles dalawa can be distinguished from congeners by the following combination of characters: (1) body size small (SVL 52.7–66.1 mm); (2) limbs tridactyl; (3) limb length small; (4) supralabials six; (5) infralabials five; (6) suparciliaries six; (7) supraoculars five; (8) midbody scale rows 22–23; (9) axilla–groin scale rows 72–75; (10) paravertebral scale rows 90–92; (11) pineal eye spot present; (12) frontoparietals contact; (13) enlarged chin shields in three pairs; (14) nuchal scales differentiated; (15) fourth and fifth supralabial below eye; (16) auricular opening covered with scales; (17) presacral vertebrae 47; (18) fusion of mental and first infralabials; and (19) non-uniform body color (Tables 4.4, 4.5). Comparisons.—Characters distinguishing Brachymeles dalawa from all non-pentadactyl, limbed species of Brachymeles are summarized in Tables 4.4 and 4.5. Brachymeles dalawa most closely resembles B. isa, B. muntingkamay, and B. tridactylus, the only other tridactyl species, but differs from these three taxa by having five infralabials, and fusion of the mental and first 255 infralabials (Table 4.5). Brachymeles dalawa further differs from B. isa by having shorter body sizes among males, shorter relative fore-limb lengths, fewer paravertebral scale rows, and a non-uniform body color (Tables 4.4, 4.5); from B. muntingkamay by having a shorter maximum body length, shorter fore-limb lengths, shorter hind limb lengths, a greater number of axilla–groin scale rows, six supraciliaries, five supraoculars, the presence of a pineal eyespot, the presence of contact between frontoparietals, the presence of differentiated nuchals, the presence of a continuous subocular scale row, and the absence of longitudinal rows of spots around the body (Tables 4.4, 4.5); and from B. tridactylus by having a shorter maximum body length, shorter relative tail length, shorter fore-limb length, shorter hind limb lenths, a greater number of presacral vertebrae, six supralabials, five infralabials, six supraciliaries, five supraoculars, the presence of contact between frontoparietals, the presence of a continuous subocular scale row, and the absence of longitudinal rows of spots around the body (Tables 4.4, 4.5). Brachymeles dalawa can be distinguished from all limbless species of Brachymeles (B. apus, B. lukbani, B. minimus, B. miriamae, B. vermis) by having limbs; and from all pentadactyl species of Brachymeles (B. boholensis, B. boulengeri, B. bicolor, B. gracilis, B. kadwa, B. makusog, B. mindorensis, B. orientalis, B. schadenbergi, B. talinis, B. taylori, B. tungaoi, B. vindumi) by having non-pentadactyl (vs. pentadactyl) limbs, shorter fore-limb lengths (less than 1.8 mm vs. greater than 5.9 mm), shorter hind limb lengths (less than 2.7 mm vs. greater than 10.3 mm), a narrower body (less than 5.9 mm vs. greater than 7.9 mm), and by the absence of a postnasal scale and auricular opening (vs. presence). Description of holotype.—Details of the head scalation are shown in Figure 4.7. Adult male, hemipenes everted; body small, slender, SVL 56.3 mm; head weakly differentiated from neck, nearly as wide as body, HW 6.5% SVL, 112.7% HL; HL 31.5% SnFa; SnFa 20.9% SVL; snout 256 short, bluntly rounded in dorsal and lateral profile, SNL 65.0% HL; ear completely hidden by scales; eyes small, ED 1.8% SVL, 28.0% HL, 60.8% END, pupil subcircular; body slightly depressed, nearly uniform in thickness, MBW 120.3% MBH; scales smooth, glossy, imbricate; longitudinal scale rows at midbody 22; paravertebral scale rows 90; axilla–groin scale rows 73; limbs short, poorly developed, with digits reduced to three claws on both fore-limbs and hind limbs, finger and toe lamellae absent; FLL 3.3% AGD, 2.5% SVL; HLL 5.3% AGD, 3.9% SVL; tail not as wide as body, gradually tapered towards end, TW 81.5% MBW, TL 83.6% SVL. Rostral projecting onto dorsal snout to point in line with posterior edge of nasal, broader than high, in contact with frontonasal; frontonasal wider than long; nostril ovoid, in center of single trapezoidal nasal, longer axis directed anteroventrally and posterodorsally; supranasals present, large, broadly separated; postnasals absent; prefrontals moderately separated; frontal nearly diamond-shaped, its anterior margin in moderate contact with frontonasal, in contact with first two anterior supraoculars, 4× wider than anterior supraocular; supraoculars five; frontoparietals moderate, in moderate medial contact, each frontoparietal in contact with interior two supraoculars; interparietal moderate, its length roughly equal to midline length of frontoparietal, longer than wide, kite-shaped, wider anteriorly; parietals as broad as frontoparietals, in moderate contact behind interparietal; enlarged nuchals present; two loreals, decreasing in size from anterior to posterior, anterior loreal about as long as and slightly higher than posterior loreal; one preocular; one presubocular; supraciliaries six, the anteriormost contacting prefrontal and separating posterior loreal from first supraocular, posteriomost extending to middle of fifth supraocular; single subocular scale row complete, in contact with supralabials; lower eyelid with one row of scales; supralabials six, first 2× size of other supralabials, third, fourth, and fifth below eye; infralabials five (Fig. 4.6). 257 Mental wider than long, fused with first infralabials on both sides; postmental single, enlarged, its width greater than width of mental; followed by three pairs of enlarged chin shields, first pair in broad medial contact, equal in width to third pair, second pair wider than first and third, separated by single medial scale, third pair separated by three medial scales (Fig. 4.6). Scales on limbs smaller than body scales; scales on dorsal surfaces of digits wrapping around lateral edges of digits; lamellae absent; palmar surfaces of hands and plantar surfaces of feet with several small, irregular scales, each with irregular raised anterior edges; fore-limb digits equal in size; hind limb digits unequal in size, middle digit greatest in length, first and third digits equal in length. Coloration in preservative.—The ground color of the body is dark brown, with each dorsal scale having a dark, chocolate-brown streak on the anterior one third to one half of the scale with cream posterior. Posterior edge of all body scales transparent. The streaks are present around the entire body. Beige coloration on scales more dominant on ventral scales. Caudals and subcaudals have less beige coloration on scales, giving appearance of a darker tail color. Streaks on each individual scale consist of four to seven longitudinal thin stripes of chocolate-brown pigment, with smudges of brown between each. Forelimb scales are the same color as surrounding body scales. Hind limb scales are dark brown and slightly darker than surrounding body scales. Precloacal scales match surrounding ventral scales. Head scales have mottled light and dark brown coloration and match the body color. The rostral, nasal, supranasal and first supralabial scales have a light gray coloration. Supraocular scales and other supralabial scales possess the darkest brown coloration of all head scales with umber brown color. The mental scale is cream. The chin shields and postmental scale match the bordering ventral scales. 258 Coloration in life.—(Fig. 4.8). Coloration in life closely matches the coloration in preservative with minor differences. Head scales are mottled medium brown to dark brown or black. The ground color of the body is medium to dark brown. The streaks of pigmentation on each scale are dark brown to black. Variation.—Morphometric variation of the series is summarized in Table 4.6. We observed variation in the degree of head scale contact: (1) prefrontals were observed in point contact medially in seven specimens (KU 320444, 320449, 320458–60, 320462, 320465), and separated for the remaining examined specimens (CAS-SU 27554, 27556, 28453–5, KU 320428–43, 320445–8, 320450–57, 320461, 320463–4, 320466–7); (2) frontoparietals were observed in point contact for a single specimen (KU 320467), and separated for the remaining examined specimens (CAS-SU 27554, 27556, 28453–5, KU 320428–66); (3) first pair of enlarged chin shiels were observed separated in a single specimen (KU 320451), and in contact medially for the remaining examined specimens (CAS-SU 27554, 27556, 28453–5, KU 320428–50, 320452–67). Additionally, the degree of fusion between loreals was observed to vary among the type series. The majority of specimens examined have two loreals and no fused scales (CAS-SU 27554, 27556, 28453–55, KU 320431–7, 320439–42, 320445–46, 320448, 320450–51, 320455, 320457–60, 320462, 320464, 320466), five specimens have single, enlarged loreals on both sides of the head (KU 320444, 320449, 320452, 320456, 320467), five specimens have single, enlarged loreals on the left side of the head (KU 320430, 320453–54, 320463, 320465), and six specimens have single, enlarged loreals on the right side of the head (KU 320428–29, 320438, 320443, 320447, 320461). Distribution.—Brachymeles dalawa is known from Lapinig Chico, Lapinig Grande, Tilmubo, and Tintiman islands off the northeast coast of Bohol Island (Fig. 4.3). 259 Ecology and natural history.—Brachymeles dalawa occurs in agricultural habitats, and disturbed forest habitat. No original forest remains on any of the Lapinig Group Islands, and common habitat consists of grassland, rice fields, agricultural habitats, and human habitations. Surprisingly, B. dalawa on Lapinig Grande Island was observed to be the more common than any other known species of Brachymeles. Individuals were regularly observed under piles of rotting cocounuts, in loose soil around trees and root systems, and in loose leaf litter. Interestingly, this species seems to be a ubiquitous habitat generalist on the Lapinig Group Islands, but has not been recorded from the nearby island of Bohol, whereas its congeners, B. orientalis and B. boholensis, are known. It remains possible that populations of this species will eventually be discovered on the northeast coast of Bohol Island. Sympatric lizard species observed in the Lapinig Group islands include: (Gekkonidae) Hemidactylus frenatus and H. platyurus. Etymology.—We are pleased to name this new species in honor of Carlos Polestico Garcia. Born on Bohol Island, Carlos P. Garcia later became the 8th President of the Philippines. He was the first Philippine president to be laid to rest in the Libingan ng mga Bayani, or Cemetary of the Heroes, located within Fort Bonifacio in Manila, Philippines. The municipality of Carlos P. Garcia, and type locality for Brachymeles dalawa, was named after this Philippine hero. The word “dalawa” is derived from the phrase Libingan ng mga Bayani. Suggested common name: Lapinig Islands’ Slender Skink. 260 Table 4.4. Summary of meristic and mensural characters in all known limbed, non-pentadactyl species of Brachymeles. Sample size, body length and total length among males and females, and general geographical distribution (PAIC = Pleistocene Aggregate Island Complexes, sensu Brown and Diesmos, 2002) are included for reference (SVL, TotL, MBW, FLL, and HLL given as range over mean ± standard deviation; all body proportions given as percentage over mean ± standard deviation). In cases of scale count variation within species, numbers of individuals showing specific counts are given in parentheses. 261 sa m ar en sis (1 m , 5 f) isa (3 m , 9 f) da la wa (1 0 m , 2 5 f) lim a (6 m , 1 0 f) ap at (9 f) ta tlo (1 m , 2 f) Ra ng e Sa m ar Is la nd Le yt e P A IC La pin ig Gro up Is la nd s Ce nt ra l B ico l P en in su la Ca ta nd ua ne s I sla nd So ut her n Bi col P en in su la SV L (f) SV L (m ) 62 .4 –6 6. 1 (6 3. 4 ± 1. 5) 57 .9 47 .2 –6 1. 4 (5 6. 5 ± 4. 2) 62 .4 –6 6. 1 (6 3. 4 ± 1. 5) 52 .8 –6 6. 1 (5 8. 6 ± 3. 3) 52 .7 –5 7. 4 (5 6. 0 ± 1. 6) 46 .4 –6 7. 4 (5 9. 0 ± 6. 7) 56 .4 –6 6. 1 (6 1. 7 ± 3. 5) 54 .0 –6 4. 4 (5 8. 7 ± 3. 5) — 54 .0 , 6 0. 0 56 .8 To tL (f ) To tL (m ) 97 .7 –1 12 .9 (1 07 .3 ± 8 .3 ) 93 .0 99 .5 –1 08 .5 (1 02 .6 ± 5 .1 ) 10 6. 7– 11 4. 6 (1 10 .6 ± 5 .6 ) 91 .4 –1 11 .2 (1 02 .2 ± 6 .4 ) 92 .1 –1 03 .4 (9 9. 4 ± 4. 5) 94 .1 –1 12 .7 (1 02 .1 ± 8 .8 ) 99 .6 –1 07 .9 (1 04 .1 ± 4 .2 ) 10 2. 2– 10 9. 4 (1 06 .2 ± 2 .7 ) — 92 .3 , 9 5. 2 10 2. 0 TL /S V L 57 –8 1 (6 8 ± 12 ) 69 –7 9 (7 5 ± 4) 63 –8 4 (7 7 ± 6) 58 –9 3 (7 5 ± 12 ) 76 –9 6 (8 8 ± 8) 59 –8 0 (7 0 ± 11 ) FL L 1. 1– 2. 6 (1 .8 ± 0 .5 ) 1. 3– 1. 7 (1 .5 ± 0 .1 ) 1. 1– 1. 8 (1 .3 ± 0 .2 ) 1. 1– 1. 9 (1 .4 ± 0 .3 ) 1. 4– 2. 1 (1 .7 ± 0 .2 ) 1. 1– 1. 5 (1 .5 ± 0 .2 ) FL L/ SV L 2– 4 (3 ± 1 ) 2– 4 (3 ± 0 ) 2– 3 (2 ± 0 ) 2– 4 (2 ± 0 ) 3 (3 ± 0 ) 2– 3 (3 ± 0 ) H LL 2. 5– 3. 1 (2 .9 ± 0 .2 ) 2. 3– 3. 0 (2 .6 ± 0 .3 ) 2. 0– 2. 7 (2 .4 ± 0 .2 ) 1. 9– 3. 1 (2 .6 ± 0 .3 ) 2. 5– 3. 6 (3 .0 ± 0 .3 ) 2. 1– 2 .7 (2 .5 ± 0 .3 ) H LL /S V L 4– 5 (5 ± 0 ) 4– 5 (4 ± 0 ) 3– 5 (4 ± 0 ) 3– 5 (4 ± 1 ) 4– 6 (5 ± 1 ) 4– 5 (4 ± 0 ) To eI V la m 0 0 0 0 0 0 262 T A B L E 4 .4 .— C on tin ue d. m un tin gk am ay (1 2 f) tr id ac ty lu s (9 m , 1 1 f) bo ni ta e (6 m , 7 f) ce bu en si s (8 f) el er ae (2 m , 1 f) pa th fin de ri (1 4 m , 2 3 f) wri gh ti (1 m , 1 f) Ran ge Lu zon Isl an d Visa ya n PA IC M in do ro & L uzo n PA ICs Ceb u Isla nd Lu zon Isl an d M in da na o Isla nd Lu zon Isl an d SVL (f) SVL (m ) 61 .8 –8 1. 3 (7 3. 6 ± 5. 9) N/A 45 .5 –5 9. 1 (5 2. 1 ± 5. 0) 55 .7 –7 8. 3 (6 8. 5 ± 7. 4) 49 .7 –5 9. 8 (5 6. 4 ± 3. 9) 65 .1 –8 0. 0 (7 3. 5 ± 6. 4) 51 .5 –6 7. 9 (6 1. 8 ± 5. 3) N/A 68 .2 , 7 1. 9 71 .5 55 .8 –6 8. 3 (6 2. 0 ± 3. 4) 54 .5 –6 5. 1 (5 9. 4 ± 3. 8) 11 3. 0 12 5. 8 Tot L (f) Tot L (m ) 10 7. 4– 13 6. 0 (1 24 .0 ± 8 .6 ) N/A 10 2. 6– 15 4. 1 (1 32 .6 ± 1 4. 0) 10 5. 3– 13 3. 67 (1 15 .9 ± 1 5. 4) 93 .4 –1 50 .4 (1 26 .7 ± 1 9. 9) 10 2. 6– 14 4. 5 (1 21 .3 ± 1 5. 6) 10 4. 3– 12 8. 0 (1 19 .0 ± 8 .5 ) N/A 10 9. 9, 13 1. 9 N/A 11 1. 1– 13 3. 2 (1 19 .7 ± 8 .2 ) 10 1. 4– 10 7. 0 (1 04 .2 ± 4 .0 ) 20 5. 6 21 6. 4 TL/S VL 50 –7 9 (6 5 ± 10 ) 69 –1 12 (9 2 ± 12 ) 35 –9 3 (6 9 ± 18 ) 78 –1 15 (9 2 ± 13 ) 61 –8 4 (7 2 ± 16 ) 69 –9 5 (8 4 ± 10 ) 72 , 8 2 FL L 2. 4– 3. 0 (2 .7 ± 0 .2 ) 1. 5– 2. 5 (2 .0 ± 0 .3 ) 1. 0– 1. 5 (1 .3 ± 0 .1 ) 1. 1– 1. 8 (1 .5 ± 0 .3 ) 3. 3– 3. 5 (3 .4 ± 0 .1 ) 4. 4– 6. 9 (5 .8 ± 0 .5 ) 7. 5, 7. 5 FL L/S VL 3– 4 (4 ± 0 ) 2– 3 (3 ± 0 ) 1– 2 (2 ± 0 ) 2– 3 (2 ± 0 ) 5– 5 (5 ± 0 ) 8– 11 (1 0 ± 1) 6, 7 H LL 5. 3– 6. 0 (5 .7 ± 0 .2 ) 2. 6– 3. 6 (3 .1 ± 0 .3 ) 1. 3– 2. 0 (1 .6 ± 0 .2 ) 2. 3– 3. 0 (2 .7 ± 0 .3 ) 4. 3– 5. 4 (5 .0 ± 0 .6 ) 8. 4– 12 .9 (1 0. 8 ± 1. 0) 10 .9 , 1 3. 9 H LL /SVL 7– 9 (8 ± 1 ) 3– 6 (5 ± 1 ) 2– 3 (2 ± 0 ) 3– 5 (4 ± 0 ) 6– 8 (7 ± 1 ) 15 –2 1 (1 8 ± 1) 10 , 1 1 Toe IVla m 0 0 0 0 3 5– 8 4, 5 263 Table 4.5. Summary of qualitative diagnostic characters (present, absent) in all known limbed, non-pentadactyl species of Brachymeles. The pairs of enlarged scales posterior to the postmental scale are abbreviated as chin shield pairs with reference to the 1st, 2nd, and 3rd pairs (when present). 264 sa m ar en si s (1 m , 5 f ) is a (3 m , 9 f ) da la w a (1 0 m , 2 5 f) li m a (6 m , 1 0 f) ap at (9 f ) ta tl o ( 1 m , 2 f ) N um be r of d ig it s (f or e/ hi nd ) 2/ 2 3/ 3 3/ 3 2/ 2 2/ 2 2/ 2 P S V 45 47 47 46 –4 9 45 47 –4 8 M B S R 19 –2 2 21 –2 2 22 –2 3 20 –2 2 21 –2 2 20 A G S R 66 –6 9 71 –7 4 72 –7 5 68 –7 3 68 –7 2 73 –7 7 P V S R 86 –8 8 93 –9 6 90 –9 2 85 –9 0 85 –8 9 90 –9 4 S L 6 (6 ) 6 (1 2) 6 (3 5) 6 (1 6) 6 (9 ) 6 (3 ) IF L 6 (6 ) 5 (4 ) 6 (8 ) 5 (3 5) 5 (1 1) 6 (5 ) 6 (9 ) 6 (3 ) S C 6 (6 ) 6 (1 2) 6 (3 5) 6 (1 6) 6 (9 ) 6 (3 ) S O 5 (6 ) 5 (1 2) 5 (3 5) 5 (1 6) 5 (9 ) 5 (3 ) P in ea l e ye sp ot P re se nt P re se nt P re se nt P re se nt P re se nt P re se nt P re fr on ta l c on ta ct A bs en t A bs en t P oi nt c on ta ct o r A bs en t A bs en t A bs en t A bs en t F ro nt op ar ie ta l c on ta ct P re se nt P re se nt P re se nt P re se nt o r A bs en t P re se nt P re se nt 1s t c hi n sh ie ld p ai r co nt ac t P re se nt P re se nt o r A bs en t P re se nt o r A bs en t P re se nt o r A bs en t P re se nt A bs en t 3r d ch in s hi el d pa ir P re se nt P re se nt P re se nt P re se nt P re se nt P re se nt C hi n sh ie ld p ai r si ze 3 < 1 ! 2 3 < 1 ! 2 3 < 1 < 2 3 < 1 < 2 3 < 1 ! 2 3 < 1 < 2 C hi n sh ie ld p ai r se pa ra ti on 1 1( 0) ; 2 (1 ); 3 (3 ) 1( 0/ 1) ; 2 (1 ); 3 (3 ) 1( 0/ 1) ; 2 (1 ); 3 (3 ) 1( 0/ 1) ; 2 (1 ); 3 (3 ) 1( 0) ; 2 (1 ); 3 (3 ) 1( 0) ; 2 (1 ); 3 (3 ) 1s t /2 nd lo re al f us io n P re se nt o r A bs en t P re se nt o r A bs en t P re se nt o r A bs en t P re se nt o r A bs en t A bs en t A bs en t M en ta l/ 1s t I F L f us io n A bs en t P re se nt o r A bs en t P re se nt P re se nt o r A bs en t A bs en t A bs en t D if fe re nt ia te d nu ch al s P re se nt P re se nt P re se nt P re se nt P re se nt P re se nt C on ti nu ou s su bo cu la r sc al e ro w P re se nt P re se nt P re se nt P re se nt P re se nt P re se nt A ur ic ul ar o pe ni ng A bs en t A bs en t A bs en t A bs en t A bs en t A bs en t D or so la te ra l s tr ip es A bs en t A bs en t A bs en t A bs en t A bs en t A bs en t L on gi tu di na l r ow s of d ar k sp ot s A bs en t A bs en t A bs en t A bs en t A bs en t A bs en t 1 P ar en th es es s ho w th e nu m be r of s m al l v en tr al s ca le r ow s se pa ra ti ng e ac h en la rg ed p ai r of c hi n sh ie ld s. 265 T A B L E 4 .5 .— C on tin ue d. m un tin gk am ay (1 2 f) tr id ac ty lu s (9 m , 1 1 f) bo ni ta e (6 m , 7 f) ce bu en si s (8 f) el er ae (2 m , 1 f) pa th fin de ri (1 4 m , 2 3 f) w ri gh ti (1 m , 1 f) N um be r o f d ig its (fo re /h in d) 3/ 3 3/ 3 0– 2/ 0– 2 3/ 2 4/ 4 5/ 4 4/ 4 PS V 42 , 4 4 47 47 –5 7 45 43 34 — M BS R 22 –2 4 22 –2 4 21 –2 3 22 –2 4 22 –2 4 23 –2 5 28 , 2 8 A G SR 65 –7 0 70 –7 9 73 –9 0 65 –6 9 63 –6 7 44 –4 8 85 , 8 5 PV SR 85 –9 0 88 –9 8 90 –1 09 84 –8 8 84 –8 7 64 –6 7 10 6, 1 08 SL 6 (1 2) 6 (1 2) 7 (8 ) 6 (1 2) 7 (1 ) 6 (8 ) 6 (3 ) 6 (3 7) 6 (1 ) 7 (1 ) IF L 6 (1 2) 6 (1 2) 7 (8 ) 5 (1 ) 6 (1 0) 7 (2 ) 6 (5 ) 7 (3 ) 6 (3 ) 6 (3 7) 7 (2 ) SC 6 (1 0) 7 (2 ) 5 (2 0) 5 (1 2) 6 (1 ) 6 (8 ) 5 (2 ) 6 (1 ) 5 (1 7) 6 (1 9) 6 SO 5 (1 1) 6 (1 ) 4 (2 0) 4 (1 3) 5 (8 ) 4 (2 ) 5( 1) 5 (3 7) 5 Pi ne al e ye sp ot A bs en t Pr es en t Pr es en t Pr es en t A bs en t Pr es en t Pr es en t Pr ef ro nt al c on ta ct Pr es en t A bs en t A bs en t Pr es en t o r A bs en t Pr es en t A bs en t Pr es en t o r A bs en t Fr on to pa rie ta l c on ta ct A bs en t A bs en t A bs en t Pr es en t Pr es en t Pr es en t o r A bs en t Pr es en t 1s t c hi n sh ie ld p ai r c on ta ct A bs en t Pr es en t o r A bs en t A bs en t Pr es en t A bs en t A bs en t A bs en t 3r d c hi n sh ie ld p ai r Pr es en t Pr es en t Pr es en t Pr es en t Pr es en t A bs en t Pr es en t Ch in sh ie ld p ai r s iz e 3 < 1 < 2 3 < 1 < 2 3 < 2 < 1 1 = 3 < 2 1 < 3 < 2 1 < 2 2 < 1 Ch in sh ie ld p ai r s ep ar at io n1 1( 1) ; 2 (1 ); 3( 3) 1( 0/ 1) ; 2 (1 ); 3( 3) 1( 1) ; 2 (1 ); 3( 3) 1( 0) ; 2 (1 ); 3( 3) 1( 1) ; 2 (1 ); 3( 3) 1( 1) ; 2 (1 ) 1( 1) ; 2 (3 ) 1s t /2 nd lo re al fu sio n A bs en t A bs en t A bs en t A bs en t A bs en t A bs en t A bs en t M en ta l/1 st IF L fu sio n A bs en t A bs en t Pr es en t o r A bs en t A bs en t A bs en t A bs en t A bs en t D iff er en tia te d nu ch al s A bs en t Pr es en t Pr es en t Pr es en t A bs en t A bs en t Pr es en t2 Co nt in uo us su bo cu la r s ca le ro w A bs en t A bs en t Pr es en t Pr es en t Pr es en t Pr es en t Pr es en t A ur ic ul ar o pe ni ng A bs en t A bs en t A bs en t A bs en t A bs en t Pr es en t A bs en t D or so la te ra l s tri pe s A bs en t A bs en t A bs en t A bs en t A bs en t Pr es en t A bs en t Lo ng itu di na l r ow s o f d ar k sp ot s Pr es en t, ar ou nd b od y Pr es en t, va gu e to in di sti nc t A bs en t A bs en t Pr es en t, ar ou nd bo dy Pr es en t, 6 Pr es en t 1 P ar en th es es sh ow th e nu m be r o f s m al l v en tra l s ca le ro w s s ep ar at in g ea ch e nl ar ge d pa ir of c hi n sh ie ld s. 2 D ue to h ea d da m ag e in th e nu ch al re gi on fo r b ot h kn ow n sp ec im en s o f B . w ri gh ti, th e pr es en ce o f d iff er en tia te d nu ch al s r em ai ns te nt at iv e. 266 Table 4.6. Summary of univariate morphological variation among mensural characters in series of Brachymeles samarensis, B. isa, B. dalawa, B. lima, B. apat, and B. tatlo. samarensis (1 m; 5 f) isa (3 m; 9 f) dalawa (10 m; 25 f) lima (6 m; 10 f) apat (9 f) tatlo (1 m; 2 f) SVL (m) 57.9 59.7–64.1 (61.8 ± 2.2) 52.7–57.4 (56.0 ± 1.6) 56.4–66.1 (61.7 ± 3.5) — 56.8 SVL (f) 62.4–66.1 (63.4 ± 1.5) 47.2–61.4 (56.5 ± 4.2) 52.8–66.1 (58.6 ± 3.3) 46.4–67.4 (59.0 ± 6.7) 54.0–64.4 (58.7 ± 3.5) 54.0, 60.0 AGD (m) 40.3 44.1–48.2 (46.0 ± 2.1) 39.5–43.6 (42.1 ± 1.2) 42.9–52.0 (47.4 ± 3.4) — 43.8 AGD (f) 45.3–50.3 (47.6 ± 1.8) 35.6–46.5 (43.2 ± 3.1) 39.4–50.6 (44.7 ± 2.8) 32.9–52.3 (44.8 ± 5.8) 41.0–49.1 (44.6 ± 2.3) 45.5, 45.8 TotL (m) 93.0 106.7–114.6 (110.6 ± 5.6) 92.1–103.4 (99.4 ± 4.5) 99.6–107.9 (104.1 ± 4.2) — 102.0 TotL (f) 97.7–112.9 (107.3 ± 99.5–108.5 (102.7 ± 91.4–111.2 94.1–112.7 102.2–109.4 92.3, 95.2 267 8.3) 5.1) (102.2 ± 6.4) (102.1 ± 8.8) (106.2 ± 2.7) MBW (m) 5.7 5.0–5.3 (5.1 ± 0.2) 4.0–4.7 (4.4 ± 0.3) 4.2–5.1 (4.5 ± 0.3) — 4.0 MBW (f) 5.2–6.4 (5.7 ± 0.5) 3.7–5.0 (4.2 ± 0.4) 3.4–5.9 (4.5 ± 0.6) 3.8–4.8 (4.4 ± 0.3) 4.2–5.4 (4.8 ± 0.4) 3.2, 4.8 MBH (m) 4.0 2.9–4.5 (3.8 ± 0.8) 3.2–4.7 (3.6 ± 0.5) 3.0–5.1 (3.6 ± 0.8) — 3.2 MBH (f) 4.3–4.8 (4.5 ± 0.2) 3.0–4.7 (3.9 ± 0.5) 2.9–5.3 (3.7 ± 0.8) 2.9–5.0 (3.7 ± 0.8) 3.4–4.4 (3.8 ± 0.4) 2.5, 4.3 TL (m) 35.1 45.0–50.5 (47.8 ± 3.9) 39.3–47.1 (43.6 ± 3.4) 38.7–51.5 (43.2 ± 7.2) — 45.2 TL (f) 35.3–50.4 (44.5 ± 8.1) 41.0–47.1 (43.9 ± 3.1) 38.3–50.1 (44.2 ± 4.1) 32.3–52.1 (42.5 ± 7.4) 45.6–53.5 (49.5 ± 3.1) 38.3, 35.2 TW (m) 4.1 3.8–4.1 (4.0 ± 0.2) 3.1–3.9 (3.4 ± 0.2) 3.4–4.3 (3.7 ± 0.3) — 3.7 TW (f) 4.1–4.6 (4.4 ± 0.2) 3.3–3.8 (3.4 ± 0.2) 2.8–4.6 (3.5 ± 0.5) 2.8–4.2 (3.5 ± 0.4) 3.6–4.5 (4.0 ± 0.3) 2.4, 3.6 TH (m) 3.5 3.2–3.4 (3.3 ± 0.1) 2.8–3.5 (3.1 ± 0.2) 2.6–3.6 (3.0 ± 0.4) — 2.6 TH (f) 3.5–3.9 2.9–3.4 2.5–4.5 2.3–3.4 2.7–3.9 2.3, 3.2 268 (3.8 ± 0.2) (3.1 ± 0.2) (3.1 ± 0.5) (2.8 ± 0.4) (3.1 ± 0.4) HL (m) 5.3 4.5–4.8 (4.6 ± 0.2) 3.7–4.7 (4.1 ± 0.4) 3.6–4.2 (3.8 ± 0.2) — 3.9 HL (f) 4.8–5.2 (5.0 ± 0.2) 3.5–4.4 (4.1 ± 0.3) 3.5–4.5 (4.0 ± 0.3) 3.5–5.3 (4.1 ± 0.6) 3.8–5.5 (4.3 ± 0.6) 3.1, 4.2 HW (m) 5.1 4.6–4.7 (4.6 ± 0.1) 3.9–4.6 (4.2 ± 0.2) 3.9–4.9 (4.2 ± 0.4) — 4.0 HW (f) 4.6–5.8 (5.2 ± 0.5) 3.8–4.6 (4.1 ± 0.2) 3.6–5.2 (4.2 ± 0.4) 3.7–5.4 (4.2 ± 0.5) 4.0–5.3 (4.4 ± 0.4) 3.5, 4.2 HH (m) 3.5 3.0–3.8 (3.4 ± 0.4) 2.7–3.1 (2.9 ± 0.2) 2.8–3.6 (3.0 ± 0.3) — 2.9 HH (f) 3.4–4.2 (3.9 ± 0.3) 2.9–3.4 (3.1 ± 0.2) 2.5–3.9 (3.0 ± 0.4) 2.5–3.9 (3.0 ± 0.5) 2.9–3.9 (3.3 ± 0.3) 2.5, 3.1 SnFa (m) 13.6 11.6–12.8 (12.0 ± 0.6) 10.9–12.2 (11.6 ± 0.4) 11.3–12.3 (11.8 ± 0.3) — 11.9 SnFa (f) 11.7–14.1 (12.9 ± 0.9) 10.1–11.9 (11.2 ± 0.6) 10.9–12.5 (11.6 ± 0.5) 10.6–13.0 (11.7 ± 0.8) 11.3–13.2 (11.8 ± 0.6) 11.5, 12.1 ED (m) 0.9 1.0–1.1 (1.0 ± 0.1) 1.0–1.1 (1.0 ± 0.0) 0.8–0.9 (0.9 ± 0.0) — 0.9 ED (f) 0.8–1.0 (0.9 ± 0.1) 0.8–1.1 (1.0 ± 0.1) 0.9–1.1 (1.0 ± 0.1) 0.8–0.9 (0.9 ± 0.1) 0.9–1.1 (1.0 ± 0.1) 1.0, 1.0 269 END (m) 1.9 1.1–1.7 (1.5 ± 0.3) 1.5–1.9 (1.7 ± 0.1) 1.6–1.9 (1.7 ± 0.1) — 1.6 END (f) 1.8–2.2 (1.9 ± 0.1) 1.6–1.8 (1.7 ± 0.1) 1.5–1.9 (1.7 ± 0.1) 1.4–1.9 (1.7 ± 0.2) 1.6–1.9 (1.8 ± 0.1) 1.7, 1.9 SNL (m) 2.7 1.8–2.5 (2.2 ± 0.4) 2.1–2.5 (2.4 ± 0.1) 2.2–2.5 (2.4 ± 0.1) — 2.3 SNL (f) 2.6–2.9 (2.7 ± 0.1) 2.2–2.6 (2.3 ± 0.1) 2.2–2.6 (2.4 ± 0.1) 2.1–2.7 (2.4 ± 0.2) 2.3–2.6 (2.4 ± 0.1) 2.4, 2.6 IND (m) 1.4 1.2–1.4 (1.3 ± 0.1) 1.2–1.4 (1.3 ± 0.1) 1.1–1.5 (1.3 ± 0.1) — 1.1 IND (f) 1.1–1.4 (1.3 ± 0.1) 1.2–1.4 (1.3 ± 0.1) 1.1–1.5 (1.3 ± 0.1) 1.0–1.4 (1.3 ± 0.1) 1.1–1.5 (1.3 ± 0.1) 1.1, 1.3 FLL (m) 2.3 1.4–1.7 (1.6 ± 0.1) 1.1–1.5 (1.3 ± 0.1) 1.1–1.6 (1.3 ± 0.2) — 1.4 FLL (f) 1.1–2.6 (1.7 ± 0.5) 1.2–1.7 (1.4 ± 0.1) 1.1–1.8 (1.3 ± 0.2) 1.1–1.9 (1.5 ± 0.3) 1.4–2.1 (1.7 ± 0.2) 1.1, 1.5 HLL (m) 2.9 2.3–3.0 (2.6 ± 0.4) 2.1–2.4 (2.3 ± 0.1) 2.4–2.8 (2.6 ± 0.2) — 2.6 HLL (f) 2.5–3.1 (2.8 ± 0.2) 2.3–2.9 (2.6 ± 0.2) 2.0–2.7 (2.4 ± 0.2) 1.9–3.1 (2.7 ± 0.4) 2.5–3.6 (3.0 ± 0.3) 2.1, 2.7 270 Brachymeles lima sp. nov. Figs. 4.3, 4.5 Holotype.—PNM 9756 (CDS Field No. 4050, formerly KU 324003), adult male, collected under rotting coconut husks in secondary-growth forest (10:00–12:30 hr) on 1 June 2009, in Barangay Common, Municipality of Tabaco City, Albay Province, Luzon Island, Philippines (13°14' N, 123°38' E; WGS-84), by J. Fernandez. Paratopotypes.—Four adult males (KU 324015–6, PNM 9759–60), six adult females (KU 323087, 324005–7, 324009–10), and four juveniles (KU 324008, 324011, PNM 9757–58), collected between 1 and 23 June 2009. Paratypes.—One adult male (CAS 152025) and two adult females (CAS 140065, 152026) collected on 16 December 1991, in an Abaca plantation, Barangay Labnig, Municipality of Malinao, Albay Province, Luzon Island, Philippines (13°22'38" N, 123°40'59" E; WGS-84), by C. A. Ross; two adult females (CAS-SU 24173, 24413) collected between 26 March and 22 April 1961, on Mt. Isarog, Bario Curry, Municipality of Pili, Camarines Sur Province, Luzon Island, Philippines (13°38'35" N, 123°21'4" E; WGS-84), by D. S. Rabor. Diagnosis.—Brachymeles lima can be distinguished from congeners by the following combination of characters: (1) body size small (SVL 46.4–66.1 mm); (2) limbs bidactyl; (3) limb length small; (4) supralabials six; (5) infralabials five or six; (6) suparciliaries six; (7) supraoculars five; (8) midbody scale rows 20–22; (9) axilla–groin scale rows 68–73; (10) paravertebral scale rows 85–90; (11) pineal eye spot present; (12) prefrontals not contacting on midline; (13) postnasals absent; (14) enlarged chin shields in three pairs; (15) nuchals enlarged; (16) fourth and fifth supralabial below eye; (17) mental and first infralabials fused or separated; 271 (18) auricular opening absent; (19) presacral vertebrae 46–49; and (20) uniform body color (Tables 4.4, 4.5). Comparisons.—Characters distinguishing Brachymeles lima from all non-pentadactyl, limbed species of Brachymeles are summarized in Tables 4.4 and 4.5. Brachymeles lima most closely resembles B. samarensis, B. apat, B. tatlo, and populations of B. bonitae, the only other species to be bidactyl or have bidactyl populations. However, B. lima differs from these four taxa by having five or six infralabials (Table 4.5). Brachymeles lima further differs from B. samarensis, B. apat, B. tatlo by the presence or absence of mental and first infralabial fusion (Table 4.5); from B. samarensis by having a greater number of presacral vertebrae, and a tendancy towards a greater number of midbody, axilla–groin, and paravertebral scale rows (Table 4.5); from B. apat by having a smaller relative fore-limb length and a greater number of presacral vertebrae (Tables 4.4, 4.5); from B. tatlo by having a smaller relative fore-limb length, and a tendancy towards having fewer axilla–groin and paravertebral scale rows (Tables 4.4, 4.5); and from B. bonitae by having only bidactyl body forms, longer relative fore- and hind limb lengths, six supralabials, five or six infralabials, six supraciliaries, five supraoculars, and a tendancey towards fewer presacral vertebrae, axilla–groin, and paravertebral scale rows (Tables 4.4, 4.5). Brachymeles lima can be distinguished from all limbless species of Brachymeles (B. apus, B. lukbani, B. minimus, B. miriamae, B. vermis) by having limbs; and from all pentadactyl species of Brachymeles (B. boholensis, B. boulengeri, B. bicolor, B. gracilis, B. kadwa, B. makusog, B. mindorensis, B. orientalis, B. schadenbergi, B. talinis, B. taylori, B. tungaoi, B. vindumi) by having non-pentadactyl (vs. pentadactyl) limbs, shorter fore-limb lengths (less than 1.9 mm vs. greater than 5.9 mm), shorter hind limb lengths (less than 3.1 mm vs. greater than 10.3 mm), a 272 narrower body (less than 5.1 mm vs. greater than 7.9 mm), and by the absence of a postnasal scale and auricular opening (vs. presence). Description of holotype.—Details of the head scalation are shown in Figure 4.6. Adult male, body small, slender, SVL 60.2 mm; head weakly differentiated from neck, nearly as wide as body, HW 6.7% SVL, 104.9% HL; HL 33.1% SnFa; SnFa 19.3% SVL; snout short, bluntly rounded in dorsal and lateral profile, SNL 58.2% HL; ear completely hidden by scales; eyes small, ED 1.4% SVL, 22.6% HL, 55.4% END, pupil subcircular; body slightly depressed, nearly uniform in thickness, MBW 124.0% MBH; scales smooth, glossy, imbricate; longitudinal scale rows at midbody 22; paravertebral scale rows 85; axilla–groin scale rows 68; limbs short, poorly developed, with digits reduced to two claws on both fore-limbs and hind limbs, finger and toe lamellae absent; FLL 2.7% AGD, 2.1% SVL; HLL 6.1% AGD, 4.7% SVL [6.9]; tail nearly as wide as body, gradually tapered at end, TW 88.9% MBW, TL 65.6% SVL. Rostral projecting onto dorsal snout to point just past poasterior edge of nasal, broader than high, in broad contact with frontonasal; frontonasal wider than long; nostril ovoid, in center of single trapezoidal nasal, longer axis directed anteroventrally and posterodorsally; supranasals present, large, broadly separated; postnasals absent; prefrontals moderately separated; frontal octagonal, its anterior margin in moderate contact with frontonasal, in contact with first two anterior supraoculars, 5× wider than anterior supraocular; supraoculars five; frontoparietals moderate, just barely separated by anterior point of interparietal in contact with frontal, each frontoparietal in contact with interior three supraoculars; interparietal large, its length roughly 1.5× midline length of frontoparietal, longer than wide, diamond-shaped, wider anteriorly; parietals as broad as frontoparietals, in broad contact behind interparietal; enlarged nuchals present; anterior and posterior loreals fused into single, enlarged loreal (Fig. 4.5), or distinct; one 273 preocular; one presubocular; supraciliaries six, the anteriormost contacting prefrontal and separating posterior loreal from first supraocular, posteriomost extending to middle of fifth supraocular; single subocular scale row complete, in contact with supralabials; lower eyelid with one row of scales; supralabials six, first 1.5× size of other supralabials, third, fourth, and fifth below eye; infralabials five (Fig. 4.5). Mental wider than long, fused with first infralabials; postmental single, enlarged, its width less than width of mental; followed by three pairs of enlarged chin shields, first pair in broad medial contact, greater in width than third pair, narrower than second pair, second pair broadly separated by single medial scale, third pair separated by three medial scales (Fig. 4.5). Scales on limbs smaller than body scales; scales on dorsal surfaces of digits wrapping around lateral edges of digits; lamellae absent; palmar surfaces of hands and plantar surfaces of feet with several small, irregular scales, each with irregular raised anterior edges; fore-limb digits equal in size; hind limb digits unequal in size, second digit greatest in length. Coloration in preservative.—The ground color of the body is medium brown, with each dorsal scale having a dark, auburn streak on the anterior two thirds to one half of the scale with light brown posterior. Posterior edge of all body scales transparent. The streaks are present around the entire body. Ventral scales have more distinct, smaller streaks restricted to the anterior one-third to one half of scale. Ventral scales have sandy brown posterior coloration. Posterior portion of ventral caudal and subcaudal scales have lighter shade of sandy brown. Streaks on each individual scale consist of four to five longitudinal thin stripes of auburn pigment. Forelimb and hind limb scales are dark shade of brown with weakly defined scale boundaries. Auburn streaks are more dominant on precloacal scales, giving them a slightly darker appearance. Head scales have mottled light and dark brown coloration, matching dorsal 274 body scales. Supraocular scales possess the darkest brown coloration of all head scales with brown umber color. The rostral, nasal, supranasal, and first supralabial scales have a cream coloration, lacking any brown color. The mental, infralabial, postmental, and chin shield scales are cream with light brown mottling. Coloration in life.—Coloration in life is unrecorded; however, because Brachymeles specimens do not change significantly during preservation (CDS, RMB personal observation), we suspect that the preserved coloration and patterns are much like those in life. Variation.—Morphometric variation of the series is summarized in Table 4.6. A single instance of digit variation was observed, where one specimen (KU 324006) has three fore-limb claws and two hind limb claws. We observed variation in the degree of head scale contact and the number of infralabials: (1) frontoparietals were observed in point contact medially for a single specimen (KU 324003), in moderate to broad contact medially for eleven specimens (CAS-SU 24173, 24413, CAS 140065, KU 323087, 324006–8, 324011–3, 324018), and separated for eight specimens (CAS 152025–6, KU 324005, 324014–6, 324009–10); (2) parietals were observed in point contact medially for a single specimen (CAS-SU 24413), in moderate to broad contact medially for seventeen specimens (CAS-SU 24173, CAS 140065, CAS 152025–6, KU 323087, 324003, 324005–9, 324011, 324013–6, 234018), and separated for two specimens (KU 324010, 324012); (3) first pair of enlarged chin shiels were observed in point contact medially for a single specimen (CAS 152025), in moderate to broad contact medially for seventeen specimens (CAS-SU 24173, 24413, CAS 140065, 152026, KU 324003, 324005–13, 324016, 324018), and separated in three specimens (KU 324014–5, 323087); (4) the number of infralabials varied among the type series, with eight specimens observed to have six infralabials 275 (CAS-SU 24413, KU 324009–14, 324018), and twelve observed to have five infralabials (CAS-SU 24173, CAS 140065, 152025–6, KU 323087, 324003, 324005–8, 324015–6). Additionally, the degree of fusion between loreals, and between the mental and 1st infralabials, was observed to vary in the type series. All specimens examined have two loreals with the exception of a single specimen (KU 324003) with single, enlarged loreals on both sides of the head. Eleven specimens were observed with enlarged mental scales resulting from fusion with the 1st infralabial on both sides of the head (CAS-SU 24173, CAS 152025–6, KU 323087, 324003, 324005–8, 324015–6), a single specimen was observed with fused scales only on the right side of the head (CAS 140065), and eight specimens were observed to have distinct mentals and infralabials, with no scale fusion (CAS-SU 24413, KU 324009–14, 324018). Distribution.—Brachymeles lima is known only from the central Bicol Peninsula of Luzon Island (Fig. 4.3). Ecology and natural history.—Brachymeles lima occurs in agricultural habitats, as well as in disturbed and secondary-growth forest, and is found in sympatry with B. boulengeri and B. makusog. Three additional species of Brachymeles have also been recorded from the Bicol Peninsula of Luzon Island: B. kadwa, B. lukbani, and B. tatlo. Sympatric lizard species occurring in the Bicol Peninsula include: (Agamidae) Bronchocela cristatella, Draco spilopterus, Gonocephalus sophiae, Hydrosaurus pustulatus; (Gekkonidae) Cyrtodactylus philippinicus, Hemidactylus frenatus, H. platyurus, Gehyra mutilata, Gekko gecko, G. mindorensis, Luperosaurus cumingii, Pseudogekko smaragdina, P. compressicorpus; (Scincidae) Emoia atrocostata, Eutropis multicarinata borealis, E. multifasciata, Lamprolepis smaragdina, Lipinia pulchella pulchella, Sphenomorphus abdictus abdictus, S. decipiens, S. cumingi, Sphenomorphus jagori, S. laterimaculatus, S. leucospilos, S. steerei, Tropidophorus 276 grayi; (Varanidae) Varanus marmoratus, V. olivaceus. Etymology.—The specific epithet is chosen in reference to the biogeographically and culturally distinct Bicol Region of southern Luzon Island (Albay, Camarines Norte, Camarines Sur, Catanduanes and Sorsogon Provinces). Inhabited by peaceful and particularly hospitable Bicolanos, the unique peninsula is home to many dozens of endemic vertebrates, delicious local cuisine, unique linguistic stock, and rich cultural traditions. Suggested common name: Bicol Slender Skink. Brachymeles apat sp. nov. Figs. 4.3, 4.5 Holotype.—PNM 9761 (CDS Field No. 5255, formerly KU 324023), adult female, collected under rotting coconut husks in secondary-growth forest (10:00–12:30 hr) on 8 October 2009, in Barangay Palta Small, Municipality of Virac, Catanduanes Province, Catanduanes Island, Philippines (13°34'44" N, 124°13'52" E; WGS-84), by J. Fernandez. Paratopotypes.—Eight adult females (KU 306311, 308077, 324019–20, 324025–26, PNM 9562–63) and one juvenile (KU 324021) collected between 4 and 7 June 2009 by CDS and J. Fernandez. Diagnosis.