Mitochondrial DNA contains highly informative polymorphic sites and its simple maternal inheritance without recombination makes it useful for phylogenetic analyses and population studies in many organisms. In present work, molecular phylogenetic relationships and biogeography of Niviventer in China was inferred from complete mitochondrial cytochrome b gene sequences. Phylogeographic structure and population history of house mice（Mus musculus）in China was investigated based on complete mitochondrial control region sequences. Chinese species of the genus Niviventer, predominantly distributed in the southeastern Tibetan Plateau and in Taiwan, have a blurry phylogenetic status and have not been included in previous molecular systematic analysis. Phylogenetic relationships of 32 specimens representing nine Chinese species of Niviventer were reconstructed in this study, based on sequences of the complete mitochondrial cytochrome b gene. Maximum parsimony, maximum likelihood and Bayesian analysis resulted in three consistent trees supported by high bootstrap values. The phylogeny showed that the genus Niviventer is monophyletic. The nine species in the study were classified into three distinct genetic clades: Clade A with Niviventer brahma, N. confucianus, N. coxingi, N. culturatus, N. eha and N. fulvescens; Clade B with N. andersoni and N. excelsior; and Clade C with N. cremoriventer. Our results also suggested that N. culturatus should be a valid species rather than a subspecies of N. confucianus. Divergence times among species were calibrated according to the middle-late Pleistocene (1.2-0.13 Mya) fossil records of N. confucianus. The results demonstrated that the first radiation event of the genus Niviventer occurred in early Pleistocene (about 1.66 Mya), followed by the divergence of Clades A and B at about 1.46 Mya. Most of the extant Niviventer species appeared during early to middle Pleistocene (about 1.29-0.67 Mya). These divergence times are coincident with the last uplift events of the Tibetan Plateau, Kun-Huang movement, Pleistocene glaciations, and vicariance of the Taiwan Strait. Our results suggested geographical events and Pleistocene glaciations might have played great roles in the speciation of Niviventer. In order to detect the phylogeographical pattern, to describe the genetic relationship, and to infer demographic and biogeographic process, we sequenced 876 bp full length of the mitochondrial DNA control region of 184 house mice (Mus musculus) from 12 locations. Both Bayesian and Neighbor-joining analyses support the same conclusion of two well-differentiated lineages (northern lineage and southern lineage), separated by the Yangtze River. There is no shared haplotype between lineages. An analysis of molecular variance (AMOVA) identified significant population genetic divergence within both two lineages, suggesting restricted gene flow and regional population isolation with lineages. Nested clade analysis of haplotypes indicated that such a division was a consequence of allopatric fragmentation. High haplotype diversities, low nucleotide diversities and unimodal mismatch distribution within lineages suggest recent expansion . The expansion time of southern lineage and northern lineage was 20 000 (40 000-6 700) and 16 000(22 000-11 000) years ago, respectively. The present distribution of house mice was best explained by fast expansion events during and following the last glacial era. Activities of humankind might have an important impact on the migration of house mice.
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