Data from: Deep mitochondrial introgression and hybridization among ecologically divergent vole species

The completion of speciation is typically difficult to ascertain in rapidly diverging taxa but the amount of hybridization and gene flow in sympatry or parapatry contains important information about the level of reproductive isolation achieved. Here we examined the progress in speciation between the Mediterranean (Microtus duodecimcostatus) and the Lusitanian pine vole (M. lusitanicus) which are part of the most rapid radiation of species known in mammals. These two Iberian pine voles are classified as separate species because of differences in morphology and ecology, but relatively many ambiguous individuals can be found in sympatric conditions. Our phylogenetic analyses of rangewide data from the mitochondrial cytochrome b gene (mtDNA) demonstrated high levels of diversity and a basal separation in two parapatric lineages. However, mtDNA affiliation was at odds with morphological classification or geographical distribution of the taxa. In contrast, statistical analyses of microsatellites (nucDNA) showed two clear genetic clusters in allopatry and sympatry generally matching morphological classification. This cytonuclear discordance over a large geographic area suggests historical introgression of mtDNA from M. duodecimcostatus to M. lusitanicus. There was statistical evidence for at least two recent hybrids in the sympatry zone but gene flow is apparently low given clear-cut differences in nucDNA. Our results indicate a relatively advanced speciation process in these Iberian pine voles without fully established reproductive isolation. This situation enables use of combined population genomic and experimental approaches for the separation of patterns and mechanisms in the ongoing explosive diversification of these and other Arvicoline rodents in the future.在快速分化的类群中，物种形成完成的判定通常颇具难度；而同域分布（sympatry）或邻域分布（parapatry）类群间的杂交水平与基因流强度，则可为其已达成的生殖隔离程度提供关键信息。本研究以哺乳类中已知演化速率最快的类群之一——地中海松田鼠（Microtus duodecimcostatus）与卢西塔尼亚松田鼠（M. lusitanicus）为研究对象，解析二者的物种形成进程。这两种伊比利亚松田鼠因形态与生态特征差异被划分为独立物种，但在同域分布区域中却存在相当数量的分类地位模糊的个体。我们对线粒体细胞色素b基因（mtDNA）的全分布区数据开展系统发育分析，结果显示二者具有较高的遗传多样性，且在两个邻域支系间存在基部分化。然而，线粒体DNA的类群归属与该类群的形态分类或地理分布并不一致。与之相反，微卫星标记（microsatellites，核DNA(nucDNA)）的统计分析显示，无论在异域分布（allopatry）还是同域分布区域中，均存在两个清晰的遗传聚类簇，且整体与形态分类结果相符。这种大范围的核质不一致现象，暗示了线粒体DNA从地中海松田鼠向卢西塔尼亚松田鼠发生过历史渐渗。统计分析显示，同域分布区域中至少存在两个近期杂交个体，但核DNA存在显著差异，说明当前基因流水平较低。本研究结果表明，这两种伊比利亚松田鼠正处于相对成熟的物种形成进程中，但尚未建立完全的生殖隔离。这种研究体系可为未来结合群体基因组学与实验手段，解析该类群及其他田鼠亚科啮齿动物正在进行的爆发式物种分化的模式与机制提供契机。