The evolutionary history of multiple mountain ungulates reveals refugia and population expansion in response to Quaternary change in the east Himalaya-Hengduan Mountains region

In this study, three mountain ungulates taxa (Capricornis spp., Naemorhedus spp. and Muntiacus spp.) who have overlapping niches and similar life-history strategies were selected to analyze the impact of historical events on the evolution and population dynamics. Our samples were obtained from ungulates of natural death during multiple field trips and from forest police confiscated from hunters, including skull, skin and dry meat. The mitogenomes were used as molecular markers. Molecular divergence analyses indicate that the divergence of three mountain ungulates have same driving factors, which are five main dramatic uplift of Qinghai-Tibet Plateau and a series of glaciations. We also speculated multiple refugia were formed in the EHHM region during Quaternary. The C. sumatraensis, N. cranbrooki, N. evansi and M. gongshanensis in the east Himalaya-Hengduan Mountains region were selected for historical dynamics analysis. The population expansions are detected for all species. The population expansion of N. cranbrooki, N. evansi and M. gongshanensis occurred in the mid-Holocene period due to the warm and humid climate. The expansion of C. sumatraensis occurred in the late Holocene, mainly affected by the retreated forests and human settlement, grazing activity.