Data from: Speciation processes in putative island endemic sister bat species: false impressions from mitochondrial DNA and microsatellite data

Cases of geographically restricted co-occurring sister taxa are rare and may point to potential divergence with gene flow. The two bat species Murina gracilis and M. recondita are both endemic to Taiwan and are putative sister species. To test for non-allopatric divergence and gene flow in these taxa, we generated sequences using Sanger and Next Generation Sequencing, and combined these with microsatellite data for coalescent-based analyses. MtDNA phylogenies supported the reciprocally monophyletic sister relationship between M. gracilis and M. recondita, however, clustering of microsatellite genotypes revealed several cases of species admixture suggesting possible introgression. Sequencing of microsatellite flanking regions revealed that admixture signatures stemmed from microsatellite allele homoplasy rather than recent introgressive hybridization, and also uncovered an unexpected sister relationship between M. recondita and the continental species M. eleryi, to the exclusion of M. gracilis. To dissect the basis of these conflicts between ncDNA and mtDNA, we analysed sequences from 10 anonymous ncDNA loci with *BEAST and isolation-with-migration (IM) and found two distinct clades of M. eleryi, one of which was sister to M. recondita. We conclude that Taiwan was colonized by the ancestor of M. gracilis first, followed by the ancestor of M. recondita after a period of allopatric divergence. After colonization, the mitochondrial genome of M. recondita was replaced by that of the resident M. gracilis. This study illustrates how apparent signatures of sympatric divergence can arise from complex histories of allopatric divergence, colonization and hybridization, thus highlighting the need for rigorous analyses to distinguish between such scenarios.

地理受限的同域共存姊妹类群案例较为罕见，此类案例或可揭示存在基因流时的物种分化潜力。长翼蝠属（Murina）的纤细长翼蝠（Murina gracilis）与隐体长翼蝠（Murina recondita）均为台湾特有种，且被推测为姊妹物种。为检验这些类群是否存在非异域分化与基因流，我们通过桑格测序（Sanger sequencing）与下一代测序技术获取序列，并结合微卫星数据开展基于溯祖理论的分析。线粒体DNA（mitochondrial DNA, MtDNA）系统发育树支持纤细长翼蝠与隐体长翼蝠互为单系的姊妹群关系，但微卫星基因型聚类分析显示存在多例物种混合现象，提示可能存在基因渐渗。对微卫星侧翼区域的测序结果表明，此类混合信号源于微卫星等位基因同态，而非近期的渐渗杂交；同时还发现隐体长翼蝠与大陆物种埃利长翼蝠（Murina eleryi）构成意外的姊妹群关系，纤细长翼蝠并未被纳入该分支。为解析核DNA（nuclear DNA, ncDNA）与线粒体DNA之间的冲突根源，我们利用*BEAST与迁徙隔离（isolation-with-migration, IM）模型分析了10个匿名核DNA位点序列，结果发现埃利长翼蝠存在两个显著分支，其中一支与隐体长翼蝠互为姊妹群。我们推断，台湾地区最先由纤细长翼蝠的祖先定居，随后隐体长翼蝠的祖先在经历一段异域分化后抵达此地。定居后，隐体长翼蝠的线粒体基因组被当地栖息的纤细长翼蝠的线粒体基因组所替换。本研究表明，看似同域分化的信号可源于异域分化、定居与杂交的复杂演化历史，这也凸显了采用严谨分析方法区分此类演化场景的必要性。