—Brachymeles apat can be distinguished from congeners by the following combination of characters: (1) body size small (SVL 54.0–64.4 mm); (2) limbs bidactyl; (3) limb length small; (4) supralabials six; (5) infralabials six; (6) suparciliaries six; (7) supraoculars five; (8) midbody scale rows 21–22; (9) axilla–groin scale rows 68–72; (10) paravertebral scale rows 85–89; (11) pineal eye spot present; (12) prefrontals not contacting on midline; (13) frontoparietals contact; (14) postnasals absent; (15) enlarged chin shields in three pairs; (16) 277 nuchals enlarged; (17) fourth and fifth supralabial below eye; (18) auricular opening absent; (19) presacral vertebrae 45; (20) non-fusion of mental and first infralabials; (21) non-fusion of loreals; and (22) uniform body color (Tables 4.4, 4.5). Comparisons.—Characters distinguishing Brachymeles apat from all non-pentadactyl, limbed species of Brachymeles are summarized in Tables 4.4 and 4.5. Brachymeles apat most closely resembles B. samarensis, B. lima, B. tatlo, and populations of B. bonitae, the only other species to be bidactyl or have bidactyl populations. However, B. apat can be distinguished from B. samarensis by having non-fusion of the loreals and a tendancy towards a greater number of axilla–groin scale rows (Table 4.5); from B. lima by having a greater relative fore-limb length, fewer presacral vertebrae, six infralabials, the presence of contact between frontoparietals, the presence of contact between the first pair of enlarged chin shields, non-fusion of the loreals, and non-fusion of the mental and first infralabials (Tables 4.4, 4.5); from B. tatlo by having fewer presacral vertebrae, a greater number of midbody scale rows, fewer axilla–groin and paravertebral scale rows, and the presence of contact between the first pair of enlarged chin shields (Table 4.5); and from B. bonitae by having only bidactyl body forms, longer relative fore- and hind limb lengths, fewer presacral vertebrae, fewer axilla–groin and paravertebral scale rows, six supralabials, six infralabials, six supraciliaries, five supraoculars, the presence of contact between frontoparietals, the presence of contact between the first pair of enlarged chin shields, and non-fusion of the mental and first infralabials (Tables 4.4, 4.5). Brachymeles apat can be distinguished from all limbless species of Brachymeles (B. apus, B. lukbani, B. minimus, B. miriamae, B. vermis) by having limbs; and from all pentadactyl species of Brachymeles (B. boholensis, B. boulengeri, B. bicolor, B. gracilis, B. kadwa, B. makusog, B. mindorensis, B. orientalis, B. schadenbergi, B. talinis, B. taylori, B. tungaoi, B. vindumi) by 278 having non-pentadactyl (vs. pentadactyl) limbs, shorter fore-limb lengths (less than 2.1 mm vs. greater than 5.9 mm), shorter hind limb lengths (less than 3.6 mm vs. greater than 10.3 mm), a narrower body (less than 5.4 mm vs. greater than 7.9 mm), and by the absence of a postnasal scale and auricular opening (vs. presence). Description of holotype.—Details of the head scalation are shown in Figure 4.6. Adult female, body small, slender, SVL 60.2 mm; head weakly differentiated from neck, nearly as wide as body, HW 7.0% SVL, 107.1% HL; HL 33.8% SnFa; SnFa 19.2% SVL; snout short, bluntly rounded in dorsal and lateral profile, SNL 63.0% HL; ear completely hidden by scales; eyes small, ED 1.7% SVL, 26.5% HL, 62.7% END, pupil subcircular; body slightly depressed, nearly uniform in thickness, MBW 120.4% MBH; scales smooth, glossy, imbricate; longitudinal scale rows at midbody 22; paravertebral scale rows 85; axilla–groin scale rows 68; limbs short, poorly developed, with digits reduced to two claws on both fore-limbs and hind limbs, finger and toe lamellae absent; FLL 3.4% AGD, 2.6% SVL; HLL 6.2% AGD, 4.7% SVL; tail as wide as body, tail tip regenerated, sharply tapered at end, TW 87.6% MBW, TL 75.6% SVL. Rostral projecting onto dorsal snout to point in line with middle of nasal, broader than high, in contact with frontonasal; frontonasal wider than long; nostril ovoid, in center of single trapezoidal nasal, longer axis directed anteroventrally and posterodorsally; supranasals present, large, broadly separated; postnasals absent; prefrontals moderately separated; frontal octagonal-shaped, its anterior margin in moderate contact with frontonasal, in contact with first two anterior supraoculars, 4× wider than anterior supraocular; supraoculars five; frontoparietals large, in broad medial contact, each frontoparietal in contact with interior three supraoculars; interparietal moderate, its length equal to midline length of frontoparietal, longer than wide, diamond-shaped, wider anteriorly; parietals narrower than frontoparietals, in broad contact behind interparietal; 279 nuchals enlarged; two loreals, decreasing in size from anterior to posterior, anterior loreal about as long as and slightly higher than posterior loreal; one preocular; one presubocular; supraciliaries six, the anteriormost contacting prefrontal and separating posterior loreal from first supraocular, posteriomost extending nearly to middle of fifth supraocular; single subocular scale row complete, in contact with supralabials; lower eyelid with one row of scales; supralabials six, first 2× size of other supralabials, third, fourth, and fifth below eye; infralabials six (Fig. 4.5). Mental wider than long, fused with first infralabials; postmental single, enlarged, its width greater than width of mental; followed by three pairs of enlarged chin shields, first pair in broad medial contact, its width greater than width of third pair, narrower than second pair, second pair broadly separated by single medial scale, third pair separated by three medial scales (Fig. 4.5). Scales on limbs smaller than body scales; scales on dorsal surfaces of digits wrapping around lateral edges of digits; lamellae absent; palmar surfaces of hands and plantar surfaces of feet with several small, irregular scales, each with irregular raised anterior edges; fore-limb digits equal in size; hind limb digits unequal in size on right foot, second digit greatest in length, digits absent on left foot. Coloration in preservative.—The ground color of the body is medium brown, with each dorsal scale having a dark, auburn streak on the anterior two thirds to one half of the scale with light brown posterior. Posterior edge of all body scales transparent. The streaks are present around the entire body. Ventral scales have lighter color, with auburn streaks in anterior and light cream in posterior. Caudals and subcaudals match the bordering body scales. Streaks on each individual scale consist of four to seven longitudinal thin streaks of auburn with smudges of auburn between streaks. Forelimb and hind limb scales are brown and have darker coloration than their surrounding body scales. Forelimb and hind limb scales have weakly defined scale 280 boundaries. Precloacal scale coloration matches surrounding ventral scale coloration. Head scales have mottled light and dark brown coloration that match dorsal body scales. Supraocular scales possess the darkest brown coloration of all head scales with brown umber color. The rostral, nasal, supranasal, and first supralabial scales possess a cream color. The other supralabials have a slightly darker, gray cream coloration. The mental, postmental, and chin shield scales are mottled brown on a light cream background that match bordering body scales. Coloration in life.—Ground color of body medium to dark brown; streaks of darker pigmentation on body dark-brown. Variation.—Morphometric variation of the series is summarized in Table 4.6. We observed no variation among the type series in digit number, head scale counts, or in the degree of head scale contact. Distribution.—Brachymeles apat is known only from Catanduanes Island (Fig. 4.3). Ecology and natural history.—Brachymeles apat occurs in residential and agricultural habitats, as well as in disturbed and secondary-growth forest. No original, low elevation forest remains on Catanduanes Island, but we assume the species once also occurred in first growth forest at low elevations. Individuals have been observed under piles of rotting coconut husks, in the rotting material within fallen logs, and in loose soil and leaf litter surrounding the root networks of trees. This species occurs sympatrically with the pentadactyl species, B. makusog, and the limbless species, B. minimus. On Catanduanes Island, both B. makusog and B. minimus have only been observed in disturbed, secondary-growth forest, whereas B. apat appears to be a habitat generalist. Sympatric lizard species occurring on Catanduanes Island include: (Agamidae) Bronchocela cristatella, Draco spilopterus, Gonocephalus sophiae, Hydrosaurus pustulatus; (Gekkonidae) 281 Cyrtodactylus philippinicus, Hemidactylus frenatus, H. platyurus, Gehyra mutilata, Gekko gecko, G. mindorensis, Luperosaurus cumingii, Pseudogekko smaragdina, P. compressicorpus; (Scincidae) Dasia atrocostata, Eutropis multicarinata borealis, E. indepresa, E. multifasciata, Lamprolepis smaragdina, Lipinia pulchella pulchella, Sphenomorphus abdictus, S.decipiens, S.cumingi, S.jagori, S. laterimaculatus, S. lawtoni, S. leucospilos, S.steerei, Tropidophorus grayi; (Varanidae) Varanus marmoratus, V. olivaceus. Etymology.—The specific epithet is chosen in recognition of the Catanduanes indigenous people’s group for which the first adopted name for the island, “Isla de Apat,” was coined. The name was adopted by the Spanish conquistadores who encountered the original Catanduanes tribes living in thatched huts called “apat.” Suggested common name: Catanduanes Slender Skink. Brachymeles tatlo sp. nov. Figs. 4.3, 4.4 Holotype.—PNM 9764 (CDS Field No. 4099, formerly KU 324017), adult male, collected under pile of rotting coconut husks in secondary-growth forest (10:00–12:30 hr) on 18 June 2009, in the Municipality of Irosin, Sorsogon Province, Luzon Island, Philippines (15°50' N, 123°55' E; WGS-84), by J. Fernandez. Paratypes.—Adult female (TNHC 62469) collected in a rotting log on ridge above lake Bulusan on 24 November 2001, 500–700 m elevation, Mt. Balusan National Park, Barangay San Roque, Municipality of Irosin, Sorsogon Province, Luzon Island, Philippines, by RMB and B. Fernandez; adult female (PNM 4856) collected 1 July 1995, in Barangay Salvacion, Municipality of Santa Magdalena, Sorsogon Province, Luzon Island, Philippines, by R. V. Sison. 282 Diagnosis.—Brachymeles tatlo can be distinguished from congeners by the following combination of characters: (1) body size small (SVL 54.0–60.0 mm); (2) limbs bidactyl; (3) limb length small; (4) supralabials six; (5) infralabials six; (6) suparciliaries six; (7) supraoculars five; (8) midbody scale rows 20; (9) axilla–groin scale rows 73–77; (10) paravertebral scale rows 90–94; (11) pineal eye spot present; (12) prefrontals not contacting on midline; (13) frontoparietals contact; (14) postnasals absent; (15) enlarged chin shields in three pairs; (16) nuchals elnlarged; (17) fourth and fifth supralabial below eye; (18) auricular opening absent; (19) presacral vertebrae 47–48; (20) non-fusion of mental and first infralabials; (21) non-fusion of loreals; and (22) uniform body color (Tables 4.4, 4.5). Comparisons.—Characters distinguishing Brachymeles tatlo from all non-pentadactyl, limbed species of Brachymeles are summarized in Tables 4.4 and 4.5. Brachymeles tatlo most closely resembles B. samarensis, B. lima, B. apat, and populations of B. bonitae, the only other species to be bidactyl or have bidactyl populations. However, B. tatlo can be distinguished from B. samarensis by having a greater number of presacral vertebrae, a greater number of axilla–groin and paravertebral scale rows, and non-fusion of the mental and the first infralabials (Table 4.5); from B. lima by having a greater relative fore-limb length, six infralabials, non-fusion of the mental and the first infralabials, non-fusion of the loreals, a tendancy towards a greater number of axilla–groin and paravertebral scale rows, and by the presence of contact between frontoparietals (Tables 4.4, 4.5); from B. apat by having a greater number of presacral vertebrae, fewer midbody scale rows, and a greater number of axilla–groin and paravertebral scale rows (Table 4.5); and from B. bonitae by having only bidactyl body forms, longer relative fore- and hind limb lengths, fewer midbody scale rows, six supralabials, six infralabials, six supraciliaries, 283 five supraoculars, the presence of contact between frontoparietals, anda tendancy towards fewer presacral vertebrae, axilla–groin, and paravertebral scale rows (Tables 4.4, 4.5). Brachymeles tatlo can be distinguished from all limbless species of Brachymeles (B. apus, B. lukbani, B. minimus, B. miriamae, B. vermis) by having limbs; and from all pentadactyl species of Brachymeles (B. boholensis, B. boulengeri, B. bicolor, B. gracilis, B. kadwa, B. makusog, B. mindorensis, B. orientalis, B. schadenbergi, B. talinis, B. taylori, B. tungaoi, B. vindumi) by having non-pentadactyl (vs. pentadactyl) limbs, shorter fore-limb lengths (less than 2.1 mm vs. greater than 5.9 mm), shorter hind limb lengths (less than 3.6 mm vs. greater than 10.3 mm), a narrower body (less than 5.4 mm vs. greater than 7.9 mm), and by the absence of a postnasal scale and auricular opening (vs. presence). Description of holotype.—Details of the head scalation are shown in Figure 4.5. Adult male, body small, slender, SVL 56.8 mm; head weakly differentiated from neck, nearly as wide as body, HW 7.0% SVL, 103.6% HL; HL 32.4% SnFa; SnFa 20.9% SVL; snout short, bluntly rounded in dorsal and lateral profile, SNL 59.2% HL; ear completely hidden by scales; eyes small, ED 1.6% SVL, 24.2% HL, 59.6% END, pupil subcircular; body slightly depressed, nearly uniform in thickness, MBW 125.2% MBH; scales smooth, glossy, imbricate; longitudinal scale rows at midbody 20; paravertebral scale rows 90; axilla–groin scale rows 73; limbs short, poorly developed, with digits highly reduced to two small claws on both fore-limbs and hind limbs, finger and toe lamellae absent; FLL 3.3% AGD, 2.5% SVL; HLL 5.9% AGD, 4.5% SVL; tail nearly as wide as body, gradually tapered at end, TW 91.5% MBW, TL 79.5% SVL. Rostral projecting onto dorsal snout to point just past posterior edge of nasal, broader than high, in broad contact with frontonasal; frontonasal wider than long; nostril ovoid, in center of single trapezoidal nasal, longer axis directed anterodorsally and posteroventrally; supranasals 284 present, large, broadly separated; postnasals absent; prefrontals broadly separated; frontal octagonal-shaped, its anterior margin in broad contact with frontonasal, in contact with first two anterior supraoculars, 5× wider than anterior supraocular; supraoculars five; frontoparietals large, in moderate medial contact, each frontoparietal in contact with interior three supraoculars; interparietal large, its length greater than midline length of frontoparietal, longer than wide, diamond-shaped, wider anteriorly; parietals as broad as frontoparietals, in broad contact behind interparietal; nuchals enlarged; two loreals, decreasing in size from anterior to posterior, anterior loreal about as long as and slightly higher than posterior loreal; one preocular; one presubocular; supraciliaries six, the anteriormost contacting prefrontal and separating posterior loreal from first supraocular, posteriomost extending to middle of fifth supraocular; single subocular scale row complete, in contact with supralabials; lower eyelid with one row of scales; supralabials six, first 2× size of other supralabials, third, fourth, and fifth below eye; infralabials six (Fig. 4.4). Mental wider than long, fused with first infralabials; postmental single, enlarged, its width narrower than width of mental; followed by three pairs of enlarged chin shields, first pair in broad medial contact, its width greater than width of third pair, narrower than second pair, second pair broadly separated by single medial scale, third pair separated by three medial scales (Fig. 4.4). Scales on limbs smaller than body scales; scales on dorsal surfaces of digits wrapping around lateral edges of digits; lamellae absent; palmar surfaces of hands and plantar surfaces of feet with several small, irregular scales, each with irregular raised anterior edges; fore-limb digits absent on left hand, highly reduced to two small claw tips on right hand; hind limb digits unequal in size, first digit highly reduced to small claw tip, second digit greatest in length. 285 Coloration in preservative.—The ground color of the body is medium brown, with each dorsal scale having a dark, auburn streak on the anterior one third to one half of the scale with light brown posterior. Streaks on each individual scale consist of four to six longitudinal thin streaks of auburn with smudges of auburn between streaks. The streaks are present around the entire body. Posterior edge of all body scales transparent. Ventral scales have more distinct streaks, with sandy brown color posterior. Forelimb and hind limb scales are same shade of color as caudal scales. Scales are light sandy brown with brown mottling. Scale boundaries more clearly seen on hind limbs than on forelimbs. Precloacal scales match surrounding ventral scales. Head scales have mottled light and dark brown coloration and slightly lighter appearance compared with bordering dorsal body scales. Supraocular scales possess the darkest brown coloration of all head scales with umber brown color. The rostral, nasal, supranasal and supralabial scales have the lightest coloration of beige-umber. The mental and infralabial scales are cream. The chin shields and postmental scale are cream with slight brown mottling. Coloration in life.—Coloration in life is unrecorded; however, because Brachymeles specimens do not change significantly during preservation (CDS, RMB personal observation), we suspect that the preserved coloration and patterns are much like those in life. Variation.—Morphometric variation of the series is summarized in Table 4.6. We observed no variation among the type series in digit number, head scale counts, or in the degree of head scale contact. Distribution.—Brachymeles tatlo is known only from the southern Bicol Peninsula (Fig. 4.3). Ecology and natural history.—Brachymeles tatlo occurs in disturbed and secondary-growth forest, and is found in sympatry with B. boulengeri; however, B. tatlo, B. kadwa, B. lukbani, and B. makusog are also recognized to occur on the Bicol Peninsula of Luzon Island. 286 Sympatric lizard species occurring in the Bicol Peninsula include: (Agamidae) Bronchocela cristatella, Draco spilopterus, Gonocephalus sophiae, Hydrosaurus pustulatus; (Gekkonidae) Cyrtodactylus philippinicus, Hemidactylus frenatus, H. platyurus, Gehyra mutilata, Gekko gecko, G. mindorensis, Luperosaurus cumingii, Pseudogekko smaragdina, P. compressicorpus; (Scincidae) Dasia atrocostata, Eutropis multicarinata borealis, E. multifasciata, Lamprolepis smaragdina, Lipinia pulchella pulchella, Sphenomorphus abdictus abdictus, S. decipiens, S. cumingi, S. jagori, S. laterimaculatus, S. leucospilos, S. steerei, Tropidophorus grayi; (Varanidae) Varanus marmoratus, V. olivaceus. Etymology.—The name of the new species is derived from the Latin root word “brevis”, meaning short, and “dactylus,” meaning digit, to represent the species’ small, highly reduced digits. Suggested common name: Southern Bicol Slender Skink. DISCUSSION Analyses of the two mitochondrial genes (ND1, ND2) and two nuclear loci (α-enolase, PTGER4) resulted in topologies with high ML bootstrap support and posterior probabilities for six lineages formerly part of the Brachymeles samarensis species complex (Fig. 4.2). No analyses supported the monophyly of species formerly part of Brachymeles samarensis (B. isa, B. dalawa, B. lima, B. apat, B. tatlo, and B. samarensis). However, all analyses show strong support for the sister relationship between B. isa and B. dalawa, as well as for the clade including the Greater Luzon PAIC species (B. lima, B. apat, B. tatlo; Fig. 4.2). All nodes received high support and all analyses resulted in identical topologies. In addition to the supported paraphyly of species formerly part of Brachymeles samarensis, several other recognized species were recovered as part of the B. samarensis Complex. 287 Brachymeles cebuensis, one of only two recognized species to have unequal numbers of fore- and hind limb digits, was supported to be part of a clade of species (B. cebuensis + B. isa + B. dalawa) with three fingers and two or three toes (Fig. 4.2). Sister to this three-finger clade, all analyses recovered B. minimus and B. lukbani, both limbless species, nested within a didactyl clade of species formerly part of B. samarensis (true B. samarensis, B. lima, B. apat, B. tatlo; Fig. 4.2). All three previously recognized species (B. cebuensis, B. lukbani, B. minimus) have geographical distributions that overlap, or are in close proximity to, the known ranges of other species in the B. samarensis Complex (Fig. 4.3). The six species recognized in this paper are supported to be part of two clades with different body plans (Fig. 4.2). One of these clades, made up of B. cebuensis, B. isa, and B. dalawa, consists of species with three digits on their fore-limbs and two to three digits on their hind limbs (Fig. 4.2). In contrast, the remaining species (B. samarensis, B. tatlo, B. apat, B. lima) are part of a second clade consisting of limbless and bidactyl body forms (Fig. 4.2). Two of the five recognized species of limbless Brachymeles (B. minimus and B. lukbani) are sister to clade of bidactyl species from the Bicol Peninsula of Luzon Island and Catanduanes Island. As previously recognized, Brachymeles samarensis spanned two distinct, recognized faunal regions: Greater Luzon PAIC and Greater Mindanao PAIC. Given this formerly wide geographical distribution, it is not surprising that populations between the two PAICs are distinct; however, we were surprised to discover high levels of intra-PAIC species diversity (Fig. 4.2). The species recognized in this paper increase the total number of known species of Brachymeles to 30, and all but two of these are endemic to the Philippines. The species-level diversity within the genus has doubled in the last two years as the result of large-scale sampling efforts across the Philippines and the detailed analyses of morphological variation among species 288 and populations (Siler, 2010; Siler et al., 2009a, 2010a,b; Siler and Brown, 2010, 2011; Siler et al., 2011, in press a,b,c,d). Brachymeles has long been considered a small clade of SE Asian lizards, and estimates of species diversity have remained nearly constant for more than 30 years (but see Brown and Alcala, 1995). This vast underestimation of true diversity within the genus is a testament to the extent of morphological similarity among species and a lack of systematic studies of the group. Despite the past taxonomic assessments (review: Brown and Alcala, 1980), it comes as little surprise that allopatric populations of “B. samarensis” from the Luzon and Mindanao Pleistocene Aggregate Island Complexes have proven with improved sampling to be morphologically diagnosable independent lineages. This study adds to a growing line of evidence suggesting a need for reevaluation of amphibian and reptile species boundaries within the Philippines. Few examples exist of truly “widespread” reptile species that have geographic distributions spanning recognized zoogeographic boundaries, and as is often the case, these species frequently turn out to constitute multiple evolutionary lineages (McGuire and Alcala, 2000; Brown et al., 2009; Gaulke et al, 2007; Welton et al., 2009, 2010a,b; Siler et al., 2010c, 2011). The exceptions, in contrast, appear to be invasive species and human-mediated range expansions (Diesmos et al., 2006; Brown et al., 2010). All species of Brachymeles live a semi-fossorial existence, specializing in dry rotting material inside and underneath fallen decomposing logs, leaf litter, and other forest floor detritus. Many are habitat specialists found exclusively in rotting logs, loose soil, or leaf litter, whereas others are common beneath piles of rotting coconut husks in disturbed, agricultural habitat. We assume that the species now found in residential and agricultural areas were once native to forested habitats and were possibly forest edge specialists. 289 Prior to recent, focused survey efforts, the modest sample sizes of specimens of Brachymeles available in museum collections limited appropriate, lineage-based species delimitations. Although the rarity of Brachymeles in collections may be due to their secretive, semi-fossorial lifestyle, focused survey efforts that target the appropriate microhabitat have proven effective in sampling Brachymeles in their native environments (CDS pers. observ.; Siler and Brown, 2010; Siler et al., in press a,b,c,d). Recent fine- and broad-scale phylogenetic analyses of species of the genus Brachymeles have made it apparent that species diversity in the clade has been considerably underestimated; accordingly, discovery of additional undocumented (possibly cryptic) diversity is anticipated in other species groups (e.g., Siler et al., 2009a, 2010a,b, in press a,b,c,d; Siler and Brown, 2010, 2011). A number of studies have shown that the evolution of a burrowing lifestyle is correlated with decreasing dispersal abilities (Selander et al., 1974; Patton and Yang, 1977; Patton and Feder, 1978; Nevo, 1979; Siler et al., 2011). Many Brachymeles lineages have experienced reduction or loss of limbs, which may further reduce vagility (Siler and Brown, 2010, 2011; Siler et al., 2011). Through time, reduced dispersal abilities and semi-fossorial lifestyles may lead to an increasingly patchy distributions, reduced gene flow among populations, and the accumulation of inter-population differences (Nevo, 1979). Still, the role that reduced dispersal abilities associated with fossoriality play on the dispersal abilities and diversification patterns of Brachymeles species remains unknown. Regardless of which processes produce species diversity, we suspect that additional species await discovery. Following the recognition of Brachymeles samarensis, B. lima, B. tatlo, B. apat, B. isa, and B. dalawa there are now 13 non-pentadactyl, limbed species of Brachymeles. Of these, four species are bidactyl (B. samarensis, B. tatlo, B. lima, B. apat), four are tridactyl (B. muntingkamay, B. 290 tridactylus, B. isa, B. dalawa), and two are tetradactyl (B. elerae, B. wrighti). Additionally, two species have unequal fore- and hind limb digit numbers (B. cebuensis, 3/2; B. pathfinderi, 5/4), and populations of B. bonitae have been observed to have 0–2 fore- and hind limb digits. All non-pentadactyl species have smaller body sizes with the exception of B. wrighti (Taylor, 1925; Siler et al., in press b). Interestingly, the distribution of limbed, non-pentadactyl species in the Philippines is relatively uneven across the major biogeographic regions of the Philippines, with seven species known to occur in the Luzon Faunal Region, four in the Mindanao Faunal Region, two in the Visayan Faunal Region, and one in the Mindoro Faunal Region (Brown and Alcala, 1980, Brown and Alcala, 1995; Brown and Diesmos, 2002; Siler et al., 2010a). Additionally, the distribution of total species diversity in the genus is also uneven, with 13 species known from the Luzon Faunal Region versus eight in the Mindanao Faunal Region, six in the Visayan Faunal Region, and only two and two in the Sulu archipelago and Mindoro Faunal Region respectively (Brown and Alcala, 1980; Brown and Alcala, 1995; Brown and Diesmos, 2002; Siler et al., 2009a, 2010a,b; Siler and Brown, 2010). New species discoveries on Luzon Island have occurred with consistency during the last two decades; given the island’s complex mountain ranges (Sierra Madres, Cordillera, Zambales, Bicol Peninsula volcanoes) and geographic complexity (Defant et al., 1989; Yumul et al., 2009), the increase in the faunal region’s diversity is likely to continue (Ross and Gonzales, 1992; Brown et. al. 1995a,b, 1999, 2000a; Linkem et al., 2010; Siler et al., 2009a, 2010a,b,c, in press c,d; Welton et al., 2010a,b). It is worth noting that efforts to survey Mindanao have been less extensive than efforts on Luzon; this may account for some of the differences in diversity between the regons—which may be artifacts of sampling biases. 291 At present there remains one polytypic species (B. gracilis) and one “widespread” species (B. bonitae) in the genus, both with distributions spanning boundaries between recognized faunal regions (Brown and Alcala, 1980; Siler and Brown, 2010; Siler et al., in press d). Closer investigation of island populations within each of these species may result in the discovery of new species diversity. Furthermore, recent phylogenetic studies of the genus Brachymeles have not supported the monophyly of either of these widespread species, an indication that taxonomic revisions are needed (Siler and Brown, 2011; Siler et al., 2011). As our understanding of the total diversity within Brachymeles increases, it is important that continued efforts be made to conduct surveys focused on rotting log and leaf litter microhabitats throughout the ranges of all species. Accurate data on the distributions of these species will allow for a complete assessment of the geographic ranges of the species and appropriate assessment of conservation status can be made. At present, all nine species of the B. samarensis Complex are known or believed to be common throughout their ranges. Although these species currently inhabit highly disturbed, agricultural and residential areas, no studies on the long-term effect of deforestation on populations of Brachymeles exist. Therefore, according to the IUCN categories and classification structure, we consider the conservation status of these species as “Least Concern (LC),” pending the collection of additional information that might suggest otherwise. 292 Figure 4.4. Illustration of head of adult female Brachymeles samarensis (KU 310849) and adult female Brachymeles tatlo (PNM 4856; formerly KU 324004) in dorsal, lateral, and ventral views. Taxonomically diagnostic head scales are labeled as follows: C, chin shield; F, frontal; FN, frontonasal; FP, frontoparietal; IL, infralabial; IP, interparietal; L, loreal; M, mental; N, nasal; Nu, nuchal; P, parietal; PF, prefrontal; PM, postmental; PN, postnasal; PO, preocular; PSO, presubocular; R, rostral; SC, supraciliary; SL, supralabial; SN, supranasal; and SO, supraocular. Roman numerals indicate scales in the supraocular series, with Arabic numbers indicating scales in the supraciliary series. Illustrations by CDS, AMF, and RMJ. 293 294 Figure 4.5. Illustration of head of adult male holotype Brachymeles lima (PNM 9756; formerly KU 324003) and adult female holotype Brachymeles apat (PNM 9761; formerly KU 324023) in dorsal, lateral, and ventral views. Labels for taxonomically diagnostic head scales follow those shown in Figure 4.4. Illustrations by CDS, AMF, and RMJ. 295 296 Figure 4.6. Illustration of head of adult female holotype Brachymeles isa (PNM 9746; formerly KU 311228) and adult male holotype Brachymeles dalawa (PNM 9749; formerly KU 320466) in dorsal, lateral, and ventral views. Labels for taxonomically diagnostic head scales follow those shown in Figure 4.4. Illustrations by CDS, AMF, and RMJ. 297 298 Figure 4.7. Photograph in life of Brachymeles isa (PNM 9746; formerly KU 311228), SVL = 59.1 mm. Photograph by CDS. 299 300 Figure 4.8. Photographs in life of Brachymeles dalawa (PNM 9749; formerly KU 320466), SVL = 56.3 mm. Photographs by CDS. 301 302 CHAPTER 5 Phylogeny-based species delimitation in Philippine slender skinks (Reptilia: Squamata: Scincidae: Brachymeles) III: taxonomic revision of the Brachymeles gracilis Complex, with description of three new species Few genera of scincid lizards are known to possess species representing a full spectrum of body forms, from fully limbed, pentadactyl species to limbless species (see Siler and Brown, 2010, 2011; Siler et al., 2011). Within one of them, the genus Brachymeles Duméril and Bibron, 1839, all but two of the 30 recognized species are endemic to the Philippines, the exceptions being a single species (B. apus) from northern Borneo and another (B. miriamae) from Thailand (Brown and Alcala, 1980; Hikida, 1982; Siler et al., 2009a, 2010a,b, 2011, in press a,b,c; Siler, 2010; Siler and Brown, 2010, 2011). Thirteen species of Brachymeles are pentadactyl (bicolor, boholensis, boulengeri, gracilis, kadwa, makusog, mindorensis, orientalis, schadenbergi, talinis, taylori, tungaoi, and vindumi), thirteen are non-pentadactyl, with incompletely developed limbs and a reduced numbers of digits (bonitae, cebuensis, elerae, muntingkamay, pathfinderi, samarensis, tridactylus, wright, sp. nov. [Leyte Island; Siler et al., in press c], sp. nov. [Lapinig Group Islands; Siler et al., in press c], sp. nov. [Catanduanes Island; Siler et al., in press c], sp. nov. [Central Bicol Peninsula, Luzon Island; Siler et al., in press c], and sp. nov. [Southern Bicol Peninsula, Luzon Island; Siler et al., in press c]), and five are entirely limbless (apus, minimus, miriamae, lukbani, and vermis). The non-pentadactyl species have been the subject of recent studies which have documented a wide range of limb- and digit-reduced states, from minute limbs that lack full digits (bonitae, cebuensis, muntingkamay, samarensis, tridactylus, sp. nov. [Leyte Island; Siler et al., in press c], 303 sp. nov. [Lapinig Group Islands; Siler et al., in press c], sp. nov. [Catanduanes Island; Siler et al., in press c], sp. nov. [Central Bicol Peninsula, Luzon Island; Siler et al., in press c], and sp. nov. [Southern Bicol Peninsula, Luzon Island; Siler et al., in press c]), to moderately developed limbs with four to five digits on the hands and feet (elerae, pathfinderi, wrighti: Duméril and Bibron, 1839; Brown, 1956; Brown and Rabor, 1967; Brown and Alcala, 1980; Taylor, 1917, 1918, 1925; Siler et al., 2009a, 2010b, 2011, in press a,b,c; Siler, 2010; Siler and Brown, 2010, 2011). All species are semi-fossorial and typically found in dry, rotting material inside or underneath decaying logs or in loose soil, forest floor detritus, and leaf litter. Most species in the genus are recognized from hot, lowland forests; however, several species do occur in cooler high elevation forests (e.g., B. apus, B. elerae, B. wrighti). Named over 150 years ago (Duméril and Bibron, 1839), the genus reached 15 species by 1980 (Brown and Alcala, 1980) and only one additional species, B. minimus, a legless species, was described in invervening years (Brown and Alcala, 1995). We assume that until recent work, guided by extensive field based survey work combined with molecular phylogenetic studies, conservative body plans and external morphological features among species of Brachymeles led earlier reseachers to conclude that the genus was relatively species-poor (Taylor, 1917; Brown, 1956; Brown and Rabor, 1967; Brown and Alcala, 1980). Recent studies have revealed that this assessment of limited spercies diversity is cleally an underestimate. Phylogeny-based exercises in species delimitation have identified and revised numerous non-monophyletic species complexes within the Philippines (Siler et al., 2009a, 2010a,b, 2011, in press a,b,c; Siler, 2010; Siler and Brown, 2010, 2011). Additionally, several rare, mid-to-high elevation species long represented by only a few specimens (e.g., Brachymeles bicolor, B. elerae, B. wrighti, B. pathfinderi), have recently been rediscovered and redescribed as 304 valid taxa (Siler, 2010; Siler et al., in press a,b). Together, these studies, coupled with increased sampling throughout the Philippines, and a new, robust molecular dataset now allows us to begin evalutating variation across the isolated populations of widespread species. Recently, Siler and Brown (2010) revised two polytypic species (B. boulengeri and B. schadenbergi) and one widespread species (B. talinis), and inferred the presence of ten genetically and morphologically distinct allopatric evolutionary lineages (species). Following this study, Siler et al. (in press c) revised the B. samarensis Complex, restricting the range of B. samarensis to Samar Island only, and describing five new, non-pentadactyl species. Another another species, B. bonitae, is still recognized as having a widespread distribution (Brown, 1956; Brown and Rabor, 1967; Brown and Alcala, 1980) that spans historical faunal demarcations in the Philippines (Heaney, 1985; Brown and Guttman, 2002; Brown and Diesmos, 2002, 2009). Only a single polytypic species still is recognized (B. gracilis; Brown, 1956; Brown and Rabor, 1967; Brown and Alcala, 1980); this lineage is the focus of the present study. Taxonomic History The genus Brachymeles was first described by Duméril and Bibron (1839) for the small, limb-reduced species Brachymeles bonitae. Three additional species (Senira bicolor [Gray, 1845], Eumeces (Riopa) gracilis [Fischer, 1885], E. (R.) schadenbergi [Fischer, 1885]) were transferred to the genus by Boettger (1886) and Boulenger (1887). Fischer’s (1885) description of E. gracilis was based on single specimen with the collection No. 846 (reported to be deposited in the Dresden Museum), and only a single line drawing of the dorsal view of the head was provided (Fischer, 1885: plate III, Fig. 5.1). Three decades later, in Taylor’s (1917) review of the genus, he incorrectly revised B. gracilis to include not only populations in the Mindanao 305 Faunal Region, but also populations on Negros and Mindoro islands (Fig. 5.1). At the time, Taylor did not have access to Fischer’s (1885) original description, and based his evaluation on a series of 27 specimens from Negros and Mindoro, inferring that the specimen reported by Fischer (1885) from Mindanao was actually B. schadenbergi (sensu Siler and Bown, 2010). Taylor (1917) provided an illustration of the ventral view of head likely based on a specimen of B. taylori or B. mindorensis. One year later, Taylor (1918) described B. sampu based on a single specimen from Bubuan Island of the Tapiantana Island Group off southern the coast of Basilan. He provided line drawings of the dorsal, lateral, and ventral profiles of the head of the type specimen. With what was known of the species diversity in the genus at the time, Taylor (1918) described B. sampu as “…another link in the chain of retrogression in the genus Brachymeles…between Brachymeles schadenbergii and B. bicolor.” Taylor (1918) described the type specimen (Philippine Bureau of Science collection No. 1989:254) of B. sampu; this specimen was lost in the World War II firebombing of Manila (Brown and Alcala, 1978), as were 32 other type specimens of Philippine amphibians and reptiles (Welton et al., 2009). In a subsequent revision Taylor (1922a) placed B. sampu in the synonymy of B. gracilis. In this revision, Taylor used the original head profile line drawings of B. sampu to illustrate head scale patterns for B. gracilis (Taylor, 1922a:248), suggesting that he clearly considered B. sampu to be a junior synonym of B. gracilis. Thirty years later, Brown (1956) described B. gracilis taylori, and included B. boulengeri as one of three subspecies of the polytypic species B. gracilis. Brown and Rabor’s (1967) description of B. gracilis boholensis and B. g. mindorensis brought the number of subspecies within B. gracilis to five. It was not until 1980 that Brown and Alcala (1980) resurrected the polytypic species B. boulengeri, and included four subspecies (B. b. boulengeri, B. b. boholensis, 306 B. b. mindorensis, B. b. taylori), all believed to be distinct from B. gracilis. Their restriction of B. gracilis to the southern and southeastern islands of the Philippines resulted in the recognition of only two subspecies, B. gracilis gracilis and B. gracilis hilong (Brown and Alcala, 1980). This view has characterized the taxonomy of B. gracilis for the past 30 years. To date, Brachymeles gracilis remains a widespread species spanning most major islands of the Mindanao Pleistocene Aggregate Island Complex (PAICs; Brown and Guttman, 2002; Brown and Diesmos, 2002; Fig. 5.1). Widespread distributions such as this have been the focus of many recent studies (Brown et al., 2000a; Siler et al., 2010a,b, in press c; Siler and Brown, 2010; Welton et al., 2009, 2010a,b), which have revealed that few endemic Philippine reptiles actually possess broad distributions spanning these regional faunistic boundaries (review: Brown and Diesmos, 2009). The goal of the present study is to revise the taxonomy of the B. gracilis complex such that individual units (species) represent independently evolving, cohesive lineage segments (sensu Simpson, 1961; Wiley 1978; Frost and Hillis, 1990; de Queiroz, 1998, 1999). Comprehensive examination of all recently collected specimens from throughout the known range of B. gracilis, and historically collected specimens available in museum collections, results in the reorganization of the species complex into six distinct evolutionary lineages (species). In this paper we provide a phylogenetic analysis and the first illustrations of five of these taxa, fully describe each species, and clarify taxonomic boundaries. We also provide information on each species’ natural history, ecology, and geographic distribution and comment on additional, presently unrecognized putative new species. 