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Publication Chloroplast Genome Provides Insights into Molecular Evolution and Species Relationship of Fleabanes (: Tribe Astereae, Asteraceae) in the Juan Fernández Islands, Chile(MDPI, 2024-02-23) Kim, Seung-Chul; Crawford, Daniel J; Stuessy, Tod F; Cho, Myong-Suk; Yang, JiYoung; Kim, Seon-HeeErigeron represents the third largest genus on the Juan Fernández Islands, with six endemic species, five of which occur exclusively on the younger Alejandro Selkirk Island with one species on both islands. While its continental sister species is unknown, Erigeron on the Juan Fernández Islands appears to be monophyletic and most likely evolved from South American progenitor species. We characterized the complete chloroplast genomes of five Erigeron species, including accessions of E. fernandezia and one each from Alejandro Selkirk and Robinson Crusoe Islands, with the purposes of elucidating molecular evolution and phylogenetic relationships. We found highly conserved chloroplast genomes in size, gene order and contents, and further identified several mutation hotspot regions. In addition, we found two positively selected chloroplast genes (ccsA and ndhF) among species in the islands. The complete plastome sequences confirmed the monophyly of Erigeron in the islands and corroborated previous phylogenetic relationships among species. New findings in the current study include (1) two major lineages, E. turricola–E. luteoviridis and E. fernandezia–E. ingae–E. rupicola, (2) the non-monophyly of E. fernandezia occurring on the two islands, and (3) the non-monophyly of the alpine species E. ingae complex.Publication Integrative methods reveal multiple drivers of diversification in rice paddy snakes(Nature Research, 2024-03-12) Ruane, Sara; Soto-Centeno, J Angel; Gehara, Marcelo; Brown, Rafe M; Calderón-Acevedo, Camilo A; Riyanto, Awal; Iskandar, Djoko T; McGuire, Jimmy A; Karns, Daryl R; Stuart, Bryan L; Voris, Harold K; Bernstein, Justin MDivergence dating analyses in systematics provide a framework to develop and test biogeographic hypotheses regarding speciation. However, as molecular datasets grow from multilocus to genomic, sample sizes decrease due to computational burdens, and the testing of fine-scale biogeographic hypotheses becomes difficult. In this study, we use coalescent demographic models to investigate the diversification of poorly known rice paddy snakes from Southeast Asia (Homalopsidae: Hypsiscopus), which have conflicting dates of origin based on previous studies. We use coalescent modeling to test the hypothesis that Hypsiscopus diversified 2.5 mya during the Khorat Plateau uplift in Thailand. Additionally, we use ecological niche analyses to identify potential differences in the niche space of the two most widely distributed species in the past and present. Our results suggest Hypsiscopus diversified ~ 2.4 mya, supporting that the Khorat Plateau may have initiated the diversification of rice paddy snakes. We also find significant niche differentiation and shifts between species of Hypsiscopus, indicating that environmental differences may have sustained differentiation of this genus after the Khorat Plateau uplift. Our study expands on the diversification history of snakes in Southeast Asia, and highlights how results from smaller multilocus datasets can be useful in developing and testing biogeographic hypotheses alongside genomic datasets.Publication Range-Wide Phylogeography and Ecological Niche Modeling Provide Insights into the Evolutionary History of the Mongolian Racerunner () in Northeast Asia(MDPI, 2024-04-07) Guo, XianguangThe Mongolian racerunner, , is a small lizard endemic to Northeast Asia that can serve as an excellent model for investigating how geography and past climate change have jointly influenced the evolution of biodiversity in this region. To elucidate the processes underlying its diversification and demography, we reconstructed the range-wide phylogeographic pattern and evolutionary trajectory, using phylogenetic, population genetic, landscape genetic, Bayesian phylogeographic reconstruction and ecological niche modeling approaches. Phylogenetic analyses of the mtDNA cyt gene revealed eight lineages that were unbounded by geographic region. The genetic structure of was mainly determined by geographic distance. Divergence dating indicated that and diverged during the Mid-Pliocene Warm Period. was estimated to have coalesced at~0.4351 Ma (Marine Isotope Stage 19). Bayesian phylogeographic diffusion analysis revealed out-of-Inner Mongolia and rapid colonization events from the