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

Abstract

Aim 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.Location South China, mainland Southeast Asia and the South Himalayas.Methods 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.Results 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 malebiased 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.

Integrative taxonomy of theRhinolophus macrotiscomplex (Chiroptera, Rhinolophidae) in Vietnam and nearby regions

“…are recognized as forest‐interior specialists (Kingston, Francis, Akbar, & Kunz, ), contraction and expansion of forests during Plio‐Pleistocene have been regarded as major factors driving their biogeographical history (Flanders, Wei, Rossiter, & Zhang, ; Mao, He et al., ; Mao, Zhu, Zhang, & Rossiter, ; Rossiter, Benda, Dietz, Zhang, & Jones, ; Tu et al., ). For the R. macrotis group, we suggest that the vicariance of the most common ancestors of recent taxa might have taken place due to the persistence of different allopatric refugia across the region during Pleistocene glacial periods (Bird, Taylor, & Hunt, ; Gathorne‐Hardy, Syaukani Davies, Eggleton, & Jones, ; Lin et al., ; Morgan, Somboon, & Walto, ; Tu et al., , ). As a consequence, vicariant populations adaptively evolved under different ecological selections imposed by isolated refugia which may have led to shifts in their morphology (noseleaf structure and body, skull, glans penis, and baculum morphology) and echolocation systems, and subsequently their own SMRSs.…”

Morphology, genetics and echolocation calls of the genus Kerivoula (Chiroptera: Vespertilionidae: Kerivoulinae) in Thailand

“…However, the genetic analysis in this study is only based on one mitochondrial gene (COI). Further study, including cytochrome b (Cytb) and/or nuclear genes may help considerably in resolv ing the taxonomy of this species complex (Anwarali et al 2010, Nesi et al 2011, Francis and Eger 2012, Thong et al 2012, Lin et al 2014. As, currently, there are no additional supporting data, the specimens referred to K. papillosa are here separated into three distinct taxa or monophyl etic clades.…”

“…Clade names are explained in the caption to Figure 9. are cryptic species "hidden" within this taxon (Anwarali et al 2010, Nesi et al 2011, Francis and Eger 2012, Thong et al 2012, Lin et al 2014. As there is no additional sup porting information, specimens with domed skulls are here assigned to K. hardwickii.…”

A new species of the genus Odorrana (Amphibia: Ranidae) and the first record of Odorrana bacboensis from China

“…Sea level oscillation due to glacial-interglacial climate fluctuations is believed to occur between Hainan Island and its nearby mainland during the Quaternary period (Voris 2000). Previous studies demonstrate that these series of geological dynamics can promote either isolation or gene flow in variable animals, including insects, reptiles, birds and mammals Huang et al 2013;Lin et al 2013) …”