Diversification and Colonisation in the Indo‐Australian Archipelago: Genomic Insights From Colubrid Snakes

ABSTRACT Aim The Indo‐Australian Archipelago (IAA) is one of the most geologically complex and species‐rich regions on Earth. However, our knowledge of the geological processes and dispersal mechanisms that generate archipelago‐wide distributions across the IAA is limited to a few vertebrate groups and often solely attributed to Plio‐Pleistocene sea‐level fluctuations. In this study, we use phylogenomics‐based analyses to investigate two speciose and closely related genera of snakes, Lycodon and Stegonotus (Serpentes: Colubridae), which are widely distributed across the IAA to identify which biogeographic and environmental processes have shaped snake diversity in this region. Location South Asia and the Indo‐Australian Archipelago (Indochina, Sundaland, Philippines, Wallacea, Australasia). Taxon Snakes (Colubridae: Lycodon, Stegonotus ). Methods We inferred a phylogeny using a genomic dataset consisting of ultraconserved elements, anchored hybrid enrichment loci, and protein‐coding genes (~5400 nuclear loci) from 38 species (154 samples) of Lycodon and Stegonotus . We used ancestral range estimation analysis to identify dispersal patterns across the IAA. Additionally, we implemented ensemble species distribution models to identify potential hotspots of Lycodon and Stegonotus species richness and determined the environmental influence on geographic distributions and species diversity. Results We find that these snakes comprise six deeply divergent lineages (genera) that initially originated in Mainland Southeast Asia during the Oligocene. Diversification of these lineages is influenced not by Plio‐Pleistocene sea‐level fluctuations but by multiple historical processes, including in situ diversification, island hopping, long‐distance rafting, possible microcontinental block drifting, Cenozoic land bridge migrations and founder events. The species distribution models do not consistently estimate lower or higher species richness in any particular region within the IAA, but precipitation overall is considered an important factor in estimated species richness. Main Conclusion Although Plio‐Pleistocene sea‐level fluctuations are notorious species pump diversification paradigms in the IAA, multiple and more ancient geological processes and environmental factors contributed to current diversity levels and distributions. Our approach expands future investigations of alternative hypotheses of biodiversity sources in the IAA and greatly expands the diversity of causal mechanisms for discussions of terrestrial Southeast Asian biodiversity beyond dispersal versus vicariance hypotheses.