end of the Last Interglacial to the Last Glacial Maximum, which is consistent with the expanded suitable range of the Last Glacial Maximum. Pre-Last Glacial Maximum growth of population is presented for most lineages of The Glacial Maximum contraction model and the previous multiple glacial refugia hypotheses are rejected. This may be due to an increase in the amount of climatically favorable habitats in Northeast Asia. Furthermore, most likely represents an invalid taxon. The present study is the first to report a range-wide phylogeography of reptiles over such a large region in Northeast Asia. Our results make a significant contribution towards understanding the biogeography of the entire Northeast Asia.Publication SRC-1 controls growth cone polarity and protrusion with the UNC-6/Netrin receptor UNC-5 in Caenorhabditis elegans(PLOS One, 2024-05-21) Lundquist, Erik A; Burt, Emily K; Mahadik, Snehal SThe Polarity/Protusion model of UNC-6/Netrin function in axon repulsion does not rely on a gradient of UNC-6/Netrin. Instead, the UNC-5 receptor polarizes the VD growth cone such that filopodial protrusions are biased to the dorsal leading edge. UNC-5 then inhibits growth cone protrusion ventrally based upon this polarity, resulting in dorsally-biased protrusion and dorsal migration away from UNC-6/Netrin. While previous studies have shown that UNC-5 inhibits growth cone protrusion by destabilizing actin, preventing microtubule + end entry, and preventing vesicle fusion, the signaling pathways involved are unclear. The SRC-1 tyrosine kinase has been previously shown to physically interact with and phosphorylate UNC-5, and to act with UNC-5 in axon guidance and cell migration. Here, the role of SRC-1 in VD growth cone polarity and protrusion is investigated. A precise deletion of src-1 was generated, and mutants displayed unpolarized growth cones with increased size, similar to unc-5 mutants. Transgenic expression of src-1(+) in VD/DD neurons resulted in smaller growth cones, and rescued growth cone polarity defects of src-1 mutants, indicating cell-autonomous function. Transgenic expression of a putative kinase-dead src-1(D831A) mutant caused a phenotype similar to src-1 loss-of-function, suggesting that this is a dominant negative mutation. The D381A mutation was introduced into the endogenous src-1 gene by genome editing, which also had a dominant-negative effect. Genetic interactions of src-1 and unc-5 suggest they act in the same pathway on growth cone polarity and protrusion, but might have overlapping, parallel functions in other aspects of axon guidance. src-1 function was not required for the effects of activated myr::unc-5, suggesting that SRC-1 might be involved in UNC-5 dimerization and activation by UNC-6, of which myr::unc-5 is independent. In sum, these results show that SRC-1 acts with UNC-5 in growth cone polarity and inhibition of protrusion.Publication Ecological niche conservatism spurs diversification in response to climate change(Nature Portfolio, 2024-02-19) Saupe, Erin ELengthy debate has surrounded the theoretical and empirical science of whether climatic niche evolution is related to increased or decreased rates of biological diversification. Because species can persist for thousands to millions of years, these questions cross broad scales of time and space. Thus, short-term experiments may not provide comprehensive understanding of the system, leading to the emergence of contrasting opinions: niche evolution may increase diversity by allowing species to explore and colonize new geographic areas across which they could speciate; or, niche conservatism might augment biodiversity by supporting isolation of populations that may then undergo allopatric speciation. Here, we use a simulation approach to test how biological diversification responds to different rates and modes of niche evolution. We find that niche conservatism promotes biological diversification, whereas labile niches-whether adapting to the conditions available or changing randomly-generally led to slower diversification rates. These novel results provide a framework for understanding how Earth-life interactions produced such a diverse biota.Publication Land-cover change in Cuba and implications for the area of distribution of a specialist's host-plant(PeerJ, 2024-06-25) Soberon, JorgeChanges in land cover directly affect biodiversity. Here, we assessed land-cover change in Cuba in the past 35 years and analyzed how this change may affect the distribution of plants and moths. We analyzed the vegetation cover of the Cuban archipelago for 1985 and 2020. We used Google Earth Engine