307 Figure 5.1. Map of the Philippine islands, with island labels provided for islands with representative samples used for this study. The five recognized major Pleistocene Aggregate Island Complexes (PAICs), major island groups, and additional deep-water islands are labeled for reference. Current islands in the Philippines are shown in medium grey; light gray areas enclosed in black 120 m bathymetric contours indicate the hypothesized maximum extent of land during the mid- to late Pleistocene. 308 309 Materials and Methods Field work, sample collection, and specimen preservation Fieldwork was conducted on Camiguin Sur, Leyte, Mindanao, and Samar islands, all in the Philippines (Fig. 5.1) between 1991 and 2010. Specimens were collected between 900 and 1600 hr, euthenized in aqueous chloretone, dissected for genetic samples (liver preserved in 95% ethanol or flash frozen in liquid nitrogen), fixed in 10% formalin and eventually (< 2 mo) transferred to 70% ethanol. Specimens measured or sequenced in this study are deposited in the University of Kansas Natural History Museum (KU), the Texas Natural History Collections (TNHC) of the Texas Memorial Museum of the University of Texas at Austin, the Philippine National Museum (PNM), the Cincinnati Museum Center (CMC), the California Academy of Sciences (CAS), and the Museum of Comparative Zoology (MCZ) (Acknowledgments and Specimens Examined); voucher information corresponding to data from GenBank sequences is included in Table 5.1. Taxon sampling and outgroup selection for phylogenetic analyses Because our primary goal was to estimate phylogenetic relationships among the various populations of Brachymeles gracilis we sequenced 2–4 exemplars per sampled population. We included samples of Plestiodon and Lygosoma, as well as samples of Brachymeles apus, B. bonitae, and B. miriamae, as outgroup representatives based on relationships presented in a recent phylogenetic analyses of the genus Brachymeles (Siler et al., 2011). The results of Siler et al. (2011) revealed the Brachymeles gracilis species complex to be non-monophyletic, and we therefore included samples of Brachymeles pathfinderi to explore the sister group relationships 310 within the B. gracilis complex. A total of 21 ingroup samples were used in phylogenetic inferences. Genetic samples of B. sampu were not available for inclusion. DNA extraction, purification, and amplification We extracted total genomic DNA from tissues (Table 5.1) using the modified guanidine thiocyanate extraction method of Esselstyn et al. (2008). The mitochondrial NADH Dehydrogenase Subunit 1 (ND1), NADH Dehydrogenase Subunit 2 (ND2), and the nuclear loci, Brain-derived Neurotrophic Factor (BDNF) and PTGER4, were completely sequenced for nearly all samples using the primers and protocols provided in Siler et al. (2011). We visualized amplified products on 1.0% agarose gels, then purified them with 1 µL of a 20% solution of ExoSAP-IT (US78201, Amersham Biosciences, Piscataway, NJ) on the following thermal cycler profile: 31 min at 37º, followed by 15 min at 80˚. Upon successful amplification of targeted fragments, cycle-sequencing reactions were completed with the same primers and ABI Prism BigDye Terminator chemistry (Ver. 3.1; Applied Biosystems, Foster City, CA). Cycle-sequencing products were purified with Sephadex Medium (NC9406038, Amersham Biosciences, Piscataway, NJ) in Centri-Sep 96 spin plates (CS-961, Princeton Separations, Princeton, NJ). We analyzed purified products using an ABI Prism 3130xl Genetic Analyzer (Applied Biosystems), and gene sequences were assembled with Sequencher 4.8 (Gene Codes Corp., Ann Arbor, MI). Alignment and phylogenetic analysis An initial alignment was produced in Muscle v3.7 (Edgar, 2004), and manual adjustments were made in MacClade 4.08 (Maddison and Maddison, 2005). No instances of insertions or 311 deletions, or ambiguously aligned regions, were observed in the data, and all data were used for analyses. The final alignment thus consisted of 3,032 characters. Phylogenetic analyses were conducted using likelihood optimality criteria and Bayesian methods. Partitioned maximum likelihood (ML) analyses were conducted in RAxMLHPC v7.04 (Stamatakis, 2006). The alignment was partitioned into eight regions consisting of the codon positions of ND1 and ND2, and the two nuclear loci, BDNF and PTGER4, following the methods of Siler et al. (2011). Analyses that partition protein-coding genes by codon position have been shown to improve resulting inferences (Brandley et al., 2005). The partitions were run under the same model (GTR + G) with 100 replicate best-tree inferences. Each inference was performed with a random starting tree, and relied on the rapid hill-climbing algorithm (Stamatakis 2006). Clade support was assessed with 1000 bootstrap pseudoreplicates. We considered branches receiving ≥70% bootstrap support to be well-supported (Hillis and Bull, 1993; see also Wilcox et al., 2002). The Akaike Information Criterion (AIC), as implemented in jModeltest v0.1.1 (Guindon and Gascuel, 2003; Posada, 2008), was used to select the best model of nucleotide substitution for each partition (Table 5.2). The best-fit model for each of the eight partitions (Table 5.2) was used for Bayesian analyses performed in MrBayes 3.1 (Ronquist and Huelsenbeck, 2003). The same partitioning strategy used for maximum likelihood analyses was used for Bayesian inferences. Searches over tree space were conducted with four runs, each with four chains, and were run for 2 × 107 generations. Trees were sampled every 1000 generations, with 4000 samples discarded as burn-in; this left 16001 post-burn-in trees from each run included in the posterior distribution of topologies. Visual inspection for chain stationarity and high ESS values was conducted within the program Tracer v1.4 (Rambaut and Drummond, 2007). Additionally, 312 correlations of split frequencies and cumulative split frequencies were examined using the program AWTY (Nylander et al., 2008). We considered topologies with posterior probabilities ≥0.95 to be well supported (Wilcox et al., 2002; Leaché and Reeder, 2002). Morphological data We examined fluid-preserved specimens (Appendix VI) for variation in qualitative and mensural characters. Sex was determined by gonadal inspection, and measurements were taken to the nearest 0.1 mm with digital calipers by CDS. X-rays were taken with a company cabinet X-ray on Kodak paper exposed at 5 miliampheres and 30 volts for 1 minute 15 seconds. Museum abbreviations for specimens examined follow Leviton et al. (1985). Meristic and mensural characters were chosen based on Siler et al. (2010a): snout–vent length (SVL), axilla–groin distance (AGD), total length (TotL), midbody width (MBW), midbody height (MBH), tail length (TL), tail width (TW), tail height (TH), head length (HL), head width (HW), head height (HH), snout–forearm length (SnFa), eye diameter (ED), eye–narial distance (END), snout length (SNL), internarial distance (IND), fore-limb length (FLL), hind limb length (HLL), midbody scale-row count (MBSR), paravertebral scale-row count (PVSR), axilla–groin scale-row count (AGSR), Finger-III lamellae count (FinIIIlam), Toe-IV lamellae count (ToeIVlam), supralabial count (SL), infralabial count (IFL), supraciliary count (SC), and supraocular count (SO). Additionally, we counted the number of presacral vertebrae (PSV) from x-ray images of specimens. In the description, ranges are followed by mean ± standard deviation in parentheses. 313 Table 5.1. Summary of specimens corresponding to genetic samples included in the study. PNM/CMNH = deposited in the Cincinnati Museum of Natural History; SP = Sabah Parks Reference Collection; KU = University of Kansas Natural History Museum; LSUHC = La Sierra University Herpetological Collections; * = Holotypes of new species described in this paper. 314 Sp ec ie s V ou ch er Lo ca lit y G en ba nk A cc es si on N um be rs N D 1 N D 2 PT G ER 4 B D N F Lyg os om a bo wr in gi LS U H C 6 97 0 W es t M al ay si a Ple sti od on fa sc ia tu s K U 2 89 46 2 U ni te d St at es , T ex as , S m ith C ou nt y — H Q 90 74 23 H Q 90 75 26 H Q 90 72 24 Br ac hy m el es a pu s SP 0 69 15 M al ay si a, B or ne o, S ab ah , M t. K in ab al u H Q 90 73 31 H Q 90 74 33 H Q 90 75 33 H Q 90 72 33 Br ac hy m el es b on ita e K U 3 07 74 7 Ph ili pp in es , P ol ill o Is la nd , M un ic ip al ity o f P ol ill o Br ac hy m el es b on ita e K U 3 26 08 0 Ph ili pp in es , P ol ill o Is la nd , M un ic ip al ity o f P ol ill o Br ac hy m el es g ra ci lis PN M /C M N H H -1 16 9 Ph ili pp in es , M in da na o Is la nd , M un ic ip al ity o f T or il, M t. A po Br ac hy m el es g ra ci lis K U 3 26 09 8 Ph ili pp in es , M in da na o Is la nd , M un ic ip al ity o f K ib la w an H Q 90 73 91 H Q 90 74 94 H Q 90 75 94 H Q 90 72 94 Br ac hy m el es g ra ci lis K U 3 26 09 9 Ph ili pp in es , M in da na o Is la nd , M un ic ip al ity o f K ib la w an H Q 90 73 92 H Q 90 74 95 H Q 90 75 95 H Q 90 75 94 Br ac hy m el es g ra ci lis PN M /C M N H H -1 17 5 Ph ili pp in es , M in da na o Is la nd , M un ic ip al ity o f T or il, M t. A po — H Q 90 74 92 H Q 90 75 92 H Q 90 72 92 Br ac hy m el es g ra ci lis PN M /C M N H H -1 17 6 Ph ili pp in es , M in da na o Is la nd , M un ic ip al ity o f T or il, M t. A po H Q 90 73 90 H Q 90 74 93 H Q 90 75 93 H Q 90 72 93 Br ac hy m el es g ra ci lis PN M /C M N H H -1 42 8 Ph ili pp in es , M in da na o Is la nd , M al ag os E ag le S ta tio n Br ac hy m el es g ra ci lis PN M /C M N H H -1 64 1 Ph ili pp in es , M in da na o Is la nd , M un ic ip al ity o f K ia m ba , M t. B us a Br ac hy m el es p ito K U 3 27 93 5 Ph ili pp in es , M in da na o Is la nd , M un ic ip al ity o f R TR Br ac hy m el es p ito K U 3 27 93 6 Ph ili pp in es , M in da na o Is la nd , M un ic ip al ity o f R TR Br ac hy m el es p ito K U 3 27 93 7 Ph ili pp in es , M in da na o Is la nd , M un ic ip al ity o f R TR Br ac hy m el es a ni m PN M 9 76 6* Ph ili pp in es , C am ig ui n Su r I sl an d, M un ic ip al ity o f M am ba ja o Br ac hy m el es m iri am ae K U 3 27 69 2 Th ai la nd , N ak ho n R at ch as im a, S ak ae ra t E nv iro nm en ta l R es ea rc h C en te r H Q 90 73 33 H Q 90 74 35 H Q 90 75 35 H Q 90 72 35 Br ac hy m el es p at hf in de ri K U 3 24 06 3 Ph ili pp in es , M in da na o Is la nd , M un ic ip al ity o f G la n Br ac hy m el es p at hf in de ri K U 3 24 06 5 Ph ili pp in es , M in da na o Is la nd , M un ic ip al ity o f G la n Br ac hy m el es p at hf in de ri K U 3 24 06 6 Ph ili pp in es , M in da na o Is la nd , M un ic ip al ity o f G la n Br ac hy m el es sy am K U 3 10 94 1 Ph ili pp in es , S am ar Is la nd , M un ic ip al ity o f S an Jo se d e B ua n Br ac hy m el es sy am K U 3 10 82 5 Ph ili pp in es , S am ar Is la nd , M un ic ip al ity o f T af t Br ac hy m el es sy am K U 3 11 21 6 Ph ili pp in es , L ey te Is la nd , M un ic ip al ity o f B ay ba y H Q 90 73 83 H Q 90 74 85 H Q 90 75 85 H Q 90 72 85 Br ac hy m el es sy am K U 3 11 22 0 Ph ili pp in es , L ey te Is la nd , M un ic ip al ity o f B ay ba y H Q 90 73 84 H Q 90 74 86 H Q 90 75 86 H Q 90 72 86 Br ac hy m el es w al o K U 3 26 10 9 Ph ili pp in es , M in da na o Is la nd , M un ic ip al ity o f T ub ig an Br ac hy m el es w al o PN M 9 77 6 Ph ili pp in es , M in da na o Is la nd , M un ic ip al ity o f T am pa ka n, B ar an ga y Ta bl u, D at al M an gi si Br ac hy m el es w al o PN M 9 77 7* Ph ili pp in es , M in da na o Is la nd , M un ic ip al ity o f T am pa ka n, B ar an ga y Ta bl u, D at al M an gi si 315 Table 5.2. Models of evolution selected by AIC and applied for partitioned, Bayesian phylogenetic analyses1. Partition AIC Model Number of Characters ND1, 1st codon position GTR + Γ 322 ND1, 2nd codon position GTR + Γ 322 ND1, 3rd codon position GTR + Γ 322 ND2, 1st codon position GTR + Γ 287 ND2, 2nd codon position GTR + Γ 287 ND2, 3rd codon position GTR + Γ 287 BDNF GTR + Γ 715 PTGER4 HKY + Γ 490 1The model GTR + I + G was used for partitioned RAxMLHPC analyses. 316 Table 5.3. Uncorrected pairwise sequence divergence (%) for mitochondrial data (below diagonal) and nuclear data (above diagonal), for Brachymeles gracilis, B. pito, B. anim, B. syam, B. walo, and B. pathfinderi (Fig. 5.2). Percentages on the diagonal represent intraspecific genetic diversity for mitochondrial data (bolded for emphasis). 317 gra c il is pit o a n im sy a m wa lo pa th fin d e ri gra c il is 0 .4 – 3 .4 0 .5 – 0 .7 1 .0 0 .0 – 0 .2 0 .1 – 0 .4 0 .0 – 0 .2 pit o 8 .7 – 9 .4 0 .0 – 0 .3 0 .4 – 0 .5 0 .5 – 0 .7 0 .2 – 0 .7 0 .3 a n im 8 .4 – 8 .8 4 .2 — 0 .4 – 0 .5 0 .7 – 1 .0 0 .7 sy a m 9 .3 – 9 .9 9 .2 – 9 .6 8 .9 – 9 .4 0 .3 – 1 .9 0 .5 – 0 .9 0 .0 – 0 .2 wa lo 9 .1 – 1 0 .4 1 0 .1 – 1 0 .6 8 .9 – 1 0 .1 8 .1 – 1 0 .0 0 .0 – 5 .9 0 .1 – 0 .4 pa th fin d e ri 6 .0 – 6 .5 9 .2 – 9 .3 9 .2 9 .1 – 9 .5 9 .4 – 1 0 .0 0 .0 318 Species concept We follow the General Lineage Concept of species (de Queiroz, 1998, 1999) as a logical extension of the Evolutionary Species Concept (Simpson, 1961; Wiley, 1978; Frost and Hillis, 1990). We consider as distinct lineages those populations that are morphologically, and genetically distinct, especially if allopatric. Lineage-based species concepts have been successfully employed in the recognition of Philippine biodiversity (Brown et al., 2000, 2002, 2008, 2009; Brown and Guttman, 2002; Gaulke et al., 2007; Welton et al., 2009, 2010 a,b; Siler and Brown, 2010; Siler et al., 2011) due to the highly partitioned nature of the archipelago (Brown and Diesmos, 2009), and because the geological history of the islands has been so well documented (Voris, 2000; Hall, 2002; Yumul, 2009). In this study we use an estimate of Phylogenetic relationships as a guide for delimiting species but restrict our diagnoses of new species to those populations unambiguously diagnosed by differences in non-overlapping morphological character states. Results Phylogeny Trees recovered from ML and Bayesian analyses are identical in their support for five evolutionary lineages within the Brachymeles gracilis Complex (Fig. 5.2). The resulting 100 inferences from the partitioned RAxML maximum likelihood analysis show an average likelihood score of –ln L 12804.013201, with a single inference having the highest likelihood score of –ln L 12803.989734. No inferences support the monophyly of Brachymeles gracilis (Fig. 5.2). All analyses recover four major clades (Fig. 5.2, Clades A–C, F) within the B. gracilis Complex; however, we recover only weak support for interclade relationships in most 319 instances. The Camiguin Island population and B. gracilis hilong were recovered as a strongly supported clade in all analyses (Fig. 5.2, Clade A), as were populations of B. gracilis gracilis and B. pathfinderi (Fig. 5.2, Clade E). Populations from northwestern and southwestern Mindanao Island were always recovered as a monophyletic group (Fig. 5.2, Clade B), as were populations from the islands of Samar and Leyte (Fig. 5.2, Clade C). True B. gracilis hilong was never recovered as part of a monophyletic group with true B. gracilis gracilis. Uncorrected pairwise sequence divergences are generally low within the lineages defined here as species and high between these lineages (Table 5.3). Percent divergences for the mitochondrial and nuclear data, respectively, show that the monophyletic lineages defined by our phylogenetic analyses (B. gracilis gracilis, B. gracilis hilong, B. sp. nov. [Samar and Leyte islands], B. sp. nov. [Camiguin Sur Island], and B. sp. nov. [western Mindanao Island]) are distinguished from congeners by levels of genetic divergence nearly equal to, or greater than, those between previously defined species—viz., B. pathfinderi (Table 5.3; Fig. 5.2). The two most closely related lineages (B. sp. nov. [Camiguin Sur Island] and B. gracilis hilong) are separated by 4.2% mitochondrial sequence divergence. Sequence divergences among the other lineages within the B. gracilis Complex are greater than 8.1% (Table 5.3; Fig. 5.2). Intraspecific sequence divergences are low in comparison to divergences among monophyletic lineages with one exception being B. sp. nov. (western Mindanao Island; Table 5.3; Fig. 5.2). Although samples from the southwestern Mindanao populations are genetically similar to each other (Fig. 5.2, Populations 2, 3) and form a monophyletic group, there is a 5.9% sequence divergence between these populations and the northwestern (Fig. 5.2, Population 1) Mindanao population (Table 5.3; Fig. 5.2). We suspect that this highly supported clade (Fig. 5.2, Clade B) actually represents a complex of morphologically similar species; however, only a single juvenile from 320 the northwestern Mindanao population has ever been collected. Therefore, we conservatively consider all western Mindanao popluations (Fig. 5.2, Clade B, Populations 1–3) as members of a single, unique evolutionary lineage, pending the collection of additional samples from throughout western Mindanao Island. Unfortunately, no tissues of B. sampu have ever been collected, but we suspect, on the basis of overwhelming morphological similarity, that this species would be recovered within the B. gracilis Complex (Fig. 5.2). Morphology Superficially, the six lineages within the B. gracilis complex appear morphologically similar, especially in overall body size; however, upon closer inspection, numerous non-overlapping differences were detected in meristic, mensural, osteological, and color pattern characters for each complex member, readily defining six distinct lineages within the complex (Tables 5.4–5.6). Variation in morphological characters (Tables 5.4–5.6) mirrors the results observed in phylogenetic analyses, and supports the recognition of six Brachymeles gracilis group lineages. Characters differing among these six lineages include: relative tail length, presacral vertebrae number, head and body scale counts and patterns, and pigmentation patterns (Tables 5.4–5.6; species accounts below), all of which are typical morphological diagnostic characters employed historically by taxonomists working with this genus (review: Siler and Brown, 2010; Siler et al., in press c). We observed no intraspecific mensural or meristic differences between the sexes of any of the six species. In summary, each lineage (all but two of which are allopatric) possesses unique and non-overlapping suites of diagnostic character states of morphology, perfectly corresponding to the six clades defined in phylogenetic analyses of DNA sequence data. Combined with 321 Figure 5.2. Maximum clade credibility topology of Brachymeles inferred in this study resulting from Bayesian analyses of the combined mitochondrial + nuclear dataset (preferred ML tree, -ln L 12803.989734; ND1, ND2, BDNF, PTGER4). Terminals are labeled with taxonomic names, fore- and hind limb digit states, number of presacral vertebrae, and geographic distributions. 322 323 Figure 5.3. (Left) Map of the Philippine islands showing previously recognized distribution of Brachymeles gracilis (indicated by black shaded islands), and recognized distribution of B. pathfinderi (indicated by a star). (Right) Hypothesized distributions of B. gracilis, B. pito, B. anim, B. syam, B. walo, and B. sampu in the southern and southeastern Philippines. Sampling localities are indicated by shapes: black shapes represent sites where both specimens and tissues have been sampled, white shapes represent sites where only specimens have been sampled. Numbered sites correspond to population labels shown in Figure 5.2. The hypothesized geographic range of each species is indicated by shaded polygons. Shapes and color shades correspond to the map’s key 324 325 Table 5.4. Summary of meristic and mensural characters in all known medium-sized, pentadactyl species of Brachymeles. Sample size, body length and total length among males and females, and general geographical distribution (PAIC = Pleistocene Aggregate Island Complexes, sensu Brown and Diesmos, 2002) are included for reference (SVL, TotL, MBW, FLL, and HLL given as range over mean ± standard deviation; all body proportions given as percentage over mean ± standard deviation). In cases of scale count variation within species, numbers of individuals showing specific counts are given in parentheses. 326 g ra ci li s (1 3 m , 2 4 f) p it o ( 1 1 m , 1 4 f) a n im (1 m , 1 0 f) sy a m ( 9 m , 1 8 f) w a lo (1 m , 1 f) sa m p u ( 1 f) R an g e S o u th er n M in d an ao Is la n d E as te rn M in d an ao Isl an d C am ig u in S u r Isl an d S am ar & L ey te is la n d s Wes te rn M in d an ao Isl an d B as il an Is la n d G ro u p S VL (f) S VL (m ) 5 8 .6 – 8 3 .4 (6 9 .9 ± 6 .1 ) 6 0 .1 – 8 2 .3 (6 9 .6 ± 7. 9 ) 5 9 .9 – 8 1 .5 (71 .7 ± 6 .5 ) 6 1 .5 – 78 .5 (6 9 .8 ± 4 .5 ) 5 3 .6 – 8 0 .1 (75 .4 ± 5 .1 ) 75 .8 6 4 .2 – 76 .9 (71 .5 ± 3 .7) 6 5 .0 – 74 .6 (70 .2 ± 3 .2 ) 75 .5 6 1 .6 71 .9 — T o tL (f) T o tL (m ) 1 1 6 .4 – 1 4 6 .0 (1 2 7.7 ± 8 .0 ) 1 2 4 .4 – 1 6 1 .3 (1 3 7.8 ± 1 4 .8 1 1 7.8 – 1 5 9 .2 (1 3 2 .0 ± 1 2 .0 ) 1 1 6 .7 – 1 3 9 .4 (1 2 8 .0 ± 7.5 ) 1 1 7.6 – 1 4 1 .4 (1 2 8 .3 ± 8 .7 ) — 1 3 5 .8 – 1 5 9 .7 (1 4 7.7 ± 7. 9 ) 1 3 2 .4 – 1 4 6 .9 (1 4 0 .6 ± 7.4 ) 1 4 2 .6 1 1 7.3 — — M B W 8 .0 – 1 2 .0 (9 .4 ± 1 .0 ) 7.9 – 1 2 .1 (9 .9 ± 1 .1 ) 8 .9 – 1 2 .3 (1 0 .7 ± 1 .1 ) 7.7 – 1 1 .2 (9 .5 ± 0 .8 ) 8 .5 , 8 .0 8 .2 T L /S VL 7 9 – 1 0 2 (9 3 ± 6 ) 5 7 – 9 8 (79 ± 1 4 ) 5 4 – 8 4 (72 ± 1 2 ) 9 2 – 1 2 6 (1 0 8 ± 9 ) 9 0 , 8 9 — T W/M B W 5 7 – 79 (70 ± 5 ) 5 7 – 8 1 (70 ± 7) 6 1 – 8 2 (70 ± 8 ) 5 9 – 8 7 (74 ± 6 ) 8 7, 8 6 71 F L L 5 .9 – 8 .6 (7.2 ± 0 .8 ) 7.1 – 9 .3 (8 .3 ± 0 .6 ) 7.9 – 9 .1 (8 .3 ± 0 . 4 ) 8 .2 – 9 .9 (9 .1 ± 0 .5 ) 7.5 , 7.1 7.2 F L L /S VL 9 – 1 2 (1 0 ± 1 ) 1 0 – 1 4 (1 2 ± 1 ) 1 0 – 1 2 (1 1 ± 1 ) 1 1 – 1 5 (1 3 ± 1 ) 1 2 , 9 1 0 H L L 1 0 .3 – 1 4 .8 (1 2 .4 ± 1 .0 ) 1 2 .2 – 1 6 .0 (1 4 .0 ± 1 .1 ) 1 3 .6 – 1 5 .6 (1 4 .2 ± 0 . 6 ) 1 2 .3 – 1 6 .7 (1 4 .3 ± 1 .0 ) 1 2 .1 , 1 0 .3 1 3 .1 H L L /S VL 1 4 – 2 3 (1 8 ± 2 ) 1 7 – 2 3 (2 0 ± 1 ) 1 7 – 2 1 (1 9 ± 1 ) 1 7 – 2 3 (2 0 ± 2 ) 2 0 , 1 4 1 8 F in IIIla m 4 ( 1 1 ) 5 ( 2 6 ) 5 (2 5 ) 5 (1 1 ) 5 (2 7 ) 4 ( 1 ) 5 (1 ) 5 ( 1 ) T o eIVl am 7 ( 2 0 ) 8 ( 1 7 ) 8 (1 8 ) 9 (7) 8 ( 1 0 ) 9 (1 ) 8 ( 4 ) 9 ( 2 3 ) 6 (2 ) 8 (1 ) 327 T A B L E 5 .4 .— C on ti n u ed . bo ho le ns is (5 m , 1 4 f) bo ul en ge ri (7 m , 8 f) m in do re ns is (6 m , 1 2 f) ta yl or i (8 m , 1 3 f) R an ge B oh ol Is la nd L uzo n P A IC M in do ro Is la nd N eg ro s & C eb u Isl an d S VL (f) S VL (m ) 83 .8 –9 4. 0 (88 .4 ± 3 .1 ) 84 .1 –9 3. 6 (89 .1 ± 4 .1 ) 60 .5 –9 5. 5 (84 .0 ± 1 1. 2) 72. 3 –9 3. 1 (82 .5 ± 6 .7) 90 .0 –1 06 .8 (98 .8 ± 5 .3 ) 93 .9 –1 04 .2 (10 0. 2 ± 4 .1 ) 65 .8 –9 3. 2 (83 .9 ± 7.4 ) 83 .1 –9 9. 2 (87. 0 ± 5 .2 ) T ot L (f) T ot L (m ) 12 9. 6– 174 .8 (15 4. 1 ± 1 4. 7) 15 4. 5– 16 6. 2 (16 0. 7 ± 5 .9 ) 12 9. 7– 16 7.4 (15 9. 3 ± 1 3. 1) 12 4. 3– 173 .1 (15 1 .4 ± 1 9. 4) 16 2. 5– 20 6. 7 (18 0. 2 ± 1 4. 2) 16 5. 3– 19 7.0 (18 4. 9 ± 1 1. 5) 13 0. 3– 16 8. 5 (14 9. 9 ± 1 3. 0) 14 9. 6– 176 .7 (16 4. 3 ± 1 1. 3) M B W 11 .9 –1 5. 0 (13 .4 ± 1 .0 ) 9. 9– 14 .7 (12 .4 ± 1 .7) 12 .8 –2 0. 8 (16 .0 ± 1 .8 ) 11 .0 –1 6. 8 (13 .8 ± 1 .7) T L /S VL 53 –9 0 (76 ± 1 3) 67 –1 14 (89 ± 1 6) 60 –9 9 (85 ± 1 1) 69 –1 03 (83 ± 1 0) T W/M B W 62 –78 (70 ± 5 ) 60 –8 1 (70 ± 6 ) 54 –8 0 (69 ± 8 ) 54 –8 0 (69 ± 7) F L L 9. 0– 11 .2 (10 .1 ± 0 .7) 8. 2– 11 .7 (10 .5 ± 0 .8 ) 10 .0 –1 3. 0 (11 .4 ± 0 .8 ) 9. 0– 10 .4 (9. 8 ± 0 .4 ) F L L /S VL 10 –1 3 (11 ± 1 ) 12 –1 4 (13 ± 1 ) 10 –1 3 (11 ± 1 ) 10 –1 4 (1 2 ± 1 ) H L L 15 .4 –1 8. 7 (17. 2 ± 1 .0 ) 14 .3 –1 8. 7 (17. 2 ± 1 .1 ) 18 .8 –2 3. 1 (20 .6 ± 1 .2 ) 15 .6 –1 8. 7 (17. 0 ± 1 .0 ) H L L /S VL 18 –2 2 (19 ± 1 ) 18 –2 4 (21 ± 2 ) 18 –2 4 (21 ± 2 ) 18 –2 5 (20 ± 2 ) F in IIIla m 6 (19 ) 5 (14 ) 6 (1) 5 (16 ) 6 (2) 5 (12 ) 6 (9) T oe IVla m 9 (7) 10 (1 2) 9 (13 ) 10 (2 ) 8 (14 ) 9 (4) 9 (10 ) 10 (1 1) 328 Table 5.5. Summary of qualitative diagnostic characters (present, absent) in all known medium-sized, pentadactyl species of Brachymeles. The pairs of enlarged scales posterior to the postmental scale are abbreviated as chin shield pairs with reference to the 1st, 2nd, and 3rd pairs (when present). 329 gr ac il is (1 3 m , 2 4 f) pi to (1 1 m , 1 4 f) an im (1 m , 1 0 f) sy am (9 m , 1 8 f) w al o (1 m , 1 f ) sa m pu (1 f , 1 ju v. ) PS V 34 32 32 31 33 31 M B SR 24 –2 7 27 –3 0 26 –2 8 25 –2 6 26 , 2 6 24 A G SR 46 –4 9 44 –5 0 44 –4 9 42 –4 5 47 , 5 0 48 , 4 7 PV SR 67 –7 0 66 –7 3 65 –7 0 64 –6 7 70 , 7 2 69 SL 6 (3 7) 6 (2 5) 6 (1 1) 6 (2 7) 6 (2 ) 6 (1 ) IF L 6 (1 9) 7 (1 8) 6 (2 5) 6 (1 1) 6 (2 7) 6 (2 ) 6 (1 ) SC 6 (3 7) 6 (2 5) 6 (1 1) 6 (2 7) 6 (2 ) 6 (1 ) SO 5 (3 7) 5 (2 5) 5 (1 1) 5 (2 7) 5 (2 ) 5 (1 ) Pi ne al e ye sp ot – or + + – or + + – or + + Su pr an as al c on ta ct – – – – – – Pr ef ro nt al c on ta ct – or + – – or p oi nt – or p oi nt – or + – Fr on to pa ri et al c on ta ct – or + – or + + + + – Pa ri et al s co nt ac t + – or + + + + – or p oi nt 1s t c hi n sh ie ld p ai r co nt ac t – or + – or + – – – or + + E nl ar ge d ch in s hi el d pa ir s 2 2 or 3 2 3 3 3 C hi n sh ie ld p ai r si ze 1 < 2 or 1 > 2 1 < 2 or 3 < 1 < 2 1 < 2 3 < 1 < 2 3 < 1 < 2 3 < 1 < 2 C hi n sh ie ld p ai r se pa ra tio n1 1( 0/ 1) ; 2 (1 –3 ) 1( 0/ 1) ; 2 (1 –3 ) or 1( 0/ 1) ; 2 (1 ); 3 (3 ) 1( 1) ; 2 (1 –3 ) 1( 1) ; 2 (1 ); 3 (3 ) 1( 0/ 1) ; 2 (1 ); 3 (3 ) 1( 0) ; 2 (1 ); 3 (3 ) Su bo cu la r su pr al ab ia l 4t h an d 5t h 4t h an d 5t h 4t h an d 5t h 4t h an d 5t h 4t h an d 5t h 4t h an d 5t h Po st na sa l sm al l o r ab se nt 2 sm al l t o m od er at e sm al l t o m od er at e sm al l t o m od er at e sm al l t o m od er at e sm al l t o m od er at e D if fe re nt ia te d nu ch al s – – – – – – 1 P ar en th es es s ho w th e nu m be r of s m al l v en tr al s ca le r ow s se pa ra tin g ea ch e nl ar ge d pa ir o f ch in s hi el ds . 2 P os tn as al /s up ra na sa l f us io n 31 o f 51 s pe ci m en s (a du lts a nd ju ve ni le s) e xam in ed f or th is c ha ra ct er . 330 T A B L E 5. 5. — C on ti n u ed . bo ho le ns is (5 m , 1 4 f) bo ul en ge ri (7 m , 8 f ) m in do re ns is (6 m , 1 2 f) ta yl or i (8 m , 1 3 f) P S V 31 32 31 31 M B S R 26 –2 8 26 –2 7 26 –2 8 26 –2 8 A G S R 42 –4 6 42 –4 6 42 –4 5 42 –4 7 P V S R 63 –6 6 63 –6 6 63 –6 5 62 –6 9 S L 7 (1 9) 6 (1 2) 7 (3 ) 7 (1 8) 6 (2 1) IF L 7 (1 9) 7 (1 5) 6 (1 8) 7 (2 1) S C 6 (1 9) 5 (1 ) 6 (1 4) 6 (1 8) 6 (2 1) S O 5( 19 ) 5 (1 5) 5 (1 8) 5 (2 1) P in ea l e ye sp ot + + + + S up ra na sa l c on ta ct – – – or + – P re fr on ta l c on ta ct – – – or + – F ro nt op ar ie ta l c on ta ct + + + + P ar ie ta ls c on ta ct – or + – or + – or + – or + 1s t c hi n sh ie ld p ai r co nt ac t – or + + + – or + Enl ar ge d ch in s hi el d pa ir s 3 2 2 2 C hi n sh ie ld p ai r si ze 3 < 1 < 2 1 < 2 1 < 2 1 < 2 C hi n sh ie ld p ai r se pa ra ti on 1 1( 0/ 1) ; 2 (1 ); 3( 3) 1( 0/ 1) ; 2 (1 ) 1( 0) ; 2 (1 ) 1( 0) ; 2 (1 ) S ub oc ul ar s up ra la bi al 5t h an d 6t h 4t h an d 5t h 5t h an d 6t h 4t h an d 5t h P os tn as al m od er at e m od er at e m od er at e m od er at e D if fe re nt ia te d nu ch al s – – – – 1 P ar en th es es s ho w th e nu m be r of s m al l v en tr al s ca le r ow s se pa ra ti ng e ac h en la rg ed p ai r of c hi n sh ie ld s. 331 Table 5.6. Summary of univariate morphological variation among mensural characters in series of Brachymeles gracilis, B. pito, B. anim, B. syam, B. walo and B. sampu. gracilis (13 m; 24 f) pito (11 m; 14 f) anim (1 m; 10 f) syam (9 m; 18 f) walo (1 m; 1 f) sampu (1 f) SVL (m) 60.1–82.3 (69.4 ± 7.9) 61.5–71.5 (69.8 ± 4.5) 75.8 65.0–74.6 (70.1 ± 3.2) 61.6 — SVL (f) 58.6–83.4 (69.9 ± 3.1) 59.9–81.5 (71.7 ± 6.5) 63.6–80.1 (75.4 ± 5.1) 64.2–76.9 (71.5 ± 3.7) 75.5 71.9 AGD (m) 39.5–58.1 (46.3 ± 6.1) 38.8–54.1 (45.6 ± 3.8) 49.3 41.5–48.7 (44.7 ± 2.4) 38.9 — AGD (f) 39.6–56.6 (47.5 ± 4.4) 37.9–53.4 (46.0 ± 4.6) 39.8–54.2 (49.7 ± 4.3) 40.4–52.9 (46.6 ± 3.1) 49.3 49.7 TotL (m) 124.4–161.3 (137.8 ± 14.8) 116.7–139.4 (128.0 ± 7.5) 134.2 132.4–146.9 (140.6 ± 7.4) 117.3 — TotL (f) 116.4–146.0 (127.7 ± 8.0) 117.8–159.2 (132.0 ± 12.0) 117.6–141.4 (128.3 ± 8.7) 135.8–159.7 (147.7 ± 7.9) 142.6 110.1 MBW (m) 8.3–12.0 (9.6 ± 1.2) 8.6–11.6 (9.6 ± 0.9) 9.9 8.8–11.0 (9.4 ± 0.6) 8.5 — 332 MBW (f) 8.0–10.8 (9.3 ± 0.8) 7.9–12.1 (10.1 ± 1.2) 8.9–12.3 (10.8 ± 1.1) 7.7–11.2 (9.5 ± 0.9) 8.0 8.2 MBH (m) 5.6–9.9 (7.5 ± 1.3) 6.3–9.0 (7.8 ± 1.0) 7.8 6.4–8.4 (7.0 ± 0.7) 6.9 — MBH (f) 5.6–10.1 (7.3 ± 1.2) 5.3–9.6 (7.8 ± 1.4) 7.8–10.3 (9.2 ± 0.8) 5.6–8.0 (6.8 ± 0.7) 6.8 5.2 TL (m) 53.2–79.4 (63.5 ± 8.6) 44.3–67.0 (57.7 ± 8.2) 58.4 66.5–78.3 (72.9 ± 5.2) 55.7 — TL (f) 49.4–66.9 (58.9 ± 5.6) 34.4–77.7 (54.6 ± 11.9) 41.3–64.5 (53.8 ± 8.6) 66.5–89.1 (76.7 ± 6.4) 67.1 38.2 TW (m) 5.4–8.7 (6.9 ± 0.9) 6.1–7.7 (6.8 ± 0.4) 8.1 5.7–7.8 (7.0 ± 0.6) 7.4 — TW (f) 5.7–7.8 (6.4 ± 0.5) 6.2–8.0 (7.0 ± 0.5) 6.7–8.3 (7.5 ± 0.6) 5.9–8.6 (7.0 ± 0.6) 6.9 5.8 TH (m) 4.6–6.7 (5.5 ± 0.6) 5.0–6.4 (5.7 ± 0.4) 6.9 5.1–6.6 (5.8 ± 0.5) 5.1 — TH (f) 4.4–6.1 (5.3 ± 0.4) 4.6–6.7 (5.6 ± 0.7) 5.5–6.9 (6.1 ± 0.5) 4.7–6.8 (5.6 ± 0.6) 5.6 4.6 HL (m) 5.1–7.7 (6.6 ± 0.7) 6.3–7.5 (7.0 ± 0.4) 7.1 6.0–7.6 (6.7 ± 0.4) 4.8 — HL (f) 5.1–7.6 (6.5 ± 0.6) 6.4–8.3 (7.2 ± 0.4) 5.9–8.2 (7.3 ± 0.7) 6.3–7.8 (6.8 ± 0.4) 6.1 6.8 333 HW (m) 6.6–8.4 (7.4 ± 0.5) 6.7–8.0 (7.4 ± 0.4) 7.8 6.5–7.7 (7.1 ± 0.3) 6.4 — HW (f) 6.2–8.2 (7.0 ± 0.4) 6.4–9.1 (7.7 ± 0.7) 6.7–8.2 (7.6 ± 0.5) 6.5–8.4 (7.1 ± 0.5) 6.3 6.7 HH (m) 4.1–6.1 (5.1 ± 0.6) 4.6–6.4 (5.5 ± 0.5) 5.1 4.0–55.5 (5.1 ± 0.5) 4.0 — HH (f) 3.9–5.6 (4.9 ± 0.5) 4.5–6.5 (5.5 ± 0.6) 4.7–6.0 (5.5 ± 0.4) 3.9–5.3 (4.6 ± 0.5) 4.2 4.6 SnFa (m) 15.6–22.0 (18.3 ± 2.0) 16.2–19.6 (18.7 ± 1.0) 20.8 18.5–20.8 (19.6 ± 0.8) 16.4 — SnFa (f) 16.0–20.7 (17.7 ± 1.2) 17.2–20.8 (19.5 ± 1.0) 18.4–20.6 (19.5 ± 0.6) 183–21.0 (19.6 ± 0.8) 19.7 17.5 ED (m) 1.0–1.5 (1.3 ± 0.1) 1.2–1.5 (1.4 ± 0.1) 1.4 1.2–1.7 (1.4 ± 0.1) 1.3 — ED (f) 1.0–1.5 (1.3 ± 0.1) 1.3–1.8 (1.4 ± 0.2) 1.1–1.6 (1.4 ± 0.2) 1.2–1.4 (1.3 ± 0.1) 1.4 1.8 END (m) 2.2–3.5 (2.8 ± 0.3) 2.8–3.1 (2.9 ± 0.1) 3.1 2.7–3.5 (3.1 ± 0.2) 2.8 — END (f) 2.3–3.1 (2.6 ± 0.2) 2.4–3.1 (2.8 ± 0.2) 3.0–3.3 (3.1 ± 0.1) 2.9–3.4 (3.1 ± 0.1) 3.0 2.6 SNL (m) 3.5–4.7 (4.0 ± 0.4) 3.8–4.5 (4.1 ± 0.2) 4.4 3.8–4.4 (4.2 ± 0.2) 3.9 — SNL (f) 3.3–4.2 3.5–4.2 4.1–4.5 3.8–4.4 3.7 3.8 334 (3.8 ± 0.3) (3.9 ± 0.2) (4.4 ± 0.1) (4.1 ± 0.1) IND (m) 1.9–2.8 (2.3 ± 0.3) 2.1–2.4 (2.2 ± 0.1) 2.5 2.1–2.3 (2.2 ± 0.1) 2.1 — IND (f) 1.9–2.6 (2.2 ± 0.2) 2.1–2.5 (2.3 ± 0.1) 2.0–2.5 (2.4 ± 0.2) 1.9–2.4 (2.1 ± 0.1) 2.6 2.3 FLL (m) 5.9–8.6 (7.3 ± 0.9) 7.1–8.8 (8.1 ± 0.6) 8.7 8.8–9.8 (9.3 ± 0.3) 7.5 — FLL (f) 6.2–8.6 (7.1 ± 0.7) 7.5–9.3 (8.4 ± 0.5) 7.9–9.1 (8.3 ± 0.4) 8.2–9.9 (9.0 ± 0.5) 7.1 7.2 HLL (m) 11.3–14.8 (12.4 ± 1.0) 12.2–15.7 (13.6 ± 1.1) 13.6 12.5–15.7 (14.5 ± 1.0) 12.1 — HLL (f) 10.3–14.7 (12.4 ± 1.0) 13.1–16.0 (14.3 ± 1.0) 13.8–15.6 (14.3 ± 0.6) 12.3–16.7 (14.2 ± 1.1) 10.3 13.1 335 biogeographic evidence, and clearly separate geographical ranges (with one exception), our data suggest the presence of six evolutionary lineages, worthy of taxonomic recognition. Taxonomic conclusions Our estimate of phylogeny (Fig. 5.2), biogeographically separate ranges on islands or distinct geologic components of islands, diagnostic, non-overlapping morphological character states, and genetic distances between the taxa (Table 5.3) indicate the presence of a new species from Samar and Leyte islands, a new species from Camiguin Sur Island, and a new species from western Mindanao Island (Table 5.3; Fig. 5.2) and the distinctiveness of B. sampu from Basilan and Bubuan islands. Each of the six species of the B. gracilis complex is morphologically distinct from all others and each of the six species of the B. gracilis Complex included in phylogenetic analyses are genetically distinct. Each monophyletic lineage, with the exception of the one occurring on Samar and Leyte islands and the one occurring on Basilan and Bubuan islands, is endemic to single islands within the Mindanao PAIC, thereby providing additional support for the distinctiveness of each clade’s evolutionary history and lineage integrity. Previous descriptions of members of the B. gracilis Complex have applied the name B. gracilis to southern Mindanao populations (Taylor, 1922a; Brown, 1956; Brown and Rabor, 1967; Brown and Alcala, 1980; Siler et al., 2010a; Siler and Brown, 2010). One of the unique diagnostic characters consistently reported for Brachymeles gracilis has been the absence of postnasals resulting from the fusion of the postnasal with the supranasal scale (Brown and Rabor, 1967; Brown and Alcala, 1980). Brown and Rabor (1967) and Brown and Alcala (1980) report this fused scale to be present in more than 60% and 50%, respectively, of the B. gracilis individuals examined. This unique character (fused postnasal/supranasal) has never been 336 recorded for any other member of the B. gracilis Complex. Accordingly, we recognize Brachymeles gracilis as a species that occurs only in central and southcentral Mindanao Island, based on a suite of morphological characters that closely allies it with all previously published accounts (Taylor, 1922a; Brown, 1956; Brown and Rabor, 1967; Brown and Alcala, 1980; Siler et al., 2010a; Siler and Brown, 2010): (1) supralabials six; (2) infralabials six or seven; (3) midbody scale rows 24–27; (4) axilla–groin scale rows 46–49; and (5) postnasal/supranasal fusion present in more than 50% of population. The two examined specimens of B. cf. gracilis from Basilan Island housed at the California Academy of Sciences closely match Taylor’s (1918) description of B. sampu based on the following suite of morphological characters: (1) supralabials six; (2) infralabials six; (3) midbody scale rows 24; and (4) supranasals separated; (5) frontoparietals separated; (6) parietals separated or in point contact; (7) first pair of enlarged chin shields moderately to broadly contacting on midline; and (8) enlarged chin shields in three pairs. We therefore recognize B. sampu as a species that occurs on Basilan and its surrounding islets (including Buban Island; Fig. 5.2). Finally, we recognize B. pito as a species that occurs only in northeast Mindanao Island, and hereby recognize the three additional lineages within the B. gracilis species complex each as new species. TAXONOMIC ACCOUNTS Brachymeles gracilis (Fischer 1885) Fig. 5.4 Senira bicolor (part), Gray, 1845:98. Eumeces (Riopa) gracilis, Fischer, 1885:85, Type locality: “Mindanao Island,” Philippines (No. 337 846 reported to be deposited in the Dresden Museum). Brachymeles gracilis, Boettger, 1886:103; Boulenger, 1887:378; Boettger, 1893:112; Taylor, 1917:270; 1918:257; 1922 a:247; 1922 b:287; (part) Brown and Alcala, 1970:112. Brachymeles gracilis gracilis, Brown, 1956:10; Brown and Rabor, 1967:537; Brown and Alcala, 1980:37. Brachymeles sampu, Taylor, 1918:254. Diagnosis.