• Gene flow;
  • leaf-nosed bats;
  • palaeoclimate;
  • phylogeography;
  • population expansion events;
  • South China;
  • Southeast Asia;
  • sex-biased dispersal;
  • wide distribution



The goals of our study were to assess the population history and genetic structure of the widespread bat Hipposideros armiger, and to evaluate the effect of palaeoclimatic changes and dispersal patterns on this species.


South China, mainland Southeast Asia and the South Himalayas.


We amplified two mitochondrial DNA (mtDNA) regions (cyt b and D-loop) and seven nuclear microsatellite loci (nSSRs) from 216 individuals of H. armiger. To examine the evolutionary history of this species, we constructed maximum likelihood and Bayesian phylogenetic trees based on the two mtDNA regions. From the mtDNA and/or nSSR data, we assessed population genetic structure using analysis of molecular variance (AMOVA) and median-joining network and structure analyses. We also estimated demographic history and gene flow using a Bayesian skyline plot and the program IMa2.


Phylogenetic and median-joining network analyses revealed that H. armiger comprises two distinct mtDNA clades divided into seven subclades. The results of AMOVA suggested strong population genetic structure based on mtDNA, but weak structure based on nSSRs. structure analysis identified three population clusters and also showed weak genetic structure at the nuclear level. Demographic analyses revealed two population expansion events c. 0.62 Ma and c. 0.25 Ma. The basic phylogeographical structure of H. armiger was established by 0.24 Ma. IMa2 analysis demonstrated that substantial gene flow has occurred between different regions since then. Additionally, non-significant population structure and significant gene flow were detected between Taiwan and Hainan island populations and those from mainland China.

Main conclusions

Our results suggest that divergence and population expansion of H. armiger occurred in association with Pleistocene climatic changes and that multiple refugia may have existed for this species. Post-glacial male-biased dispersal was likely to be the primary contributor to the contemporary genetic structure of H. armiger populations. Gene flow may have contributed greatly to the genetic structure of insular populations and populations from mainland China.