to classify two satellite image compositions into seven cover types: forest and shrubs, mangrove, soil without vegetation cover, wetlands, pine forest, agriculture, and water bodies. We considered four different areas for quantifications of land-cover change: (1) Cuban archipelago, (2) protected areas, (3) areas of potential distribution of , and (4) areas of potential distribution of the plant within the protected areas. We found that "forest and shrubs", which is cover type in which populations have been reported, has increased significantly in Cuba in the past 35 years, and that most of the gained forest and shrub areas were agricultural land in the past. This same pattern was observed in the areas of potential distribution of ; whereas almost all cover types were mostly stable inside the protected areas. The transformation of agricultural areas into forest and shrubs could represent an interesting opportunity for biodiversity conservation in Cuba. Other detailed studies about biodiversity composition in areas of forest and shrubs gain would greatly benefit our understanding of the value of such areas for conservation.Publication Ecological niche divergence or ecological niche partitioning in a widespread Neotropical bird lineage(PeerJ, 2024-04-30) Cooper, Jacob CEcological niche divergence is generally considered to be a facet of evolution that may accompany geographic isolation and diversification in allopatry, contributing to species' evolutionary distinctiveness through time. The null expectation for any two diverging species in geographic isolation is that of niche conservatism, wherein populations do not rapidly shift to or adapt to novel environments. Here, I test ecological niche divergence for a widespread, pan-American lineage, the avian genus of martins (). The genus includes migrant and resident species, as well as geographically restricted taxa and widespread, intercontinentally distributed taxa, thus providing an ideal group in which to study the nature of niche divergence within a broad geographic mosaic. I obtained distributional information for the genus from publicly available databases and created ecological niche models for each species to create pairwise comparisons of environmental space. I combined these data with the most up-to-date phylogeny of currently available to examine the patterns of niche evolution within the genus. I found limited evidence for niche divergence across the breeding distributions of , and much stronger support for niche conservatism with patterns of niche partitioning. The ancestral had a relatively broad ecological niche, like extant basal lineages, and several geographically localized descendant species occupy only portions of this larger ancestral niche. I recovered strong evidence of breeding niche divergence for four of 36 taxon pairs but only one of these divergent pairs involved two widespread species (Southern Martin . Gray-breasted Martin ). Potential niche expansion from the ancestral species was observed in the most wide-ranging present-day species, namely the North American Purple Martin and . I analyzed populations of separately, as a microcosm of evolution, and again found only limited evidence of niche divergence. This study adds to the mounting evidence for niche conservatism as a dominant feature of diversifying lineages, and sheds light on the ways in which apparently divergent niches may arise through allopatry while not involving any true niche shifts through evolutionary time. Even taxa that appear unique in terms of habitat or behavior may not be diversifying with respect to their ecological niches, but merely partitioning ancestral niches among descendant taxa.Publication New species of redbait from the Philippines (Teleostei, Emmelichthyidae, )(ZooKeys, 2024-03-22) Bemis, Katherine EDito pinakita namin ang isang kakaibang isda na may Tagalog name na Rebentador pula at English name na Redbait na kabilang sa genus na nakuha sa mga pamilihan ng isda sa isla ng Panay at Cebu sa Visayas, Philippines. Ang isdang ito ay may panglabas na anyo kamukha ng pero naiba ito dahil meron itong dalawa (2) prominenteng fleshy papillae na parte ng cleithrum, may mas konting pectoral-fin rays na may bilang na 18–19 at gill rakers na may bilang na 30–33. Iniiba ng mitochondrial DNA ang taxon na ito mula sa iba pang mga species ng . Binuo, sinuri at kinumpara namin ang mitochondrial genomes ng dalawang type specimens ng kakaibang isda at iba pang isda na kabilang sa emmelichthyids para malaman kung bago nga ba ito. Lumabas sa pagsusuri, gamit ang lahat ng protein-coding mitochondrial loci, na bago nga