Evolution of the aquatic beetle family Noteridae (Coleoptera: Adephaga): integrating methods to examine patterns of diversification across temporal scales.

Abstract

Parsing the evolutionary patterns and processes that underly beetle diversity has been the subject of countless investigations. With an estimated crown age of 300 million years and millions of species, beetle evolution has unfolded over broad temporal and spatial scales. My dissertation focuses on the evolution of the aquatic beetle family Noteridae (Coleoptera: Adephaga). By integrating a wide variety of methods, I investigate patterns of noterid evolution across hundreds of millions of years of evolutionary time, from major lineages over 250 million years old, to the level of species and populations, potentially less than 1 million years old. Adephaga has been the subject of many phylogenetic investigations using a variety of data types, without strong consensus on the relationships of its aquatic members. We conducted the first phylogenomic study of Adephaga with ultraconserved elements (UCEs). UCEs are captured by targeted, probe-based, enrichment and subsequent next-gen sequencing, and are known for effective phylogenetic reconstructions at both deep and shallow time scales. Capturing over 300 loci, we showed that aquatic adephagans, or ‘Hydradephaga’, are not monophyletic and further proved the efficacy of UCEs for coleopteran phylogenomics. As Adephaga is the parent suborder of Noteridae, this chapter is provided a contextual and methodological basis for my dissertation research. Within Noteridae, the subfamily of minute beetles, Notomicrinae, presents a partial Gondwanan distribution, occupying Oceania, Indomalaya and the New World. My dissertation research shows that several species in the largest genus of the group, Notomicrus, are yet undescribed, and the subfamily displays a wide range of habitat preference among species with varying degrees of specificity. To investigate these patterns, we constructed a Sanger-based dataset of five markers and robust sampling of Notomicrinae, with a strong emphasis on New World species of Notomicrus. We used this to reconstruct the phylogeny of Notomicrinae and estimate divergence times for a biogeographic reconstruction. We recovered a monophyletic Notomicrus, divided into five species groups of Notomicrus, and affirmed the existence of several undescribed species. The crown age of Notomicrus is estimated to be ca. 72 million years (ma), with Old and New World clades reciprocally monophyletic and separating in a time-span consistent with Gondwanan vicariance. The results of the phylogenetic reconstruction are then used to guide the taxonomic circumscription of the five species groups of Notomicrus. Provided is a key and diagnosis to each species group and insertae sedis species. We additionally performed the first of four reviews of the four New World groups, and review the josiahi group, complete with a description of a new species, N. interstinctus Baca and Short, 2021. The phylogenetic reconstruction and taxonomic research of Notomicrinae showed that there exists a large species complex within Notomicrus, namely, the traili complex. Individuals of this complex can be found throughout South American and north into Mexico and the West Indies, with often overlapping distributions among phylogenetically distinct groups. To examine the evolution of this group and guide taxonomy, we designed a tailored noterid UCE probe set. We captured data from a robust population level sampling of the traili complex (45 individuals) and generated UCE data matrices at different levels of completeness and trimming regimes. With up to UCE 1,252 loci, we reconstructed the phylogeny of the complex. We recovered two distinct species N. gracilipes Sharp, 1882 and a tentative new species as successive sisters to the greater complex. In most analyses the complex split into four main clades with extensive and often overlapping ranges throughout south America. We discuss the taxonomic and biogeographic implications of this reconstruction and establish a foundation for future research in the traili complex.