Quaternary climate and environmental changes have shaped genetic differentiation in a Chinese pheasant endemic to the eastern margin of the Qinghai-Tibetan Plateau.

The geological complexity generated by the uplift of the Qinghai-Tibetan Plateau and the resulting habitat heterogeneity have functioned together with climatic oscillations in the Quaternary to have a profound impact on the patterns of genetic diversity and demography of the fauna in this region. To understand the effect of the climatic and environmental shifts of the Quaternary on intraspecific genetic patterns and evolutionary history, we investigated the population genetic structure of the blue eared pheasant (Crossoptilon auritum), an endemic bird inhabiting the easternmost region of the plateau. Our phylogeographic analysis of mitochondrial DNA sequences and eight autosomal microsatellites reveals that the blue eared pheasant is subdivided into four distinct subpopulations: a central group (Huzhu and Taizi Mountains), a southern Zoige group, a southernmost Wanglang group and the northernmost Helan Mountain group. These groups are likely to have diverged in the Pleistocene, corresponding to geological changes and the interglacial-glacial climate oscillations that occurred at the eastern margin of the Qinghai-Tibetan Plateau. These subpopulations thus represent major conservation units, especially for the isolated Helan subpopulation. Our findings provide evidence of population divergence driven by complex Quaternary climate and environmental changes and, once more, highlight the importance of phylogeographic studies for conservation endeavours.