Diversification, introgression, and rampant cytonuclear discordance in Rocky Mountains Chipmunks (Sciuridae: Tamias)

Evidence from natural systems suggests that hybridization between animal species is more common than traditionally thought, but the overall contribution of introgression to standing genetic variation within species remains unclear for most animal systems. Here, we use targeted exon-capture to sequence thousands of nuclear loci and complete mitochondrial genomes from closely related chipmunk species in the Tamias quadrivittatus group that are distributed across the Great Basin and the central and southern Rocky Mountains of North America. This recent radiation includes six overlapping, ecologically distinct species (T. canipes, T. cinereicollis, T. dorsalis, T. quadrivittatus, T. rufus, and T. umbrinus) that show evidence for widespread mitochondrial introgression across species boundaries. Such evidence has historically derived from a handful of markers, typically focused on mitochondrial loci, to describe patterns of introgression; consequently, the extent of introgression of nuclear g...

自然系统的证据表明，动物物种间的杂交（hybridization）比传统认为的更为普遍，但基因渗入（introgression）对物种内现有遗传变异的整体贡献，在大多数动物系统中仍不明确。在此，我们采用靶向外显子捕获（targeted exon-capture）技术，对分布于北美大盆地及落基山脉中部和南部的金花地松鼠四纹种组（Tamias quadrivittatus group）中近缘物种的数千个核基因座及完整线粒体基因组进行测序。这一近期辐射演化支系包含6个分布重叠、生态位分化显著的物种（T. canipes、T. cinereicollis、T. dorsalis、T. quadrivittatus、T. rufus及T. umbrinus），它们均显示出跨物种边界的广泛线粒体基因渗入迹象。历史上，这类证据多来自少量分子标记（通常聚焦于线粒体基因座），用于描述基因渗入模式；因此，核基因的渗入程度……