—Brachymeles gracilis can be distinguished from congeners by the following combination of characters: (1) body size medium (SVL 58.6–83.4 mm); (2) limbs pentadactyl; (3) limb length moderate; (4) relative tail length long; (5) Finger-III lamellae four or five; (6) Toe-IV lamellae seven or eight; (7) supralabials six; (8) infralabials six or seven; (9) suparciliaries six; (10) supraoculars five; (11) midbody scale rows 24–27; (12) axilla–groin scale rows 46–49; (13) paravertebral scale rows 67–70; (14) supranasals separate; (15) parietals in contact; (16) postnasal/supranasal fusion present or absent; (17) enlarged chin shields in two pairs; (18) nuchal scales undifferentiated; (19) fourth and fifth supralabial below eye; (20) auricular opening present; and (21) presacral vertebrae 34 (Tables 5.4, 5.5). Comparisons.—Characters distinguishing Brachymeles gracilis from all medium-sized, pentadactyl species of Brachymeles are summarized in Tables 5.4 and 5.5. Brachymeles gracilis most closely resembles B. anim, B. walo, and B. sampu. However, B. gracilis differs from these three taxa by having seven or eight Toe-IV lamellae (vs. eight or nine [B. anim], six [B. tiboli], eight [B. sampu]), a greater number of presacral vertebrae (34 vs. 31 [B. sampu], 32 [B. anim], 33 [B. tiboli]), six or seven infralabials (vs. six), and the presence or absence of a fused postnasal/supranasal scale (vs. absence; Fig. 5.4). Brachymeles gracilis further differs from B. anim and B. sampu by having four or five Finger-III lamellae (vs. five); from B. anim and B. 338 walo by having a tendancy towards a longer relative tail length (TL/SVL up to 102% vs. less than 90%); from B. walo and B. sampu by having enlarged chind shields in two pairs (vs. 3); and from B. sampu by the presence of contact between parietal scales (vs. presence or absence). Brachymeles gracilis can be distinguished from all limbless species of Brachymeles (B. apus, B. lukbani, B. minimus, B. miriamae, B. vermis) by having limbs; and from all non-pentadactyl species of Brachymeles (B. bonitae, B. cebuensis, B. elerae, B. muntingkamay, B. pathfinderi, B. samarensis, B. tridactylus, B. wright, sp. nov. [Leyte Island; Siler et al., in press c], sp. nov. [Lapinig Group Islands; Siler et al., in press c], sp. nov. [Catanduanes Island; Siler et al., in press c], sp. nov. [Central Bicol Peninsula, Luzon Island; Siler et al., in press c], and sp. nov. [Southern Bicol Peninsula, Luzon Island; Siler et al., in press c]) by having pentadactyl (vs. non-pentadactyl) limbs. Description (based on holotype description [Fischer, 1885] and 37 referred specimens).—Details of the head scalation of an adult male (KU 326097) are shown in Figure 5.4. Measurements of the holotype are provided below in brackets. Body medium-sized, moderately slender; maximum SVL 82.3 mm for males, 83.4 mm for females, [67.0, subadult] (Tables 5.4, 5.5); head weakly differentiated from neck, nearly as wide as body, HW 8.7–12.3% (10.2 ± 0.8) SVL, 93.0–130.9% (109.8 ± 9.4) HL; HL 28.9–44.4% (36.8 ± 4.7) SnFa; SnFa 22.5–29.8% (25.6 ± 1.5) SVL; snout short, rounded in dorsal and lateral profile, SNL 47.1–71.4% (59.5 ± 7.2) HL; ear opening visible, small; eyes small, ED 1.3–2.4% (1.8 ± 0.3) SVL, 15.3–25.7% (19.7 ± 2.6) HL, 34.7–58.4% (48.0 ± 6.2) END, pupil subcircular; body slightly depressed, nearly uniform in thickness, MBW 94.2–190.8% (130.4 ± 20.5) MBH; scales smooth, glossy, imbricate; longitudinal scale rows at midbody 24 (CAS 124804, 124808, 124811, 139293, 139300, 139309, CAS-SU 24165, KU 326101, 326103, 326106, MCZ 26539, 26549), 25 (CAS 139295, 139307, 339 MCZ 26550), 26 (CAS 124803, 124806–07, 139294, 139303–05, 139308, CAS-SU 24163, CMC 12170, 12171, KU 326096, 326099, 326104, 326107, 326299, MCZ 26541, 26543, 26548, TNHC 59948, 60016), or 27 (MCZ 26546) [24]; paravertebral scale rows 67 (CAS 124804, 124806, 139293, 139300, 139304, 139309, CAS-SU 24165, MCZ 26549, TNHC 59948), 68 (CAS 124808, 124811, 139295, 139303, CAS-SU 24163, CMC 12171, KU 326101, 326106, MCZ 26543, 26550, TNHC 60016), 69 (CAS 124803, 124807, 139294, 139305, CMC 12170, KU 326096, MCZ 26548), or 70 (CAS 139307–08, KU 326099, 326103–04, 326107, 236299, MCZ 26539, 26541, 26546); axilla–groin scale rows 46 (CAS 124804, 124806, 139293, 139300, 139304, CAS-SU 24165, MCZ 26549), 47 (CAS 124808, 124811, 139295, 139309, CAS-SU 24163, CMC 12171, KU 326101, 326106, MCZ 26543, 26550), 48 (CAS 124803, 124807, 139294, 139303, 139305, CMC 12170, KU 326096, MCZ 26548, TNHC 59948), or 49 (CAS 139307–08, KU 326099, 326103–04, 326107, 326299, MCZ 26539, 26541, 26546, TNHC 60016) [49]; limbs short, well developed, pentadactyl, digits small; FinIIIlam four (CAS 124808, 124811, 139295, 139300, 139304–05, 139307–08, CMC 12171, TNHC 59948, 60016) or five (CAS 124803–04, 124806–07, 139293–94, 139303, 139309, CAS-SU 24163, 24165, CMC 12170, KU 326096, 326099, 326101, 326103–04, 326106–07, 326299, MCZ 26539, 26541, 26543, 26546, 26548–50); ToeIVlam seven (CAS 124808, 124811, 139295, 139305, CMC 12171, KU 326096, 326099, 326101, 326103–04, 326106–07, MCZ 26539, 26541, 26543, 26546, 26548–50, TNHC 59948) or eight (CAS 124803–04, 124806–07, 139293–94, 139300, 139303–04, 139307–09, CAS-SU 24163, 24165, CMC 12170, KU 326299, TNHC 60016); FLL 12.4–19.4% (15.4 ± 1.7) AGD [13.3], 8.6–12.4% (10.3 ± 1.0) SVL [9.0]; HLL 20.6–35.1% (26.5 ± 2.7) AGD [26.7], 14.0–22.6% (17.8 ± 1.6) SVL [17.9]; order of digits from shortest to longest 340 for hand: V = I < IV = II < III, for foot: V = I < II < III < IV; tail not as wide as body, gradually tapered towards end, TW 56.8–78.9% (70.3 ± 5.5) MBW, TL 79.5–102.1% (92.5 ± 5.8) SVL. Rostral projecting onto dorsal snout to point in line with middle of nasal, broader than high, in contact with frontonasal; frontonasal wider than long; nostril ovoid, in center of single pentagonal nasal, longer axis directed anterodorsally and posteroventrally; supranasals present, large, broadly separated; postnasals present and small (CAS 124807, 124812, 139307–08, 139310, CAS-SU 24160, KU 326096, 326100, MCZ 26539, 26541, 26543–44, 26546, 26548–50), present and highly reduced (CAS 124808, 139294, 139301–02), fused to supranasal on one side of the head (CAS 139303, 139306, CAS-SU 24158, 24162, KU 326106), or fused to supranasals on both sides of the head (CAS 124806, 124809–11, 139296–300, 139309, 139311, CAS-SU 24159, 24161, 24163–65, 24171, KU 326089, 326099, 326101–05, 326107–08); prefrontals separated (CAS 124806, 124808, 139293–96, 139299, 139301–05, CMC 12170–71, KU 326089, 326096, 326099, 326100–05, 326107–08, 326299, MCZ 26539, 26541, 26543), in point medial contact (FMNH 52642, KU 326106, MCZ 26544), or in moderate medial contact (FMNH 52647, MCZ 26546, 26548–50); frontal diamond-shaped, its anterior margin in narrow to broad contact with frontonasal, narrowly separated from frontonasal, or in moderate medial contact with frontonasal, in contact with first two anterior supraoculars, 4× wider than anterior supraocular; supraoculars five; frontoparietals large, each in contact with supraoculars II–IV, frontoparietals separated (CAS 124806, 124808, 139295, 139301, 139303–05, KU 326299), in point medial contact (KU 326101), or in moderate medial contact (CAS 139293–94, 139296, 139299, 139302, CMC 12170–71, FMNH 52642, 52647, KU 326089, 326096, 326099–100, 326102–08, MCZ 26539, 26543–44, 26546, 26548–50); interparietal large, its length roughly equal to midline length of frontoparietal, longer than wide, subdiamond-shaped, wider anteriorly, 341 with pineal eyespots present and distinct (CAS 139296, CMC 12170–71, FMNH 52642, KU 326089, 326096, 326099, 326100–08, 326299, MCZ 26539, 26541, 26543–44, 26546, 26549–50), present and indistinct (CAS 124806, 124808, 139294–95, 139299, 139302, 139304–05), or absent (FMNH 52647, CAS 139293, 139301, 139303, MCZ 26548); parietals broader than frontoparietals, in broad contact behind interparietal; nuchals undifferentiated; two loreals, decreasing in height from anterior to posterior, anterior loreal slightly narrow than and higher than posterior loreal; preocular single; supraciliaries six, the anteriormost contacting prefrontal and separating posterior loreal from first supraocular, posteriomost extending to posterior edge of fifth supraocular; single subocular scale row complete, in contact with supralabials; lower eyelid with one row of scales on dorsal margin; supralabials six, first 1.5× size of others, fourth and fifth below eye; infralabials six (CMC 12170–71, KU 326096, 326099, 326101, 326103–04, 326106–07, 326299, MCZ 26539, 26541, 26543, 26546, 26548–50, TNHC 59948, 60016) or seven (CAS 124803–04, 124806–08, 124811, 139293–95, 139300, 139303–05, 139307–09, CAS-SU 24163, 24165) (Fig. 5.4). Mental wider than long, in contact with first infralabials; postmental single, enlarged, its width greater than width of mental; followed by two pairs of enlarged chin shields, first pair of enlarged chin shields separated (CAS 139294, CMC 12170–71, KU 326099, 326299, MCZ 26550), in point medial contact (CAS 124808, 139293, MCZ 26541), or in moderate to broad medial contact (CAS 124806, 139295–96, 139299, 139301–05, FMNH 52642, 52647, KU 326089, 326096, 326100–08, MCZ 26539, 26543–44, 26546, 26548–49); second pair wider than, or narrower than, first, broadly separated by one, two, or three medial scales (Fig. 5.4). Scales on limbs smaller than body scales; scales on dorsal surfaces of digits large, wrapping around lateral edges of digits; lamellae undivided; palmar surfaces of hands and plantar surfaces 342 of feet covered by small, irregular scales, each with raised anterior edges; scales on dorsal surface of hands and feet smaller than limb scales, lacking raised edges. Coloration in preservative (based on holotype description and 37 referred specimens).—Ground color of body is medium brown throughout or with distinctly darker middorsal region (KU 319934–35, 319938–39, 326097, 326105–06, 326108). Light dorsolateral stripes are present in some specimens (KU 326096–98, 326100–04, 326107), absent in remainder. Dorsal surfaces of head, and snout are uniformly medium brown (majority of specimens) or with darker marbling (e.g., KU 319936, 319938, 326100–03). Lateral surfaces of the head are nearly uniformly dark brown; supraocculars are slightly darker than surrounding scales. Postocculr and tympanic regions are distinctly darker than remaining portions of the head and neck in some specimens (KU 326100, 326105–06, 326108). The rostral, supranasals, postnasals, first suprlabials and infralabials and mental scales are all medium gray. Suprlabials are dark brown and infralabials, mental, and chin shields are a lighter shade of orange-brown. Trunk coloration is variable, with dorsal surfaces dark to medium brown with a series of faint longitudinal streaks, each composed of a series of distinct dark spots either confined to the distal edge of each scale or traversing the whole scale. Lateral surfaces, lack longitudinal streaks and are either homogeneous dark brown or possess equally spaced spots of dark pigment, with each spot on distal tip of each scale. Ventral surfaces exhibit a wide range of variation with homogeneous dark brown in some specimens (KU 319937–38, 326103, 326106, 326108) to very light orange-brown withalmost no dark pigment in others (KU 319939–40, 326096, 326099, 326104, 326299). In specimens of intermediate hues of pigmentation (KU 319935–36 and remainder of series), ventral surfaces are marked by evenly spaced dark brown spots (corresponding to the distal edge of each scale) on a 343 light ornge-brown background. Ventral surfaces of the head and neck devoid of any dark pigmentation (KU 326096–97, 326099, 326103) or with a light ornge-brown ground coloration with dark streaks composed of dark brown spots on each scale. The posterior portion of trunk with dark brown spots or clusters of striations at the distal edge of each scale, becoming more pronounced posteriorly; subcaudal regions nearly solid dark brown (e.g., KU 326106, 326108), with dark brown spots on the distal edge of each scale (e.g., KU 326100, 326104), or with clusters of faint, dark, striations on the distal edges of scales (remainder). Tail coloration becomes more distinct distally, with contrasting darker shades of brown and lighter ground colration at the tail’s tip, which is nearly black in many specimens. Ventral surfaces of hands and feet are light gray to cream, with slightly darker fingers and toes. The precloacals region is slightly lighter than the surrounding ventrals and subcaudals. Coloration in life.—Coloration in life is unrecorded; however, because Brachymeles specimens do not change significantly during preservation (CDS, RMB personal observation), we suspect that the preserved coloration and patterns are much like those in life. Distribution.—Brachymeles gracilis is known only from central, southern, and southeastern Mindanao Island (Fig. 5.3). No mention of the specific locality, or province, on Mindanao Island was ever given for the holotype (Fischer, 1885). Although we are certain of our identification of B. gracilis, that specimens referred here to this species match the type description, and that no other species can possibly be confused with B. gracilis, we are unable to pinpoint the type locality on the basis of available specimens. Ecology and natural history.—Brachymeles gracilis occurs in primary- and secondary-growth forest habitats. In South Cotabato Province, Mindanao Island (Fig. 5.2), B. gracilis has been documented to occur in sympatry with B. schadenbergi (Siler and Brown, 2010) and B. 344 tiboli. Interestingly, this is the first documented case of two species of Brachymeles in the same body form and body size class (B. gracilis and B. tiboli) occuring in sympatry. All other sympatric communities of Brachymeles are made up of distinctly different body forms (e.g., large pentadactyl, medium pentadactyl, non-pentadactyl, limbless). The eastern populations of B. gracilis (e.g., Davao Province populations) are documented to occur in sympatry with B. orientalis (a large-bodied form; Siler and Brown, 2010). In addition to B. gracilis, B. tiboli, B. orientalis, and B. schadenbergi, two other species of Brachymeles have been confirmed to occur on Mindanao Island (B. pito and B. pathfinderi; Siler and Brown, 2010; Siler et al., in press a). We have evaluated this species against the IUCN criteria for classification, and find that it does not qualify for Critically Endangered, Endangered, Vulnerable, or Near Threatened status. Brachymeles gracilis has been documented to have a broad geographic distribution and is quite abundant at all sampled localities. We therefore classify this species as Least Concern, LC (IUCN, 2010). Other sympatric scincid species observed on Mindanao Island include: Eutropis indeprensa, E. multicarinata, E. multifasciata, E. englei, Lamprolepis smaragdina, L. pulchella, L. quadrivittata, Sphenomorphus abdictus abdictus, S. acutus, S. atrigularis, S. cumingi, S. cf. mindanensis, S. coxi, S. fasciatus, S. jagori, S. llanosi, S. steerei, S. variegatus, Tropidophorus misaminus, T. partelloi. Brachymeles pito Brown and Rabor 1967 Fig. 5.4 Brachymeles pito, Brown and Rabor, 1967:543 (type locality: Barrio Balang-balang, Mt. Hilong-hilong, Diuata Mountains, Agusan Province, Mindanao Island, Philippines, 9° 03' 345 20.77" N, 125° 37' 40.8" E [holotype: CAS-SU 24407]). Brachymeles gracilis hilong, Brown and Alcala, 1970:113; Brown and Alcala, 1980:39. Diagnosis.—Brachymeles pito can be distinguished from congeners by the following combination of characters: (1) body size medium (SVL 59.9–81.5 mm); (2) limbs pentadactyl; (3) limb length moderate; (4) relative tail length moderate; (5) Finger-III lamellae five; (6) Toe-IV lamellae eight or nine; (7) supralabials six; (8) infralabials six; (9) suparciliaries six; (10) supraoculars five; (11) midbody scale rows 27–30; (12) axilla–groin scale rows 44–50; (13) paravertebral scale rows 66–73; (14) pineal eyespot present; (15) supranasals separate; (16) prefrontals separate; (17) postnasal/supranasal fusion absent; (18) enlarged chin shields in two or three pairs; (19) nuchal scales undifferentiated; (20) fourth and fifth supralabial below eye; (21) auricular opening present; and (22) presacral vertebrae 32 (Tables 5.4, 5.5). Comparisons.—Characters distinguishing Brachymeles pito from all medium-sized, pentadactyl species of Brachymeles are summarized in Tables 5.4 and 5.5. Brachymeles pito most closely resembles B. syam; however, B. pito differs from this taxon by having a shorter relative tail length (TL/SVL up to 126% vs. less than 98%), a greater number of presacral vertebrae (32 vs. 31), a greater number of midbody scale rows (27–30 vs. 25–26), a tendency towards a greater number of axilla–groin scale rows (up to 50 vs. less than or equal to 45), a tendency towards a greater number of paravertebral scale rows (up to 73 vs. less than or equal to 67), enlarged chind shields in two or three pairs (vs. three), and the absence of contact between prefrontal scales (vs. presence or absence). Brachymeles pito can be distinguished from all limbless species of Brachymeles (B. apus, B. lukbani, B. minimus, B. miriamae, B. vermis) by having limbs; and from all non-pentadactyl species of Brachymeles (B. bonitae, B. cebuensis, B. elerae, B. muntingkamay, B. pathfinderi, B. 346 samarensis, B. tridactylus, B. wright, sp. nov. [Leyte Island; Siler et al., in press c], sp. nov. [Lapinig Group Islands; Siler et al., in press c], sp. nov. [Catanduanes Island; Siler et al., in press c], sp. nov. [Central Bicol Peninsula, Luzon Island; Siler et al., in press c], and sp. nov. [Southern Bicol Peninsula, Luzon Island; Siler et al., in press c]) by having pentadactyl (vs. non-pentadactyl) limbs. Description (based on holotype and 25 referred specimens).—Details of the head scalation of an adult female are shown in Figure 5.4. Measurements of the holotype (CAS-SU 22407) are provided below in brackets. Body medium-sized, moderately slender; maximum SVL 78.5 mm for males, 81.5 mm for females, [61.5, subadult] (Tables 5.4, 5.5); head weakly differentiated from neck, nearly as wide as body, HW 9.6–12.9% (10.7 ± 0.8) SVL, 98.9–122.7% (106.3 ± 5.0) HL; HL 32.5–43.5% (37.2 ± 2.2) SnFa; SnFa 23.3–30.1% (27.1 ± 1.5) SVL; snout short, rounded in dorsal and lateral profile, SNL 47.2–71.9% (56.4 ± 5.1) HL; ear opening visible, small; eyes small, ED 1.7–3.0% (2.0 ± 0.3) SVL, 16.9–27.9% (20.0 ± 2.2) HL, 40.4–74.8% (50.0 ± 6.7) END, pupil subcircular; body slightly depressed, nearly uniform in thickness, MBW 102.4–154.7% (128.9 ± 14.9) MBH; scales smooth, glossy, imbricate; longitudinal scale rows at midbody 27 (CAS 102406, 133577–78, 133581, 133692, 133704, KU 319937–38, 319940), 28 (CAS 133582, 133609, 133612, 133693, 133703, 133705–06, 133743, 133745–46, 133747, CAS-SU 24315, 24411, KU 319935–36), or 30 (CAS-SU 24407) [30]; paravertebral scale rows 66 (CAS 102406), 67 (CAS 133704, CAS-SU 24315), 68 (CAS 133578, 133581–82, 133609, 133703, 133745–47, CAS-SU 24411, KU 319936–38, 319940), 69 (CAS 133612, 133692–93, KU 319935), 70 (CAS 133577, 133706, 133743, CAS-SU 24407), or 73 (CAS 133705) [70]; axilla–groin scale rows 44 (CAS 102406), 45 (CAS 133747, CAS-SU 24315), 46 (CAS 133582, 133609, 133612, 133692, 133703, CAS-SU 24411, KU 319936–38, 319940), 47 (CAS 133578, 347 133581, 133693, 133704, 133743, 133746, CAS-SU 24407, KU 319935), 48 (CAS 133577, 133706, 133745), or 50 (CAS 133705) [47]; limbs short, well developed, pentadactyl, digits short; FinIIIlam 5 [5]; ToeIVlam eight (CAS 102406, 133581, 133609, 133693, 133703–04, 133706, 133743, 133745–47, CAS-SU 24315, 24411, KU 319935–38, 319940) or nine (CAS 133577–78, 133582, 133612, 133692, 133705, CAS-SU 24407) [9]; FLL 15.3–22.0% (18.2 ± 1.7) AGD, 10.3–14.0% (11.8 ± 0.9) SVL; HLL 27.0–37.2% (30.8 ± 2.8) AGD, 17.5–23.4% (19.8 ± 1.5) SVL; order of digits from shortest to longest for hand: I = V < IV = II < III, for foot: V < I < II < IV = III; tail not as wide as body, gradually tapered towards end, TW 56.9–81.4% (70.5 ± 6.6) MBW, TL 57.5–97.9% (78.8 ± 13.8) SVL [89.7]. Rostral projecting onto dorsal snout to point in line with middle of nasal, broader than high, in broad contact with frontonasal; frontonasal wider than long; nostril ovoid, in center of single trapezoidal nasal, longer axis directed anterodorsally and posteroventrally; supranasals present, large, broadly separated; postnasals present, small to moderate; prefrontals moderately separated; frontal nearly diamond-shaped, its anterior margin in moderate contact with frontonasal, in contact with first two anterior supraoculars, 3.5× wider than anterior supraocular; supraoculars five; frontoparietals moderate, each in contact with supraoculars II–IV, frontoparietals separated (CAS 133578, 133704, 133743, KU 319940), in point medial contact (CAS 133579, KU 319937), or in moderate medial contact (CAS 133581, 133705, KU 319934–36, 319938–39); interparietal large, its length roughly 2× length of frontoparietal, longer than wide, subdiamond- shaped, wider anteriorly; parietals roughly as broad as frontoparietals, separated (KU 319935, 319940), in point medial contact (KU 319934–38), or in moderate medial contact (CAS 133578–79, 133581, 133704–05, 133743, KU 319934, 319936, 319939); nuchals undifferentiated; two loreals, decreasing in size from anterior to posterior, anterior loreal about as long and slightly 348 higher than posterior loreal; preocular single; supraciliaries six, the anteriormost contacting prefrontal and separating posterior loreal from first supraocular, posteriomost extending to midline of fifth supraocular; single subocular scale row complete, in contact with supralabials; lower eyelid with one row of scales on dorsal margin; supralabials six, first 1.5× size of others, fourth and fifth below eye; infralabials six (Fig. 5.4). Mental wider than long, in contact with first infralabials; postmental single, enlarged, its width greater than width of mental; followed by two or three pairs of enlarged chin shields, first pair of enlarged chin shields separated (CAS 133578–79, 133743, KU 319934–40), in point medial contact (CAS 133704), or in moderate medial contact (CAS 133581, 133705), second pair wider than first, broadly separated by single medial scale, third pair absent (CAS 133578, 133581, 133704–05, 133743), or present (CAS 133579, KU 319934–40) and separated by three to five medial scales (Fig. 5.4). Scales on limbs smaller than body scales; scales on dorsal surfaces of digits large, wrapping around lateral edges of digits; lamellae undivided; palmar surfaces of hands and plantar surfaces of feet covered by small, irregular scales, each with raised anterior edges; scales on dorsal surface of hands and feet smaller than limb scales, lacking raised edges. Coloration in preservative (based on holotype description and 25 referred specimens).—The ground color of the body of B. pito is medium brown with dark brown longitudinal streaks, with dark streaks traversing each scale. The species lacks any sign of color pattern differentiation between dorsal and lateral surfaces except for a tendency towards more darkly pigmented streaks in middoorsal region and a progressively lighter pattern on ventral surfaces. Light dorsolateral stripes are completely absent. Dorsal surfaces of head, and snout are uniformly light brown (CAS 133704), light brown with darker marbling (CAS 133581, 133704), or are uniformly dark 349 brown (CAS 133579, 133743). Lateral surfaces of the head are uniformly dark brown with light scale sutures; supraocculars are slightly darker than surrounding scales. The rostral, supranasals, postnasals, first suprlabials and infralabials and mental scales are all medium gray. Suprlabials are dark brown and infralabials, mental, and chin shields are a slightly lighter shade of orange-brown. Trunk coloration is relatively invariant. Lateral surfaces, lack possess longitudinal streaks similar to those of dorsum and become increasingly lighter ventrally. Ventral surfaces distinctly lighter than lateral and dorsal coloration, either nearly devoid of dark pigment (CAS 133581) or with very faint streaks of diffuse darker brown spots (on per scale). Ventral surfaces of the head and neck devoid of any dark pigmentation (CAS133581, 133704–05) darker brown ground color with light scale margins (CAS133579, 133743). Ventral tail is not distinctly different from ventral trunk coloration, but some specimens exhibit slightly darker tail tips (CAS 133581, 133743). Ventral surfaces of hands and feet are medium gray, with slightly darker fingers and toes. The precloacals region is not noticeably different form the surrounding ventrals and subcaudals. Coloration in life.—Coloration in life is unrecorded; however, because Brachymeles specimens do not change significantly during preservation (CDS, RMB personal observation), we suspect that the preserved coloration and patterns are much like those in life. Distribution.—Brachymeles pito is known only from northwestern Mindanao Island (Fig. 5.3). Ecology and natural history.—Brachymeles pito occurs in primary- and secondary-growth forest habitats. In contrast to B. gracilis and B. tiboli, B. pito does not occur in sympatry with any other medium-sized, pentadactyl species of Brachymeles. However, B. orientalis also occurs 350 throughout the recognized range of B. pito. In addition to B. pito and B. orientalis, four other species of Brachymeles have been confirmed to occur on Mindanao Island (B. gracilis, B. tiboli, B. pathfinderi, and B. schadenbergi; Siler and Brown, 2010; Siler et al., in press a). Based on our expectation that this species will likely qualify for a threatened category in the near future, we would recommend classification of B. pito as Near Threatened, NT, based on the following criteria: VU B1ab(iii); D2 (IUCN, 2010). Other sympatric scincid species observed on Mindanao Island include: Eutropis indeprensa, E. multicarinata, E. multifasciata, E. englei, Lamprolepis smaragdina, L. pulchella, L. quadrivittata, Sphenomorphus abdictus abdictus, S. acutus, S. atrigularis, S. cumingi, S. cf. mindanensis, S. coxi, S. fasciatus, S. jagori, S. llanosi, S. steerei, S. variegatus, Tropidophorus misaminus, T. partelloi. Brachymeles sampu Taylor 1918: 254 Fig. 5.5 Brachymeles sampu, Taylor, 1918:254, Type locality: Bubuan Island, Tapiantana Group, Sulu Province, Philippines. Brachymeles gracilis, Taylor, 1922 a:247; 1922 b:287; (part) Brown and Alcala, 1970:112. Brachymeles gracilis gracilis, Brown, 1956:10; Brown and Rabor, 1967:537; Brown and Alcala, 1980:37. Designation of a neotype for Brachymeles sampu.—Taylor (1918) clearly declared a type specimen, deposited at the Philippine Bureau of Science under collection No. 1989, for B. sampu. In a subsequent revision he (Taylor 1922a), synonymized B. sampu with B. gracilis, basing the revised description of B. gracilis on the type specimen of B. sampu which he then 351 (incorrectly) reported to be Philippine Bureau of Science collection No. 1666. We assume that Taylor’s (1922a) reference to specimen No. 1666 as the type specimen of B. sampu was in error, that Philippine Bureau of Science No. 1989 was the valid holotype for B. sampu, and that Philippine Bureau of Science No. 1666 was a non-type specimen of B. gracilis. Unfortunately the Philippine Bureau of Science was destroyed and all specimens destroyed during the firebombing of Manila in World War II (see Brown and Alcala, 1978). In the absence of an existing holotype and in accordance with article No. 75 of the International Code of Zoological Nomenclature (ICZN, 1979), we designate a neotype for this species. Accordingly, we choose an adult female specimen from the geographically proximate island of Basilan (Fig. 5.3). Two specimens from Taylor’s collections on Basilan Island have been examined in the collections at CAS. Both specimens agree with Taylor’s (1918) holotype description; from these collections we have chosen a female neotype. Neotype.—CAS 60366 (E. H. Taylor Field No. 1173), adult female, collected in Isabela City, Basilan Province, Basilan Island, Philippines, by E. H. Taylor. Diagnosis.—Brachymeles sampu can be distinguished from congeners by the following combination of characters: (1) body size medium (SVL 71.9 mm); (2) limbs pentadactyl; (3) limb length moderate; (4) Finger-III lamellae five; (5) Toe-IV lamellae eight; (6) supralabials six; (7) infralabials six; (8) suparciliaries six; (9) supraoculars five; (10) midbody scale rows 24; (11) axilla–groin scale rows 48; (12) paravertebral scale rows 69; (13) pineal eyespot present; (14) supranasals separate; (15) prefrontals separate; (16) frontoparietals separate; (17) first pair of enlarged chin shields in contact; (18) postnasal/supranasal fusion absent; (19) enlarged chin shields in three pairs; (20) nuchal scales undifferentiated; (21) fourth and fifth supralabial below eye; (22) auricular opening present; and (23) presacral vertebrae 31 (Tables 5.4, 5.5). 352 Comparisons.—Characters distinguishing Brachymeles sampu from all medium-sized, pentadactyl species of Brachymeles are summarized in Tables 5.4 and 5.5. Brachymeles sampu most closely resembles B. gracilis, B. anim, and B. tiboli. However, B. sampu differs from these three taxa by having eight Toe-IV lamellae (vs. six [B. tiboli], seven or eight [B. gracilis], eight or nine [B. anim]), fewer presacral vertebrae (31 vs. 32 [B. anim], 33 [B. tiboli], 34 [B. gracilis]), the presence of a pineal eyespot (vs. presence or absence), the absence of contact between prefrontal scales (vs. presence or absence), the absence of contact between frontoparietal scales (vs. presence or absence [B. gracilis], presence [B. anim, B. tiboli]), and the presence of contact between the first pair of enlarged chin shields (vs. presence or absence [B. gracilis, B. tiboli], absence [B. anim]). Brachymeles sampu further differs from B. gracilis and B. walo by having five Finger-III lamellae (vs. four or five); from B. gracilis and B. anim by having enlarged chin shields in three pairs (vs. two); and from B. gracilis by having six infralabials (vs. six or seven) and by the absence of a fused postnasal/supranasal scale (vs. presence or absence). Brachymeles sampu can be distinguished from all limbless species of Brachymeles (B. apus, B. lukbani, B. minimus, B. miriamae, B. vermis) by having limbs; and from all non-pentadactyl species of Brachymeles (B. bonitae, B. cebuensis, B. elerae, B. muntingkamay, B. pathfinderi, B. samarensis, B. tridactylus, B. wright, sp. nov. [Leyte Island; Siler et al., in press c], sp. nov. [Lapinig Group Islands; Siler et al., in press c], sp. nov. [Catanduanes Island; Siler et al., in press c], sp. nov. [Central Bicol Peninsula, Luzon Island; Siler et al., in press c], and sp. nov. [Southern Bicol Peninsula, Luzon Island; Siler et al., in press c]) by having pentadactyl (vs. non-pentadactyl) limbs. Description of neotype.—Details of head scalation in CAS 60366 are shown in Figure 5.5. Adult female, body medium in size, moderately slender, SVL 71.9 mm; head weakly 353 differentiated from neck, nearly as wide as body, HW 9.3% SVL, 97.8% HL; HL 38.9% SnFa; SnFa 24.3% SVL; snout short, broadly rounded in dorsal profile, bluntly rounded in lateral profile, SNL 55.2% HL; ear opening visible, small; eyes small, ED 2.4% SVL, 25.8% HL, 69.0% END, pupil subcircular; body slightly depressed, nearly uniform in thickness, MBW 158.1% MBH; scales smooth, glossy, imbricate; longitudinal scale rows at midbody 24; paravertebral scale rows 69; axilla–groin scale rows 48; limbs short, well developed, pentadactyl, digits small; FinIIIlam 5; ToeIVlam 8; FLL 14.4% AGD, 10.0% SVL; HLL 26.2% AGD, 18.1% SVL; order of digits from shortest to longest for hand: I = V < IV = II < III, for foot: V = I < II < IV = III; tail regenerated, not as wide as body, gradually tapered towards end, TW 70.8% MBW. Rostral projecting onto dorsal snout to point in line with anterior edge of nasal, broader than high, in broad contact with frontonasal; frontonasal wider than long; nostril ovoid, in center of single trapezoidal nasal, longer axis directed anterodorsally and posteroventrally; supranasals present, large, broadly separated; postnasals present, small; prefrontals moderately separated; frontal suboctagonal-shaped, fragmented posteriorly (Fig. 5), its anterior margin in moderate contact with frontonasal, in contact with first two anterior supraoculars, 4× wider than anterior supraocular; supraoculars five; frontoparietals moderate, broadly separated, each frontoparietal in contact with supraoculars II–IV; interparietal large, its length roughly 2× length of frontoparietal, longer than wide, diamond-shaped; parietals roughly as broad as frontoparietals, moderately separated behind interparietal; nuchals undifferentiated; two loreals, decreasing in size from anterior to posterior, anterior loreal about as long as and moderately higher than posterior loreal; preocular single; supraciliaries six, the anteriormost contacting prefrontal and separating posterior loreal from first supraocular, posteriomost extending to midline of fifth 354 supraocular; single subocular scale row complete, in contact with supralabials; lower eyelid with one row of scales on dorsal margin; supralabials six, first 1.5× size of other supralabials, fourth and fifth below eye; infralabials six (Fig. 5.5). Mental wider than long, in contact with first infralabials; postmental single, enlarged, its width greater than width of mental; followed by three pairs of enlarged chin shields, first pair in moderate medial contact, second pair wider than first, moderately separated by single medial scale, third pair narrower than first and second pairs, separated by three medial scales (Fig. 5.5). Scales on limbs smaller than body scales; scales on dorsal surfaces of digits large, wrapping around lateral edges of digits; lamellae undivided; palmar surfaces of hands and plantar surfaces of feet covered by small, irregular scales, each with raised anterior edges; scales on dorsal surface of hands and feet smaller than limb scales, lacking raised edges. Coloration of neotype in preservative.