ang kakaibang isda. Pero napag-alaman din na mukhang isang grupo lang at malapit na mag kamag-anak ang 2 genus ( and ) na kasama sa Family Emmelichthyidae kung kaya’t kailangan pa ang ibayong pagsusri sa pagkakakilanlan ng nasabing 2 genus.Publication Human Impacts on the Vegetation of the Juan Fernández (Robinson Crusoe) Archipelago(MDPI, 2023-11-30) Greimler, JosefThe human footprint on marine and terrestrial ecosystems of the planet has been substantial, largely due to the increase in the human population with associated activities and resource utilization. Oceanic islands have been particularly susceptible to such pressures, resulting in high levels of loss of biodiversity and reductions in the numbers and sizes of wild populations. One archipelago that has suffered from human impact has been the Juan Fernández (Robinson Crusoe) Archipelago, a Chilean national park located 667 km west of Valparaíso at 33° S. latitude. The park consists of three principal islands: Robinson Crusoe Island (48 km); Santa Clara Island (2.2 km); and Alejandro Selkirk Island (50 km). The latter island lies 181 kms further west into the Pacific Ocean. No indigenous peoples ever visited or lived on any of these islands; they were first discovered by the Spanish navigator, Juan Fernández, in 1574. From that point onward, a series of European visitors arrived, especially to Robinson Crusoe Island. They began to cut the forests, and such activity increased with the establishment of a permanent colony in 1750 that has persisted to the present day. Pressures on the native and endemic flora increased due to the introduction of animals, such as goats, rats, dogs, cats, pigs, and rabbits. Numerous invasive plants also arrived, some deliberately introduced and others arriving inadvertently. At present, more than three-quarters of the endemic and native vascular species of the flora are either threatened or endangered. The loss of vegetation has also resulted in a loss of genetic variability in some species as populations are reduced in size or go extinct. It is critical that the remaining genetic diversity be conserved, and genomic markers would provide guidelines for the conservation of the diversity of the endemic flora. To preserve the unique flora of these islands, further conservation measures are needed, especially in education and phytosanitary monitoring.Publication An evaluation of the ecological niche of Orf virus (Poxviridae): Challenges of distinguishing broad niches from no niches(PLOS One, 2024-01-18) Peterson, A TownsendContagious ecthyma is a skin disease, caused by Orf virus, creating great economic threats to livestock farming worldwide. Zoonotic potential of this disease has gained recent attention owing to the re-emergence of disease in several parts of the world. Increased public health concern emphasizes the need for a predictive understanding of the geographic distributional potential of Orf virus. Here, we mapped the current distribution using occurrence records, and estimated the ecological niche in both geographical and environmental spaces. Twenty modeling experiments, resulting from two- and three-partition models, were performed to choose the candidate models that best represent the geographic distributional potential of Orf virus. For all of our models, it was possible to reject the null hypothesis of predictive performance no better than random expectations. However, statistical significance must be accompanied by sufficiently good predictive performance if a model is to be useful. In our case, omission of known distribution of the virus was noticed in all Maxent models, indicating inferior quality of our models. This conclusion was further confirmed by the independent final evaluation, using occurrence records sourced from the Centre for Agriculture and Bioscience International. Minimum volume ellipsoid (MVE) models indicated the broad range of environmental conditions under which Orf virus infections are found. The excluded climatic conditions from MVEs could not be considered as unsuitable owing to the broad distribution of Orf virus. These results suggest two possibilities: that the niche models fail to identify niche limits that constrain the virus, or that the virus has no detectable niche, as it can be found throughout the geographic distributions of its hosts. This potential limitation of component-based pathogen-only ENMs is discussed in detail.Publication Physiognomy datasets across two sub-montane tropical forests: Bakossi National Park and Mt. Nlonako in the continental Cameroon mountains(Elsevier, 2024-04-25) Sainge, Moses Nsanyi; Lyonga, Ngoh