Low coverage shotgun sequencing from 12 Arborophila species

The advent of the phylogenomic era has improved our understanding of the biogeographic patterns and evolutionary histories of the avian fauna of Southeast Asia. However, there remains many Southeast Asian bird taxa whose evolutionary histories remain poorly resolved, especially those that have experienced both ancient and recent geological and climatic events. In this study, we examined the evolutionary history of hill partridges (Galliformes: Phasianidae: Arborophila spp.), which is thought to be an early colonizer into Southeast Asia from Africa and currently the second most speciose galliform genus. We used low coverage shotgun sequencing to generate ultra-conserved elements, exon, and mitochondrial genomes from both fresh and old museum tissue samples of almost complete coverage of all Arborophila species. Our results suggest that although the ancestor of Arborophila arrived in Indochina during the early Miocene, the initial divergence within Arborophila did not occur until ~10 Ma when global cooling intensified. Subsequent dispersal and diversification of Arborophila was affected by a number of tectonic and climatic events. In particular, we found evidence of rapid radiation in Indochinese Arborophila during the Pliocene global cooling, and extensive dispersal and radiation of Sundaic Arborophila during Pleistocene sea level fluctuations. Taken together, these results suggest that the evolutionary history of Arborophila were influenced by complex interactions among historical, geological and climatic events in Southeast Asia. Furthermore, our study highlights that phylogenomic studies can provide unprecedented opportunities to explore biogeographic patterns and the evolutionary history in biologically complex parts of Asia that support high species diversity.