Our knowledge of the biodiversity of Asia and Australasia continues to expand with more focused studies on the systematics of various groups and their 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 species dispersal events may be better explanations for the biodiversity in these regions. In a recent paper, Berstein et al. (2023) 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. Berstein et al. (2023) also used 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 supported 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. Alternatively, geological shifts in mainland Southeast Asia may have been a significant driver of diversity in this group. Bernstein et al. also emphasize the importance of using fresh and degraded tissues, nuclear and mitochondrial DNA, to fill knowledge gaps in poorly known but highly diverse and conceptually essential groups. Here, Homalopsidae represents a non-traditional but effective model study system for understanding transitions between terrestrial, marine, and freshwater environments.
The authors successfully generated nuclear DNA alignments ≥200 bp for 10 of the 41 museum specimens of the fangless homalopsids Brachyorrhos gastrotaenius (3) and Calamophis ruuddelangi (1) and the rear-fanged Dieurostus dussumieri (2), Ferania sieboldii (1), Hypsiscopus plumbea (1), Mintonophis pakistanicus (1), and Miralia alternans (1). However, the recovery of homologous loci among these specimens was minimal, and high levels of missing data of targeted nuclear loci precluded their use. Thus, they relied on the cyt-b sequences obtained as mitochondrial bycatch from Calamophis ruuddelangi, Brachyorrhos gastrotaenius, Ferania sieboldii, Mintonophis pakistanicus, Dieurostus dussumieri, Miralia alternans, and Homalophis doriae and included these only in the cyt-b tree.
The concatenated nuclear tree (fresh samples only) is topologically identical to the species tree with solid support at most nodes (Supplementary Figs. S1–S3). All species are monophyletic in the concatenated nuclear tree except Cerberus schneiderii, Homalopsis buccata, and Hypsiscopus plumbea. Cerberus microlepis and C. dunsoni are nested within C. schneiderii, Homalopsis semizonata is embedded in H. buccata, and H. plumbea is paraphyletic concerning H. matannensis.
The homalopsid species tree with only fresh specimens recovers a monophyletic Homalopsidae with strong support (Bpp=1) at all nodes except the divergence between Enhydris enhydris and E. longicauda+E. innominata. The fangless genus Brachyorrhos is sister to the rear-fanged clade, which comprises all other homalopsids. The rear-fanged homalopsids consist of two subclades (subclade I and II; Fig 2B). The species tree is broadly consistent with the cyt-b (constrained by the genomic tree topology) tree regarding the fangless/rear-fanged split and the two subclades of rear-fanged taxa. The cyt-b tree recovered a poorly supported fangless clade (UFB=66), sister to the strongly supported rear-fanged clade (UFB=96), with all genera as monophyletic and most nodes strongly supported (Fig. 2B; Supplementary Figure S4). The poorly known New Guinea endemic Calamophis diverges from Brachyorrhos for the fangless taxa. The rear-fanged South Asian homalopsids Ferania sieboldii, Mintonophis pakistanicus, and Dieurostus dussumieri are the closest related group to all other homalopsids in Subclade I with solid support (Fig. 2B). Miralia alternans is strongly supported as sister to Myrrrophis. Enhydris jagorii is minimally divergent from E. innominata and E. longicauda. Additionally, Homalophis doriae is recovered as part of a clade consisting of the Sundaic taxa Raclitia indica and Phytolopsis punctata.