Michael; Nchu, Felix; Peterson, A. TownsendThe submontane forests in the Congo Basin have not been studied sufficiently in terms of floristic diversity, biomass, and geographic distribution. The region's lack of resources and rugged terrain are among the barriers to sampling biodiversity. This study focuses on two understudied submontane forest areas, Bakossi National Park (BNP) and Mt. Nlonako (MN), which form part of the continental Cameroon Mountains and are believed to have high species diversity and endemism. However, significant gaps exist in biodiversity data across the continental Cameroon Mountains. This study is the first detailed quantitative survey of forests in the BNP and MN through permanent plot sampling. The results of this study can be used to guide policies for managing montane ecosystems in Cameroon and enhancing conservation efforts. The study also provides an opportunity for long-term monitoring of forest health and REDD+ status.Publication Predicting climate-driven distribution shifts in Hyalomma marginatum (Ixodidae)(Cambridge University Press, 2023-07-31) Hekimoglu, Olcay; Elverici, Can; Cem Kuyucu, ArdaHyalomma marginatum is an important tick species which is the main vector of Crimean–Congo haemorrhagic fever and spotted fever. The species is predominantly distributed in parts of southern Europe, North Africa and West Asia. However, due to ongoing climate change and increasing reports of H. marginatum in central and northern Europe, the expansion of this range poses a potential future risk. In this study, an ecological niche modelling approach to model the current and future climatic suitability of H. marginatum was followed. Using high-resolution climatic variables from the Chelsa dataset and an updated list of locations for H. marginatum, ecological niche models were constructed under current environmental conditions using MaxEnt for both current conditions and future projections under the ssp370 and ssp585 scenarios. Models show that the climatically suitable region for H. marginatum matches the current distributional area in the Mediterranean basin and West Asia. When applied to future projections, the models suggest a considerable expansion of H. marginatum's range in the north in Europe as a result of rising temperatures. However, a decline in central Anatolia is also predicted, potentially due to the exacerbation of drought conditions in that region.Publication Predicting climate-driven distribution shifts in Hyalomma marginatum (Ixodidae)(Cambridge University Press, 2023-07-31) Hekimoglu, Olcay; Elverici, Can; Cem Kuyucu, ArdaHyalomma marginatum is an important tick species which is the main vector of Crimean–Congo haemorrhagic fever and spotted fever. The species is predominantly distributed in parts of southern Europe, North Africa and West Asia. However, due to ongoing climate change and increasing reports of H. marginatum in central and northern Europe, the expansion of this range poses a potential future risk. In this study, an ecological niche modelling approach to model the current and future climatic suitability of H. marginatum was followed. Using high-resolution climatic variables from the Chelsa dataset and an updated list of locations for H. marginatum, ecological niche models were constructed under current environmental conditions using MaxEnt for both current conditions and future projections under the ssp370 and ssp585 scenarios. Models show that the climatically suitable region for H. marginatum matches the current distributional area in the Mediterranean basin and West Asia. When applied to future projections, the models suggest a considerable expansion of H. marginatum's range in the north in Europe as a result of rising temperatures. However, a decline in central Anatolia is also predicted, potentially due to the exacerbation of drought conditions in that region.Publication Species Delimitation, Phylogenomics, and Biogeography of Sulawesi Flying Lizards: A Diversification History Complicated by Ancient Hybridization, Cryptic Species, and Arrested Speciation(Oxford University Press, 2023-04-19) Mcguire, Jimmy A.; Huang, Xiaoting; Reilly, Sean B.; Iskandar, Djoko T.; Wang-Claypool, Cynthia Y.; Werning, Sarah; Chong, Rebecca A.; Lawalata, Shobi Z. S.; Stubbs, Alexander L.; Frederick, Jeffrey H.; Brown, Rafe M.; Evans, Ben J.; Arifin, Umilaela; Riyanto, Awal; Hamidy, Amir; Arida, Evy; Koo, Michelle S.; Supriatna, Jatna; Andayani, Noviar; Hall, RobertThe biota of Sulawesi is noted for its high degree of endemism and for its substantial levels of in situ biological diversification. While the island’s long period