Population differentiation within species can be stimulated by various geographic and climatic factors. In this study, we analyzed the population structure of the Common Pheasant (Phasianus colchicus) in the Loess Plateau and its adjacent eastern areas (named eastern China). We sequenced mitochondrial cytochrome b and control regions of 249 samples collected from 42 populations that covered the whole Loess Plateau and eastern China. Two groups (one containing populations 1-27 and the other populations 28-42) were identified using Analysis of Molecular Variance, Spatial Analysis of Molecular Variance, median-joining network analysis and maximum-parsimony analysis. The results demonstrated that although populations were distributed continuously throughout the study area, there was clear differentiation between populations. Geographically, population differentiation was sutured along the eastern edge of the Loess Plateau. The Migration Divergence (MDIV) analysis suggested that the two groups diverged at about 0.21 million years ago, which corresponded to a period when numerous large inland paleo-lakes greatly receded across the Loess Plateau during 0.25-0.20 million years before present (Ma BP). We inferred that the rapid recession of the Loess Plateau paleo-lakes caused dramatic shifts from a relatively humid climate, to one that was significantly more arid. Such severe climate transition combined with a dry-cold starting of one of multi-cycled climate fluctuations from warm-humid to dry-cold since about 0.24-0.22 Ma BP on the Loess Plateau may have been the impetus that effectively facilitated differentiation between different pheasant populations.
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