Phylogeography of <i>Hipposideros armiger</i> (Chiroptera: Hipposideridae) in the Oriental Region: the contribution of multiple Pleistocene glacial refugia and intrinsic factors to contemporary population genetic structure

Abstract

Abstract Aim The goals of our study were to assess the population history and genetic structure of the widespread bat H ipposideros armiger , and to evaluate the effect of palaeoclimatic changes and dispersal patterns on this species. Location S outh C hina, mainland S outheast A sia and the S outh H imalayas. Methods We amplified two mitochondrial DNA (mt DNA ) regions (cyt b and D ‐loop) and seven nuclear microsatellite loci (n SSR s) 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 mt DNA regions. From the mt DNA and/or n SSR 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 B ayesian skyline plot and the program I Ma 2. Results Phylogenetic and median‐joining network analyses revealed that H . armiger comprises two distinct mt DNA clades divided into seven subclades. The results of AMOVA suggested strong population genetic structure based on mt DNA , but weak structure based on n SSR s. 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. I Ma 2 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 T aiwan and H ainan island populations and those from mainland C hina. Main conclusions Our results suggest that divergence and population expansion of H . armiger occurred in association with P leistocene 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 C hina.