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Homalopsids (Old World Mud Snakes) include 59 semiaquatic species in Asia and Australasia that display an array of morphological adaptations, behaviors, and microhabitat preferences. These attributes make homalopsids an ideal model system for broader questions in evolutionary biology, but the diversity of this understudied group of snakes is still being described. Recognized species diversity in rice paddy snakes (Hypsiscopus) has recently doubled after nearly 200 years of taxonomic stability. However, the evolutionary distinctiveness of some populations remains in question. In this study, we compare mainland Southeast Asian populations of Hypsiscopus east and west of the Red River Basin in Vietnam, a known biogeographic barrier in Asia, using an iterative approach with molecular phylogenetic reconstruction, machine-learning morphological quantitative statistics, and ecological niche modeling. Our analyses show that populations west of the Red River Basin represent an independent evolutionary lineage that is distinct in genetics, morphospace, and habitat suitability, and so warrants species recognition. The holotype of H. wettsteini, a species originally described in error from Costa Rica, grouped morphometrically with the population at the Red River Basin and eastward, and those west of the Red River Basin are referred to the recently described H. murphyi. The two species may have diversified due to a variety of geological and environmental factors, and their recognition exemplifies the importance of multifaceted approaches in taxonomy for downstream biogeographic studies on speciation scenarios.  

Abstract 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 thatHypsiscopusdiversified 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 suggestHypsiscopusdiversified ~ 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 ofHypsiscopus, 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. 

Abstract Comprehensive assessments of species’ extinction risks have documented the extinction crisis 1 and underpinned strategies for reducing those risks 2 . Global assessments reveal that, among tetrapods, 40.7% of amphibians, 25.4% of mammals and 13.6% of birds are threatened with extinction 3 . Because global assessments have been lacking, reptiles have been omitted from conservation-prioritization analyses that encompass other tetrapods 4–7 . Reptiles are unusually diverse in arid regions, suggesting that they may have different conservation needs 6 . Here we provide a comprehensive extinction-risk assessment of reptiles and show that at least 1,829 out of 10,196 species (21.1%) are threatened—confirming a previous extrapolation 8 and representing 15.6 billion years of phylogenetic diversity. Reptiles are threatened by the same major factors that threaten other tetrapods—agriculture, logging, urban development and invasive species—although the threat posed by climate change remains uncertain. Reptiles inhabiting forests, where these threats are strongest, are more threatened than those in arid habitats, contrary to our prediction. Birds, mammals and amphibians are unexpectedly good surrogates for the conservation of reptiles, although threatened reptiles with the smallest ranges tend to be isolated from other threatened tetrapods. Although some reptiles—including most species of crocodiles and turtles—require urgent, targeted action to prevent extinctions, efforts to protect other tetrapods, such as habitat preservation and control of trade and invasive species, will probably also benefit many reptiles.