Phylogenomics of fresh and formalin specimens resolves the systematics of old world mud snakes (Serpentes: Homalopsidae) and expands biogeographic inference
Creators: name: Bernstein, Justin
Publisher: name: Zenodo
Year: 2024
Subjects: Ancient DNA
natural history collections
Phylogenomics
sea-level fluctuations
Southeast Asia

description: The known biodiversity of Asia and Australasia is continuously expanding with more focused studies on systematics of various groups and the respective biogeography. Historically, fluctuating sea-levels and cyclic connection and separation of now-disjunct landmasses have been invoked to explain the accumulation of biodiversity via species pump mechanisms. However, recent research has shown that geological shifts of the mainland and dispersal events may be better explanations of the biodiversity in these regions. We investigate these processes using the poorly-studied and geographically widespread Mud Snakes (Serpentes: Homalopsidae) using a target capture approach of ~4,800 nuclear loci from fresh tissues and supplemental mitochondrial data from formalin tissues from museum specimens. We use these datasets to reconstruct the first resolved phylogeny of the group, identify their biogeographic origins, and test hypotheses regarding the roles of sea-level change and habitat selection on their diversification. Divergence dating and ancestral range estimation yielded support for an Oligocene origin and diversification from mainland Southeast Asia and Sundaland in the rear-fanged group ~20 million years ago, followed by eastward and westward dispersal. GeoHiSSE models indicate that niche expansion of ancestral rear-fanged lineages into aquatic environments did not impact their diversification rates. Our results highlight that Pleistocene sea-level changes and habitat specificity did not primarily lead to the extant species richness of Homalopsidae, and that, alternatively, geological shifts in mainland Southeast Asia may be a major driver of diversity in this group. We also emphasize the importance of using fresh and degraded tissues, and both nuclear and mitochondrial DNA, for filling in knowledge gaps in poorly known, but highly diverse and conceptually important groups, constituting a non-traditional model study system for understanding transitions between terrestrial, marine, and freshwater environments.
description: Text editor applications (e.g., Notepad++) can be used to open .nexus, .phylip, .docx, and .tre files. The .tre and .tree files can also be opened using FigTree phylogenetic tree visualizer. Adobe or another version of PDF viewer will be needed to viwe .pdf files.
Funding provided by: National Science FoundationROR ID: https://ror.org/021nxhr62Award Number: DEB 2224119
Funding provided by: National Science FoundationROR ID: https://ror.org/021nxhr62Award Number: DEB 0743491
Funding provided by: National Science FoundationROR ID: https://ror.org/021nxhr62Award Number: DEB 1654388
Funding provided by: National Science FoundationROR ID: https://ror.org/021nxhr62Award Number: DEB 0804115
Funding provided by: National Institute of General Medical SciencesROR ID: https://ror.org/04q48ey07Award Number: 2P20GM103432
Funding provided by: Field Museum of Natural History's Grainger Bioinformatics Center *Crossref Funder Registry ID: Award Number:
description: Data was collected using target capture approach, using the Squamate Conserved Loci v2 probeset from Singhal et a. 2017.