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.

地理局限分布的同域共存姊妹类群案例较为罕见，此类案例或可指示存在基因流条件下的潜在物种分化过程。格雷氏管鼻蝠（*Murina gracilis*）与隐管鼻蝠（*Murina recondita*）这两种蝙蝠均为台湾特有类群，且被推测为姊妹物种。为验证此类群是否存在非异域分化与基因流，本研究采用桑格测序（Sanger Sequencing）与下一代测序（Next Generation Sequencing）技术获取序列数据，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）系统发育分析结果支持格雷氏管鼻蝠与隐管鼻蝠互为单系姊妹群的关系，但微卫星基因型聚类分析却揭示了多例物种混合现象，暗示可能存在基因渐渗。对微卫星侧翼序列的测序分析显示，物种混合的信号实则源于微卫星等位基因同塑，而非近期的渐渗杂交；同时还发现了一个出乎意料的类群关系：隐管鼻蝠与大陆分布的伊氏管鼻蝠（*Murina eleryi*）构成姊妹群，而格雷氏管鼻蝠并未被纳入该演化分支。为解析核DNA（ncDNA）与线粒体DNA之间的冲突机制，本研究采用BEAST与迁移隔离模型（isolation-with-migration, IM）对10个匿名核DNA位点的序列进行分析，结果发现伊氏管鼻蝠存在两个独立演化支，其中一支与隐管鼻蝠构成姊妹群。本研究推断，台湾岛首先被格雷氏管鼻蝠的祖先类群定居，随后隐管鼻蝠的祖先类群在经历一段异域分化后抵达该区域。定居完成后，隐管鼻蝠的线粒体基因组被本地栖息的格雷氏管鼻蝠的线粒体基因组所替换。本研究阐明了看似同域分化的分子信号，实则可由异域分化、定居与杂交的复杂演化历史所产生，这也凸显了开展严谨分析以区分此类演化场景的必要性。