— Ground color of body dark gray-brown, with few color features and no apparent differences between dorsal, lateral and ventral surfaces of trunk and tail. Dorsal surfaces of head, and limbs, colored like trunk, with few lighter brown blotches on head scales; snout slightly darker than remainder of head. Suprlabials slightly darker brown than infralabials, mental, and chin shields. Regenerated portion of tail (distal one third) slightly lighter than remainder. Trunk coloration invariant; all surfaces medium brown with a series of very faintly indistinct longitudinal streaks, each composed of a series slightly darker spots on the distal edge of each scale. Ventral body surfaces dark homogeneous gray-brown; subcaudal region similar with slightly lighter regenerated portion towards tail tip. Ventral surfaces of hands and feet light gray; fingers 355 and toes light gray. Precloacals slightly not noticeably lighter than surrounding ventrals. We assume that coloration has considerably faded in the 95 years since the neotype was preserved. Coloration in life.—“Above and below light brown, each scale with a large slightly darker spot; a lighter stripe from behind eye to hind leg” (Taylor, 1918). Measurements and scale counts of neotype in mm.—SVL 71.9; AGD 49.7; TotL 110.1; MBW 8.2; MBH 5.2; TL 38.2; TW 5.8; TH 4.6; HL 6.8; HW 6.7; HH 4.6; SnFa 17.5; ED 1.8; END 2.6; SNL 3.8; IND 2.3; FLL 7.2; HLL 13.1; MBSR 24; PVSR 69; AGSR 48; FinIIIlam 5; ToeIVlam 8; SL 6; IFL 6; SC 6; SO 5. Variation.—Morphometric variation of the series is summarized in Table 5.6. We are aware of only one adult and one subadult specimen of B. sampu in museum collections (CAS 60365–66). We observed the following minor variation in scale contact and scale row counts between the neotype and the subadult specimen: axilla–groin scale row counts of 47 (CAS 60365; subadult) or 48 (CAS 60366; neotype); parietals separated (CAS 60366; neotype) or in point medial contact (CAS 60365; subadult); frontal fragmented posteriorly (CAS 60366; neotype) or unbroken (CAS 60365; subadult). The subadult has noticeably more distinct longitudinal streaks on the dorsal survaces of the body (each stream composed of spots, confinded to distal edges of dorsal scales), distint light dorsolateral stripes, a darker tail tip, uniformly brown head scales, and a light brown ventral surfaces of the hed and neck. Distribution.—Brachymeles sampu is known only from Basilan and Bubuan islands (Fig. 5.3). Ecology and natural history.—Taylor (1918) did not provide any information regarding the microhabitat preferences of Brachymeles sampu; however, we assume that the species occurs in disturbed and secondary-growth forest on the islands of Basilan and Bubuan. On Basilan Island, 356 B. sampu is found in sympatry with B. schadenbergi. We have evaluated this species against the IUCN criteria for classification, and find that it qualifies for the status of Vulnerable, VU, based on the following criteria: VU B2ab(iii); D2 (IUCN, 2010). Other sympatric scincid species observed on Basilan Island include: Emoia atrocostata, Eutropis multicarinata, E. rudis, E. multifasciata, Lamprolepis smaragdina, Lipinia quadrivittata, Sphenomorphus atrigularis, S. fasciatus, S. jagori, S. variagatus, Tropidophorus misaminus. Brachymeles anim sp. nov. Figs. 5.3, 5.5 Holotype.—PNM 9766 (RMB Field No. 8223, formerly KU 310359), adult male, collected under rotting logs in secondary-growth forest (10:00–12:30 hr) on 19 June 2007, in Sitio Pamahawan, Barangay Pandan, Municipality of Mambajao, Camiguin Sur Province, Camiguin Sur Island, Philippines (09°15'00" N, 124°42'57.6" E; WGS-84), by J. Fernandez. Paratypes.—Four adult females (CAS-SU 26142, 26144, 26231, 26236) and two juveniles of undetermined sex (CAS-SU 26145–46), collected on 30 June 1966, in Dago-okan, 2 km south of Catibawasan Falls, Municipality of Mambajao, Camiguin Sur Province, Camiguin Sur Island, Philippines (09°11'24.9" N, 124°43'36.01" E; WGS-84), by L. C. Alcala; one juvenile of undetermined sex (CAS-SU 26294) collected on 3 July 1966, in Sitio Basiao, Barrio Naasag, Municipality of Mambajao, Camiguin Sur Province, Camiguin Sur Island, Philippines (09°13'9.95" N, 124°39'18" E; WGS-84), by L. C. Alcala; one juvenile of undetermined sex (CAS-SU 26295) collected on 3 July 1966, on the northwest side of Nasawa crater, Municipality of Mambajao, Camiguin Sur Province, Camiguin Sur Island, Philippines (09°11'14.17" N, 357 124°41'45.6" E; WGS-84), by L. C. Alcala; two adult females (CAS-SU 26166, 26185), one juvenile female (CAS-SU 26165), one juvenile male (CAS-SU 16184), collected on 4 July 1966, in Barrio Naasag, Municipality of Mambajao, Camiguin Sur Province, Camiguin Sur Island, Philippines (09°13'9.95" N, 124°39'18" E; WGS-84), by L. C. Alcala; three adult females (CAS-SU 28199, 28331, 28358), one juvenile female (CAS-SU 28359), and two juveniles of undetermined sex (CAS-SU 28314, 28329) collected between 15 and 27 May 1967, 4.5–8.0 km NE of Catarman Town, Municipality of Catarman, Camiguin Sur Province, Camiguin Sur Island, Philippines (09°07'32.02" N, 124°40'32.02" E; WGS-84), by L. C. Alcala; one adult female (CAS 139031) collected on 1 March 1973, in Kantinbay, Municipality of Mambajao, Camiguin Sur Province, Camiguin Sur Island, Philippines (09°11'50.1" N, 124°43'12" E; WGS-84), by L. C. Alcala. Diagnosis.—Brachymeles anim can be distinguished from congeners by the following combination of characters: (1) body size medium (SVL 53.6–80.1 mm); (2) limbs pentadactyl; (3) limb length moderate; (4) relative tail length short; (5) Finger-III lamellae five; (6) Toe-IV lamellae eight or nine; (7) supralabials six; (8) infralabials six; (9) suparciliaries six; (10) supraoculars five; (11) midbody scale rows 26–28; (12) axilla–groin scale rows 44–49; (13) paravertebral scale rows 65–70; (14) supranasals separate; (15) frontoparietals in contact; (16) parietals in contact; (17) first pair of enlarged chin shields separate; (18) postnasal/supranasal fusion absent; (19) enlarged chin shields in two pairs; (20) nuchal scales undifferentiated; (21) fourth and fifth supralabial below eye; (22) auricular opening present; and (23) presacral vertebrae 32 (Tables 5.4, 5.5). Comparisons.—Characters distinguishing Brachymeles anim from all medium-sized, pentadactyl species of Brachymeles are summarized in Tables 5.4 and 5.5. Brachymeles anim 358 most closely resembles B. gracilis, B. tiboli, and B. sampu. However, B. anim differs from these three taxa by having eight or nine Toe-IV lamellae [vs. six [B. tiboli], seven or eight [B. gracilis], eight [B. sampu], 32 presacral vertebrae (vs. 31 [B. sampu], 33 [B. tiboli], 34 [B. gracilis]), and by the absence of contact between the first pair of enlarged chin shields (vs. presence or absence [B. gracilis, B. tiboli], presence [B. sampu]). Brachymeles anim further differs from B. gracilis and B. walo by having a shorter relative tail length (TL/SVL less than 84% vs. up to 102% [B. gracilis] and 90% [B. tiboli]) and five Finger-III lamellae (vs. four or five); from B. walo and B. sampu by having enlarged chin shields in two pairs (vs. three); from B. gracilis and B. sampu by the presence of contact between frontoparietal scales (vs. presence or absence [B. gracilis], absence [B. sampu]); from B. gracilis by having six infralabials (vs. six or seven) and by the absence of a fused postnasal/supranasal scale (vs. presence or absence); and from B. sampu by having a greater number of midbody scale rows (26–28 vs. 24). Brachymeles anim can be distinguished from all limbless species of Brachymeles (B. apus, B. lukbani, B. minimus, B. miriamae, B. vermis) by having limbs; and from all non-pentadactyl species of Brachymeles (B. bonitae, B. cebuensis, B. elerae, B. muntingkamay, B. pathfinderi, B. samarensis, B. tridactylus, B. wright, sp. nov. [Leyte Island; Siler et al., in press c], sp. nov. [Lapinig Group Islands; Siler et al., in press c], sp. nov. [Catanduanes Island; Siler et al., in press c], sp. nov. [Central Bicol Peninsula, Luzon Island; Siler et al., in press c], and sp. nov. [Southern Bicol Peninsula, Luzon Island; Siler et al., in press c]) by having pentadactyl (vs. non-pentadactyl) limbs. Description of holotype.—Details of the head scalation are shown in Figure 5.5. Adult male, body medium in size, moderately slender, SVL 75.8 mm; head weakly differentiated from neck, nearly as wide as body, HW 10.2% SVL, 109.6% HL; HL 34.1% SnFa; SnFa 27.4% SVL; snout 359 short, broadly rounded in dorsal and lateral profile, SNL 61.9% HL; ear opening visible, small; eyes small, ED 1.8% SVL, 19.5% HL, 45.1% END, pupil subcircular; body slightly depressed, nearly uniform in thickness, MBW 127.0% MBH; scales smooth, glossy, imbricate; longitudinal scale rows at midbody 26; paravertebral scale rows 68; axilla–groin scale rows 49; limbs short, well developed, pentadactyl, digits small; FinIIIlam 5; ToeIVlam 8; FLL 17.6% AGD, 11.5% SVL; HLL 27.6% AGD, 18.0% SVL; order of digits from shortest to longest for hand: V < I < IV = II < III, for foot: I < V < II < IV = III; tail regenerated, not as wide as body, gradually tapered towards end, TW 81.6% MBW. Rostral projecting onto dorsal snout to point in line with anterior one third of nasal, broader than high, in broad contact with frontonasal; frontonasal wider than long; nostril ovoid, in center of single trapezoidal nasal, longer axis directed anteroventrally and posterodorsally; supranasals present, large, broadly separated; postnasals present, moderate; prefrontals moderately separated; frontal subdiamond-shaped, its anterior margin in moderate contact with frontonasal, in contact with first two anterior supraoculars, 2.5× wider than anterior supraocular; supraoculars five; frontoparietals moderate, in moderate medial contact, each frontoparietal in contact with interior three supraoculars; interparietal moderate, its length roughly 1.5× length of frontoparietal, slightly longer than wide, subdiamond-shaped, wider anteriorly; parietals roughly as broad as frontoparietals, in broad medial contact behind interparietal; nuchals undifferentiated; two loreals, decreasing in size from anterior to posterior, anterior loreal slightly longer than and about as high as posterior loreal; preocular single; presubocular single; supraciliaries six, the anteriormost contacting prefrontal and separating posterior loreal from first supraocular, posteriomost extending to posterior edge of fifth supraocular; single subocular scale row complete, in contact 360 with supralabials; lower eyelid with one row of scales on dorsal margin; supralabials six, first nearly 2× size of other supralabials, fourth and fifth below eye; infralabials six (Fig. 5.5). Mental wider than long, in contact with first infralabials; postmental single, enlarged, its width greater than width of mental; followed by two pairs of enlarged chin shields, first pair moderately separated by singl medial scale, second pair wider than first, moderately separated by one, two, or three medial scales (Fig. 5.5). Scales on limbs smaller than body scales; scales on dorsal surfaces of digits large, wrapping around lateral edges of digits; lamellae undivided; palmar surfaces of hands and plantar surfaces of feet covered by small, irregular scales, each with raised anterior edges; scales on dorsal surface of hands and feet smaller than limb scales, lacking raised edges. Coloration of holotype in preservative.—The ground color of the body is light (lateral surfaces) to medium (middorsal surface) brown,with very two faintly lighter dorsolateral stripes enclosing a distinctly darker middorsal region. Dorsal surfaces of the head, forelimbs, hind limbs, and basal tail region darker brown. Head scales mottled light and dark brown, similar to dorsal body scales but slightly darker. Temporal region distinctly darker than remaining portions of the head and neck. Supraocular scales and other supralabial scales ligher gray-umber. Rostral, supranasals, postnasals, first suprlabials and infralabials and mental scale medium gray. Trunk coloration variable; each dorsal scale with dark brown blotch on the anterior and posterior one fourth to one third of the scale. The resulting color pattern. a field of uniformly distributed dark brown spots not corresponding to underlying scales. Each spot consequently lies at the distal margin of each scale and bleeds over on to the basal edge of the next posteriorly adjacent scale. On lateral surfaces, each spot more or less confined to distal tip of each scale; on the ventrum, distal edge of each scale marked with fine array of three to four radiating lines, 361 together giving the appearance of dark smudge pigmentation at the distal edge of each scale. Ventral body surfaces rich orange-brown; ventral surfaces of head, neck and subcaudal coloration similar to remaining ventrum. Ventral surfaces of hands and feet dark gray; fingers and toes nearly black. Precloacals slightly lighter than surrounding ventrals. Coloration of holotype in life.—Coloration in life is unrecorded; however, because Brachymeles specimens do not change significantly during preservation (CDS, RMB personal observation), we suspect that the preserved coloration and patterns are much like those in life. Measurements and scale counts of holotype in mm.—SVL 75.8; AGD 49.3; TotL 134.2; MBW 9.9; MBH 7.8; TL 58.4; TW 8.1; TH 6.9; HL 7.1; HW 7.8; HH 5.1; SnFa 20.8; ED 1.4; END 3.1; SNL 4.4; IND 2.5; FLL 8.7; HLL 13.6; MBSR 26; PVSR 68; AGSR 49; FinIIIlam 5; ToeIVlam 8; SL 6; IFL 6; SC 6; SO 5. Variation.—Morphometric variation of the series is summarized in Table 5.6. Among the 20 specimens examined for the degree of contact between head scales, we observed the following variation: prefrontals in point medial contact (CAS 139031, CAS-SU 26142, 26231, 26236, 28331, 28359, KU 310359) or separated (CAS-SU 16184, 26144–46, 26165–66, 26185, 26294–95, 28199, 28314, 29329, 28358); frontoparietals in moderate to broad medial contact (CAS 139031, CAS-SU 16184, 26142, 26144–46, 26166, 26185, 26231, 26294–95, 28199, 28314, 28329, 28331, 28358, 28359, KU 310359) or in point medial contact (CAS-SU 26165, 26236). A single individual (CAS-SU 26142) was observed to possess a single, large frontoparietal scale, resulting from the fusion of the frontoparietals. Scale counts were observed to vary among the measured series. Specimens were observed to have midbody scale row counts of 26 (CAS-SU 26166, 28199, 28358, KU 310359) and 28 (CAS 139031, CAS-SU 16184, 26142, 26144, 26165, 26185, 26231, 26236, 26295, 28331); axilla– 362 groin scale row counts of 44 (CAS-SU 26166), 45 (CAS-SU 28199, 28358), 47 (CAS-SU 26142, 26144, 26231, 26236, 28331), 49 (CAS 139031, CAS-SU 26165, 26185, KU 310359), and 50 (CAS-SU 16184, 26295); and paravertebral scale row counts of 65 (CAS-SU 26166), 66 (CAS-SU 28199, 28358), 68 (CAS-SU 26142, 26144, 26231, 26236, 28331, KU 310359), 69 (CAS 139031, CAS-SU 26165), and 70 (CAS-SU 16184, 26185, 26295). We also observed lamellae counts and the presence of a pineal eyespot to vary among the specimens examined. The number of Toe-IV lamellae varied between eight (CAS-SU 26142, 26144, 26146, 26166, 26185, 26231, 26236, 26294, 28199, 28314, 28331, 28358, 28359, KU 310359) and nine (CAS 139031, CAS-SU 16184, 26145, 26165, 26295, 28329). Pineal eyespots were observed to be present (CAS 139031, CAS-SU 16184, 26145–46, 26165, 26185, 26231, 26236, 26294–95, 28199, 28329, 28331, 28358–59) or absent (CAS-SU 26142, 26144, 26166, 28314, KU 310359). Coloration of the type series is generally very consistent. Some specimens (holotype, CAS-SU 26144, 26231) have a distinctly darker temporal and tympanic region; others have well developed dorsolater lines (CAS-SU 26144, 28358). Most specimens possess ventral coloration matching the holotype; four have nearly immaculate cream ventral surfaces (CAS-SU 26166, 28199, 28314, 28359). Distribution.—Brachymeles anim is known only from Camiguin Sur Island (Fig. 5.3). Ecology and natural history.—Brachymeles anim occurs in agricultural habitats, as well as in disturbed and secondary-growth forest. Little original, forest remains on Camiguin Sur Island, but we assume the species once also occurred in first-growth forest at low elevations. Individuals have been observed in the rotting material within fallen logs. Over the last several years, multiple herpetological expeditions to Camiguin Sur Island have resulted in the 363 observation of only a single specimen of this island endemic species. However, not enough data is available to determine if this is an indication of a declining population on the island. This species is found in sympatry with B. orientalis (Siler and Brown, 2010). We have evaluated this species against the IUCN criteria for classification, and find that it qualifies for the status of Vulnerable, VU, based on the following criteria: VU B2ab(iii); D2 (IUCN, 2010). Other sympatric scincid species observed on Camiguin Sur Island include: Eutropis multifasciata, Lamprolepis smaragdina, Sphenomorphus abdictus abdictus, S. coxi, S. fasciatus, S. variegatus, Tropidophorus misaminus. Etymology.—The island of Camiguin Sur is volcanic in origin, with five major volcanic structures: Mt. Hibok-Hibok, Mt. Vulcan, Mt. Mambajao, M. Guinsiliban, and Mt. Uhay. Since its formation, the island has experienced regular volcanic activity, with several major eruptions resulting in the death of thousands of the island’s inhabitants and the complete destruction of several coastal towns. The specific epithet is chosen in recognition of the island’s volatile geologic history, and is derived from the latin word “Vulcan,” the ancient Roman god of fire. Suggested common name: Camiguin Sur Slender Skink. Brachymeles syam sp. nov. Figs. 5.3, 5.6, 5.7 Holotype.—PNM 9767 (CDS Field No. 2772, formerly KU 310828), adult male, collected under rotting coconut husks in secondary-growth forest (10:00–12:30 hr) on 18 October 2007, in Taft Forest, Barangay San Rafael, Municipality of Taft, Eastern Samar Province, Samar Island, Philippines (11°48'9.18" N, 125°17'33.936" E; WGS-84), by CDS and J. Fernandez. 364 Paratopotypes.—Five adult males (KU 310826, 310830–31, 310834, 310941), 14 adult females (KU 310731, 310820–21, 310827, 310829, 310835, 310928–31, 310933–34, 310937, 310939), one juvenile male (KU 310838) and 11 juveniles of undetermined sex (KU 310730, 310822–25, 310832–33, 310836–37, 310932, 310935) collected between 11 and 26 October 2007. Paratypes.—Three adult males (KU 311216, 311218, PNM 9768), four adult females (KU 311223, PNM 9769, 9773–74), and six juveniles of undetermined sex (KU 311220–21, PNM 9770–72, 9775, ) collected under rotting logs in secondary-growth forest (10:00–12:30 hr) between 29 October and 7 November 2007, in the Sitio San Vicente Tree Nursery, Barangay Pilim, Baybay City, Leyte Province, Leyte Island, Philippines (10°43'35" N, 124°49'05" E; WGS-84), by CDS and J. Fernandez. Diagnosis.—Brachymeles syam can be distinguished from congeners by the following combination of characters: (1) body size medium (SVL 64.2–76.9 mm); (2) limbs pentadactyl; (3) limb length moderate; (4) relative tail length long; (5) Finger-III lamellae five; (6) Toe-IV lamellae eight or nine; (7) supralabials six; (8) infralabials six; (9) suparciliaries six; (10) supraoculars five; (11) midbody scale rows 25–26; (12) axilla–groin scale rows 42–45; (13) paravertebral scale rows 64–67; (14) pineal eyespot present; (15) supranasals separate; (16) frontoparietals in contact; (17) parietals in contact; (18) first pair of enlarged chin shields separate; (19) postnasal/supranasal fusion absent; (20) enlarged chin shields in three pairs; (21) nuchal scales undifferentiated; (22) fourth and fifth supralabial below eye; (23) auricular opening present; and (24) presacral vertebrae 31 (Tables 5.4, 5.5). Comparisons.—Characters distinguishing Brachymeles syam from all medium-sized, pentadactyl species of Brachymeles are summarized in Tables 5.4 and 5.5. Brachymeles syam 365 most closely resembles B. pito; however, B. syam differs from this taxa by having a longer relative tail length (TL/SVL up to 126% vs. less than 98%), fewer presacral vertebrae (31 vs. 32), fewer midbody scale rows (25–26 vs. 27–30), a tendency towards fewer axilla–groin scale rows (less than 45 vs. up to 50), a tendency towards fewer paravertebral scale rows (less than 67 vs. up to 70), enlarged chind shields in three pairs (vs. two or three), the presence of contact between frontoparietal scales (vs. presence or absence), the presence of contact between paretal scales (vs. presence or absence), and the absence of contact between the first pair of enlarged chin shields (vs. presence or absence). Brachymeles syam can be distinguished from all limbless species of Brachymeles (B. apus, B. lukbani, B. minimus, B. miriamae, B. vermis) by having limbs; and from all non-pentadactyl species of Brachymeles (B. bonitae, B. cebuensis, B. elerae, B. muntingkamay, B. pathfinderi, B. samarensis, B. tridactylus, B. wright, sp. nov. [Leyte Island; Siler et al., in press c], sp. nov. [Lapinig Group Islands; Siler et al., in press c], sp. nov. [Catanduanes Island; Siler et al., in press c], sp. nov. [Central Bicol Peninsula, Luzon Island; Siler et al., in press c], and sp. nov. [Southern Bicol Peninsula, Luzon Island; Siler et al., in press c]) by having pentadactyl (vs. non-pentadactyl) limbs. Description of holotype.—Details of the head scalation are shown in Figure 5.6. Adult male, body medium in size, moderately slender, SVL 68.6 mm; head weakly differentiated from neck, nearly as wide as body, HW 10.4% SVL, 113.5% HL; HL 31.6% SnFa; SnFa 29.0% SVL; snout short, broadly rounded in dorsal and lateral profile, SNL 69.8% HL; ear opening visible, small; eyes small, ED 1.9% SVL, 20.3% HL, 37.1% END, pupil subcircular; body slightly depressed, nearly uniform in thickness, MBW 140.3% MBH; scales smooth, glossy, imbricate; longitudinal scale rows at midbody 26; paravertebral scale rows 65; axilla–groin scale rows 43; limbs short, 366 well developed, pentadactyl, digits small; FinIIIlam 5; ToeIVlam 9; FLL 19.9% AGD, 12.9% SVL; HLL 31.2% AGD, 20.3% SVL; order of digits from shortest to longest for hand: I = V < II < IV = III, for foot: I < V < II < III < IV; tail long, not as wide as body, gradually tapered towards end, TW 77.6% MBW; TL 114.1% SVL. Rostral projecting onto dorsal snout to point in line with midline of nasal, broader than high, in broad contact with frontonasal; frontonasal wider than long; nostril ovoid, in center of single trapezoidal nasal, longer axis directed anteroventrally and posterodorsally; supranasals present, large, moderately separated; postnasals present, moderate; prefrontals in point medial contact; frontal suboctagonal-shaped, its anterior margin narrowly separated from frontonasal, in contact with first two anterior supraoculars, 3× wider than anterior supraocular; supraoculars five; frontoparietals moderate, in moderate medial contact, each in contact with supraoculars II–IV; interparietal moderate, its length roughly equal to length of frontoparietal, slightly longer than wide, subdiamond-shaped, wider anteriorly; parietals roughly as broad as frontoparietals, in broad contact behind interparietal; nuchals undifferentiated; two loreals, increasing in size from anterior to posterior, anterior loreal narrower than and slightly higher than posterior loreal; preocular single; presubocular single; supraciliaries six, the anteriormost contacting prefrontal and separating posterior loreal from first supraocular, posteriomost extending to posterior edge of fifth supraocular; single subocular scale row complete, in contact with supralabials; lower eyelid with one row of scales on dorsal margin; supralabials six, first 1.2× size of other supralabials, fourth and fifth below eye; infralabials six (Fig. 5.6). Mental wider than long, in contact with first infralabials; postmental single, enlarged, its width greater than width of mental; followed by three pairs of enlarged chin shields, first pair 367 moderately separated, second pair wider than first, moderately separated by single medial scale, third pair narrower than first and second pairs, separated by three medial scales (Fig. 5.6). Scales on limbs smaller than body scales; scales on dorsal surfaces of digits large, wrapping around lateral edges of digits; lamellae undivided; palmar surfaces of hands and plantar surfaces of feet covered by small, irregular scales, each with raised anterior edges; scales on dorsal surface of hands and feet smaller than limb scales, lacking raised edges. Coloration of holotype in preservative.—Ground color of body light (lateral surfaces) to dark (middorsal surface) brown, with distinctly darker middorsal region; light dorsolateral stripes absent. Dorsal surfaces of head, and snout darker brown but dorsal surfaces of limbs match that of trunk. Scales of dorsal and lateral surfaces of head nearly uniformly dark brown; supraocculars nearly black. Nuchal and supratympanic regions distinctly darker than remaining portions of the head and neck. Rostral, supranasals, postnasals, first suprlabials and infralabials and mental scale medium gray. Suprlabials dark brown but infralabials, mental, and chin shields light orange-brown. Trunk coloration variable; dorsal surfaces medium brown with a series of indistinct longitudinal streaks, each composed of a series of indstinct dark spots either confined to the distal edge of each scale or traversing the whole scale. Lateral surfaces, lack the appearance of longitudinal streaks but instead possess equally spaced spots of dark pigment, with each spot on distal tip of each scale. Ventral body surfaces rich orange-brown; ventral surfaces of head and neck devoid of any dark pigmentation; posterior portion of trunk with faint brown striations at the distal edge of each scale, becoming more pronounced posteriorly; subcaudal regions with dark brown spots or clusters of striations on distal edge of each scale, becoming more contrasting distally with darker 368 shades of brown and lighter ground colration at the tail’s tip. Ventral surfaces of hands and feet light gray; fingers and toes dark gray. Precloacals slightly lighter than surrounding ventrals. Coloration of holotype in life.—(Differences from preserved specimens; Fig. 5.7). Light, dorsolateral stripes absent to nearly indistinct. Trunk coloration medium to dark brown; dorsal surfaces dark brown with a series of distinct to indistinct longitudinal streaks, each composed of a series of dark brown to black spots confined to the distal edge of each scale or traversing the whole scale. Lateral surfaces possess longitudinal rows of dark spots of pigment, indistinct anteriorly, distinct posteriorly, with each spot on distal tip of each scale. Ventral body surfaces rich orange-brown or medium brown. Ventral surfaces of hands and feet light gray to tan; fingers and toes dark gray. Measurements and scale counts of holotype in mm.—SVL 68.6; AGD 44.6; TotL 146.9; MBW 9.4; MBH 6.7; TL 78.3; TW 7.3; TH 5.3; HL 6.3; HW 7.2; HH 4.8; SnFa 19.9; ED 1.3; END 3.5; SNL 4.4; IND 2.1; FLL 8.9; HLL 13.9; MBSR 26; PVSR 65; AGSR 43; FinIIIlam 5; ToeIVlam 9; SL 6; IFL 6; SC 6; SO 5. Variation.—Morphometric variation of the series is summarized in Table 5.6. Among the 45 specimens examined for the degree of contact between head scales, we observed the following variation: prefrontals in point medial contact (KU 310827–29, 310931, 311218) or separated (KU 310730–31, 310820–26, 310830–38, 310929–30, 310932–41, 311214–17, 311219–23). A single individual (KU 310830) was observed to possess a single, large parietal scale, resulting from the fusion of the parietals. Scale counts were observed to vary among the measured series. Specimens were observed to have midbody scale row counts of 25 (KU 310929, 310936) and 26 (KU 310731, 310820–21, 310826–31, 310834–35, 310928, 310930–31, 310933–34, 310937–39, 310941, 311214–16, 369 311218, 311223); axilla–groin scale row counts of 42 (KU 310829–30, 310929, 310933, 310938, 311215), 43 (KU 310826, 310828, 310831, 310835, 310931, 310934, 310936–37, 310941, 311214), 44 (KU 310731, 310820–21, 310834, 310928, 310930, 310939, 311223), and 45 (KU 310827, 311216, 311218); and paravertebral scale row counts of 64 (KU 310829–30, 310929, 310933, 310938, 311215), 65 (KU 310826, 310828, 310831, 310835, 310931, 310934, 310936–37, 310941, 311214), 66 (KU 310731, 310820–21, 310834, 310928, 310930, 310939, 311223), and 67 (KU 310827, 311216, 311218). We also observed lamellae counts to vary among the specimens examined, with the number of Toe-IV lamellae observed to vary between eight (KU 310930, 310937, 311216, 311218) and nine (KU 310820–21, 310826–31, 310834–35, 310928–29, 310931, 310933–34, 310936, 310938–39, 310941, 311214–15, 311223). Color in the type series is remarkably invariant. Several specimens possess slightly lighter dorsolateral reions, suggesting the presence of dorsolateral “stripes” (KU 310831, 310937, 310928, 310939, 311214); in one small juvenile, this color feature is particularly evident (KU 311211) but in others (KU 310822, 311220, 311222) it is absent. In some specimens, overall pigmentation is markedly darker on both dorsal and ventral surfaces (KU 310820, 310821, 3190931, 310933, 310934, 310936) and in some specimens dorsal coloration is slightly lighter and ventral ground color nerly immaculate orange-brown (KU 310731, 311218). In two specimens ventral surfaces are marked by indistinct midventral streaks of dark minute flecks and spots. Distribution.—Brachymeles syam is known only from Samar and Leyte islands (Fig. 5.3). Ecology and natural history.—Brachymeles syam occurs in primary- and secondary-growth forest, as well as disturbed and agricultural habitats. In contrast to the other members of the B. 370 gracilis complex, this species appears to be quite common throughout its range (CDS pers. observ.). Three species of Brachymeles have been confirmed to occur on Samar Island (B. orientalis, B. syam, and B. samarensis; Siler and Brown, 2010; Siler et al., in press c). We have evaluated this species against the IUCN criteria for classification, and find that it does not qualify for Critically Endangered, Endangered, Vulnerable, or Near Threatened status. Brachymeles syam has been documented to have a broad geographic distribution and is quite abundant at all sampled localities. We therefore classify this species as Least Concern, LC (IUCN, 2010). Other sympatric sincid species observed on Samar and Leyte islands include: Emoia atrocostata, Eutropis multicarinata, E. multifasciata, Lamprolepis smaragdina, Lipinia pulchella, L. quadrivittata, Sphenomorphus acutus, S. cumingi, S. fasciatus, S. jagori, S. cf. mindanensis, S. steerei, S. variegatus, Tropidophorus misaminus. Etymology.—Prior to the Spanish colonization of the Philippines, numerous names (Samal, Ibabao, Tandaya) had been colloquially given to Samar Island. The name Samar was originally derived from the local dialect “syam”, meaning wound or cut, which described the geographically complex features of the island, and the rough terrain dissected by streams. Suggested common name: Eastern Visayas Slender Skink. Brachymeles walo sp. nov. Figs. 5.3, 5.6 Holotype.—PNM 9777 (ACD Field No. 5747), adult female, collected under a rotting log in secondary-growth forest (10:00–12:30 hr) on 23 October 2009, in Barangay Tablu, Municipality of Tampakan, South Cotabato Province, Mindanao Island, Philippines, by ACD and J. Fernandez. 371 Paratopotype.—One subadult male (PNM 9776) collected on 21 October 2009 by ACD and J. Fernandez. Paratype.—One juvenile of undetermined sex (KU 326109) collected on 24 May 2001, in Initao National Park, Barangay Initao, Municipality of Tubigan, Misamis Oriental Province, Mindanao Island, Philippines (08°50'2.4" N, 123°52'30" E; WGS-84), by ACD. Diagnosis.—Brachymeles walo can be distinguished from congeners by the following combination of characters: (1) body size medium (SVL 61.6, 75.5 mm); (2) limbs pentadactyl; (3) limb length moderate; (4) relative tail length moderate; (5) Finger-III lamellae four or five; (6) Toe-IV lamellae six; (7) supralabials six; (8) infralabials six; (9) suparciliaries six; (10) supraoculars five; (11) midbody scale rows 26; (12) axilla–groin scale rows 46–47; (13) paravertebral scale rows 68–70; (14) supranasals separate; (15) frontoparietals in contact; (16) parietals in contact; (17) postnasal/supranasal fusion absent; (18) enlarged chin shields in three pairs; (19) nuchal scales undifferentiated; (20) fourth and fifth supralabial below eye; (21) auricular opening present; and (22) presacral vertebrae 33 (Tables 5.4, 5.5). Comparisons.—Characters distinguishing Brachymeles walo from all medium-sized, pentadactyl species of Brachymeles are summarized in Tables 5.4 and 5.5. Brachymeles walo most closely resembles B. gracilis, B. anim, and B. sampu. However, B. walo differs from these three taxa by having six Toe-IV lamellae (vs. seven or eight [B. gracilis], eight [B. sampu], eight or nine [B. anim]), a tendency towards a greater number of paravertebral scale rows (up to 72 vs. less than or equal to 70), and 33 presacral vertebrae (vs. 31 [B. sampu], 32 [B. anim], 34 [B. gracilis]). Brachymeles walo further differs from B. anim and B. sampu by having four or five Finger-III lamellae (vs. five); from B. gracilis and B. anim by having enlarged chin shields in three pairs (vs. two); from B. gracilis and B. sampu by the presence of contact between 372 frontoparietal scales (vs. presence or absence [B. gracilis], absence [B. sampu]); from B. gracilis by having six infralabials (vs. six or seven) and the absence of a fused postnasal/supranasal scale (vs. presence or absence); and from B. sampu by having a greater number of midbody scale rows (26 vs. 24) and by the presence of contact between parietals scales (vs. presence or absence). Brachymeles walo can be distinguished from all limbless species of Brachymeles (B. apus, B. lukbani, B. minimus, B. miriamae, B. vermis) by having limbs; and from all non-pentadactyl species of Brachymeles (B. bonitae, B. cebuensis, B. elerae, B. muntingkamay, B. pathfinderi, B. samarensis, B. tridactylus, B. wright, sp. nov. [Leyte Island; Siler et al., in press c], sp. nov. [Lapinig Group Islands; Siler et al., in press c], sp. nov. [Catanduanes Island; Siler et al., in press c], sp. nov. [Central Bicol Peninsula, Luzon Island; Siler et al., in press c], and sp. nov. [Southern Bicol Peninsula, Luzon Island; Siler et al., in press c]) by having pentadactyl (vs. non-pentadactyl) limbs. Description of holotype.—Details of the head scalation are shown in Figure 5.6. Adult female, body medium in size, moderately slender, SVL 75.5 mm; head weakly differentiated from neck, nearly as wide as body, HW 8.3% SVL, 103.3% HL; HL 31.0% SnFa; SnFa 26.1% SVL; snout short, rounded in dorsal profile, bluntly rounded in lateral profile, SNL 60.7% HL; ear opening visible, small; eyes small, ED 1.9% SVL, 23.0% HL, 46.7% END, pupil subcircular; body slightly depressed, nearly uniform in thickness, MBW 117.6% MBH; scales smooth, glossy, imbricate; longitudinal scale rows at midbody 26; paravertebral scale rows 72; axilla–groin scale rows 50; limbs short, well developed, pentadactyl, digits small; FinIIIlam 4; ToeIVlam 6; FLL 14.4% AGD, 9.4% SVL; HLL 20.9% AGD, 13.6% SVL; order of digits from shortest to longest for hand: I = V < IV = II < III, for foot: V = I < II < IV = III; tail moderate in length, not as wide as body, gradually tapered towards end, TW 86.3% MBW; TL 88.9% SVL. 373 Rostral projecting onto dorsal snout to point in line with anterior edge of nasal, broader than high, in broad contact with frontonasal; frontonasal wider than long; nostril ovoid, in center of single trapezoidal nasal, longer axis directed anteroventrally and posterodorsally; supranasals present, large, broadly separated; postnasals present, moderate; prefrontals broadly separated; frontal suboctagonal-shaped, its anterior margin in broad contact with, or narrowly separated from, frontonasal, in contact with first two anterior supraoculars, 4.5× wider than anterior supraocular; supraoculars five; frontoparietals moderate, in moderate medial contact, each in contact with supraoculars II–IV; interparietal large, its length roughly equal to length of frontoparietal, slightly longer than wide, subdiamond-shaped, wider anteriorly; parietals narrower than frontoparietals, in broad contact behind interparietal; nuchals undifferentiated; two loreals, decreasing in size from anterior to posterior, anterior loreal about as long as and moderately higher than posterior loreal; preocular single; supraciliaries six, the anteriormost contacting prefrontal and separating posterior loreal from first supraocular, posteriomost extending to posterior edge of fifth supraocular; single subocular scale row complete, in contact with supralabials; lower eyelid with one row of scales on dorsal margin; supralabials six, first 2× size of other supralabials, fourth and fifth below eye; infralabials six (Fig. 5.6). Mental wider than long, in contact with first infralabials; postmental single, enlarged, its width greater than width of mental; followed by three pairs of enlarged chin shields, first pair narrowly separated, second pair wider than first, moderately separated by single medial scale, third pair narrower than first and second pairs, separated by three medial scales (Fig. 5.6). Scales on limbs smaller than body scales; scales on dorsal surfaces of digits large, wrapping around lateral edges of digits; lamellae undivided; palmar surfaces of hands and plantar surfaces 374 of feet covered by small, irregular scales, each with raised anterior edges; scales on dorsal surface of hands and feet smaller than limb scales, lacking raised edges. Coloration of holotype in preservative.