of isolation and dynamic tectonic history have been implicated as drivers of the regional diversification, this has rarely been tested in the context of an explicit geological framework. Here, we provide a tectonically informed biogeographical framework that we use to explore the diversification history of Sulawesi flying lizards (the Draco lineatus Group), a radiation that is endemic to Sulawesi and its surrounding islands. We employ a framework for inferring cryptic speciation that involves phylogeographic and genetic clustering analyses as a means of identifying potential species followed by population demographic assessment of divergence-timing and rates of bi-directional migration as means of confirming lineage independence (and thus species status). Using this approach, phylogenetic and population genetic analyses of mitochondrial sequence data obtained for 613 samples, a 50-SNP data set for 370 samples, and a 1249-locus exon-capture data set for 106 samples indicate that the current taxonomy substantially understates the true number of Sulawesi Draco species, that both cryptic and arrested speciations have taken place, and that ancient hybridization confounds phylogenetic analyses that do not explicitly account for reticulation. The Draco lineatus Group appears to comprise 15 species—9 on Sulawesi proper and 6 on peripheral islands. The common ancestor of this group colonized Sulawesi ~11 Ma when proto-Sulawesi was likely composed of two ancestral islands, and began to radiate ~6 Ma as new islands formed and were colonized via overwater dispersal. The enlargement and amalgamation of many of these proto-islands into modern Sulawesi, especially during the past 3 Ma, set in motion dynamic species interactions as once-isolated lineages came into secondary contact, some of which resulted in lineage merger, and others surviving to the present.Publication The Fergana Valley Is an Isolate of Biodiversity: A Discussion of the Endemic Herpetofauna and Description of Two New Species of Alsophylax (Sauria: Gekkonidae) from Eastern Uzbekistan(MDPI, 2023-08-04) Nazarov, Roman A.; Abduraupov, Timur V.; Shepelya, Evgeniya Yu.; Gritsina, Mariya A.; Melnikov, Daniel A.; Buehler, Matthew D.; Lapin, Jack D.; Poyarkov, Nikolay A.; Grismer, Jesse L.The high level of endemism in Fergana Valley has been well documented in numerous studies for various groups of animals and plants. In a relatively small area, there are 45 endemic plant species, five endemic insect species, and five endemic reptile species. In surveying this area for data on distribution, abundance, acoustics, and genetic samples for species of reptiles, we discovered two new species of gecko from the genus Alsophylax. Phylogenetic analyses of mitochondrial DNA sequences indicate the relatives of these new species are the even-fingered gecko, Alsophylax pipiens, and the southern even-fingered gecko, Alsophylax laevis, located hundreds of kilometers to the northwest and southwest of the Fergana Valley. The threats to these new endemic species are significant given the amount of continued agricultural development that involves new territories previously considered “unsuitable” for any species of significance that is leading to the further reduction in, fragmentation of, and degradation of the remaining natural ecosystems in the Fergana Valley. The conservation of these rare and locally endemic species depends directly on the readiness of the state to create areas with IUCN I and II protection. The many studies documenting levels of endemism, along with the data published in this study, are the basis for the justification for state-protected areas in the Fergana Valley.Publication Anthropogenic uranium signatures in turtles, tortoises, and sea turtles from nuclear sites(Oxford University Press, 2023-08-22) Conrad, Cyler; Inglis, Jeremy; Wende, Allison; Sanborn, Matthew; Mukundan, Nilesh; Price, Allison; Tenner, Travis; Wurth, Kimberly; Naes, Benjamin; Fair, Jeanne; Middlebrook, Earl; Gaukler, Shannon; Whicker, Jeffrey; Gerard, Jamie L.; Aguilera, Washington Tapia; Gibbs, James P.; Wolf, Blair; Kattil-deBrum, Tonie K; Hagemann, Molly; Seminoff, Jeffrey A.; Brys, Timothy; Brown, Rafe M.; Derieg, Katrina M.Chelonians (turtles, tortoises, and sea turtles) grow scute keratin in sequential layers over time. Once formed, scute keratin acts as an inert reservoir of environmental information. For chelonians inhabiting areas with legacy or modern nuclear activities, their scute has the potential to act as a time-stamped record of radionuclide contamination in the environment. Here, we measure bulk (i.e. homogenized scute) and