Integrative methods reveal multiple drivers of diversification in rice paddy snakes.

Divergence 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.

Phylogeography of the Mekong mud snake (Enhydris subtaeniata): the biogeographic importance of dynamic river drainages and fluctuating sea levels for semiaquatic taxa in Indochina.

During the Cenozoic, Southeast Asia was profoundly affected by plate tectonic events, dynamic river systems, fluctuating sea levels, shifting coastlines, and climatic variation, which have influenced the ecological and evolutionary trajectories of the Southeast Asian flora and fauna. We examined the role of these paleogeographic factors on shaping phylogeographic patterns focusing on a species of semiaquatic snake, Enhydris subtaeniata (Serpentes: Homalopsidae) using sequence data from three mitochondrial fragments (cytochrome b, ND4, and ATPase-2785 bp). We sampled E. subtaeniata from seven locations in three river drainage basins that encompassed most of this species' range. Genetic diversities were typically low within locations but high across locations. Moreover, each location had a unique suite of haplotypes not shared among locations, and pairwise φ(ST) values (0.713-0.998) were highly significant between all location pairs. Relationships among phylogroups were well resolved and analysis of molecular variance (AMOVA) revealed strong geographical partitioning of genetic variance among the three river drainage basins surveyed. The genetic differences observed among the populations of E. subtaeniata were likely shaped by the Quaternary landscapes of Indochina and the Sunda Shelf. Historically, the middle and lower Mekong consisted of strongly dissected river valleys separated by low mountain ranges and much of the Sunda Shelf consisted of lowland river valleys that served to connect faunas associated with major regional rivers. It is thus likely that the contemporary genetic patterns observed among populations of E. subtaeniata are the result of their histories in a complex terrain that created abundant opportunities for genetic isolation and divergence yet also provided lowland connections across now drowned river valleys.

Phylogeny, evolutionary history, and biogeography of Oriental-Australian rear-fanged water snakes (Colubroidea: Homalopsidae) inferred from mitochondrial and nuclear DNA sequences.

Homalopsid snakes are widely distributed throughout Southeast Asia and form the ecologically dominant component of the herpetofauna over much of their range. Although they are considered well differentiated from other colubrid lineages, several aspects of their radiation including within-family relationships, temporal patterns of species diversification, and biogeographic history remain under studied. We analyzed sequence data from four genes (three mitochondrial and one nuclear) for 22 species of the Homalopsidae to generate the most comprehensive phylogeny of the family to date. We also estimated divergence times within the family using a model of independent but log-normally distributed rates of evolution in conjunction with two external fossil calibrations. Using this chronogram, we inferred historical patterns of species diversification within the family. Finally, we used previously published sequence data for 172 snake species to test for the monophyly of the Homalopsidae. Phylogenetic analysis reveals strong support for homalopsid monophyly with an estimate age of the crown group of approximately 22 MYA. The family comprises three major clades which all originated 18-20 MY. Lineage through time plots reveal that homalopsids experienced a significantly higher rate of effective cladogenesis in their early history, consistent with a hypothesis of adaptive radiation. We discuss several Miocene and Pliocene paleogeographic factors that might underlie observed patterns of temporal diversification and biogeography.