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Mitochondrial cytochrome b gene sequences and morphological data (body length, hind foot length, etc.) for twelve populations with pairwise distances 27-600 km in Qinghai-Tibetan Plateau (distributed in Qinghai, Gansu and Sichuan Province, and at the altitude 3020-4550 m) in Western China were used to investigate the phylogeographical pattern of Plateau zokor (Myospalax baileyi Thomas). There was a little disparity between mtDNA genetic distance and morphological Euclidean distance on population relationships. However, there is a significant correlation (P <0.001) calculated by Mantel's tests was validated between mtDNA and morphology distances. Analysis of Molecular Variance showed that most of the observed genetic variations occurred between populations, indicating little maternal gene flow between them, as a result of geographical restrictions. Phylogenetic analysis coupled with cluster analysis together showed that the substantial population structuring and phylogenetic discontinuities existed within this species. The evident allopatric population structuring of this subterranean rodent may mostly result from its specialized subterranean excavating behavior with high energy costs, predation from grassland raptors and also the influences of perennial tundra and environmental desiccation in the Qinghai-Tibetan Plateau.
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