Diversification, Introgression, and Rampant Cytonuclear Discordance in Rocky Mountains Chipmunks (Sciuridae: Tamias).
Diversification, Introgression, and Rampant Cytonuclear Discordance in Rocky Mountains Chipmunks (Sciuridae: Tamias).
复制标题
DOI：
10.1093/sysbio/syaa085
复制
发表时间：
2021-01
影响因子：
6.5
通讯作者：
B. Sarver;N. D. Herrera;David Sneddon;Samuel S. Hunter;M. Settles;Zev N. Kronenberg;J. Demboski;J. Good;J. Sullivan
中科院分区：
文献类型：
--
作者：
B. Sarver;N. D. Herrera;David Sneddon;Samuel S. Hunter;M. Settles;Zev N. Kronenberg;J. Demboski;J. Good;J. Sullivan
来自自然系统的证据表明，动物物种之间的杂交比传统认为的更为普遍，但对于大多数动物系统来说，物种内遗传变异的遗传渗入的总体贡献仍不清楚。在这里，我们使用靶向外显子捕获对分布在北美大盆地和落基山脉中部和南部的Tamias quadrivittatus组中密切相关的花栗鼠物种的数千个核位点和完整的线粒体基因组进行测序。最近的辐射包括六个重叠的，生态上不同的物种（T. canipes， T. cinereicollis， T. dorsalis， T. quadrivitatus， T. rufus和T. umbrinus），显示出跨物种边界广泛渗透的证据。历史上，这种证据来源于少数标记，通常集中在线粒体位点上，用来描述基因渗入的模式；因此，核基因的渗入程度没有很好地表征。我们进行了一系列的系统基因组和种树分析，以解决该群体中6个物种的系统发育问题。此外，我们进行了几个群体基因组分析，以表征核基因组并推断个体之间的共祖。此外，我们使用基于新兴四重奏的方法同时推断物种树（SVDquartets）和识别渗入（HyDe）。我们发现，尽管线粒体基因组在某些物种对之间（有时涉及多达三个物种）存在猖獗的渗入，但似乎几乎没有证据表明存在核渗入。这些发现反映了其他基因组的结果，在没有明显的核基因流动的情况下，花栗鼠物种之间发生了完全的线粒体捕获。在这个群体中，反复出现大量细胞核不一致的潜在原因仍未得到解决，但线粒体DNA似乎对整个群体历史具有高度误导性。总的来说，似乎花栗鼠的物种边界在很大程度上不受核基因流动的影响，而杂交虽然在mtDNA方面普遍存在，但在这一群体的进化史上可能起着相对较小的作用。
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 introgression across species boundaries. Such evidence has historically been derived from a handful of markers, typically focused on mitochondrial loci, to describe patterns of introgression; consequently, the extent of introgression of nuclear genes is less well characterized. We conducted a series of phylogenomic and species-tree analyses to resolve the phylogeny of six species in this group. In addition, we performed several population genomic analyses to characterize nuclear genomes and infer coancestry among individuals. Furthermore, we used emerging quartets-based approaches to simultaneously infer the species tree (SVDquartets) and identify introgression (HyDe). We found that, in spite of rampant introgression of mitochondrial genomes between some species pairs (and sometimes involving up to three species), there appears to be little to no evidence for nuclear introgression. These findings mirror other genomic results where complete mitochondrial capture has occurred between chipmunk species in the absence of appreciable nuclear gene flow. The underlying causes of recurrent massive cytonuclear discordance remain unresolved in this group but mitochondrial DNA appears highly misleading of population histories as a whole. Collectively, it appears that chipmunk species boundaries are largely impermeable to nuclear gene flow and that hybridization, while pervasive with respect to mtDNA, has likely played a relatively minor role in the evolutionary history of this group.