—Ground color of body dark (lateral surfaces) to miedium (middorsal surface) brown, with distinctly lighter tan dorsolateral stripes, continuing from postorbital region to base of tail. Dorsal surfaces of head, and snout marbled light and dark brown, with distinct tan spots on prefrontals and first supralabials and dark gray to black supraoccular coloration posteriorly. Scales of dorsal and lateral surfaces of snout and lateral surfaces of head homogenous dark brown. Rostral, supranasals, postnasals, first suprlabials and infralabials and mental scale medium gray. Suprlabials medium brown; infralabials orange-brown; mental, and chin shields light immaculate creram. Trunk coloration variable; middorsal reguion between light tan dorsolateral stripes medium brown with a series of six faint longitudinal dark brown streaks, each composed of a indistinct dark blotches either on the distal edge of each scale and traversing the whole scale in posterior portions of trunk. Lateral surfaces nearly uniformly dark brown, with lighter margins of each scale. Dorsal surfaces of limbs similar to lateral body coloration. Ventral surfaces of head, neck and body light brown, with light yellowish cream margins to each scale. Subcaudal regions uniform dark brown with slighter scale margins becoming more evident distally. Ventral surfaces of hands and feet dark gray; fingers and toes slightly darker. Precloacals colored as surrounding ventrals. Coloration of holotype in life.—Coloration in life is unrecorded; however, because Brachymeles specimens do not change significantly during preservation (CDS, RMB personal observation), we suspect that the preserved coloration and patterns are much like those in life. 375 Measurements and scale counts of holotype in mm.—SVL 75.5; AGD 49.3; TotL 142.6; MBW 8.0; MBH 6.8; TL 67.1; TW 6.9; TH 5.6; HL 6.1; HW 6.3; HH 4.2; SnFa 19.7; ED 1.4; END 3.0; SNL 3.7; IND 2.6; FLL 7.1; HLL 10.3; MBSR 26; PVSR 72; AGSR 50; FinIIIlam 4; ToeIVlam 6; SL 6; IFL 6; SC 6; SO 5. Variation.—Morphometric variation of the series is summarized in Table 5.6. We observed the following variation in the degree of contact between head scales: prefrontals in moderate medial contact (ACD 5727) or separated (KU 326109, ACD 5747); first pair of enlarged chin shields in moderate medial contact (KU 326109, ACD 5727) or separated (ACD 5747). Scale and lamellae counts were observed to vary among the measured series. Specimens were observed to have axilla–groin scale row counts of 47 (ACD 5727) and 50 (ACD 5747); and paravertebral scale row counts of 70 (ACD 5727) and 72 (ACD 5747). The number of Finger-III lamellae varied between four (ACD 5747) and five (ACD 5727). Distribution.—Brachymeles walo is known only from western Mindanao Island (Fig. 5.3). Ecology and natural history.—Brachymeles walo occurs in primary- and secondary-growth forest habitats, and occurs in sympatry throughout its currently recognized range with B. schadenbergi (Siler and Brown, 2010). The population found in South Cotabato Province, Mindanao Island (Fig. 2) also has been documented to occur in sympatry with B. gracilis. As previously mentioned, this is the first documented case of two species of Brachymeles in the same body form and body size class occuring in sympatry. In addition to B. gracilis and B. schadenbergi, four other species of Brachymeles have been confirmed to occur on Mindanao Island (B. pito, B. orientalis, and B. pathfinderi; Siler and Brown, 2010; Siler et al., in press a). Due to the observation of a high degree of sequence divergence (up to 5.9%; Table 5.3) between the northern and southern populations sampled for this species, we suspect that B. walo 376 may actually represent a complex of morphologically similar species. However, due to the absence of additional, adult samples for both populations, currently we cannot evaluate this hypothesis. Given what little we know about this unique species (or species complex), B. walo cannot be directly, or indirectly, assessed for risk of extinction based on the IUCN criteria. Therefore, we classify this species as Data Deficient, DD, pending the collection of additional information (IUCN, 2010). Other sympatric sincid species observed on Mindanao Island include: Eutropis indeprensa, E. multicarinata, E. multifasciata, E. englei, Lamprolepis smaragdina, L. pulchella, L. quadrivittata, Sphenomorphus abdictus abdictus, S. acutus, S. atrigularis, S. cumingi, S. cf. mindanensis, S. coxi, S. fasciatus, S. jagori, S. llanosi, S. steerei, S. variegatus, Tropidophorus misaminus, T. partelloi. Etymology.—The specific epithet is chosen to recognize the T’boli indigenous peoples from South Mindanao Island. The T’boli possess ancestral tribal domains from Buluan Lake in the Cotabato Basin to Agusan del Norte Province in northeastern Mindanao Island, encompassing much of the known distribution of this new species. Suggested common name: Western Mindanao Slender Skink. DISCUSSION Analyses of the two mitochondrial gene fragments (ND1, ND2) and two unlinked nuclear loci (BDNF, PTGER4) resulted in topologies with high ML bootstrap support and posterior probabilities for five lineages formerly part of the Brachymeles gracilis Complex (Fig. 5.2). No analyses supported the monophyly of species formerly part of Brachymeles gracilis (B. gracilis, 377 B. pito, B. anim, B. syam, and B. tiboli). However, all analyses show strong support for the sister relationship between B. anim and B. pito (Fig. 5.2). In addition to the apparent paraphyly of species formerly part of Brachymeles gracilis, B. pathfinderi was recovered as part of the B. gracilis Complex. Brachymeles pathfinderi, one of only two recognized species to have unequal numbers of fore- and hind limb digits, was placed by our analyses sister to B. gracilis (Fig. 5.2, Clade E). Although each of the five genetically sampled species formerly part of the B. gracilis Complex were recovered in all analyses with strong support, the interspecific relationships remain incompletely resolved, and the diversity of species within the complex is recovered as a polytomy of four, well supported clades (Fig. 5.2, Clades A–C, E). The previously recognized species B. pathfinderi has an abutting distribution with true B. gracilis in southcentral Mindanao Island (Fig. 5.3). The species recognized in this paper increase the total number of known species of Brachymeles to 34, and all but two of these are endemic to the Philippines. Having nearly doubled the known number of species of Brachymeles in the last several years (Siler, 2010; Siler et al., 2009a, 2010a,b, 2011, in press a,b,c; Siler and Brown, 2010), we are left with two general questions: do many more species in this clade await discovery? And will the results of our studies involving this group extrapolate to generalizations regarding underestimation of Philippine biodiversity? First, our comprehensive fossorial lizard field studies throughout the archipelago have targeted the major biogeographic components of the Philippines (Brown and Diesmos, 2009) and allowed for a clade-by-clade revisionary approach of the genus Brachymeles (Siler and Brown, 2010; Siler et al. in press c). Consequently, we do not expect wholesale discovery of many 378 additional clades of species and we suspect that we will soon (following the revision of the B. bonitae Complex) arrive at a reasonably accurate accounting of species diversity. Nevertheless we anticipate that additional species of Brachymeles will be discovered with continued fieldwork in isolated regions of the archipelago. To date, despite our efforts and those of our colleagues, the major montane components of Luzon and Mindanao remain poorly sampled for biodiversity due to logistical obstacles to field research. Overcoming many of these bureaucratic hurdles will undoubtedly result in the discovery of additional species of Brachymeles. Finally, many small islands (now known to harbor distinct species of Brachymeles) have not been adequately surveyed for fossorial lizard species diversity by biologists targeting this distinct microhabitat. As a result, we expect that many areas considered reasonably well known by terrestrial biodiversitry specialists may indeed possess additional undescribed of Brachymeles. This study adds to a growing body of literature suggesting that a reevaluation of amphibian and reptile species boundaries within the Philippines will result in a wholesale reappraisal of archipelago-wide biodiversity (review: Brown et al., 2002; Brown and Diesmos, 2009). In the context of this body of work, few examples of truly widespread reptile species are now known to exist, and most previous examples have turned out to constitute multiple evolutionary lineages (McGuire and Alcala, 2000; Brown et al., 2009, in press; Gaulke et al, 2007; Welton et al., 2009, 2010a,b; Siler and Brown, 2010; Siler et al., in press c) with limited geographical distributions. The exceptions to this generalization appear to be invasive species and human-mediated range expansions (Diesmos et al., 2006; Brown et al., 2010). Following the recognition of B. gracilis, B. pito, B. anim, B. syam, B. tiboli, and B. sampu there are now 18 pentadactyl species of Brachymeles. The diversity of pentadactyl species can be broken into three major body size categories. Half of the diversity of pentadactyl taxa 379 consists of medium-sized species (B. boholensis, B. boulengeri, B. mindorensis, B. taylori, B. gracilis, B. pito, B. anim, B. syam, B. tiboli, and B. sampu; Siler and Brown, 2010), and the other half consists of larger, more robust species (B. talinis, B. kadwa, B. tungaoi, B. makusog, B. orientalis, B. schadenbergi, B. vindumi; Siler and Brown, 2010). Finally, B. bicolor represents a unique species in having a large, long body; significantly longer than all other pentadactyl species (Siler et al., in press a). Interestingly, the distribution of pentadactyl species in the Philippines is markedly uneven across the major biogeographic regions of the Philippines, with four species known to occur in the Luzon Faunal Region, nine in the Mindanao Faunal Region, three in the Visayan Faunal Region, one in the Sulu Archipelago, and one in the Mindoro Faunal Region (Siler and Brown, 2010). This observation of the greatest pentadactyl species diversity being distributed across the Mindanao PAIC stands in stark contrast to the patterns observed for the diversity of limbed, non-pentadactyl species, where 13 species are known from the Luzon PAIC versus eight in the Mindanao PAIC (Siler et al., in press c). A resurgence of species discoveries on Mindanao Island have occurred during the last decade, largely due to increased sociopolitical stability in the southern Philippines resulting in renewed survey efforts. Given the island’s complex geography (Defant et al., 1989; Yumul et al., 2009), the increase in the faunal region’s diversity is likely to continue (Siler et al., 2009b, in press c; Siler and Brown, 2010; Sanguila et al., in press; Welton et al., 2009, 2010a,b) Although B. syam, B. anim, B. pito, and B. gracilis currently can be found in a variety of habitat types, from secondary-growth forest to highly disturbed, agricultural and residential areas, no studies are available on the long-term effect of deforestation on Brachymeles populations. In contrast, less is known about the natural history, abundance, and effective range of B. walo and B. sampu, and both species remain known from three and two vouchered specimens, respectively. 380 Presently, one “widespread” species complex (B. bonitae) remains in the genus, with a distribution spanning boundaries between recognized faunal regions (Brown and Alcala, 1980; Siler and Brown, 2010; Siler et al., 2011, in press c). Recent phylogenetic studies of the genus have statistically rejected the monophyly of the B. bonitae species complex (Siler et al., 2011). Closer investigations of island populations of B. bonitae will likely result in the discovery of new species diversity, and needed taxonomic revisions for this group of morphologically similar, non-pentadatyl species. 381 Figure 5.4. Illustration of head of adult male Brachymeles gracilis (KU 326079) and adult female Brachymeles pito (CAS 133705) in dorsal, lateral, and ventral views. Taxonomically diagnostic head scales are labeled as follows: C, chin shield; F, frontal; FN, frontonasal; FP, frontoparietal; IL, infralabial; IP, interparietal; L, loreal; M, mental; N, nasal; Nu, nuchal; P, parietal; PF, prefrontal; PM, postmental; PN, postnasal; PO, preocular; PSO, presubocular; R, rostral; SC, supraciliary; SL, supralabial; SN, supranasal; and SO, supraocular. Roman numerals indicate scales in the supraocular series, with Arabic numbers indicating scales in the supraciliary series. The partial lateral view for B. gracilis highlights (in gray) the absence of a postnasal scale resulting from the fusion of the supranasal and postnasal. Illustrations by RMJ and CDS. 382 383 Figure 5.5. Illustration of head of adult female neotype Brachymeles sampu (CAS 60366) and adult male holotype Brachymeles anim (PNM 9766; formerly KU 310359) in dorsal, lateral, and ventral views. Labels for taxonomically diagnostic head scales follow those shown in Figure 5.4. Illustrations by RMJ and CDS. 384 385 Figure 5.6. Illustration of head of adult male holotype Brachymeles syam (PNM 9767; formerly KU 310828) and adult female holotype Brachymeles walo (PNM 9777) in dorsal, lateral, and ventral views. Labels for taxonomically diagnostic head scales follow those shown in Figure 5.4. Illustrations by RMJ and CDS. 386 387 Figure 5.7. Photograph in life of Brachymeles syam (KU 311223), SVL = 76.9 mm, from Leyte Island, Philippines. Photograph by CDS. 388 389 Literature Cited ACKERLY, D. D., AND P. B. REICH. 1999. Convergence and correlations among leaf size and function in seed plants: a comparative test using independent contrasts. American Journal of Botony 86:1272–1281. ALBERCH, P., AND E. GALE. 1985. A developmental analysis of an evolutionary trend: digital reduction in amphibians. Evolution 39:8–23. ALFARO, M. E., D. R. KARNS, H. K. VORIS, E. ABERNATHY, AND S. L. SELLINS. 2004. Phylogeny of Cerberus (Serpentes: Homalopsinae) and phylogeography of Cerberus rynchops: diversification of a coastal marine snake in Southeast Asia. Journal of Biogeography 31:1277–1292. ARBOGAST, B. S., S. V. EDWARDS, J. WAKELEY, P. BEERLI, AND J. SLOWINSKI. 2002. Estimating divergence times from molecular data on phylogenetic and population genetic timescales. Annual Review of Ecological Systems 33:707–740. BENJAMINI, Y., AND Y. HOCHBERG. 1995. Controlling the false discovery rate—a practical and powerful approach to multiple testing. J. R. Stat. Soc. B 57:289–300. BERGMANN, P. J., AND D. J. IRSCHICK. 2010. Alternate pathways of body shape evolution translate into common patterns of locomotor evolution in two clades of lizards. Evolution. In press. BICKFORD, D., D. J. LOHMAN, N. S. SODHI, P. K. L. NG, R. MEIER, K. WINKER, K. K. INGRAM, AND I. DAS. 2007. Cryptic species as a window on diversity and conservation. Trends in Ecology and Evolution 22:148–155. BLOMBERG, S. P., T. GARLAND, JR., AND A. R. IVES, JR. 2003. Testing for phylogenetic signal in comparative data: behavioral traits are more labile. Evolution 57:717–745. 390 BOETTGER, O. 1886. Aufzahlung der von den Philippinen bekannten Reptilien und Batrachier. Ber. Senck. Natur. Ges. 1886:91–134. BOULENGER, G. A. 1887. Catalogue of lizards in the British Museum (natural history), London, 3:i–vii + 575 pp. BRANDLEY, M. C., A. SCHMITZ, AND T. W. REEDER. 2005. Partitioned Bayesian analyses, partition choice, and the phylogenetic relationships of Scincid lizards. Systematic Biology 54:373–390. BRANDLEY, M. C., J. P. HUELSENBECK, AND J. J.WIENS. 2008. Rates and patterns in the evolution of snake-like body form in squamate reptiles: Evidence for repeated re-evolution of lost digits and long-term persistence of intermediate body forms. Evolution 62:2042–2064. BROWN, R.M., AND A. C. DIESMOS. 2002. Application of lineage-based species concepts to oceanic island frog populations: the effects of differing taxonomic philosophies on the estimation of Philippine biodiversity. Silliman Journal 42:133–162. BROWN, R.M., AND A. C. DIESMOS. 2009. Philippines, Biology. In: Gillespie, R., Clague, D. (Eds.), Encyclopedia of Islands. University of California Press, Berkeley, pp. 723–732. BROWN, R. M., A. C. DIESMOS, AND A. C. ALCALA. 2001 (2002). The state of Philippine herpetology and the challenges for the next decade. Silliman Journal 42:18–87. BROWN, R. M., A. C. DIESMOS, AND C. OLIVEROS. In press. A new flap-legged forest gecko (Genus Luperosaurus) from the northeastern Philippines. Journal of Herpetology. BROWN, R.M., AND S. I. GUTTMAN. 2002. Phylogenetic systematics of the Rana signata complex of Philippine and Bornean stream frogs: reconsideration of Huxley’s modification of Wallace’s Line at the Oriental–Australian faunal zone interface. Biological Journal of the Linnean Society 76:393–461. 391 BROWN, R. M., C. W. LINKEM, C. D. SILER, J. SUKUMARAN J. A. ESSELSTYN, A. C. DIESMOS, D. T. ISKANDAR, D. BICKFORD, B. J. EVANS, J. A. MCGUIRE, L. GRISMER, J. SUPRIATNA, AND N. ANDAYANI. 2010. Phylogeography and historical demography of Polypedates leucomystax in the islands of Indonesia and the Philippines: evidence for recent human-mediated range expansion? Molecular Phylogenetics and Evolution 57:598–619. BROWN, R. M., C. OLIVEROS, C. D. SILER, AND A. C. DIESMOS. 2008. A new Gekko from the Babuyan Islands, northern Philippines. Herpetologica 64:305–320. BROWN, R. M., C. OLIVEROS, C. D. SILER, AND A. C. DIESMOS. 2009. Phylogeny of Gekko from the northern Philippines, and description of a new species from Calayan Island. Journal of Herpetology 43:620–635. BROWN, R. M., J. A. MCGUIRE, AND A. C. DIESMOS. 2000. Status of some Philippine frogs related to Rana everetti (Anura: Ranidae), description of a new species, and resurrection of Rana igorota (Taylor 1922). Herpetologica 56:81–104. BROWN, R. M., J. A. MCGUIRE, J. W. FERNER, AND A. C. ALCALA. 1999. A new diminutive species of skink (Squamata; Scincidae; Lygosominae: Sphenomorphus) from Luzon Island, Republic of the Philippines. Copeia 1999:362–370. BROWN, R. M., J. W. FERNER, AND L. A. RUEDAS. 1995a. A new species of lygosomine lizard (Reptilia: Lacertilia: Scincidae; Sphenomorphus) from Mt. Isarog, Luzon Island, Philippines. Proceedings of the Biological Society of Washington 108:18–28. BROWN, R. M., J. W. FERNER, AND R. V. SISON. 1995b. Rediscovery and redescription of Sphenomorphus beyeri Taylor (Reptilia: Lacertilia: Scincidae) from the Zambales mountains of Luzon, Philippines. Proceedings of the Biological Society of Washington 108:6–17. 392 BROWN, R. M., C. D. SILER, A. C. DIESMOS, AND A. C. ALCALA. 2009. . The Philippine frogs of the genus Leptobrachium (Anura; Megophryidae): phylogeny-based species delimitation, taxonomic revision, and descriptions of three new species. Herpetological Monographs 23:1–44. BROWN, R. M., C. W. LINKEM, C. D. SILER, J. SUKUMARAN, J. A. ESSELSTYN, A. C. DIESMOS, D. T. ISKANDAR, D. BICKFORD, B. J. EVANS, J. A. MCGUIRE, L. GRISMER, J. SUPRIATNA, AND N. ANDAYANI. 2010. Phylogeography and historical demography of Polypedates leucomystax in the islands of Indonesia and the Philippines: evidence for recent human-mediated range expansion? Molecular Phylogenetics and Evolution 57:598–619. BROWN, R. P., AND J. PESTANO. 1998. Phylogeography of skinks (Chalcides) in the Canary Islands inferred from mitochondrial DNA sequences. Molecular Ecology 7:1183–1191. BROWN, W. C. 1956. A revision of the genus Brachymeles (Scincidae), with descriptions of new species and subspecies. Breviora 54:1–19. BROWN, W. C., AND A. C. ALCALA. 1970. The zoogeography of the Philippine Islands, a fringing archipelago. Proceedings of the California Academy of Sciences 38:105–130. BROWN, W. C., AND A. C. ALCALA. 1978. In: Philippine Lizards of the Family Gekkonidae. Silliman University Press, Dumaguete City, Philippines. BROWN, W. C., AND A. C. ALCALA. 1980. In: Philippine Lizards of the Family Scincidae. Silliman University Press, Dumaguete City, Philippines. BROWN, W. C., AND A. C. ALCALA. 1995. A new species of Brachymeles (Reptilia: Scincidae) from Catanduanes Island, Philippines. Proceedings of the Biological Society of Washington 108:392–394. 393 BROWN, W. C., AND D. S. RABOR. 1967. Review of the genus Brachymeles (Scincidae), with descriptions of new species and subspecies. Proceedings of the California Academy of Sciences 15:525–548. BROWN, W. C., AND E. L. ALCALA. 1995. A new species of Brachymeles (Reptilia: Scincidae) from Catanduanes Island, Philippines. Proceedings of the Biological Society of Washington 108:392–394. CAPUTO, V., B. LANZA, AND R. PALMIERI. 1995. Body elongation and limb reduction in the genus Chalcides Laurenti 1768 (Squamata: Scincidae): a comparative study. Tropical Zoology 8:95–152. CHANARD, T., W. GROSSMANN, A. GUMPRECHT, AND K.-D. SCHULZ. 1999. Amphibians and reptiles of Peninsular Malaysia and Thailand: an illustrated checklist. Bushmaster Publications, Switzerland, pp. 1–240. CHOQUENOT, D., AND A. E. GREER. 1987. Intrapopulationsl and interspecific variation in digital limb bones and presacral vertebrae of the genus Hemiergis (Lacertilia, Scincidae). Journal of Herpetology 23:274–281. COHN, M. J., AND C. TICKLE. 1999. Developmental basis of limblessness and axial patterning in snakes. Nature, March. COLLIN, R., AND R. CIPRIANO. 2003. Dollo’s law and the re-evolution of shell coiling. Proceedings of the Royal Society of London, B 270:2551–2555. COLLIN, R., AND M. P. MIGLIETTA. 2008. Reversing opinions on Dollo’s Law. Trends in Ecology and Evolution 23:602–609. CRONQUIST, A. 1981. An integrated system of classification of flowering plants. Columbia University Press, New York, NY. 394 CROTTINI, A., J. DORDEL, J. KOHLER, F. GLAW, A. SCHMITZ, AND M. VENCES. 2009. A multilocus phylogeny of Malagasy scincid lizards elucidates the relationships of the fossorial genera Androngo and Cryptoscincus. Molecular Phylogenetics and Evolution 53:345–350. DANIELS, S. R., N. J. L. HEIDEMAN, M. G. J. HENDRICKS, M. E. MOKONE, AND K. A. CRANDALL. 2005. Unraveling evolutionary lineages in the limbless fossorial skink genus Acontias (Sauria: Scincidae): Are subspecies equivalent systematic units? Molecular Phylogenetics and Evolution 34:645–654. DAS, I. 2007. A pocket guide: amphibians and reptiles of Brunei. Natural History Publications, Borneo, pp. 1–200. DAS, I. 2010. A Field Guide to the Reptiles of South-East Asia: Myanmar, Thailand, Laos, Cambodia, Vietnam, Peninsular Malaysia, Singapore, Sumatra, Borneo, Java, Bali. New Holland Publishers, Australia, pp. 1–376. DEFANT, M. J., D. JACQUES, R. C. MAURY, J. DE BOER, AND J.-L. JORON. 1989. Geochemistry and tectonic setting of the Luzon arc, Philippines. Geological Society of America Bulletin 101:663–672. DE QUEIROZ, K. 1998. The general lineage concept of species. species criteria, and the process of speciation. Pp. 57–75. In: D.J. Howard, S.H. Berlocher (Eds.), Endless forms: Species and Speciation. Oxford University Press, New York, USA. DE QUEIROZ, K. 1999. The general lineage concept of species and the defining properties of the species category. Pp. 49–89. In: R.A. Wilson (Ed.), Species: New Interdisciplinary Essays. Massachusetts Institute of Technology Press, Cambridge, Massachusetts, USA. DICKERSON, R. E., E. R. MERRILL, R. C. MCGREGOR, W. SCHULTZE, E. H. TAYLOR, AND A. W. C. T. HERRE. 1925. Distribution of Life in the Philippines. Bureau of Science, Manila, 395 Philippines. DIESMOS, A. C., M. L. DIESMOS, AND R. M. BROWN. 2006. Status and distribution of alien invasive frogs in the Philippines. Journal of Environmental Science Management, Philippines 9:41–53. DOLLO, L. 1893. Les lois de l’ ´evolution. Bulletin de la Societe beige de Geologie, de Paleontologie et d'Hydrologie 7:164–166. DOLLO, L. 1905. Les Dinosauriens adapt´es `a la vie quadrup`ede secondaire. Bulletin de la Societe beige de Geologie, de Paleontologie et d'Hydrologie 19:441–448. DOLLO, L. 1922. Los cephalopodes deroules et l'irreversibilite de l'evolution. Bijdragen tot de Dierkunde 1922:215–227. DOMES, K., R. A. NORTON, M. MARAUN, AND S. SCHEU. 2007. Reevolution of sexuality breaks Dollo’s law. Proceedings of the National Academy of Sciences USA 104:139–144. DRUMMOND, A. J., AND A. RAMBAUT. 2007. "BEAST: Bayesian evolutionary analysis by sampling trees." BMC Evolutionary Biology 7:214 DRUMMOND, A. J., S. Y. W. HO, M. J. PHILLIPS, AND A. RAMBAUT. 2006. Relaxed Phylogenetics and Dating with Confidence. PLoS Biology 4:88. DUMÉRIL, A. M. C., AND G. BIBRON. 1839. Erp´etologie g´en´eral ou histoire naturelle complete des reptiles, V. EDGAR, R. C. 2004. MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Research 32:1792–97. ESSELSTYN, J. A., P. WIDMANN, AND L. R. HEANEY. 2004. The mammals of Palawan Island, Philippines. Proceedings of the Biological Society of Washington 117:271–302. 396 ESSELSTYN, J. A., H. J. D. GARCIA, M. G. SAULOG, AND L. R. HEANEY. 2008. A new species of Desmalopex (Pteropodidae) from the Philippines, with a phylogenetic analysis of the Pteropodini. Journal of Mammology 89:815–825. ESSELSTYN, J. A., AND R. M. BROWN. 2009. The role of repreated sea-level fluctuations in the generation of shrew (Soricidae: Crocidura) diversity in the Philippine Archipelago. Molecular Phylogenetics and Evolution 58:171–181. ESSELSTYN, J. A., R. M. TIMM, AND R. M. BROWN. 2009. Do geological or climatic processes drive speciation in dynamic archipelagos? The tempo and mode of diversification in Southeast Asian shrews. Evolution. 63:2595–2610. EVANS, B. J., R. M. BROWN, J. A. MCGUIRE, J. SUPRIATNA, N. ANDAYANI, A. C. DIESMOS, D. ISKANDAR, D. J. MELNICK, AND D. C. CANNATELLA. 2003. Phylogenetics of fanged frogs: testing biogeographical hypotheses at the interface of the Asian and Australian faunal zones. Systematic Biology 52:794–819. FELSENSTEIN, J. 1985. Phylogenies and the comparative method. American Naturalist 125:1–15. FELSENSTEIN, J. 2004. Inferring phylogenies. Sinauer Associates, Inc., Sunderland, MA. FISCHER, J. G. 1885. Ichtyologische and herpetologische Bermerkungen. Jahr. Wiss. Anst. Hamburg 2:49–121. FITZJOHN, R. G., W. P. MADDISON, AND S. P. OTTO. 2009. Estimating trait-dependent speciation and extinction rates from incompletely resolved phylogenies. Systematic Biology 58:595–611. FRECKLETON, R. P., P. H. HARVEY, AND M. PAGEL. 2002. Phylogenetic analysis and comparative data: a test and review of evidence. American Naturalist 160:712–726. 397 FRIESEN, V. L., B. C. CONGDON, H. E. WALSH, AND T. P. BIRT. 1997. Intron variation in marbled murrelets detected using analyses of single-stranded conformational polymorphisms. Molecular Ecology 6:1047–1058. FROST, D. R, AND D. M. HILLIS. 1990. Species in concept and practice: Herpetological applications. Herpetologica 46:87–104. GALIS, F., J. W. ARNTZEN, AND R. LANDE. 2010. Dollo’s law and the irreversibility of digit loss in Bachia. Evolution doi:10.1111/j.1558-5646.2010.01041.x. GALTIER, N., B. NABHOLZ, S. GLÉMIN, S., AND G. HURST. 2009. Mitochondrial DNA as a marker of molecular diversity: a reappraisal. Molecular Ecology 18:4541–4550. GARLAND, T., JR., AND A. R. IVES. 2000. Using the past to predict the present: confidence intervals for regression equations in phylogenetic omparative methods. American Naturalist 155:346–364. GARLAND, T., JR., P. H. HARVEY, AND A. R. IVES. 1992. Procedures for the analysis of comparative data using phylogenetically independent contrasts. Systematic Biology 41:18–32. GAULKE, M., H. RÖSLER, AND R. M. BROWN. 2007. A new species of Luperosaurus (Squamata; Gekkonidae) from Panay Island, Philippines, with comments on the taxonomic status of Luperosaurus cumingii (Gray, 1845). Copeia 2007:413–425. GILBERT, A. N. 1986. Mammary number and litter size in rodentia: “the one-half rule”. Proceedings of the National Academy of Sciences USA 83:4828–4830. GOLDBERG, E. E., AND B. IGIC. 2008. On phylogenetic tests of irreversible evolution. Evolution 62:2727–2741. 398 GOULD, J. S. 1970. Dollo on Dollo’s law: irreversibility and the status of evolutionary laws. Journal of Historical Biology 3:189–212. GRAY, J. E. 1845. Catalogue of the specimens of lizards in the collection of the British Museum. London, i–xxviii + 289 pp. GREER, A. E. 1987. Limb reduction in the genus Lerista. 1. Variation in the number of phalanges and presacral vertebrae. Journal of Herpetology 21:267–276. GREER, A. E. 1990. Limb reduction in the scincid lizard genus Lerista. 2. Variation in the bone complements of the front and rear limbs and the number of postsacral vertebrae. Journal of Herpetology 24:142–150. GREER, A. E. 1991. Limb reduction in squamates: Identification of the lineages and discussion of the trends. Journal of Herpetology 25: 166–173. GREER, A. E. 1992. Hyperphalangy in squamates: insight on the reacquisition of primitive character states in limb-reduced lineages. Journal of Herpetology 26:327–329. GREER, A. E. 2002. The loss of the external ear opening in scincid lizards. Journal of Herpetology 36:544–555. GREER, A. E., V. CAPUTO, B. LANZA, AND R. PALMIERI. 1998. Observations on limb reduction in the Scincid lizard genus Chalcides. Journal of Herpetology 32:244–252. GREER, A. E., P. DAVID, AND A. TEYNIE. 2006. The Southeast Asian scincid lizard Siaphos tridigitus Bourret, 1939 (Reptilia, Scincidae): A second specimen. Zoosystema 28:785–790. GRISMER L. L., T. M. YOUMANS, P. L. WOOD, JR., AND J. L. GRISMER. 2006a. Checklist of the herpetofauna of the Seribuat Archipelago, West Malaysia with comments on biogeography, natural history and adaptive types. Raffles Bulletin of Zoology 54:157–180. 399 GRISMER L. L., T. M. YOUMANS, P. L. WOOD, JR., A. PONCE, S. B. WRIGHT, B. S. JONES, R. JOHNSON, K. L. SANDERS, D. J. GOWER, S. Y. NORSHAM, AND K. K. P. LIM. 2006b. Checklist on the herpetofauna of Pulau Langkawi, Malaysia, with comments on taxonomy. Hamadryad 30:61–74. GUINDON, S., AND O. GASCUEL. 2003. A simple, fast and accurate method to estimate large phylogenies by maximum-likelihood. Systematic Biology 52:696–704. HALL, R. 2002. Cenozoic geological and plate tectonic evolution of SE Asia and the SW Pacific: computer-based reconstructions, model and animations. Journal of Asian Earth Sciences 20:353–431. HARMON, L. J., J. T. WEIR, C. D. BROCK, R. E. GLOR, AND W. CHALLENGER. 2008. GEIGER: investigating evolutionary radiations. Bioinformic Applications 24:129–131. HEANEY, L. R. 1985. Zoogeographic evidence for middle and late Pleistocene land bridges to the Philippine Islands. Modern Quaternary Research in SE Asia 9:127–143. HEANEY, L. R. 1986. Biogeography of small mammals in SE Asia: estimates of rates of colonization, extinction and speciation. Biological Journal of the Linnean Society 28:127–165. HEANEY, L. R., D. S. BALETE, M. L. DOLAR, A. C. ALCALA, A. T. L. DANS, P. C. GONZALES, N. R. INGLE, M. V. LEPITEN, W. L. R. OLIVER, P. S. ONG, E. A. RICKART, B. R. TABARANZA, AND R. B. UTZURRUM. 1998. A synopsis of the mammalian fauna of the Philippine Islands. Fieldiana: Zool. n.s. 88:1–61. HEYER, W. R. 1972. A new limbless skink (Reptilia: Scincidae) from Thailand with comments on the generic status of the limbless skinks of Southeast Asia. Fieldiana: Zoology 58:109–129. 400 HIKIDA, T. 1982. A new limbless Brachymeles (Sauria: Scincidae) from Mt. Kinabalu, North Borneo. Copeia 4:840–844. HILLIS, D. M., AND J. J. BULL. 1993. An empirical tests of bootstrapping as a method for assessing confidence in phylogenetic analysis. Systematic Biology 42:182–192. HUTCHEON, J. M., J. A. W. KIRSCH, AND T. GARLAND, JR. 2002. A comparative analysis of brain size in relation to foraging ecology and phylogeny in the chiroptera. Brain Behavior and Evolution 60:165–180. INGER, R. F. 1954. Systematics and zoogeography of Philippine Amphibia. Fieldiana 33:181–531. IUCN. 2010. IUCN Red List of Threatened Species. Version 2010.4. . Downloaded on 15 March 2011. JONES, A. W., AND R. S. KENNEDY. 2008. Evolution in a tropical archipelago: comparative phylogeography of Philippine fauna and flora reveals complex patterns of colonization and diversification. Biological Journal of the Linnean Society 95:620–639. KASS, R. E., AND A. E. RAFTERY. 1995. Bayes factors. J. Am. Stat. Assoc. 90, 773–795. KEARNEY, M., AND B. L. STUART. 2004. Repeated evolution of limblessness and digging heads in worm lizards revealed by DNA from old bones. Proceedings of the Royal Society of London, B 271:1677–1683. KELLY, C. K. 1995. Seed size in tropical trees: a comparative study of factors affecting seed size in Peruvian angiosperms. Oecologia 102:377–388. KELLY, C. K., AND D. J. BEERLING. 1995. Plant life form, stomatal density and taxonomic relatedness: a reanalysis of Salisbury (1927). Functional Ecology 9:422–431. KELLY, C. K., AND A. PURVIS. 1993. Seed size and establishment conditions in tropical trees: on 401 the use of taxonomic relatedness in determining ecological patterns. Oecologia 94:356–360. KEMBEL, S. W., P. D. COWAN, M. R. HELMUS, W. K. CORNWELL, H. MORLON, D. D. ACKERLY, S. P. BLOMBERG, AND C. O. WEBB. 2010. Picante: R tools for integrating phylogenies and ecology. Bioinformatics 26:1463–1464. KENNEDY, R. S., P. C. GONZALES, E. C. DICKINSON, H. C. MIRANDA, JR., AND T. H. FISHER. 2000. A guide to the birds of the Philippines. Oxford University Press, Oxford. KLOSS, C.B., 1929. The zoo-geographic boundaries between Asia and Australia and some Oriental sub-regions. Bulletin of the Raffles Museum 1929:1–10. KOHLSDORF, T., AND G. P. WAGNER. 2006. Evidence for the reversibility of digit loss: a phylogenetic study of limb evolution in Bachia Gymnophthalmidae: Squamata). Evolution 60:1896–1912. KOHLSDORF, T., V. J. LYNCH, M. T. RODRIGUES, M. C. BRANDLEY, AND G. P. WAGNER. 2010. Data and data interpretation in the study of limb evolution: a reply to Galis et al. on the revolution of digits in the lizard genus Bachia. Evolution. In press. KURTÉN,B. 1964. Return of a lost structure in the evolution of the felid dentition. Finnish Society of Sciences and Letters 26:1–12. LANDE, R. 1978. Evolutionary mechanisms of limb loss in tetrapods. Evolution 32, 73–92. LEACHÉ, A. D., AND T. W. REEDER. 2002. Molecular systematics of the eastern fence lizard (Sceloporus undulatus): A comparison of parsimony, likelihood, and Bayesian approaches. Systematic Biology 51:44–68. LEVITON, A. E., R. H. GIBBS, JR., E. HEAL, AND C. E. DAWSON. 1985. Standards in herpetology and ichthyology: Part I. Standard symbolic codes for institutional resource collections in herpetology and ichthyology. Copeia 1985:802–821. 402 LIHOREAU, F., J. R. BOISSERIE, AND L. VIRIOT. 2006. Anthracothere dental anatomy reveals a late Miocene Chado-Libyan bioprovince. Proceedings of the National Academy of Sciences USA 103:8763–8767. LINKEM, C. A., K. HESED, A. C. DIESMOS, AND R. M. BROWN. 2010. Species boundaries and cryptic lineage diversity in a Philippine forest skink complex (Reptilia; Squamata; Scincidae: Lygosominae). Molecular Phylogenetics and Evolution 56, 572–585. LYNCH, V. J., AND G. P. WAGNER. 2009. Did egg-laying boas break Dollo’s Law? Phylogenetic evidence for reversal to oviparity in sand boas (Eryx: Boidae). Evolution 64:207–216. MADDISON, D. R., AND W. P. MADDISON. 2005. MacClade: analysis of phylogeny and character evolution. Vers. 4.08. Sinauer, Sunderland, M.A. MADDISON, W. P., P. E. MIDFORD, AND S. P. OTTO. 2007. Estimating a binary character’s effect on speciation and extinction. Systematic Biology 56:701–710. MALKMUS, R., U. MANTHEY, G. VOGEL, P. HOFFMANN, AND J. KOSUCH. 2002. Amphibians & reptiles of Mount Kinabalu (North Borneo). Serpents Tale NHBD, Minnesota, USA, pp. 1–424. MANTHEY, U., AND W. GROSSMANN. 