Comparative rangewide phylogeography of four endemic Taiwanese bat species HAO-CHIH KUO,* SHIANG-FAN CHEN, † YIN-PING FANG, ‡ JON FLANDERS § and STEPHEN J. ROSSITER* *School of Biological and Chemical Sciences, Queen Mary University of London, London E1 4NS, UK, †Center for General Education, National Taipei University, New Taipei City 23741, Taiwan, ‡Department of Biological Resources, National Chiayi University, Chiayi City 60004, Taiwan, §School of Biological Sciences, University of Bristol, Bristol BS8 1UG, UK Abstract Phylogeographic reconstructions of codistributed taxa can help reveal the interplay between abiotic factors, such as altitude and climate, and species-specific attributes, in shaping patterns of population genetic structure. Recent studies also demonstrate the value of both rangewide sampling and species distribution modelling (SDM) in com- parative phylogeography. Here, we combine these approaches to study the population histories of four phylogenetically related forest-dependent bat species. All are endemic to the mountainous island of Taiwan but show differences in their tolerance to alti- tude, with Murina gracilis considered to be a high-altitude specialist, M. recondita and Kerivoula sp. low-altitude specialists, and M. puta an altitudinal generalist. We tested the prediction that contrasting habitat preferences would impact on patterns of past and contemporary gene flow and found broad concordance between the results of population genetic analyses and species distribution models based on the Model for Interdisciplinary Research on Climate. Both lowland species showed evidence of genetic divergence between the east and west of the island, consistent with SDMs that indicated the Central Mountain Range (CMR) has presented a long-term and continu- ous barrier to gene flow since before the Last Glacial Maximum. In contrast, Murina gracilis and M. puta showed lower degrees of historical isolation and genetic differen- tiation associated with the CMR, reflecting greater gene flow, possibly coupled with past population growth in M. puta. Together our results highlight the usefulness of combining distribution models with phylogeographic analyses to understand the driv- ers of genetic structure. Keywords: demographic analyses, gene flow, mountain barriers, species distribution modelling Received 23 July 2013; accepted 9 June 2014 Introduction Comparative phylogeography offers a powerful means of investigating the relative importance of extrinsic fac- tors in shaping the population histories and genetic structure of codistributed taxa (Bermingham & Moritz 1998; Avise 2000). Shared responses to climatic oscilla- tions and/or topographic features inferred from con- cordant patterns of spatial genetic variation are well described, particularly in terms of postglacial coloniza- tion routes among temperate European taxa (Hewitt 1999, 2000, 2001) and genetic discontinuities linked to topographic features in North American taxa (Hewitt 2004; Soltis et al. 2006). However, similar genetic pat- terns may also arise via different historical processes (e.g. Creer et al. 2001; Soltis et al. 2006) and, conversely, discordant genetic patterns among codistributed taxa may reflect differences in the way they respond to their environment, including past and future environ- mental change (e.g. Marske et al. 2012; Rossiter et al. 2012). Correspondence: Stephen Rossiter, Fax: +44 (0) 207 882 7732; E-mail: s.j.rossiter@qmul.ac.uk © 2014 John Wiley & Sons Ltd Molecular Ecology (2014) 23, 3566–3586 doi: 10.1111/mec.12838