The patterns of subspecies distribution, diversity and differentiation of the house mouse Mus musculus provide insights into past dispersal events in natural populations of this species. We investigated the molecular phylogenetics of Chinese house mice based on 466 DNA sequences from mitochondrial D-loop fragments. Our analyses revealed that Mus musculus musculus and M. m. castaneus are older colonized subspecies with broad distributions in East China, while M. m. domestics is a newly arrived subspecies currently restricted to Shanghai, indicating the elevated risk in this cosmopolitan cities. Phylogenetic analysis indicates that M. m. musculus migrated from northern China to eastern China and that M. m. castaneus invaded from southern China. The two subspecies form a hybrid zone in eastern China. There were three major well-differentiated clades within M. m. castaneus, which were designated as CAS1, CAS2 and CAS3 and confirmed previous internal sublineage differentiation of this subspecies. Of the three clades, only CAS1 was detected in all the samples from mainland China. M. m. musculus exhibited no broadly distributed clade, which might be explained by frequent human-assisted movements. Our study offers a newly detailed perspective on the subspecies distribution of M. musculus and its history of migration to eastern China.
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