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.

地理局限分布且共存的姊妹类群案例较为罕见，这类类群或可指向伴基因流的分化过程。两种管鼻蝠属（*Murina*）蝙蝠——纤小管鼻蝠（*M. gracilis*）与隐小管鼻蝠（*M. recondita*）均为台湾特有种，且被推测为姊妹类群。为检验这类类群是否存在非异域分化与基因流，本研究通过桑格测序（Sanger sequencing）与下一代测序（Next Generation Sequencing）获取序列，并结合微卫星（microsatellite）数据开展基于溯祖理论的分析。线粒体DNA（MtDNA, mitochondrial DNA）系统发育树支持纤小管鼻蝠与隐小管鼻蝠互为单系的姊妹类群关系，但微卫星基因型聚类分析却发现多例物种混杂现象，提示存在潜在的基因渐渗。对微卫星侧翼区的测序结果显示，此类混杂信号实则源于微卫星等位基因同型性，而非近期的渐渗杂交；同时还意外发现，隐小管鼻蝠与大陆物种埃雷管鼻蝠（*M. eleryi*）构成姊妹类群，而纤小管鼻蝠并未被纳入该分支。为解析核DNA（ncDNA, nuclear DNA）与线粒体DNA之间的冲突根源，我们借助*BEAST软件与隔离与迁移（isolation-with-migration, IM）模型分析了10个匿名核基因座序列，结果发现埃雷管鼻蝠存在两个显著分化的分支，其中一支与隐小管鼻蝠构成姊妹类群。研究表明，台湾地区最早由纤小管鼻蝠的祖先定殖，随后隐小管鼻蝠的祖先在经历一段异域分化后抵达该区域。定殖完成后，隐小管鼻蝠的线粒体基因组被本土纤小管鼻蝠的线粒体基因组所替换。本研究阐明，看似同域分化的信号实则可能源自异域分化、定殖与杂交的复杂演化历史，这也凸显了采用严谨分析手段区分此类演化场景的必要性。