sequential samples of chelonian scute from the Republic of the Marshall Islands and throughout the United States of America, including at the Barry M. Goldwater Air Force Range, southwestern Utah, the Savannah River Site, and the Oak Ridge Reservation. We identify legacy uranium (235U and 236U) contamination in bulk and sequential chelonian scute that matches known nuclear histories at these locations during the 20th century. Our results confirm that chelonians bioaccumulate uranium radionuclides and do so sequentially over time. This technique provides both a time series approach for reconstructing nuclear histories from significant past and present contexts throughout the world and the ability to use chelonians for long-term environmental monitoring programs (e.g. sea turtles at Enewetok and Bikini Atolls in the Republic of the Marshall Islands and in Japan near the Fukushima Daiichi reactors).Publication Range-wide phylogenomics of the Great Horned Owl (Bubo virginianus) reveals deep north-south divergence in northern Peru Emily N. Ostrow,corresponding author Lucas H. DeCicco, and Robert G. Moyle(Peej, 2023-08-09) Ostrow, Emily N.; DeCicco, Lucas H.; Moyle, Robert G.The Great Horned Owl (Bubo virginianus) inhabits myriad habitats throughout the Americas and shows complex patterns of individual and geographic morphological variation. The owl family Strigidae is known to follow ecogeographic rules, such as Gloger’s rule. Although untested at the species level, these ecogeographic rules may affect B. virginianus plumage coloration and body size. Previous studies have indicated that, despite this species’ morphological variability, little genetic differentiation exists across parts of their range. This study uses reduced representation genome-wide nuclear and complete mitochondrial DNA sequence data to assess range-wide relationships among B. virginianus populations and the disputed species status of B. v. magellanicus (Magellanic or Lesser Horned Owl) of the central and southern Andes. We found shallow phylogenetic relationships generally structured latitudinally to the north of the central Andes, and a deep divergence between a southern and northern clade close to the Marañón Valley in the central Andes, a common biogeographic barrier. We identify evidence of gene flow between B. v. magellanicus and other subspecies based on mitonuclear discordance and F-branch statistics. Overall differences in morphology, plumage coloration, voice, and genomic divergence support species status for B. v. magellanicus.Publication Identifying Climatic Drivers of Hybridization with a New Ancestral Niche Reconstruction Method(Oxford University Press, 2023-04-19) Folk, Ryan A; Gaynor, Michelle L; Engle-Wrye, Nicholas J; O'Meara, Brian C; Soltis, Pamela S; Soltis, Douglas E; Guralnick, Robert P; Smith, Stephen A; Grady, Charles J; Okuyama, YudaiApplications of molecular phylogenetic approaches have uncovered evidence of hybridization across numerous clades of life, yet the environmental factors responsible for driving opportunities for hybridization remain obscure. Verbal models implicating geographic range shifts that brought species together during the Pleistocene have often been invoked, but quantitative tests using paleoclimatic data are needed to validate these models. Here, we produce a phylogeny for Heuchereae, a clade of 15 genera and 83 species in Saxifragaceae, with complete sampling of recognized species, using 277 nuclear loci and nearly complete chloroplast genomes. We then employ an improved framework with a coalescent simulation approach to test and confirm previous hybridization hypotheses and identify one new intergeneric hybridization event. Focusing on the North American distribution of Heuchereae, we introduce and implement a newly developed approach to reconstruct potential past distributions for ancestral lineages across all species in the clade and across a paleoclimatic record extending from the late Pliocene. Time calibration based on both nuclear and chloroplast trees recovers a mid- to late-Pleistocene date for most inferred hybridization events, a timeframe concomitant with repeated geographic range restriction into overlapping refugia. Our results indicate an important role for past episodes of climate change, and the contrasting responses of species with differing ecological strategies, in generating novel patterns of range contact among plant communities and therefore new opportunities for hybridization. The new ancestral niche method flexibly models the shape of niche while incorporating diverse sources of uncertainty and will be an important