Molecular phylogeography of Jerdon’s pitviper (Protobothrops jerdonii): importance of the uplift of the Tibetan plateau

Aim To investigate the population history and demographics of Jerdon’s pitviper, Protobothrops jerdonii, and elucidate how the unique physical conditions and heterogeneous mountain environments resulting from the uplift of the Tibetan Plateau shaped the genetic diversity and evolutionary history of the species. Location China and Vietnam. Methods We sequenced and analysed a total of 1752 base pairs from two mitochondrial genes, cytochrome b (cyt b) and NADH dehydrogenase subunit (ND4), for 81 specimens sampled from 27 localities across the species’ range, and a total of 464 base pairs from two nuclear genes for 28 representative samples from all mitochondrial DNA lineages. Based on these data, we constructed the genealogical relationships and estimated the divergence times of the mitochondrial DNA clades. Results The mitochondrial DNA results revealed the existence of five distinct, strongly supported and geographically structured DNA lineages within populations of P. jerdonii that are paraphyletic with respect to Protobothrops xiangchengensis. Estimation of divergence dates suggested that P. jerdonii possibly evolved in the western Hengduan Mountains region c. 6.6 Ma in the late Miocene. Nuclear DNA data did not provide sufficient resolution to distinguish the mitochondrial DNA lineages. Main conclusions Based on the present‐day distribution and intraspecific genealogy, the evolutionary history of P. jerdonii can be explained by a pattern of dispersal followed by vicariance. All lines of evidence suggest that historical biogeographical factors, particularly the north–south orientation of the higher mountains, as well as low‐elevation areas in western China, had the greatest influence on the population structure, lineage formation and species distribution of this snake. However, highly heterogeneous habitats and glacial cycles appear to have affected patterns of intraspecific differentiation. While our mitochondrial data provide evidence for clear phylogeographical structure, our small sampling of nuclear genes does not, suggesting that nuclear markers may not have had sufficient time to coalesce to match patterns observed in the mitochondrial data.