A multifaceted approach to investigating diversity, systematics, and biogeography of old world mud snakes (Serpentes: Homalopsidae)
Creators: name: Bernstein, Justin Matthew
Publisher: name: No Publisher Supplied
Year: 2022

description: Snakes exhibit a diversity of morphological, ecological, and behavioral traits, and are widely distributed across the world. These characteristics serve as excellent systems for testing evolutionary hypotheses. Homalopsids (Old World mud snakes) are a family of primarily semi-aquatic snakes that are distributed through South and Southeast Asia, New Guinea, and Australia. The variation in natural history traits seen within homalopsids makes them useful as a system to study evolution, biogeography, and more. However, the lack of a resolved homalopsid phylogeny and detailed studies using multiple datatypes precludes their use as a system. In this study, I investigate the species richness and evolution of Homalopsidae using a variety of datatypes and methods. After using preliminary Sanger sequencing data to better understand homalopsid diversity (Chapter 1), I use genomic data to reconstruct a resolved, time-calibrated phylogeny of Homalopsidae (Chapter 2). Ancestral range estimations and hidden state models support that Homalopsidae originated in the Oligocene, with the rear-fanged species of this group likely diversifying due to geological changes in the aquatic landscape of Indochina and Sundaland and then dispersing east and west. I also provide biogeographic hypotheses of fangless and South Asian homalopsids on the basis of molecular data collected from museum specimens. Using genomic and multilocus data, with supplemental morphological data and machine learning classification, I also describe a new species of Hypsiscopus from Indochina (Chapter 3). Coalescent modeling and simulations with multilocus data suggest that this lineage may have diverged from its congeners when the Khorat Plateau in Thailand uplifted ~2.5 mya (with no subsequent migration or gene flow), but genomic divergence dating of this diversification predates the plateau at ~4 mya. Ecological niche models of Hypsiscopus suggest that the new species of the genus occupies a distinct niche when compared to the other two species. With these results, I show support that Hypsiscopus had an eastward dispersal through its range, and provide an alternative hypothesis for the diversification of the genus: ecological divergence 4 mya, and cessation of gene flow when the Khorat Plateau uplift occurred ~2.5 mya. Finally, I use museum genomics to reject that Hydrablabes periops, a poorly known snake from Borneo, is in the family Homalopsidae, and I show support for its taxonomic designation amongst other aquatic snakes in the family Natricidae. Using a multifaceted approach, I use multilocus, genomic, distributional, and ecological data, as well as phylogenetic, machine learning, and coalescent modeling and simulation methods to increase the known diversity of Homalopsidae and provide information on their evolution across their geographic distribution. I also show that using both fresh and degraded DNA can expand evolutionary, biogeographic, and taxonomic inference by using alternative pipelines for data processing and combining these data with published datasets. My study provides a phylogeny and natural history information that is novel for this group, and exemplifies how using a variety of approaches for evolutionary and biogeographic studies can find new patterns, undescribed diversity, and new biogeographic hypotheses.