addition to the current comparative methods toolkit. [Ancestral niche reconstruction; hybridization; paleoclimate; pleistocene.]Publication Movement patterns and habitat use for the sympatric species: Gambelia wislizenii and Aspidoscelis tigris(Wiley Open Access, 2023-08-10) McAlpine-Bellis, Elizabeth; Utsumi, Kaera L.; Diamond, Kelly M.; Klein, Janine; Gilbert-Smith, Sophia; Garrison, Grace E.; Eifler, Maria A.Movement is an important characteristic of an animal's ecology, reflecting the perception of and response to environmental conditions. To effectively search for food, movement patterns likely depend on habitat characteristics and the sensory systems used to find prey. We examined movements associated with foraging for two sympatric species of lizards inhabiting the Great Basin Desert of southeastern Oregon. The two species have largely overlapping diets but find prey via different sensory cues, which link to their differing foraging strategies—the long‐nosed leopard lizard, Gambelia wislizenii, is a visually‐oriented predator, while the western whiptail, Aspidoscelis tigris, relies more heavily on chemosensory cues to find prey. Using detailed focal observations, we characterized the habitat use and movement paths of each species. We placed markers at the location of focal animals every minute for the duration of each 30‐min observation. Afterward, we recorded whether each location was in the open or in vegetation, as well as the movement metrics of step length, path length, net displacement, straightness index, and turn angle, and then made statistical comparisons between the two species. The visual forager spent more time in open areas, moved less frequently over shorter distances, and differed in patterns of plant use compared to the chemosensory forager. Path characteristics of step length and turn angle differed between species. The visual predator moved in a way that was consistent with the notion that they require a clear visual path to stalk prey whereas the movement of the chemosensory predator increased their chances of detecting prey by venturing further into vegetation. Sympatric species can partition limited resources through differences in search behavior and habitat use.Publication An elevational shift facilitated the Mesoamerican diversification of Azure‐hooded Jays (Cyanolyca cucullata) during the Great American Biotic Interchange(Wiley Open Access, 2023-08-15) McCormack, John E.; Hill, Molly M.; DeRaad, Devon A.; Kirsch, Eliza J.; Reckling, Kelsey R.; Mutchler, Marquette J.; Ramirez, Brenda R.; Campbell, Russell M. L.; Salter, Jessie F.; Pizarro, Alana K.; Tsai, Whitney L. E.; Bonaccorso, ElisaThe Great American Biotic Interchange (GABI) was a key biogeographic event in the history of the Americas. The rising of the Panamanian land bridge ended the isolation of South America and ushered in a period of dispersal, mass extinction, and new community assemblages, which sparked competition, adaptation, and speciation. Diversification across many bird groups, and the elevational zonation of others, ties back to events triggered by the GABI. But the exact timing of these events is still being revealed, with recent studies suggesting a much earlier time window for faunal exchange, perhaps as early as 20 million years ago (Mya). Using a time‐calibrated phylogenetic tree, we show that the jay genus Cyanolyca is emblematic of bird dispersal trends, with an early, pre‐land bridge dispersal from Mesoamerica to South America 6.3–7.3 Mya, followed by a back‐colonization of C. cucullata to Mesoamerica 2.3–4.8 Mya, likely after the land bridge was complete. As Cyanolyca species came into contact in Mesoamerica, they avoided competition due to a prior shift to lower elevation in the ancestor of C. cucullata. This shift allowed C. cucullata to integrate itself into the Mesoamerican highland avifauna, which our time‐calibrated phylogeny suggests was already populated by higher‐elevation, congeneric dwarf‐jays (C. argentigula, C. pumilo, C. mirabilis, and C. nanus). The outcome of these events and fortuitous elevational zonation was that C. cucullata could continue colonizing new highland areas farther north during the Pleistocene. Resultingly, four C. cucullata lineages became isolated in allopatric, highland regions from Panama to Mexico, diverging in genetics, morphology, plumage, and vocalizations. At least two of these lineages are best described as species (C. mitrata and C. cucullata). Continued study will further document the influence of the GABI and help clarify how dispersal and vicariance shaped modern‐day species assemblages in the Americas.