1997. Amphibien & Reptilien Südostasiens. Natur und Tier Verlag, Münster, Germany, pp. 1–512. MARSHALL, C. R., E. C. RAFF, AND R. A. RAFF. 1994. Dollo’s law and the death and resurrection of genes. Proceedings of the National Academy of Sciences USA 91:12283–12287. MARSHALL, D. C., C. SIMON, AND T. R. BUCKLEY. 2006. Accurate branch length estimation in partitioned Bayesian analyses requires accommodation of among-partition rate variation and attention to branch length priors. Systematic Biology 55:993–1003. 403 MARSHALL, D. C. 2010. Cryptic failure of partitioned Bayesian phylogenetic analyses: lost in the land of long trees. Systematic Biology 59:108–117. MCGUIRE, J. A., AND A. C. ALCALA. 2000. A taxonomic revision of the flying lizards of the Philippine Islands (Iguania: Agamidae: Draco), with a description of a new species. Herpetological Monographs 14:92–145. MCGUIRE, J.A., AND B. H. KIEW. 2001. Phylogenetic systematics of Southeast Asian flying lizards (Iguania: Agamidae: Draco) as inferred from mitochondrial DNA sequence data. Biological Journal of the Linnean Society 72:203–229. MIDFORD P, T. GARLAND, JR, AND W. P. MADDISON. 2005. PDAP: Package of MESQUITE (version 1.07). http://mesquiteproject.org/pdap-mesquite. MULLER, H. J. 1939. Reversibility in evolution considered from the standpoint of genetics. Biological Review of the Cambridge Philosophical Society 14:261–280. MULVANEY, A., T. A. CASTOE, G. A. KYLE, L. K. KENNETH, AND C. L. PARKINSON. 2005. Evidence of population genetic structure within the Florida worm lizard, Rhineura floridana (Amphisbaenia: Rhineuridae). Journal of Herpetology 39:118–124. NEVO, E. 1979. Adaptive convergence and divergence of subterranean mammals. Annual Review 10:269–308. NYLANDER, J.A.A., F. RONQUIST, J. P. HUELSENBECK, AND J. L. NIEVES-ALDREY. 2004. Bayesian phylogenetic analysis of combined data. Systematic Biology 53:47–67. NYLANDER, J. A. A., J. C. WILGENBUSCH, D. L. WARREN, AND D. L. SWOFFORD. 2008. AWTY (are we there yet?): a system for graphical exploration of MCMC convergence in Bayesian phylogenetics. Bioinformatics 24:581–583. 404 OLIVEROS, C. H., AND R. G. MOYLE. 2010. Origin and diversification of Philippine bulbuls. Molecular Phylogenetics and Evolution 54:822–832. PAGEL, M. 1994. Detecting correlated evolution on phylogenies: a general method for the comparative analysis of discrete characters. Proceedings of the Royal Society of London, B 255:37–45. PAGEL, M. 2004. Limpets break Dollo’s Law. Trends in Ecology and Evolution 19:278–280. PAGEL, M., AND F. LUTZONI. 2002. Accounting for phylogenetic uncertainty in comparative studies of evolution and adaptation. Pp. 148–161 in M. Lassig and A. Valleriani, eds., Biological evolution and statistical physics. Springer-Verlag, Berlin, Germany. PARADIS, E., J. CLAUDE, AND K. STRIMMER. 2004. APE: Analyses of phylogenetics and evolution in R language. Bioinformatic Applications 20:289–290. PATTON, J. L., AND J. H. FEDER. 1978. Genetic divergence between populations of the pocket gopher, Thomomys umbrinus (Richardson). Saugetierkunde 43:12–30. PATTON, J. L., AND S. Y. YANG. 1977. Genetic variation in Thomomys bottae pocket gophers: Macrogeographic patterns. Evolution 31:697–720. PAUWELS, O. S. G., P. DAVID, C. CHIMSUNCHART, AND K. THIRAKHUPT. 2003. Reptiles of Phetchaburi Province, Western Thailand: a list of species, with natural history notes, and a discussion on the biogeography at the Isthmus of Kra. Natural History Journal of Chulalongkorn University 3:23–53. PESTANO, J., AND R. P. BROWN. 1999. Geographical structuring of mitochondrial DNA in Chalcides sexlineatus within the Island of Gran Canaria. Proceedings of the Royal Society of London, B 266:805–812. PFENNINGER, M., AND K. SCHWENK. 2007. Cryptic animal species are homogeneously distributed 405 among taxa and biogeographical regions. BMC Evolutionary Biology 7:121. POSADA, D. 2008. jModelTest: Phylogenetic Model Averaging. Molecular Biology and Evolution 25:1253–1256. POUGH, F. H., R. M. ANDREWS, J. E. CADLE, M. L. CRUMP, A. H. SAVITZKY, AND K. W. WELLS. 2004. Herpetology. 3rd edn. Prentice-Hall, Upper Saddle River, NJ. R DEVELOPMENT CORE TEAM, 2008. R: a language and environment for statistical computing. Vienna: R Foundation for Statistical Computing. http://www.R-project.org. RAMBAUT, A., AND A. J. DRUMMOND. 2007. Tracer v1.4, Available from http://beast.bio.ed.ac.uk/Tracer. REVELL, L. J. 2009. Size-correction and principal components for interspecific comparative studies. Evolution 63:3258–3268. RONQUIST, F., AND J. P. HUELSENBECK. 2003. MRBAYES 3: Bayesian phylogenetic inference under mixed models. Bioinformatics 19:1572–1574. ROSS, C. A., AND P. C. GONZALES. 1992. Amphibians and reptiles of Catanduanes Island, Philippines. Philippine National Museum Papers 2:50–76. SANDERSON, M. J. 1997. A nonparametric approach to estimating divergence times in the absence of rate constancy. Molecular Biology and Evolution 14:1218–1231. SANG, N. V., H. T. CUC, AND N. Q. TRUONG. 2009. Herpetofauna of Vietnam. Serpents Tale NHBD, Minnesota, USA, pp. 1–768. SANGER, T. J., AND J. J. GIBSON-BROWN. 2004. The developmental bases of limb reduction and body elongation in squamates. Evolution 58:2103–2106. 406 SANGUILA, M. B., C. D. SILER, A. C. DIESMOS, O. NUNEZAA, AND R. M. BROWN. In press. The conservation implications of geographic structure and potential species boundaries in southern Philippine river toads. Molecular Phylogenetics and Evolution. SCHMITZ, A., M. C. BRANDLEY, P. MAUSFELD, M. VENCES, F. GLAW, R. A. NUSSBAUM, AND T. W. REEDER. 2005. Molecular Phylogenetics and Evolution 34:118–133. SELANDER, R. K., D. W. KAUFMAN, R. J. BAKER, AND S. L. WILLIAMS. 1974. Genic and chromosomal differentiation in pocket gophers of the Geomys bursarius group. Evolution 28:557–64. SHAPIRO, M. D. 2002. Developmental morphology of limb reduction in Hemiergis (Squamata: Scincidae): chondrogenesis, osteogenesis, and heterochrony. Journal of Morphology 254:211–231. SHERMAN, P. W., S. BRAUDE, AND J. U. M. JARVIS. 1999. Litter sizes andmammary numbers of naked mole-rats: breaking the one-half rule. Journal of Mammalogy 80:720–733. SHIMODAIRA, H., 2002. An approximately unbiased test of phylogenetic tree selection. Systematic Biology 51:492–508. SHIMODAIRA, H., AND M. HASEGAWA. 2001. CONSEL: for assessing the confidence of phylogenetic tree selection. Bioinformatics 17:1246–1247. SHUBIN, N. H., AND P. ALBERCH. 1986. A morphogenetic approach to the origin an dbasic organization of the tetrapod limb. Evolutionary Biology 20:319–387. SILER, C. D. 2010. Squamata, Scincidae, Brachymeles elerae (Taylor, 1917): Rediscovery in Old Balbalan, Cordillera Mountain Range, Luzon Island, Philippines, and natural history. Check List 6:616–618. 407 SILER, C. D., AND R. M. BROWN. 2010. Phylogeny-based species delimitation in Philippine slender skinks (Reptilia: Squamata: Scincidae: Brachymeles): taxonomic revision of pentadactyl species groups and description of three new species. Herpetological Monographs 24:1–54. SILER, C. D., AND R. M. BROWN. 2011. Evidence for repeated acquisition and loss of complex body characters in an insular clade of Southeast Asian semi-fossorial skinks. Evolution doi:10.1111/j.1558-5646.2011.01315.x. SILER, C. D., E. L. RICO, M. R. DUYA, AND R. M. BROWN. 2009a. A new limb-reduced, loam-swimming skink (Reptilia: Squamata: Scincidae: Genus Brachymeles) from central Luzon Island, Philippines. Herpetologica 65:92–105. SILER, C. D., J. D. MCVAY, A. C. DIESMOS, AND R. M. BROWN. 2009b. A new species of fanged frog, genus Limnonectes (Amphibia: Anura: Dicroglossidae) from southeast Mindanao Island, Philippines. Herpetologica 65:105–114. SILER, C. D., A. C. DIESMOS, AND R. M. BROWN. 2010a. A new loam-swimming skink, Genus Brachymeles (Reptilia: Squamata: Scincidae) from Luzon and Catanduanes islands, Philippines. Journal of Herpetology 44:49–60. SILER, C. D., D. S. BALETE, A. C. DIESMOS, AND R. M. BROWN. 2010b. A new legless loam-swimming lizard (Reptilia: Squamata: Scincidae: Genus Brachymeles) from the Bicol Peninsula, Luzon Island, Philippines. Copeia 2010:114–122. SILER, C. D., J. R. OAKS, J. A. ESSELSTYN, A. C. DIESMOS, AND R. M. BROWN. 2010c. Phylogeny and biogeography of Philippine bent-toed geckos (Gekkonidae: Cyrtodactylus) contradict a prevailing model of Pleistocene diversification. Molecular Phylogenetics and Evolution 55:699–710. 408 SILER, C. D., A. C. DIESMOS, A. C. ALCALA, AND R. M. BROWN. 2011. Phylogeny of Philippine slender skinks (Scincidae: Brachymeles) reveals underestimated species diversity, complex biogeographical relationships, and cryptic patterns of lineage diversification. Molecular Phylogenetics and Evolution 59:53–65. SILER, C. D., R. I. CROMBIE, A. C. DIESMOS, AND R. M. BROWN. In press a. Redescription of two poorly known slender skinks, Brachymeles bicolor and Brachymeles pathfinderi (Reptilia: Squamata: Scincidae) from the Philippines. Journal of Herpetology. SILER, C. D., R. JONES, L. J. WELTON, AND R. M. BROWN. In press b. Redescription of the rare, tetradactyl, Philippine slender skinks (Squmata: Scincidae: Brachymeles) from northern Luzon Island, Philippines. Herpetologica. SILER, C. D., A. M. FUITEN, R. M. JONES, A. C. ALCALA, AND R. M. BROWN. In press c. Phylogeny-based species delimitation in Philippines slender skinks (Reptilia: Squamata: Scincidae) II: Taxonomic revision of Brachymeles samarensis and description of five new species. Herpetological Monographs. SILER, C. D., R. M. JONES, A. C. DIESMOS, M. L. DIESMOS, AND R. M. BROWN. In press d. Phylogeny-based species delimitation in Philippines slender skinks (Reptilia: Squamata: Scincidae) III: Taxonomic revision of the Brachymeles gracilis Complex, with description of three new species. Herpetological Monographs. SIMPSON, G. G. 1953. The major features of evolution. Columbia Univ. Press, New York. SIMPSON, G. G. 1961. Principles of Animal Taxonomy. Columbia University Press, New York, New York, U.S.A. SKINNER, A., 2010. Rate heterogeneity, ancestral character state reconstruction, and the evolution of limb morphology in Lerista (Scincidae, Squamata). Systematic Biology 59:723–740. 409 SKINNER, A., AND M. SY LEE. 2009. Body-form evolution in the scincid lizard clade Lerista and the mode of macroevolutionary transitions. Evolutionary Biology 36:292–300. SKINNER, A., AND M. SY LEE. 2010. Plausibility of inferred ancestral phenotypes and the evaluations of alternative models of limb evolution in scincid lizards. Biology Letters 6:354–358. SKINNER, A., M. SY LEE, AND M. N. HUTCHINSON. 2008. Rapid and repeated limb loss in a clade of scincid lizards. BMC Evolutionary Biology 8:310. STAMATAKIS, A., 2006. RAxML-VI-HPC: maximum likelihood-based phylogenetic analyses with thousands of taxa and mixed models. Bioinformatics 22:2688–2690. STAMATAKIS, A., F. BLAGOJEVIC, D. NIKOLOPOULOS, AND C. ANTONOPOULOS.2007. Exploring new search algorithms and hardware for phylogenetics: RAxML meets the IBM cell. Journal of VLSI Signal Processing 48:271–286. STAMATAKIS, A., P. HOOVER, AND J. ROUGEMONT. 2008. A Rapid Bootstrap Algorithm for the RAxML Web Servers. Systematic Biology 57:758-771. STEPPAN, S. J., C. ZAWADZKI, AND L. R. HEANEY. 2003. Molecular phylogeny of the endemic Philippine rodent Apomys (Muridae) and the dynamics of diversification in an oceanic archipelago. Biological Journal of the Linnean Society 80:699–715. STOKELY, P. 1947. Limblessness and correlated changes in the girdles of a comparative morphological series of lizards. American Midland Naturalist 38:725–754. SWOFFORD, D. L. 2002. PAUP*. Phylogenetic analysis using parsimony (*and other methods). Ver 4.0. Sinauer Associates, Sunderland, MA. TAYLOR, E. H. 1917. Brachymeles, a genus of Philippine lizards. Philippine Journal of Science 12:267–279. 410 TAYLOR, E. H. 1918. Reptiles of Sulu archipelago. Philippine Journal of Science 13:233–267. TAYLOR, E. H. 1922 a. The lizards of the Philippine Islands. Philippine Bureau of Science 17:1–269. TAYLOR, E. H. 1922 b. Additions to the herpetological fauna of the Philippine Islands, II. Philippine Journal of Science 21:257–303. TAYLOR, E. H. 1923. Additions to the herpetological fauna of the Philippine Islands, III. Philippine Journal of Science 22:515–557. TAYLOR, E. H. 1925. Additions to the herpetological fauna of the Philippine Islands, IV. Philippine Journal of Science 26:97–111. TAYLOR, E. H. 1928. Amphibians, lizards and snakes of the Philippines. Pp. 214–242. In: R. Dickerson (Ed.), Distribution of Life in the Philippines. Monograph, Bureau of Science, Manila, Philippines. TOWNSEND, T. M., A. LARSON, E. LOUIS, AND J. R. MACEY. 2004. Molecular phylogenetics of squamata: The position of snakes, amphisbaenians, and dibamids, and the root of the squamate tree. Systematic Biology 53:735–757. TRUEMAN, J. W. H., B. E. PFEIL, S. A. KELCHNER, AND D. K. YEATES. 2004. Did stick insects really regain their wings? Systematic Entomology 29:138–139. URDY, S., AND R. CHIRAT. 2005. Snail shell coiling (re-)evolution and the evodevo revolution. Journal of Zoological Systematics and Evolutionary Research 44:1–7. VAN DIJK, P. P., AND J. NABHITABHATA. 1998. A photographic guide to snakes and other reptiles of Peninsular Malaysia, Singapore and Thailand. Ralph Curtis Publishing, Florida, USA, pp. 1–144. 411 VERHOEVEN, K. J. F., K. L. SIMONSEN, AND L. M. MCINTYRE. 2005. Implementing false discovery rate control: increasing your power. Oikos 108:643–647. VORIS, H.K., 2000. Maps of Pleistocene sea levels in Southeast Asia: Shorelines, river systems and time durations. Journal of Biogeography 27:1153–1167. WELTON, L. J., C. D. SILER, A. C. DIESMOS, AND R. M. BROWN. 2009. A new bent-toed Gekko (Genus Cyrtodactylus) from southern Palawan Island, Philippines and clarification of the taxonomic status of C. annulatus. Herpetologica 65:328–343. WELTON, L. J., C. D. SILER, A. C. DIESMOS, AND R. M. BROWN. 2010a. Phylogeny-based species delimitation of souther Philippines bent-toed geckos and a new species of Cyrtodactylus (Squamata; Gekkonidae) from western Mindanao and the Sulu Archipelago. Zootaxa 2390:49–68. WELTON, L. J., C. D. SILER, A. C. DIESMOS, C. W. LINKEM, AND R. M. BROWN. 2010b. Philippine bent-toed geckos of the Cyrtodactylus agusanensis complex: phylogeny, morphological diversity, and description of three new species. Herpetological Monographs 24:55–85. WHITING, A. S., A. M. BAUER, AND J. W. SITES, JR. 2003. Phylogenetic relationships and limb loss in sub-Saharan African scincine lizards (Squamata:Scincidae). Molecular Phylogenetics and Evolution 29:582–598. WIENS, J. J. 2004. Development and evolution of body form and limb reduction in squamates: a response to Sanger and Gibson-Brown. Evolution 58:2107–2108. WIENS, J. J. 2011. Re-evolution of lost mandibular teeth in frogs after more than 200 million years, and re-evaluating Dollo’s Law. Evolution doi: 10.1111/j.1558-5646.2011.01221.x. 412 WIENS, J. J., AND J. L. SLINGLUFF. 2001. How lizards turn into snakes: a phylogenetic analysis of body-form evolution in anguid lizards. Evolution 55:2303–2318. WIENS, J. J., M. C. BRANDLEY, AND T. W. REEDER. 2006. Why does a trait evolve multiple times within a clade? Repeated evolution of snake-like body form in squamate reptiles. Evolution 60:123–141. WIENS, J. J., C. A. KUCZYNSKI, W. E. DUELLMAN, AND T. W. REEDER. 2007. Loss and re-evolution of complex life cycles in marsupial frogs: does ancestral trait reconstruction mislead? Evolution 61:1886–1899. WILCOX, T. P., D. J. ZWICKL, T. A. HEATH, AND D. M. HILLIS. 2002. Phylogenetic relationships the dwarf boas and a comparison of Bayesian and bootstrap measures of phylogenetic support. Molecular Phylogenetics and Evolution 25:361–371. WILEY, E. O. 1978. The evolutionary species concept reconsidered. Systematic Zoology 21:17–26. WILGENBUSCH, J. C., D. L. WARREN, AND D. L. SWOFFORD. 2004. AWTY: A system for graphical exploration of MCMC convergence in Bayesian phylogenetic inference. http://ceb.csit.fsu.edu/awty. YUMUL, G. P. JR., C. B. DIMALANTA, R. A. TAMAYAO, JR., AND R. C. MAURY. 2003. Collision, subduction and accretion events in the Philippines: A synthesis. Island Arc 12:77–91. YUMUL, G. P. JR., C. B. DIMALANTA, AND V. B. MAGLAMBAYAN. 2008. Tectonic setting of a composite terrain: A review of the Philippine island arc system. Geoscience Journal 12:7–17. YUMUL, G., C. DIMALANTA, K. QUEAÑO, AND E. MARQUEZ. 2009. Philippines, geology. Pp. 732–738. In: R. Gillespie, D. Calgue (Eds.), Encyclopedia of Islands. University of California Press, Berkeley, California, USA. 413 ZANGERL, R. 1945. Contributions to the osteology of the post-cranial skeleton of the Amphisbaenidae. American Midland Naturalist 33:764–780. ZUFALL, R. A., AND M. D. RAUSHER. 2004. Genetic changes associated with floral adaptation restrict future evolutionary potential. Nature 428:847–850. 414 Appendix I Summary of specimens corresponding to genetic samples included in the study. PNM/CMNH = deposited in the Cincinnati Museum of Natural History; RMBR = David Bickford/Djoko Iskandar field number, deposited at the Raffles Museum of Biology; CUMZR = Chulalongkorn Museum of Zoology Reptile collection; SP = Sabah Parks Reference Collection; KU = University of Kansas Natural History Museum; LSUHC = La Sierra University Herpetological Collections; FMNH = Field Museum of Natural History Herpetological Collections; * = currently uncataloged specimen, deposited in the National Museum of the Philippines. Species Voucher Locality Dasia grisea KU 305573 Philippines, Luzon Island, Municipality of Tobaco Davewakeum miriamae KU 327693 Thailand Davewakeum miriamae KU 327692 Thailand Emoia atrocostata KU 04896 Philippines, Calayan Island, Municipality of Calayan Eumeces quadrilineatus KU 311490 China, Guangxi State, Shiwan Dashang Nature Reserve Eutropis multifasciata KU 302904 Philippines, Tablas Island, Municipality of San Agustin Lamprolepis smaragdina KU 326565 Philippines, Palawan Island, Municipality of Narra Larutia seribuatensis LSUHC 5168 West Malaysia Lipinia pulchella pulchella RMB 1079* Philippines, Bohol Island, Municipality of 415 Carmen Lygosoma bowringii LSUHC 6998 West Malaysia Lygosoma sp. LSUHC 6931 West Malaysia Lygosoma quadrupes LSUHC 8403 West Malaysia Plestiodon fasciatus KU 289462 United States, Texas, Smith County Plestiodon anthracinus KU 290718 United States, Kansas, Johnson County Scincella lateralis KU 289461 United States, Texas, Smith County Scincella reevesii FMNH 255540 Lao PDR, Khammouan Prov, Thakhek District Sphenomorphus abdictus abdictus KU 306538 Philippines, Dinagat Island, Municipality of Loreto Tachydromus sexilineatus KU 311512 China, Guangxi State, Shiwan Dashang Nature Reserve Brachymeles apus SP 06915 Malaysia, Borneo, Sabah, Mt. Kinabalu Brachymeles cf. apus RMBR 2040 Malaysia, Borneo, Kalimantan Brachymeles bicolor KU 323149 Philippines, Luzon Island, Municipality of Maria Aurora Brachymeles bicolor KU 323150 Philippines, Luzon Island, Municipality of Maria Aurora Brachymeles bicolor KU 323151 Philippines, Luzon Island, Municipality of Maria Aurora Brachymeles boholensis KU 323992 Philippines, Bohol Island, Municipality of 416 Sierra Bullones Brachymeles boholensis KU 323939 Philippines, Bohol Island, Municipality of Bilar Brachymeles boholensis KU 323958 Philippines, Bohol Island, Municipality of Sierra Bullones Brachymeles bonitae KU 323086 Philippines, Luzon Island, Municipality of Baler Brachymeles bonitae KU 323085 Philippines, Luzon Island, Municipality of Baler Brachymeles bonitae KU 307748 Philippines, Mindoro Island, Municipality of Magsaysay Brachymeles bonitae KU 307749 Philippines, Mindoro Island, Municipality of Gloria Brachymeles bonitae KU 326089 Philippines, Luzon Island, Municipality of Tayabas, Mt. Banahao Brachymeles bonitae RMB 3681* Philippines, Luzon Island, Municipality of Tayabas, Mt. Banahao Brachymeles bonitae KU 320471 Philippines, Lubang Island, Municipality of Lubang Brachymeles bonitae KU 320473 Philippines, Lubang Island, Municipality of Lubang Brachymeles bonitae KU 308004 Philippines, Calayan Island, Municipality of Calayan 417 Brachymeles bonitae KU 307967 Philippines, Calayan Island, Municipality of Calayan Brachymeles bonitae KU 323937 Philippines, Masbate Island, Municipality of Masbate City Brachymeles bonitae KU 323938 Philippines, Masbate Island, Municipality of Masbate City Brachymeles boulengeri KU 323409 Philippines, Luzon Island, Municipality of Baler Brachymeles boulengeri KU 307752 Philippines, Polillo Island, Municipality of Polillo Brachymeles boulengeri KU 307753 Philippines, Polillo Island, Municipality of Polillo Brachymeles cebuensis KU 320419 Philippines, Cebu Island, Municipality of Carcar Brachymeles cebuensis KU 320421 Philippines, Cebu Island, Municipality of Carcar Brachymeles cebuensis KU 320420 Philippines, Cebu Island, Municipality of Carcar Brachymeles gracilis hilong KU 311216 Philippines, Leyte Island, Municipality of Baybay Brachymeles gracilis hilong KU 311220 Philippines, Leyte Island, Municipality of Baybay Brachymeles gracilis hilong KU 310825 Philippines, Samar Island, Municipality of 418 Taft Brachymeles gracilis hilong KU 310731 Philippines, Samar Island, Municipality of Taft Brachymeles elerae KU 326566 Philippines, Luzon Island, Municipality of Balbalan Brachymeles elerae KU 326567 Philippines, Luzon Island, Municipality of Balbalan Brachymeles gracilis gracilis PNM/CMNH 1175 Philippines, Mindanao Island, Municipality of Toril, Mt. Apo Brachymeles gracilis gracilis PNM/CMNH 1176 Philippines, Mindanao Island, Municipality of Toril, Mt. Apo Brachymeles gracilis gracilis ACD 2695* Philippines, Mindanao Island, Municipality of San Isidro, Mt. Hamiguitan Brachymeles gracilis gracilis KU 326099 Philippines, Mindanao Island, Municipality of Kiblawan Brachymeles lukbani KU 313602 Philippines, Luzon Island, Municipality of Labo Brachymeles lukbani KU 313596 Philippines, Luzon Island, Municipality of Labo Brachymeles lukbani KU 313597 Philippines, Luzon Island, Municipality of Labo Brachymeles makusog KU 313610 Philippines, Luzon Island, Municipality of Labo 419 Brachymeles makusog KU 313611 Philippines, Luzon Island, Municipality of Labo Brachymeles makusog KU 308127 Philiippines, Catanduanes Island, Municipality of Gigmoto Brachymeles makusog KU 308128 Philiippines, Catanduanes Island, Municipality of Gigmoto Brachymeles mindorensis KU 304351 Philippines, Mindoro Island, Municipality of Calayan Brachymeles mindorensis KU 307740 Philippines, Mindoro Island, Municipality of Bongabong Brachymeles mindorensis KU 308447 Philippines, Mindoro Island, Municipality of Paluan Brachymeles minimus KU 308131 Philiippines, Catanduanes Island, Municipality of Gigmoto Brachymeles minimus KU 308129 Philiippines, Catanduanes Island, Municipality of Gigmoto Brachymeles minimus KU 308130 Philiippines, Catanduanes Island, Municipality of Gigmoto Brachymeles muntingkamay KU 308866 Philippines, Luzon Island, Municipality of Quezon, Mt. Palali Brachymeles muntingkamay KU 308923 Philippines, Luzon Island, Municipality of Quezon, Mt. Palali Brachymeles muntingkamay KU 308813 Philippines, Luzon Island, Municipality of 420 Quezon, Mt. Palali Brachymeles pathfinderi KU 324057 Philippines, Mindanao Island, Municipality of Glan Brachymeles pathfinderi KU 324058 Philippines, Mindanao Island, Municipality of Glan Brachymeles pathfinderi KU 324096 Philippines, Mindanao Island, Municipality of Glan Brachymeles samarensis KU 324020 Philippines, Catanduanes Island, Municipality of Virac Brachymeles samarensis KU 324022 Philippines, Catanduanes Island, Municipality of Virac Brachymeles samarensis KU 310849 Philippines, Samar Island, Municipality of Taft Brachymeles samarensis KU 311225 Philippines, Leyte Island, Municipality of Baybay Brachymeles samarensis KU 310850 Philippines, Samar Island, Municipality of Taft Brachymeles samarensis KU 310851 Philippines, Samar Island, Municipality of Taft Brachymeles samarensis KU 311226 Philippines, Leyte Island, Municipality of Baybay Brachymeles samarensis KU 311227 Philippines, Leyte Island, Municipality of Baybay 421 Brachymeles orientalis KU 314092 Philippines, Mindanao Island, Municipality of San Francisco Brachymeles orientalis KU 310942 Philippines, Samar Island, Municipality of San Jose de Buan Brachymeles orientalis KU 311232 Philippines, Leyte Island, Municipality of Baybay Brachymeles orientalis KU 324029 Philippines, Bohol Island, Municipality of Bilar Brachymeles orientalis KU 324027 Philippines, Bohol Island, Municipality of Bilar Brachymeles schadenbergi PNM/CMNH 1457 Philippines, Mindanao Island, Municipality of Kiamba, Mt. Busa Brachymeles schadenbergi KU 314973 Philippines, Mindanao Island, Municipality of Zamboanga City Brachymeles schadenbergi KU 314998 Philippines, Mindanao Island, Municipality of Zamboanga City Brachymeles talinis RMB 3283* Philippines, Negros Island, Municipality of Valencia, Mt. Talinis Brachymeles talinis RMB 3305* Philippines, Negros Island, Municipality of Valencia, Mt. Talinis Brachymeles talinis KU 303990 Philippines, Sibuyan Island, Mt. Guiting-Guiting Natural Park Brachymeles talinis KU 306756 Philippines, Panay Island, Municipality of 422 San Remigio Brachymeles talinis KU 315355 Philippines, Tablas Island, Municipality of Calatrava Brachymeles taylori KU 320476 Philippines, Cebu Island, Municipality of Carcar Brachymeles taylori KU 320478 Philippines, Cebu Island, Municipality of Carcar Brachymeles taylori KU 307737 Philippines, Negros Island, Municipality of Valencia, Mt. Talinis Brachymeles taylori KU 320841 Philippines, Negros Island, Municipality of Valencia, Mt. Talinis Brachymeles tridactylus KU 320423 Philippines, Negros Island, Municipality of Hinoba-an Brachymeles tridactylus KU 324025 Philippines, Negros Island, Municipality of Hinoba-an Brachymeles tridactylus KU 320424 Philippines, Negros Island, Municipality of Hinoba-an Brachymeles sp. A KU 323936 Philippines, Masbate Island, Municipality of Mobo Brachymeles sp. A KU 323933 Philippines, Masbate Island, Municipality of Mobo Brachymeles sp. A KU 323934 Philippines, Masbate Island, Municipality of Mobo 423 Brachymeles sp. B KU 324041 Philippines, Luzon Island, Municipality of Tobaco Brachymeles sp. B KU 324031 Philippines, Luzon Island, Municipality of Tobaco Brachymeles sp. B KU 304897 Philippines, Calayan Island, Municipality of Calayan Brachymeles sp. B KU 304558 Philippines, Camiguin Norte Island, Municipality of Tobaco 424 Appendix II Summary of Genbank voucher numbers corresponding to genetic samples included in the study. Species Gene Genbank Voucher Number Brachymeles.apus.RMBR2040 ATP 8,6 HQ907142 BDNF HQ907234 NADH 1 HQ907332 NADH 2 HQ907434 PTGER HQ907534 R35 HQ907641 Brachymeles.apus.SP06915 ATP 8,6 HQ907141 BDNF HQ907233 NADH 1 HQ907331 NADH 2 HQ907433 PTGER HQ907533 R35 HQ907640 Brachymeles.bicolor.KU323149 ATP 8,6 HQ907181 BDNF HQ907279 NADH 1 HQ907377 NADH 2 HQ907479 PTGER HQ907579 R35 HQ907687 Brachymeles.bicolor.KU323150 ATP 8,6 HQ907182 BDNF HQ907280 425 NADH 1 HQ907378 NADH 2 HQ907480 PTGER HQ907580 R35 HQ907688 Brachymeles.bicolor.KU323151 ATP 8,6 HQ907183 BDNF HQ907281 NADH 1 HQ907379 NADH 2 HQ907481 PTGER HQ907581 R35 HQ907689 Brachymeles.bonitae.KU307748 ATP 8,6 HQ907149 BDNF HQ907241 NADH 1 HQ907339 NADH 2 HQ907441 PTGER HQ907541 R35 HQ907648 Brachymeles.bonitae.KU307749 ATP 8,6 HQ907150 BDNF HQ907242 NADH 1 HQ907340 NADH 2 HQ907442 PTGER HQ907542 R35 HQ907649 Brachymeles.bonitae.KU307967 ATP 8,6 HQ907156 426 BDNF HQ907248 NADH 1 HQ907346 R35 HQ907655 Brachymeles.bonitae.KU308004 ATP 8,6 HQ907155 BDNF HQ907247 NADH 1 HQ907345 NADH 2 HQ907447 PTGER HQ907547 R35 HQ907654 Brachymeles.bonitae.KU320471 ATP 8,6 HQ907153 BDNF HQ907245 NADH 1 HQ907343 NADH 2 HQ907445 PTGER HQ907545 R35 HQ907652 Brachymeles.bonitae.KU320473 ATP 8,6 HQ907154 BDNF HQ907246 NADH 1 HQ907344 NADH 2 HQ907446 PTGER HQ907546 R35 HQ907653 Brachymeles.bonitae.KU323085 BDNF HQ907319 NADH 1 HQ907415 427 NADH 2 HQ907519 PTGER HQ907619 R35 HQ907727 Brachymeles.bonitae.KU323086 ATP 8,6 HQ907148 BDNF HQ907240 NADH 1 HQ907338 NADH 2 HQ907440 PTGER HQ907540 R35 HQ907647 Brachymeles.bonitae.KU323937 ATP 8,6 HQ907157 BDNF HQ907249 NADH 1 HQ907347 NADH 2 HQ907448 PTGER HQ907548 R35 HQ907656 Brachymeles.bonitae.KU323938 ATP 8,6 HQ907158 BDNF HQ907250 NADH 1 HQ907348 NADH 2 HQ907449 PTGER HQ907549 R35 HQ907657 Brachymeles.bonitae.KU326089 ATP 8,6 HQ907151 BDNF HQ907243 428 NADH 1 HQ907341 NADH 2 HQ907443 PTGER HQ907543 R35 HQ907650 Brachymeles.bonitae.RMB3681 ATP 8,6 HQ907152 BDNF HQ907244 NADH 1 HQ907342 NADH 2 HQ907444 PTGER HQ907544 R35 HQ907651 Brachymeles.boulengeri.boholensis.KU323939 ATP 8,6 HQ907185 BDNF HQ907283 NADH 1 HQ907381 NADH 2 HQ907483 PTGER HQ907583 R35 HQ907691 Brachymeles.boulengeri.boholensis.KU323958 ATP 8,6 HQ907186 BDNF HQ907284 NADH 1 HQ907382 NADH 2 HQ907484 PTGER HQ907584 R35 HQ907692 Brachymeles.boulengeri.boholensis.KU323995 ATP 8,6 HQ907184 429 BDNF HQ907282 NADH 1 HQ907380 NADH 2 HQ907482 PTGER HQ907582 R35 HQ907690 Brachymeles.boulengeri.boulengeri.KU307752 ATP 8,6 HQ907164 BDNF HQ907256 NADH 1 HQ907354 NADH 2 HQ907456 PTGER HQ907556 R35 HQ907664 Brachymeles.boulengeri.boulengeri.KU307753 ATP 8,6 HQ239375 BDNF HQ907257 NADH 1 HQ907355 NADH 2 HQ907457 PTGER HQ907557 R35 HQ907665 Brachymeles.boulengeri.boulengeri.KU323409 ATP 8,6 HQ907163 NADH 1 HQ907353 NADH 2 HQ907455 PTGER HQ907555 R35 HQ907663 Brachymeles.boulengeri.mindorensis.KU304351 ATP 8,6 HQ907161 430 BDNF HQ907253 NADH 1 HQ907351 NADH 2 HQ907452 PTGER HQ907552 R35 HQ907660 Brachymeles.boulengeri.mindorensis.KU307740 ATP 8,6 HQ239372 BDNF HQ907254 NADH 1 HQ907352 NADH 2 HQ907453 PTGER HQ907553 R35 HQ907661 Brachymeles.boulengeri.mindorensis.KU308447 ATP 8,6 HQ907162 BDNF HQ907255 NADH 2 HQ907454 PTGER HQ907554 R35 HQ907662 Brachymeles.boulengeri.taylori.KU307737 ATP 8,6 HQ907167 BDNF HQ907260 NADH 1 HQ907358 NADH 2 HQ907460 PTGER HQ907560 R35 HQ907668 Brachymeles.boulengeri.taylori.KU320476 ATP 8,6 HQ907165 431 BDNF HQ907258 NADH 1 HQ907356 NADH 2 HQ907458 PTGER HQ907558 R35 HQ907666 Brachymeles.boulengeri.taylori.KU320478 ATP 8,6 HQ907166 BDNF HQ907259 NADH 1 HQ907357 NADH 2 HQ907459 PTGER HQ907559 R35 HQ907667 Brachymeles.boulengeri.taylori.KU320481 ATP 8,6 HQ907168 BDNF HQ907261 NADH 1 HQ907359 NADH 2 HQ907461 PTGER HQ907561 R35 HQ907669 Brachymeles.cebuensis.KU320419 ATP 8,6 HQ907214 BDNF HQ907314 NADH 1 HQ907410 NADH 2 HQ907514 PTGER HQ907614 R35 HQ907722 432 Brachymeles.cebuensis.KU320420 ATP 8,6 HQ907216 BDNF HQ907316 NADH 1 HQ907412 NADH 2 HQ907516 PTGER HQ907616 R35 HQ907724 Brachymeles.cebuensis.KU320421 ATP 8,6 HQ907215 BDNF HQ907315 NADH 1 HQ907411 NADH 2 HQ907515 PTGER HQ907615 R35 HQ907723 Brachymeles.elerae.KU326566 ATP 8,6 HQ907176 BDNF HQ907274 NADH 1 HQ907372 NADH 2 HQ907474 PTGER HQ907574 R35 HQ907682 Brachymeles.elerae.KU326567 ATP 8,6 HQ907177 BDNF HQ907275 NADH 1 HQ907373 NADH 2 HQ907475 PTGER HQ907575 433 R35 HQ907683 Brachymeles.gracilis.gracilis.KU326098 ATP 8,6 HQ907196 BDNF HQ907294 NADH 1 HQ907391 NADH 2 HQ907494 PTGER HQ907594 R35 HQ907702 Brachymeles.gracilis.gracilis.KU326099 ATP 8,6 HQ907197 BDNF HQ907295 NADH 1 HQ907392 NADH 2 HQ907495 PTGER HQ907595 R35 HQ907703 Brachymeles.gracilis.gracilis.PNMCMNHH1175 ATP 8,6 HQ907194 BDNF HQ907292 NADH 2 HQ907492 PTGER HQ907592 R35 HQ907700 Brachymeles.gracilis.gracilis.PNMCMNHH1176 ATP 8,6 HQ907195 BDNF HQ907293 NADH 1 HQ907390 NADH 2 HQ907493 PTGER HQ907593 434 R35 HQ907701 Brachymeles.gracilis.hilong.KU310731 ATP 8,6 HQ907190 BDNF HQ907288 NADH 1 HQ907386 NADH 2 HQ907488 PTGER HQ907588 R35 HQ907696 Brachymeles.gracilis.hilong.KU310825 ATP 8,6 HQ907189 BDNF HQ907287 NADH 1 HQ907385 NADH 2 HQ907487 PTGER HQ907587 R35 HQ907695 Brachymeles.gracilis.hilong.KU311216 ATP 8,6 HQ907187 BDNF HQ907285 NADH 1 HQ907383 NADH 2 HQ907485 PTGER HQ907585 R35 HQ907693 Brachymeles.gracilis.hilong.KU311220 ATP 8,6 HQ907188 BDNF HQ907286 NADH 1 HQ907384 NADH 2 HQ907486 435 PTGER HQ907586 R35 HQ907694 Brachymeles.lukbani.KU313596 ATP 8,6 HQ907212 BDNF HQ907312 NADH 1 HQ907408 NADH 2 HQ907512 PTGER HQ907612 R35 HQ907720 Brachymeles.lukbani.KU313597 ATP 8,6 HQ907213 BDNF HQ907313 NADH 1 HQ907409 NADH 2 HQ907513 PTGER HQ907613 R35 HQ907721 Brachymeles.lukbani.KU313602 ATP 8,6 HQ907211 BDNF HQ907311 NADH 1 HQ907407 NADH 2 HQ907511 PTGER HQ907611 R35 HQ907719 Brachymeles.makusog.KU308127 ATP 8,6 HQ907200 BDNF HQ907298 NADH 1 HQ907394 436 NADH 2 HQ907498 PTGER HQ907598 R35 HQ907706 Brachymeles.makusog.KU308128 ATP 8,6 HQ907201 BDNF HQ907299 NADH 1 HQ907395 NADH 2 HQ907499 PTGER HQ907599 R35 HQ907707 Brachymeles.makusog.KU313610 ATP 8,6 HQ907198 BDNF HQ907296 NADH 2 HQ907496 PTGER HQ907596 R35 HQ907704 Brachymeles.makusog.KU313611 ATP 8,6 HQ907199 BDNF HQ907297 NADH 1 HQ907393 NADH 2 HQ907497 PTGER HQ907597 R35 HQ907705 Brachymeles.minimus.KU308129 ATP 8,6 HQ907209 BDNF HQ907309 NADH 1 HQ907405 437 NADH 2 HQ907509 PTGER HQ907609 R35 HQ907717 Brachymeles.minimus.KU308130 ATP 8,6 HQ907210 BDNF HQ907310 NADH 1 HQ907406 NADH 2 HQ907510 PTGER HQ907610 R35 HQ907718 Brachymeles.minimus.KU308131 ATP 8,6 HQ907208 BDNF HQ907308 NADH 1 HQ907404 NADH 2 HQ907508 PTGER HQ907608 R35 HQ907716 Brachymeles.muntingkamay.KU308813 ATP 8,6 HQ907180 BDNF HQ907278 NADH 1 HQ907376 NADH 2 HQ907478 PTGER HQ907578 R35 HQ907686 Brachymeles.muntingkamay.KU308866 ATP 8,6 HQ907178 BDNF HQ907276 438 NADH 1 HQ907374 NADH 2 HQ907476 PTGER HQ907576 R35 HQ907684 Brachymeles.muntingkamay.KU308923 ATP 8,6 HQ907179 BDNF HQ907277 NADH 1 HQ907375 NADH 2 HQ907477 PTGER HQ907577 R35 HQ907685 Brachymeles.pathfinderi.KU324057 ATP 8,6 HQ907191 BDNF HQ907289 NADH 1 HQ907387 NADH 2 HQ907489 PTGER HQ907589 R35 HQ907697 Brachymeles.pathfinderi.KU324058 ATP 8,6 HQ907192 BDNF HQ907290 NADH 1 HQ907388 NADH 2 HQ907490 PTGER HQ907590 R35 HQ907698 Brachymeles.pathfinderi.KU324096 ATP 8,6 HQ907193 439 BDNF HQ907291 NADH 1 HQ907389 NADH 2 HQ907491 PTGER HQ907591 R35 HQ907699 Brachymeles.samarensis.KU310849 ATP 8,6 HQ907217 BDNF HQ907317 NADH 1 HQ907413 NADH 2 HQ907517 PTGER HQ907617 R35 HQ907725 Brachymeles.samarensis.KU310850 BDNF HQ907320 NADH 1 HQ907416 NADH 2 HQ907520 PTGER HQ907620 R35 HQ907728 Brachymeles.samarensis.KU310851 BDNF HQ907321 NADH 1 HQ907417 NADH 2 HQ907521 PTGER HQ907621 R35 HQ907729 Brachymeles.samarensis.KU311225 ATP 8,6 HQ907218 BDNF HQ907318 440 NADH 1 HQ907414 NADH 2 HQ907518 PTGER HQ907618 R35 HQ907726 Brachymeles.samarensis.KU311226 BDNF HQ907322 NADH 1 HQ907418 NADH 2 HQ907522 PTGER HQ907622 R35 HQ907730 Brachymeles.samarensis.KU311227 BDNF HQ907323 NADH 1 HQ907419 NADH 2 HQ907523 PTGER HQ907623 R35 HQ907731 Brachymeles.samarensis.KU324020 ATP 8,6 HQ907159 BDNF HQ907251 NADH 1 HQ907349 NADH 2 HQ907450 PTGER HQ907550 R35 HQ907658 Brachymeles.samarensis.KU324022 ATP 8,6 HQ907160 BDNF HQ907252 NADH 1 HQ907350 441 NADH 2 HQ907451 PTGER HQ907551 R35 HQ907659 Brachymeles.schadenbergi.orientalis.KU310942 ATP 8,6 HQ907202 BDNF HQ907301 NADH 1 HQ907397 NADH 2 HQ907501 PTGER HQ907601 R35 HQ907709 Brachymeles.schadenbergi.orientalis.KU311232 ATP 8,6 HQ907203 BDNF HQ907302 NADH 1 HQ907398 NADH 2 HQ907502 PTGER HQ907602 R35 HQ907710 Brachymeles.schadenbergi.orientalis.KU314092 BDNF HQ907300 ATP 8,6 HQ239400 NADH 1 HQ907396 NADH 2 HQ907500 PTGER HQ907600 R35 HQ907708 Brachymeles.schadenbergi.orientalis.KU324027 ATP 8,6 HQ907205 BDNF HQ907304 442 NADH 1 HQ907400 NADH 2 HQ907504 PTGER HQ907604 R35 HQ907712 Brachymeles.schadenbergi.orientalis.KU324029 ATP 8,6 HQ907204 BDNF HQ907303 NADH 1 HQ907399 NADH 2 HQ907503 PTGER HQ907603 R35 HQ907711 Brachymeles.schadenbergi.schadenbergi.KU314973 ATP 8,6 HQ907206 BDNF HQ907306 NADH 1 HQ907402 NADH 2 HQ907506 PTGER HQ907606 R35 HQ907714 Brachymeles.schadenbergi.schadenbergi.KU314998 ATP 8,6 HQ907207 BDNF HQ907307 NADH 1 HQ907403 NADH 2 HQ907507 PTGER HQ907607 R35 HQ907715 Brachymeles.schadenbergi.schadenbergi.PNMCMN ATP 8,6 HQ239397 443 HH1457 BDNF HQ907305 NADH 1 HQ907401 NADH 2 HQ907505 PTGER HQ907605 R35 HQ907713 Brachymeles.speciesA.KU323933 ATP 8,6 HQ239395 BDNF HQ907268 NADH 1 HQ907366 NADH 2 HQ907468 PTGER HQ907568 R35 HQ907676 Brachymeles.speciesA.KU323934 BDNF HQ907267 ATP 8,6 HQ239396 NADH 1 HQ907365 NADH 2 HQ907467 PTGER HQ907567 R35 HQ907675 Brachymeles.speciesA.KU323936 ATP 8,6 HQ239394 BDNF HQ907269 NADH 1 HQ907367 NADH 2 HQ907469 PTGER HQ907569 444 R35 HQ907677 Brachymeles.speciesB.KU304558 ATP 8,6 HQ907175 BDNF HQ907273 NADH 1 HQ907371 NADH 2 HQ907473 PTGER HQ907573 R35 HQ907681 Brachymeles.speciesB.KU304897 ATP 8,6 HQ907174 BDNF HQ907272 NADH 1 HQ907370 NADH 2 HQ907472 PTGER HQ907572 R35 HQ907680 Brachymeles.speciesB.KU324031 ATP 8,6 HQ907173 BDNF HQ907271 NADH 1 HQ907369 NADH 2 HQ907471 PTGER HQ907571 R35 HQ907679 Brachymeles.speciesB.KU324041 ATP 8,6 HQ907172 BDNF HQ907270 NADH 1 HQ907368 NADH 2 HQ907470 445 PTGER HQ907570 R35 HQ907678 Brachymeles.talinis.KU303990 ATP 8,6 HQ239388 BDNF HQ907264 NADH 1 HQ907362 NADH 2 HQ907464 PTGER HQ907564 R35 HQ907672 Brachymeles.talinis.KU306756 ATP 8,6 HQ907170 BDNF HQ907265 NADH 1 HQ907363 NADH 2 HQ907465 PTGER HQ907565 R35 HQ907673 Brachymeles.talinis.KU315355 ATP 8,6 HQ907171 BDNF HQ907266 NADH 1 HQ907364 NADH 2 HQ907466 PTGER HQ907566 R35 HQ907674 Brachymeles.talinis.RMB3283 ATP 8,6 HQ907169 BDNF HQ907262 NADH 1 HQ907360 446 NADH 2 HQ907462 PTGER HQ907562 R35 HQ907670 Brachymeles.talinis.RMB3305 ATP 8,6 HQ239387 BDNF HQ907263 NADH 1 HQ907361 NADH 2 HQ907463 PTGER HQ907563 R35 HQ907671 Brachymeles.tridactylus.KU320423 ATP 8,6 HQ907145 BDNF HQ907237 NADH 1 HQ907335 NADH 2 HQ907437 PTGER HQ907537 R35 HQ907644 Brachymeles.tridactylus.KU320424 ATP 8,6 HQ907146 BDNF HQ907238 NADH 1 HQ907336 NADH 2 HQ907438 PTGER HQ907538 R35 HQ907645 Brachymeles.tridactylus.KU320425 ATP 8,6 HQ907147 BDNF HQ907239 447 NADH 1 HQ907337 NADH 2 HQ907439 PTGER HQ907539 R35 HQ907646 Dasia.grisea.KU305573 BDNF HQ907226 NADH 2 HQ907425 PTGER HQ907528 R35 HQ907631 Davewakium.miriamae.KU327692 ATP 8,6 HQ907143 BDNF HQ907235 NADH 1 HQ907333 NADH 2 HQ907435 PTGER HQ907535 R35 HQ907642 Davewakium.miriamae.KU327693 ATP 8,6 HQ907144 BDNF HQ907236 NADH 1 HQ907334 NADH 2 HQ907436 PTGER HQ907536 R35 HQ907643 Emoia.atrocostata.KU304896 BDNF HQ907222 NADH 1 HQ907326 NADH 2 HQ907421 448 R35 HQ907627 Eumeces.quadrilineaturs.KU311490 BDNF HQ907223 NADH 2 HQ907422 PTGER HQ907525 R35 HQ907628 Eutropis.multifasciata.KU302904 NADH 2 HQ907427 R35 HQ907633 Lamprolepis.smaragdina.KU326565 BDNF HQ907221 NADH 1 HQ907325 R35 HQ907626 Larutia.seribuatensis.LSUHC5168 ATP 8,6 HQ907137 BDNF HQ907229 NADH 1 HQ907327 NADH 2 HQ907429 PTGER HQ907530 R35 HQ907636 Lipinia.pulchella.pulchella.RMB1079 BDNF HQ907220 NADH 1 HQ907324 R35 HQ907625 Lygosoma.bowringii.LSUHC6998 ATP 8,6 HQ907138 BDNF HQ907230 NADH 1 HQ907328 NADH 2 HQ907430 449 R35 HQ907637 Lygosoma.LSUHC9321 ATP 8,6 HQ907139 BDNF HQ907231 NADH 1 HQ907329 NADH 2 HQ907431 PTGER HQ907531 R35 HQ907638 Lygosoma.quadrupes.LSUHC8403 ATP 8,6 HQ907140 BDNF HQ907232 NADH 1 HQ907330 NADH 2 HQ907432 PTGER HQ907532 R35 HQ907639 Plestiodon.anthracinus.CAS325 BDNF HQ907225 NADH 2 HQ907424 PTGER HQ907527 R35 HQ907630 Plestiodon.fasciatus.KU289462 BDNF HQ907224 NADH 2 HQ907423 PTGER HQ907526 R35 HQ907629 Scincella.lateralis.KU289461 BDNF HQ907228 R35 HQ907635 450 Scincella.reevesii.FMNH255540 BDNF HQ907227 NADH 2 HQ907428 PTGER HQ907529 R35 HQ907634 Sphenomorphus.abdictus.abdictus.KU306539 NADH 2 HQ907426 R35 HQ907632 Tachydromus.sexilineatus.KU311512 BDNF HQ907219 NADH 2 HQ907420 PTGER HQ907524 R35 HQ907624 451 Appendix III Supporting Information—Materials and Methods VARIABLE CHOICE FOR MORPHOMETRIC SIZE CORRECTION In order to explore whether head length is an appropriate measure with which to standardize morphometric variables, and in doing so account for body size allometry, we first conducted a multivariate correlation analysis of all variables to determine which morphometric variable was most highly correlated with all measures of body size. We then conducted three sets of analyses using three different variables to correct for size. Following the methods of Lande (1978), Wiens and Slingluff (2001), and Brandley et al. (2008), we calculated measurements of relative limb and body sizes by regressing independent contrasts of limb and body-length measurements against contrasts in head length, snout–vent length, and midbody width. Each regression line was forced through the origin following Felsenstein (1985) and the standardized residuals were saved as variables. Relative measurements in each of the three sets of size-corrected morphometric variables (head-length-corrected, snout–vent-length-corrected, midbody-width-corrected) were subsequently used in bivariate and multivariate analyses. For all sets of analyses, the Benjamini and Hochberg (1995) method for controlling the false discovery rate (FDR) was applied to determine significant P-values (Verhoeven et al. 2005). SPSS 18.0 was used for all statistical analyses and JMP 8 was used for graphical output. LITERATURE CITED Benjamini, Y., and Y. Hochberg. 