The greater long-tailed hamster (Cricetulus triton) is widely distributed in the farmlands of northern China. By using DNA sequence data from the mitochondrial D-loop region, we examined genetic diversity and genetic differentiation of 3 mountain populations of the greater long-tailed hamsters in 2 river drainages and 4 plain populations in the North China Plain. Phylogenetic analyses with parsimony and Bayesian inference, nested clade analysis, and analysis of molecular variance were used. The results showed that each population was significantly differentiated from others and the species possessed a high level of phylogeographic structure. The haplotypes were grouped into 2 clades that corresponded to 2 distinct topographic ranges: the mountain and the plain region. The split between the 2 clades accounted for 24% of the genetic variance observed among the examined samples. This study indicated that contiguous mountains played a potential role in genetic differentiation of the greater long-tailed hamsters in the North China Plain. It is suggested that limited gene flow among mountain populations or between mountain and plain populations, plus the impact of inbreeding or genetic drift on the small and isolated populations, accelerated genetic differentiation of mountain populations from plain populations of the greater long-tailed hamsters.
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