Data from: Comparative rangewide phylogeography of four endemic Taiwanese bat species

Phylogeographic reconstructions of co-distributed 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 range-wide sampling and species distribution modeling (SDM) in comparative 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 altitude, 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 MIROC-based species distribution models. 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 continuous 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 differentiation 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 drivers of genetic structure.,Occurrence_dataGPS coordinates of the occurrence records used in building MaxEnt models of the four Taiwanese bat species.Bioclimatic_layers_currentThe eight selected bioclimatic layers for current conditions used in building MaxEnt models of the four Taiwanese bat species. An additional layer where Taiwan is masked (119.9-122.1ºE, 21.8-25.5ºN) is provided.Bioclimatic_layers_ccsm21kaThe eight selected bioclimatic layers for past conditions (21 ka, CCSM model) used in projecting MaxEnt models of the four Taiwanese bat species. An additional layer where a broader geographic space is masked (111.3-126.3ºE, 19.2-28.4ºN) is provided.Bioclimatic_layers_miroc21kaThe eight selected bioclimatic layers for past conditions (21 ka, MIROC model) used in projecting MaxEnt models of the four Taiwanese bat species. An additional layer where a broader geographic space is masked (111.3-126.3ºE, 19.2-28.4ºN) is provided.Mitochondrial_alignmentsA compressed file containing single-mitochondrial-locus alignments (Cyt-b or COI) for the four Taiwanese bat species and concatenated alignments of Cyt-b and COI for Murina gracilis and M. recondita. All alignments are in the FASTA format.BEAST_inputsXML input files of strict-clock BEAST analyses for dated intraspecific phylogenies of Murina gracilis and M. recondita. For each species, files were separately prepared for analyses with a constant-sized population model and a Bayesian Skyline Plot (BSP) model.BEAST_treesMaximum clade credibility trees (MCCT) obtained from strict-clock BEAST analyses applied to each of Murina gracilis and M. recondita. Tree files from analyses with a constant-sized population model and a Bayesian Skyline Plot model are both given.EBSP_inputsXML input files of the Extended Bayesian Skyline Plot (EBSP) analyses for individual local samples of Murina gracilis and M. recondita as well as for range-wide samples of M. puta and Taiwanese Kerivoula.Microsatellite_dataPanels of multi-locus microsatellite genotypes for the four Taiwanese bat species with sexes and GPS coordinates for individual bats provided. Missing values and the second alleles of males at the X-linked locus, B9, are coded as -9.,