1995. Controlling the false discovery rate—a practical and powerful approach to multiple testing. J. R. Stat. Soc. B 57:289–300. 452 Brandley, M. C., J. P. Huelsenbeck, and J. J. Wiens. 2008. Rates and patterns in the evolution of snake-like body form in squamate reptiles: Evidence for repeated re-evolution of lost digits and long-term persistence of intermediate body forms. Evolution 62:2042–2064. Felsenstein, J. 1985. Phylogenies and the comparative method. Amer. Nat. 125:1–15. Lande, R. 1978. Evolutionary mechanisms of limb loss in tetrapods. Evolution 32:73–92. Verhoeven, K. J. F., K. L. Simonsen, and L. M. McIntyre. 2005. Implementing false discovery rate control: increasing your power. Oikos 108:643–647. Wiens, J. J., and J. L. Slingluff. 2001. How lizards turn into snakes: a phylogenetic analysis of body-form evolution in anguid lizards. Evolution 55:2303–2318. 453 Supplementary Figure 1. Multivariate plot of morphometric and meristic data showing variable loadings for the first and second components for a non-phylogenetic PCA. Colored spheres indicate body form groups among Brachymeles, with shapes referring to labeled phylogenetic clades in Figure 2.1. 454 Appendix IV Additional Specimens Examined Numbers in parentheses indicate the number of specimens examined. With the exception of Brachymeles apus, all specimens examined are from the Philippines. Numbers in parentheses indicate the number of specimens examined for each species. Several sample sizes are greater than those observed in the description due to the examination of sub-adult specimens which were excluded from morphometric analyses. Brachymeles apus (1) BORNEO: MALAYSIA: Sabah: Mt. Kinabalu National Park, Sayap Sub-Station: SP 06915. Brachymeles bicolor (24) LUZON ISLAND: Aurora Province: Municipality of Maria Aurora: Barangay Villa Aurora, Sitio Dimani, Aurora Memorial National Park: KU 323149–52; CAGAYAN PROVINCE: Municipality of Baggao: Sitio Hot Springs: CAS 186111, USNM 140847, 498829–30, 498833; Isabela Province, Sierra Madres Mountain Range: KU 324097–99, PNM 5785, 9568–77; KALINGA PROVINCE: Balbalasang-Balbalan National Park: FMNH 259438. Brachymeles boholensis (19) BOHOL ISLAND: BOHOL PROVINCE: Municipality of Sierra Bullones, Barangay Danicop: KU 323944, 323948–9, 323952–6, 323960, 323962–3, 323966, 323970, 323972, 323975–6, 323981–2, 323990, 324001; BOHOL ISLAND: BOHOL PROVINCE: 6 km S of Municipality of Sierra Bullones: Teachers Park: CAS-SU (Holotype) 24528; 13 km SE Municipality of Sierra Bullones: 455 Dusita Barrio: CAS-SU (Paratypes) 24502–04, 24518, 24520–25, 24541, 24543, CAS-SU 25443–44, 25447; 1 km E Dusita Barrio: Abacjanan: CAS-SU 24867; Municipality of Sierra Bullones: Sandayong: CAS-SU 18709, 18717. Brachymeles bonitae (13) MASBATE ISLAND: MASBATE PROVINCE: Municipality of Mobo: Tugbo Barrio: CAS 144223; Mapuyo Barrio: Palangkahoy: CAS 144270; MINDORO ISLAND: MINDORO ORIENTAL PROVINCE: Mt Halcon: SE slope Barawanan Peak: CAS-SU 25713, 25793, 25886–88, 25904; Sumagui: CAS 62064 (Paratype); POLILLO ISLAND: QUEZON PROVINCE: Municipality of Polillo: Barangay Pinaglubayan: KU 307747–49, 307755. Brachymeles boulengeri (26) LUZON ISLAND: AURORA PROVINCE: Municipality of BAler: KU 322314–20; LUZON ISLAND: LAGUNA PROVINCE: Municipality of Los Banos, Barangay Batong Malake: KU 32058–60; Municipality of Los Banos: CAS 61096; Mt. Maquiling: CAS 61297; POLILLO ISLAND: QUEZON PROVINCE: Municipality of Polillo: CAS (Paratypes) 62272–73, 62276–77; Barangay Pinaglubayan: KU 307438–9, 307750–54, 307756 (Neotype), 307757–58. Brachymeles cebuensis (8) CEBU ISLAND: 40 km SW of Cebu City: Tapal Barrio, Sitio Mantalungon: CAS-SU (Holotype) 24400, (Paratypes) 24396–97, 24399, 24401, 24403; Municipality of Carcar: Tapal Barrio: CAS 102405 (Paratype); 3 km NW Cebu City, Buhisan Barrio, Buhisan Reforestation Project: CAS-SU 27537. 456 Brachymeles elerae (4) LUZON ISLAND: KALINGA PROVINCE: Municipality of Balbalan: CAS 61499–500, PNM 9563–4. Brachymeles gracilis gracilis (18) MINDANAO ISLAND: DAVAO DEL SUR PROVINCE: Municipality of Malalag: Sitio Kibawalan: CAS-SU 24163, 24165, CAS 124811, 139307–09; Davao City: Buhangin, Kabanti-an: CAS 124803–04, 139293–95, 139303–05; Digos City: Tres de Mayo Barrio: CAS 124806–08, 139300. Brachymeles gracilis hilong (20) MINDANAO ISLAND: AGUSAN DEL NORTE PROVINCE: Municipality of Cabadbaran: Diuata Mountain Range: Mt. Hilonghilong: Balangbalang : CAS-SU (Holotype) 24407, (Paratype) 102406, 133578, CAS-SU 24411, 133577, 133581–82, 133609, 133612, 133692–93, 133703–06, 133743, 133745–47; SURIGAO DEL SUR PROVINCE: Municipality of Lanuza: Diuata Mountain Range: Sibuhay Barrio: CAS-SU (Paratype) 24315. Brachymeles lukbani (14) LUZON ISLAND: CAMARINES NORTE PROVINCE: Municipality of Labo: Barangay Tulay Na Lupa, Mt. Labo: PNM (Holotype) 9567, (Paratopotypes) 9589–92, KU (Paratopotypes) 313597–99, 313601, 313603–04, 313606, 313608, FMNH (Paratopotype) 270191. Brachymeles makusog (17) 457 CATANDUANES ISLAND: CATANDUANES PROVINCE: Municipality of Gigmoto: Barangay San Pedro, Sitio Tungaw: PNM (Holotype) 9565, (Paratopotypes) 9583–9584, KU (Paratopotypes) 308126, 308128, 308136, 308208; LUZON ISLAND: CAMARINES NORTE PROVINCE: Municipality of Labo, Barangay Tulay Na Lupa, Mt. Labo: KU (Paratypes) 313612–313614, 313616, 313617, PNM (Paratypes) 9585–9588, FMNH (Paratype) 270200. Brachymeles mindorensis (34) MINDORO ISLAND: MINDORO OCCIDENTAL PROVINCE: KU 304351–5, 304412–3, 304488, 307739–42, 308404, 308447–8, 308534; MINDORO ISLAND: MINDORO ORIENTAL PROVINCE: 30 km SE Municipality of Calapan: Bank of Tarogin River: CAS-SU (Holotype) 24487; SE slope Mt Halcon, Tarogin Barrio: CAS-SU (Paratypes) 24549–54, 24561–62, 24564; 24566, 24568, 24573–74, 24577–79; Mt Halcon, SE slope Barawanan Peak: CAS-SU (Paratype) 24570. Brachymeles minimus (6) CATANDUANES ISLAND: CATANDUANES PROVINCE: Municipality of Gigmoto: Barangay San Pedro: KU 308129–31, 308210–12. Brachymeles muntingkamay (17) LUZON ISLAND: NUEVA VIZCAYA PROVINCE: Municipality of Quezon: Barangay Maddiangat, Mt. Palali: PNM (Holotype) 9566, (Paratopotypes) 9578–82, KU (Paratopotypes) 308865–66, 308900–06, 308908, 308953. Brachymeles pathfinderi (40) 458 MINDANAO ISLAND: SARANGANI PROVINCE: Municipality of Glan: Barangay Taluya: CDS 5235–42; Barangay Tanibulad, Sitio Padido: CDS 5192–5206, 5210–20, 5222–27. Brachymeles samarensis (7) SAMAR ISLAND: EASTERN SAMAR PROVINCE: Municipality of Taft: Barangay San Rafael: KU 310849–50, 310852, 311294–6; LEYTE ISLAND: LEYTE PROVINCE: Municipality of Baybay: Barangay Pilim: Sitio San Vicente: KU 311225. Brachymeles orientalis (53) BOHOL ISLAND: BOHOL PROVINCE: Municipality of Sierra Bullones: Dusita Barrio: CAS-SU (Holotype) 24436, CAS-SU (Paratypes) 24428, 24434, 24437, CAS (Paratype) 102404, CAS-SU 25452; Dusita Barrio: Abacjanan: CAS-SU (Paratypes) 24446–51, CAS-SU 25460; Cantaub Barrio: CAS-SU (Paratypes) 18702, 24442, 24458; CAMIGUIN SUR ISLAND: CAMIGUIN PROVINCE: Municipality of Catarman: Mt. Mambajao: Sitio Sangsangan: CAS 110976–83; LEYTE ISLAND: Leyte PROVINCE: Municipality of Baybay: KU 311231–5, 311241; MINDANAO ISLAND: AGUSAN DEL NORTE PROVINCE: Municipality of Cabadbaran: Diuata Mountain Range: Mt. Hilonghilong: Kasinganan: CAS-SU 133301, 133616, 133749, 133752, 133754; SAMAR ISLAND: Eastern Samar PROVINCE: Municipality of Taft: KU 305470, 310734–6, 310739, 310942–6, 310949, 310951, 310955. Brachymeles schadenbergi (45) BASILAN ISLAND: BASILAN PROVINCE: Port Holland: Sawmill: CAS 60493; MINDANAO ISLAND: MISAMIS OCCIDENTAL PROVINCE: 2 km NW of Masawan: CAS 23468–69; 4 km NW 459 of Masawan: CAS 23471; 3 km NW Masawan: south bank of Dapitan River: CAS 23479–81, 23484–85; COTABATO PROVINCE: Municipality of Tatayan: MCZ 26553, 26555–8, 26561, 26566, 26568, 26571–2, 26574; ZAMBOANGA DEL NORTE PROVINCE: Dapitan River: CAS-SU 23494–96; ZAMBOANGA CITY PROVINCE: Municipality of Pasonanca: Barangay Baluno: Pasonanca Natural Park: KU 314967, 314969, 314970–8, 314980, 314984–85, 314988–92, 314994, 314996–7. Brachymeles talinis (31) NEGROS ISLAND: NEGROS ORIENTAL PROVINCE: 6 km W Municipality of Valencia: Cuernos de Negros Mountain Range: ridge on north side of Maite River: CAS-SU (Holotype) 18358, (Paratype) 89813; Cuernos de Negros Mountain Range: Dayungan Ridge: CAS 133871; Dumaguete City: CAS-SU (Paratype) 12225; Municipality of Siaton: 20 km N Bondo Barrio: CAS-SU 22311–12; 22317, 22323; INAMPULAGAN ISLAND: GUIMARAS PROVINCE: Municipality of Sibunag: 8 km W Pulupandan Town: CAS-SU 27972, 27996–97; PANAY ISLAND: ANTIQUE PROVINCE: Municipality of San Remigio: KU 306756–60, 306762–7, 306769, 306770–6, 306786. Brachymeles taylori (34) NEGROS ISLAND: NEGROS OCCIDENTAL PROVINCE: Municipality of Silay City, Barangay Patag: KU 324044–56; NEGROS ISLAND: NEGROS ORIENTAL PROVINCE: 3 km W Municipality of Valencia: Cuernos de Negros Mountain Range: Sitio Lunga: ridge on north side of Maiti River: CAS-SU (Holotype) 18615, CAS-SU 21873; ridge on south side of Maiti River: CAS-SU (Paratype) 18641, 18656–57, 18748; Cuernos de Negros Mountain Range: CAS-SU 460 (Paratype) 18649; top of Dayungan Ridge: CAS-SU 21877, 21880, 21883–84; 24 km NW Bondo Barrio: Bantolinao: CAS-SU 22355–56; CEBU ISLAND: CEBU PROVINCE: Municipality of Carcar: Tapal Barrio: Sitio Mantalongon: CAS 154671, 154673, 154678–82, 154686. Brachymeles tridactylus (20) NEGROS ISLAND: NEGROS OCCIDENTAL PROVINCE: 16 km E Municipality of La Castellana: Barrio Cabagna-an: Southern Slope of Mt. Canlaon: CAS-SU 19424, 19426–27, 19429, 19452, 19458; 20 km E Municipality of La Castellana: Sitio Kalapnagan: CAS-SU 27082–83; NEGROS ORIENTAL PROVINCE: Hills North and Northwest of Mayaposi: CAS-SU (Holotype) 18354; PANAY ISLAND: ANTIQUE PROVINCE: Municipality of Culasi: Barangay Alojipan: KU 307726–36. Brachymeles vermis (5) JOLO ISLAND: SULU PROVINCE: CAS-SU (Paratype) 62489, CAS-SU 60720–22, 60857. 461 Appendix V Additional Specimens Examined Numbers in parentheses indicate the number of specimens examined. With the exception of Brachymeles apus and B. miriamae, all specimens examined are from the Philippines. Numbers in parentheses indicate the number of specimens examined for each species. Several sample sizes are greater than those observed in the description due to the examination of sub-adult specimens which were excluded from morphometric analyses. Brachymeles apus (1) BORNEO: MALAYSIA: Sabah: Mt. Kinabalu National Park, Sayap Sub-Station: SP 06915. Brachymeles lima (20) See type description. Brachymeles bicolor (24) LUZON ISLAND: Aurora Province: Municipality of Maria Aurora: Barangay Villa Aurora, Sitio Dimani, Aurora Memorial National Park: KU 323149–52; CAGAYAN PROVINCE: Municipality of Baggao: Sitio Hot Springs: CAS 186111, USNM 140847, 498829–30, 498833; Isabela Province, Sierra Madres Mountain Range: KU 324097–99, PNM 5785, 9568–77; KALINGA PROVINCE: Balbalasang-Balbalan National Park: FMNH 259438. Brachymeles boholensis (19) 462 BOHOL ISLAND: BOHOL PROVINCE: Municipality of Sierra Bullones, Barangay Danicop: KU 323944, 323948–9, 323952–6, 323960, 323962–3, 323966, 323970, 323972, 323975–6, 323981–2, 323990, 324001; BOHOL ISLAND: BOHOL PROVINCE: 6 km S of Municipality of Sierra Bullones: Teachers Park: CAS-SU (Holotype) 24528; 13 km SE Municipality of Sierra Bullones: Dusita Barrio: CAS-SU (Paratypes) 24502–04, 24518, 24520–25, 24541, 24543, CAS-SU 25443–44, 25447; 1 km E Dusita Barrio: Abacjanan: CAS-SU 24867; Municipality of Sierra Bullones: Sandayong: CAS-SU 18709, 18717. Brachymeles bonitae (13) MASBATE ISLAND: MASBATE PROVINCE: Municipality of Mobo: Tugbo Barrio: CAS 144223; Mapuyo Barrio: Palangkahoy: CAS 144270; MINDORO ISLAND: MINDORO ORIENTAL PROVINCE: Mt Halcon: SE slope Barawanan Peak: CAS-SU 25713, 25793, 25886–88, 25904; Sumagui: CAS 62064 (Paratype); POLILLO ISLAND: QUEZON PROVINCE: Municipality of Polillo: Barangay Pinaglubayan: KU 307747–49, 307755. Brachymeles boulengeri (26) LUZON ISLAND: AURORA PROVINCE: Municipality of BAler: KU 322314–20; LUZON ISLAND: LAGUNA PROVINCE: Municipality of Los Banos, Barangay Batong Malake: KU 32058–60; Municipality of Los Banos: CAS 61096; Mt. Maquiling: CAS 61297; POLILLO ISLAND: QUEZON PROVINCE: Municipality of Polillo: CAS (Paratypes) 62272–73, 62276–77; Barangay Pinaglubayan: KU 307438–9, 307750–54, 307756 (Neotype), 307757–58. Brachymeles tatlo (3) 463 See type description. Brachymeles cebuensis (8) CEBU ISLAND: 40 km SW of Cebu City: Tapal Barrio, Sitio Mantalungon: CAS-SU (Holotype) 24400, (Paratypes) 24396–97, 24399, 24401, 24403; Municipality of Carcar: Tapal Barrio: CAS 102405 (Paratype); 3 km NW Cebu City, Buhisan Barrio, Buhisan Reforestation Project: CAS-SU 27537. Brachymeles apat (10) See type description. Brachymeles elerae (5) LUZON ISLAND: KALINGA PROVINCE: Municipality of Balbalan: CAS 61499–500, CM (Paratype) 1717, PNM 9563–4. Brachymeles gracilis gracilis (18) MINDANAO ISLAND: DAVAO DEL SUR PROVINCE: Municipality of Malalag: Sitio Kibawalan: CAS-SU 24163, 24165, CAS 124811, 139307–09; Davao City: Buhangin, Kabanti-an: CAS 124803–04, 139293–95, 139303–05; Digos City: Tres de Mayo Barrio: CAS 124806–08, 139300. Brachymeles gracilis hilong (20) MINDANAO ISLAND: AGUSAN DEL NORTE PROVINCE: Municipality of Cabadbaran: Diuata Mountain Range: Mt. Hilonghilong: Balangbalang : CAS-SU (Holotype) 24407, (Paratype) 464 102406, 133578, CAS-SU 24411, 133577, 133581–82, 133609, 133612, 133692–93, 133703–06, 133743, 133745–47; SURIGAO DEL SUR PROVINCE: Municipality of Lanuza: Diuata Mountain Range: Sibuhay Barrio: CAS-SU (Paratype) 24315. Brachymeles kadwa (101) LUZON ISLAND: AURORA PROVINCE: Municipality of Baler: Barangay Zabali, Aurora State College of Technology campus: PNM (Holotype) 9721, KU (Paratopotypes) 232092, 323094–96, 323100, 323104, 323106, KU 323090–91, 323093, 323097–99, 323101–03, 323105, 323107; Municipality of Casiguran, IDC property: KU 323108–48; Municipality of San Luis, Barangay Real, Sitio Minoli: KU 322320; CALAYAN ISLAND: CAGAYAN PROVINCE: Municipality of Calayan: Barangay Magsidel: KU (Paratypes) 304875, 304897, 304900, 304902–3, 304905–6, 304915, 304929, 304941, KU 304908, , 304899, 304907, 304909, 304921, 304941; CAMIGUIN NORTE ISLAND: CAGAYAN PROVINCE: Municipality of Calayan: Barangay Balatubat: KU (Paratypes) 304559, 304575, 304593, 304708, 304754, 307984, 307996, 307998, 308011, KU 304558, 304562–65, 304569, 304571–74, 304627–30, 304643, 304647, 304696–99, 304704–07, 304709–12, 304714, 304753, 304755–59, 307965–66, 307985–86, 307997, 307999–8003, 308006–10, 308012–15, 308017–18. Brachymeles dalawa (46) See type description. Brachymeles lukbani (14) 465 LUZON ISLAND: CAMARINES NORTE PROVINCE: Municipality of Labo: Barangay Tulay Na Lupa, Mt. Labo: PNM (Holotype) 9567, (Paratopotypes) 9589–92, KU (Paratopotypes) 313597–99, 313601, 313603–04, 313606, 313608, FMNH (Paratopotype) 270191. Brachymeles makusog (17) CATANDUANES ISLAND: CATANDUANES PROVINCE: Municipality of Gigmoto: Barangay San Pedro, Sitio Tungaw: PNM (Holotype) 9565, (Paratopotypes) 9583–9584, KU (Paratopotypes) 308126, 308128, 308136, 308208; LUZON ISLAND: CAMARINES NORTE PROVINCE: Municipality of Labo, Barangay Tulay Na Lupa, Mt. Labo: KU (Paratypes) 313612–313614, 313616, 313617, PNM (Paratypes) 9585–9588, FMNH (Paratype) 270200. Brachymeles mindorensis (34) MINDORO ISLAND: MINDORO OCCIDENTAL PROVINCE: KU 304351–5, 304412–3, 304488, 307739–42, 308404, 308447–8, 308534; MINDORO ISLAND: MINDORO ORIENTAL PROVINCE: 30 km SE Municipality of Calapan: Bank of Tarogin River: CAS-SU (Holotype) 24487; SE slope Mt Halcon, Tarogin Barrio: CAS-SU (Paratypes) 24549–54, 24561–62, 24564; 24566, 24568, 24573–74, 24577–79; Mt Halcon, SE slope Barawanan Peak: CAS-SU (Paratype) 24570. Brachymeles minimus (6) CATANDUANES ISLAND: CATANDUANES PROVINCE: Municipality of Gigmoto: Barangay San Pedro: KU 308129–31, 308210–12. Brachymeles miriamae (2) 466 THAILAND: NAKHON RATCHASIMA PROVINCE: Wang Nam Khieo District: Sakaerat Environmental Research Station: DSM 1293, 1363 (Currently uncataloged specimens housed at KU). Brachymeles muntingkamay (17) LUZON ISLAND: NUEVA VIZCAYA PROVINCE: Municipality of Quezon: Barangay Maddiangat, Mt. Palali: PNM (Holotype) 9566, (Paratopotypes) 9578–82, KU (Paratopotypes) 308865–66, 308900–06, 308908, 308953. Brachymeles orientalis (53) BOHOL ISLAND: BOHOL PROVINCE: Municipality of Sierra Bullones: Dusita Barrio: CAS-SU (Holotype) 24436, CAS-SU (Paratypes) 24428, 24434, 24437, CAS (Paratype) 102404, CAS-SU 25452; Dusita Barrio: Abacjanan: CAS-SU (Paratypes) 24446–51, CAS-SU 25460; Cantaub Barrio: CAS-SU (Paratypes) 18702, 24442, 24458; CAMIGUIN SUR ISLAND: CAMIGUIN PROVINCE: Municipality of Catarman: Mt. Mambajao: Sitio Sangsangan: CAS 110976–83; LEYTE ISLAND: Leyte PROVINCE: Municipality of Baybay: KU 311231–5, 311241; MINDANAO ISLAND: AGUSAN DEL NORTE PROVINCE: Municipality of Cabadbaran: Diuata Mountain Range: Mt. Hilonghilong: Kasinganan: CAS-SU 133301, 133616, 133749, 133752, 133754; SAMAR ISLAND: Eastern Samar PROVINCE: Municipality of Taft: KU 305470, 310734–6, 310739, 310942–6, 310949, 310951, 310955. Brachymeles isa (17) See type description. 467 Brachymeles pathfinderi (40) MINDANAO ISLAND: SARANGANI PROVINCE: Municipality of Glan: Barangay Taluya: KU 324089–96; Barangay Tanibulad, Sitio Padido: KU 324057–88. Brachymeles samarensis (7) SAMAR ISLAND: EASTERN SAMAR PROVINCE: Municipality of Taft: Barangay San Rafael: KU 310849–52, 311294–6. Brachymeles schadenbergi (34) BASILAN ISLAND: BASILAN PROVINCE: Port Holland: Sawmill: CAS 60493; MINDANAO ISLAND: MISAMIS OCCIDENTAL PROVINCE: 2 km NW of Masawan: CAS 23468–69; 4 km NW of Masawan: CAS 23471; 3 km NW Masawan: south bank of Dapitan River: CAS 23479–81, 23484–85; ZAMBOANGA DEL NORTE PROVINCE: Dapitan River: CAS-SU 23494–96; ZAMBOANGA CITY PROVINCE: Municipality of Pasonanca: Barangay Baluno: Pasonanca Natural Park: KU 314967, 314969, 314970–8, 314980, 314984–85, 314988–92, 314994, 314996–7. Brachymeles talinis (31) NEGROS ISLAND: NEGROS ORIENTAL PROVINCE: 6 km W Municipality of Valencia: Cuernos de Negros Mountain Range: ridge on north side of Maite River: CAS-SU (Holotype) 18358, (Paratype) 89813; Cuernos de Negros Mountain Range: Dayungan Ridge: CAS 133871; Dumaguete City: CAS-SU (Paratype) 12225; Municipality of Siaton: 20 km N Bondo Barrio: CAS-SU 22311–12; 22317, 22323; INAMPULAGAN ISLAND: GUIMARAS PROVINCE: 468 Municipality of Sibunag: 8 km W Pulupandan Town: CAS-SU 27972, 27996–97; PANAY ISLAND: ANTIQUE PROVINCE: Municipality of San Remigio: KU 306756–60, 306762–7, 306769, 306770–6, 306786. Brachymeles taylori (34) NEGROS ISLAND: NEGROS OCCIDENTAL PROVINCE: Municipality of Silay City, Barangay Patag: KU 324044–56; NEGROS ISLAND: NEGROS ORIENTAL PROVINCE: 3 km W Municipality of Valencia: Cuernos de Negros Mountain Range: Sitio Lunga: ridge on north side of Maiti River: CAS-SU (Holotype) 18615, CAS-SU 21873; ridge on south side of Maiti River: CAS-SU (Paratype) 18641, 18656–57, 18748; Cuernos de Negros Mountain Range: CAS-SU (Paratype) 18649; top of Dayungan Ridge: CAS-SU 21877, 21880, 21883–84; 24 km NW Bondo Barrio: Bantolinao: CAS-SU 22355–56; CEBU ISLAND: CEBU PROVINCE: Municipality of Carcar: Tapal Barrio: Sitio Mantalongon: CAS 154671, 154673, 154678–82, 154686. Brachymeles tridactylus (20) NEGROS ISLAND: NEGROS OCCIDENTAL PROVINCE: 16 km E Municipality of La Castellana: Barrio Cabagna-an: Southern Slope of Mt. Canlaon: CAS-SU 19424, 19426–27, 19429, 19452, 19458; 20 km E Municipality of La Castellana: Sitio Kalapnagan: CAS-SU 27082–83; NEGROS ORIENTAL PROVINCE: Hills North and Northwest of Mayaposi: CAS-SU (Holotype) 18354; PANAY ISLAND: ANTIQUE PROVINCE: Municipality of Culasi: Barangay Alojipan: KU 307726–36. Brachymeles tungaoi (12) 469 MASBATE ISLAND: MASBATE PROVINCE: Municipality of Masbate City: PNM (Holotype) 9722, KU (Paratopotypes) 323934–36; Municipality of Mobo, Barangay Tugbo: CAS (Paratypes) 144229–30, 144290, 144306–7, 144313, 144341–2. Brachymeles vermis (5) JOLO ISLAND: SULU PROVINCE: CAS-SU (Paratype) 62489, CAS-SU 60720–22, 60857. Brachymeles vindumi (4) JOLO ISLAND: SULU PROVINCE: CAS (Holotype) 60724, CAS (Paratypes) 60723, 60725, MCZ (Paratype) 26577). Brachymeles wrighti (2) LUZON ISLAND: BENGUET PROVINCE: Municipality of La Trinidad: MCZ (Holotype) 26589, USNM 140756. 470 Appendix VI Additional Specimens Examined Numbers in parentheses indicate the number of specimens examined. With the exception of Brachymeles apus and B. miriamae, all specimens examined are from the Philippines. Numbers in parentheses indicate the number of specimens examined for each species. Several sample sizes are greater than those observed in the description due to the examination of sub-adult specimens which were excluded from morphometric analyses. Brachymeles apus (1) BORNEO: MALAYSIA: Sabah: Mt. Kinabalu National Park, Sayap Sub-Station: SP 06915. Brachymeles bicolor (24) LUZON ISLAND: Aurora Province: Municipality of Maria Aurora: Barangay Villa Aurora, Sitio Dimani, Aurora Memorial National Park: KU 323149–52; CAGAYAN PROVINCE: Municipality of Baggao: Sitio Hot Springs: CAS 186111, USNM 140847, 498829–30, 498833; Isabela Province, Sierra Madres Mountain Range: KU 324097–99, PNM 5785, 9568–77; KALINGA PROVINCE: Balbalasang-Balbalan National Park: FMNH 259438. Brachymeles boholensis (19) BOHOL ISLAND: BOHOL PROVINCE: Municipality of Sierra Bullones, Barangay Danicop: KU 323944, 323948–9, 323952–6, 323960, 323962–3, 323966, 323970, 323972, 323975–6, 323981–2, 323990, 324001; BOHOL ISLAND: BOHOL PROVINCE: 6 km S of Municipality of Sierra Bullones: Teachers Park: CAS-SU (Holotype) 24528; 13 km SE Municipality of Sierra Bullones: 471 Dusita Barrio: CAS-SU (Paratypes) 24502–04, 24518, 24520–25, 24541, 24543, CAS-SU 25443–44, 25447; 1 km E Dusita Barrio: Abacjanan: CAS-SU 24867; Municipality of Sierra Bullones: Sandayong: CAS-SU 18709, 18717. Brachymeles bonitae (13) MASBATE ISLAND: MASBATE PROVINCE: Municipality of Mobo: Tugbo Barrio: CAS 144223; Mapuyo Barrio: Palangkahoy: CAS 144270; MINDORO ISLAND: MINDORO ORIENTAL PROVINCE: Mt Halcon: SE slope Barawanan Peak: CAS-SU 25713, 25793, 25886–88, 25904; Sumagui: CAS 62064 (Paratype); POLILLO ISLAND: QUEZON PROVINCE: Municipality of Polillo: Barangay Pinaglubayan: KU 307747–49, 307755. Brachymeles boulengeri (26) LUZON ISLAND: AURORA PROVINCE: Municipality of BAler: KU 322314–20; LUZON ISLAND: LAGUNA PROVINCE: Municipality of Los Banos, Barangay Batong Malake: KU 32058–60; Municipality of Los Banos: CAS 61096; Mt. Maquiling: CAS 61297; POLILLO ISLAND: QUEZON PROVINCE: Municipality of Polillo: CAS (Paratypes) 62272–73, 62276–77; Barangay Pinaglubayan: KU 307438–9, 307750–54, 307756 (Neotype), 307757–58. Brachymeles cebuensis (8) CEBU ISLAND: 40 km SW of Cebu City: Tapal Barrio, Sitio Mantalungon: CAS-SU (Holotype) 24400, (Paratypes) 24396–97, 24399, 24401, 24403; Municipality of Carcar: Tapal Barrio: CAS 102405 (Paratype); 3 km NW Cebu City, Buhisan Barrio, Buhisan Reforestation Project: CAS-SU 27537. 472 Brachymeles elerae (5) LUZON ISLAND: KALINGA PROVINCE: Municipality of Balbalan: CAS 61499–500, CM (Paratype) 1717, PNM 9563–4. Brachymeles gracilis (69) MINDANAO ISLAND: DAVAO DEL SUR PROVINCE: FMNH 52642–44, 52646–47, 52662, 52669–70; Davao City: Buhangin, Kabanti-an: CAS 124803–04, 139293–95, 139301–05; Digos City: Tres de Mayo Barrio: CAS 124806–08, 139296–300; Municipality of Kiblawan: Barangay Kimlawis: KU 326096, 326098–108, 326298–99; Municipality of Malalag: Sitio Kibawalan: CAS-SU 24158–65, 24171, CAS 124809–12, 139306–11; Municipality of Toril: Barangay Baracatan, Mt. Apo, Old Eagle Station: CMC 12170–71; SOUTH COTABATO PROVINCE: MCZ 26539, 26541, 26543–44, 26546, 26548–50. Brachymeles pito (28) MINDANAO ISLAND: AGUSAN DEL NORTE PROVINCE: Municipality of Cabadbaran: Diuata Mountain Range: Mt. Hilonghilong: Balangbalang: CAS-SU (Holotype) 24407, (Paratypes) 102406, 133578, CAS-SU 24411, 133577, 133579, 133581–82, 133609, 133612, 133692–93, 133703–06, 133743, 133745–47; AGUSAN DEL SUR PROVINCE: Municipality of San Francisco: Barangay Bagusan II: Mt. Magdiwata: KU 319934–40; SURIGAO DEL SUR PROVINCE: Municipality of Lanuza: Diuata Mountain Range: Sibuhay Barrio: CAS-SU (Paratype) 24315. Brachymeles kadwa (101) 473 LUZON ISLAND: AURORA PROVINCE: Municipality of Baler: Barangay Zabali, Aurora State College of Technology campus: PNM (Holotype) 9721, KU (Paratopotypes) 232092, 323094–96, 323100, 323104, 323106, KU 323090–91, 323093, 323097–99, 323101–03, 323105, 323107; Municipality of Casiguran, IDC property: KU 323108–48; Municipality of San Luis, Barangay Real, Sitio Minoli: KU 322320; CALAYAN ISLAND: CAGAYAN PROVINCE: Municipality of Calayan: Barangay Magsidel: KU (Paratypes) 304875, 304897, 304900, 304902–3, 304905–6, 304915, 304929, 304941, KU 304908, , 304899, 304907, 304909, 304921, 304941; CAMIGUIN NORTE ISLAND: CAGAYAN PROVINCE: Municipality of Calayan: Barangay Balatubat: KU (Paratypes) 304559, 304575, 304593, 304708, 304754, 307984, 307996, 307998, 308011, KU 304558, 304562–65, 304569, 304571–74, 304627–30, 304643, 304647, 304696–99, 304704–07, 304709–12, 304714, 304753, 304755–59, 307965–66, 307985–86, 307997, 307999–8003, 308006–10, 308012–15, 308017–18. Brachymeles lukbani (14) LUZON ISLAND: CAMARINES NORTE PROVINCE: Municipality of Labo: Barangay Tulay Na Lupa, Mt. Labo: PNM (Holotype) 9567, (Paratopotypes) 9589–92, KU (Paratopotypes) 313597–99, 313601, 313603–04, 313606, 313608, FMNH (Paratopotype) 270191. Brachymeles makusog (17) CATANDUANES ISLAND: CATANDUANES PROVINCE: Municipality of Gigmoto: Barangay San Pedro, Sitio Tungaw: PNM (Holotype) 9565, (Paratopotypes) 9583–9584, KU (Paratopotypes) 308126, 308128, 308136, 308208; LUZON ISLAND: CAMARINES NORTE PROVINCE: 474 Municipality of Labo, Barangay Tulay Na Lupa, Mt. Labo: KU (Paratypes) 313612–313614, 313616, 313617, PNM (Paratypes) 9585–9588, FMNH (Paratype) 270200. Brachymeles mindorensis (34) MINDORO ISLAND: MINDORO OCCIDENTAL PROVINCE: KU 304351–5, 304412–3, 304488, 307739–42, 308404, 308447–8, 308534; MINDORO ISLAND: MINDORO ORIENTAL PROVINCE: 30 km SE Municipality of Calapan: Bank of Tarogin River: CAS-SU (Holotype) 24487; SE slope Mt Halcon, Tarogin Barrio: CAS-SU (Paratypes) 24549–54, 24561–62, 24564; 24566, 24568, 24573–74, 24577–79; Mt Halcon, SE slope Barawanan Peak: CAS-SU (Paratype) 24570. Brachymeles minimus (6) CATANDUANES ISLAND: CATANDUANES PROVINCE: Municipality of Gigmoto: Barangay San Pedro: KU 308129–31, 308210–12. Brachymeles miriamae (2) THAILAND: NAKHON RATCHASIMA PROVINCE: Wang Nam Khieo District: Sakaerat Environmental Research Station: DSM 1293, 1363 (Currently uncataloged specimens housed at KU). Brachymeles muntingkamay (17) LUZON ISLAND: NUEVA VIZCAYA PROVINCE: Municipality of Quezon: Barangay Maddiangat, Mt. Palali: PNM (Holotype) 9566, (Paratopotypes) 9578–82, KU (Paratopotypes) 308865–66, 308900–06, 308908, 308953. 475 Brachymeles orientalis (53) BOHOL ISLAND: BOHOL PROVINCE: Municipality of Sierra Bullones: Dusita Barrio: CAS-SU (Holotype) 24436, CAS-SU (Paratypes) 24428, 24434, 24437, CAS (Paratype) 102404, CAS-SU 25452; Dusita Barrio: Abacjanan: CAS-SU (Paratypes) 24446–51, CAS-SU 25460; Cantaub Barrio: CAS-SU (Paratypes) 18702, 24442, 24458; CAMIGUIN SUR ISLAND: CAMIGUIN PROVINCE: Municipality of Catarman: Mt. Mambajao: Sitio Sangsangan: CAS 110976–83; LEYTE ISLAND: Leyte PROVINCE: Municipality of Baybay: KU 311231–5, 311241; MINDANAO ISLAND: AGUSAN DEL NORTE PROVINCE: Municipality of Cabadbaran: Diuata Mountain Range: Mt. Hilonghilong: Kasinganan: CAS-SU 133301, 133616, 133749, 133752, 133754; SAMAR ISLAND: Eastern Samar PROVINCE: Municipality of Taft: KU 305470, 310734–6, 310739, 310942–6, 310949, 310951, 310955. Brachymeles pathfinderi (40) MINDANAO ISLAND: SARANGANI PROVINCE: Municipality of Glan: Barangay Taluya: KU 324089–96; Barangay Tanibulad, Sitio Padido: KU 324057–88. Brachymeles syam (45) See type description. Brachymeles samarensis (7) SAMAR ISLAND: EASTERN SAMAR PROVINCE: Municipality of Taft: Barangay San Rafael: KU 310849–52, 311294–6. 476 Brachymeles schadenbergi (34) BASILAN ISLAND: BASILAN PROVINCE: Port Holland: Sawmill: CAS 60493; MINDANAO ISLAND: MISAMIS OCCIDENTAL PROVINCE: 2 km NW of Masawan: CAS 23468–69; 4 km NW of Masawan: CAS 23471; 3 km NW Masawan: south bank of Dapitan River: CAS 23479–81, 23484–85; ZAMBOANGA DEL NORTE PROVINCE: Dapitan River: CAS-SU 23494–96; ZAMBOANGA CITY PROVINCE: Municipality of Pasonanca: Barangay Baluno: Pasonanca Natural Park: KU 314967, 314969, 314970–8, 314980, 314984–85, 314988–92, 314994, 314996–7. Brachymeles sampu (2) See neotype description. Brachymeles talinis (31) NEGROS ISLAND: NEGROS ORIENTAL PROVINCE: 6 km W Municipality of Valencia: Cuernos de Negros Mountain Range: ridge on north side of Maite River: CAS-SU (Holotype) 18358, (Paratype) 89813; Cuernos de Negros Mountain Range: Dayungan Ridge: CAS 133871; Dumaguete City: CAS-SU (Paratype) 12225; Municipality of Siaton: 20 km N Bondo Barrio: CAS-SU 22311–12; 22317, 22323; INAMPULAGAN ISLAND: GUIMARAS PROVINCE: Municipality of Sibunag: 8 km W Pulupandan Town: CAS-SU 27972, 27996–97; PANAY ISLAND: ANTIQUE PROVINCE: Municipality of San Remigio: KU 306756–60, 306762–7, 306769, 306770–6, 306786. Brachymeles taylori (34) 477 NEGROS ISLAND: NEGROS OCCIDENTAL PROVINCE: Municipality of Silay City, Barangay Patag: KU 324044–56; NEGROS ISLAND: NEGROS ORIENTAL PROVINCE: 3 km W Municipality of Valencia: Cuernos de Negros Mountain Range: Sitio Lunga: ridge on north side of Maiti River: CAS-SU (Holotype) 18615, CAS-SU 21873; ridge on south side of Maiti River: CAS-SU (Paratype) 18641, 18656–57, 18748; Cuernos de Negros Mountain Range: CAS-SU (Paratype) 18649; top of Dayungan Ridge: CAS-SU 21877, 21880, 21883–84; 24 km NW Bondo Barrio: Bantolinao: CAS-SU 22355–56; CEBU ISLAND: CEBU PROVINCE: Municipality of Carcar: Tapal Barrio: Sitio Mantalongon: CAS 154671, 154673, 154678–82, 154686. Brachymeles walo (3) See type description. Brachymeles tridactylus (20) NEGROS ISLAND: NEGROS OCCIDENTAL PROVINCE: 16 km E Municipality of La Castellana: Barrio Cabagna-an: Southern Slope of Mt. Canlaon: CAS-SU 19424, 19426–27, 19429, 19452, 19458; 20 km E Municipality of La Castellana: Sitio Kalapnagan: CAS-SU 27082–83; NEGROS ORIENTAL PROVINCE: Hills North and Northwest of Mayaposi: CAS-SU (Holotype) 18354; PANAY ISLAND: ANTIQUE PROVINCE: Municipality of Culasi: Barangay Alojipan: KU 307726–36. Brachymeles tungaoi (12) 478 MASBATE ISLAND: MASBATE PROVINCE: Municipality of Masbate City: PNM (Holotype) 9722, KU (Paratopotypes) 323934–36; Municipality of Mobo, Barangay Tugbo: CAS (Paratypes) 144229–30, 144290, 144306–7, 144313, 144341–2. Brachymeles vermis (5) JOLO ISLAND: SULU PROVINCE: CAS-SU (Paratype) 62489, CAS-SU 60720–22, 60857. Brachymeles vindumi (4) JOLO ISLAND: SULU PROVINCE: CAS (Holotype) 60724, CAS (Paratypes) 60723, 60725, MCZ (Paratype) 26577). Brachymeles anim (20) See type description. Brachymeles wrighti (2) LUZON ISLAND: BENGUET PROVINCE: Municipality of La Trinidad: MCZ (Holotype) 26589, USNM 140756. Brachymeles apat [Catanduanes Island; Siler et al., in press c] (10) CATANDUANES ISLAND: CATANDUANES PROVINCE: Municipality of Virac: Barangay Palta Small: KU (Paratopotypes) 306311, 308077, 324019–21, 324025–26, PNM (Holotype) 9761, (Paratopotypes) 9562–63. 479 Brachymeles lima [Central Bicol Peninsula, Luzon Island; Siler et al., in press c] (20) LUZON ISLAND: ALBAY PROVINCE: Municipality of Malinao: Barangay Labnig: CAS (Paratypes) 140065, 152025–26; Municipality of Tabaco City: Barangay Common: KU (Paratopotypes) 324005–11, 324015–16, 323087, PNM (Holotype) 9756, (Paratopotypes) 9757–60; CAMARINES SUR PROVINCE: Municipality of Pili: Barrio Curry, Mt. Isarog: CAS-SU (Paratypes) 24173, 24413. Brachymeles dalawa [Lapinig Group islands; Siler et al., in press c] (46) LAPINIG CHICO ISLAND: BOHOL PROVINCE: Municipality of President Carlos P. Garcia: CAS-SU (Paratypes) 27556, 28454–55; LAPINIG GRANDE ISLAND: BOHOL PROVINCE: Municipality of President Carlos P. Garcia: Barangay Villa Milagrosa: KU (Paratopotypes) 320428–30, 320435–63, 320466–67, PNM (Holotype) 9749 (Paratopotypes) 9750–55; 0.5 km SW of Barrio Pitogo: CAS-SU (Paratype) 28453; POLONG DAKO ISLAND: BOHOL PROVINCE: Municipality of President Carlos P. Garcia: CAS-SU (Paratype) 27554. Brachymeles isa [Leyte Island; Siler et al., in press c] (13) LEYTE ISLAND: LEYTE PROVINCE: Municipality of Burauen: Barrio Tambis: CAS-SU (Paratypes) 26110, 26112, 26115, 26120–23; Baybay City: Barangay Pilim, Siotio San Vicente Tree Nursery: KU (Paratopotypes) 311224–25, 311224, PNM (Holotype) 9746, (Paratopotypes) 9747–48. Brachymeles tatlo [Southern Bicol Peninsula, Luzon Island; Siler et al., in press c] (3) 480 LUZON ISLAND: SORSOGON PROVINCE: Municipality of Irosin: PNM (Holotype) 9764; Barangay San Roque, Mt. Bulusan National Park: TNHC (Paratype) 62469, PNM (Paratype) 4856.