Pleistocene glacial cycle effects on the phylogeography of the Chinese endemic bat species, Myotis davidii

M. davidii comprises three lineages (MEP, SWP and SH) based on the results of molecular variance analysis (AMOVA) and phylogenetic analyses. The results of a STRUCTURE analysis reveal multi-hierarchical population structure in M. davidii. Nuclear and mitochondrial genetic markers reveal different levels of gene flow among populations. In the case of mtDNA, populations adhere to an isolation-by-distance model, whereas the individual assignment test reveals considerable gene flow between populations. MDIV analysis indicate that the split of the MEP and SWP/SH lineages, and from the SWP and SH lineages were at 201 ka BP and 158 ka BP, respectively. The results of a mismatch distribution analysis and neutrality tests indicate a population expansion event at 79.17 ka BP and 69.12 ka BP in MEP and SWP, respectively.The complex demographic history, discontinuous extant distribution of haplotypes, and multiple-hierarchy population structure of M. davidii appear associated with climatic oscillations, topography and eco-environmental variation of China. Additionally, the three regions are genetically differentiated from one another in the entire sample set. The degree of genetic differentiation, based on the analysis of mtDNA and nDNA, suggests a male-mediated gene flow among populations. Refuges were in the MEP, SH and the lower elevations of SWP regions. This study also provides insights for conservation management units (MEP, SWP and SH).Global climatic oscillations and associated glaciation cycles have profoundly influenced species population distributions [1]. Pleistocene climate oscillations have contributed to the genetic structure of current species [2] and have played an important role in initiating intra-specific divergences of North American animal taxa [3]. However, climate condition in China during glacial periods appears to have been different from those of the rest of the world and bring about a series of eco-environmental effects, primarily due to the continui