Data from: Evolutionary neutrality of mtDNA introgression: evidence from complete mitogenome analysis in roe deer

Introgressive hybridization offers a unique platform for studying the molecular basis of natural selection acting on mitogenomes. Most of the mtDNA protein-coding genes are extremely conserved, however some of the observed variations have potentially adaptive significance. Here, we evaluated whether the evolution of mtDNA in closely related roe deer species affected by widespread mtDNA introgression is neutral or adaptive. We characterized and compared 16 complete mitogenomes of European (Capreolus capreolus) and Siberian (C. pygargus) roe deer, including four of Siberian origin introgressed into European species. The average sequence divergence of species-specific lineages was estimated at 2.8% and varied across gene classes. Only 21 of 315 fixed differences identified in protein-coding genes represented nonsynonymous changes. Only three of them were determined to have arisen in the C. pygargus lineage since the time to the most recent common ancestor (TMRCA) of both Capreolus species, reflecting a decelerated evolutionary ratio. The almost fourfold higher dN/dS ratio described for the European roe deer lineage is constrained by overall purifying selection, especially pronounced in the ND4 and ND5 genes. We suggest that the highly divergent C. capreolus lineage could have maintained a capability for genomic incorporation of the well-preserved and almost ancestral type of mtDNA present in C. pygargus. Our analyses did not indicate any signs of positive selection for Siberian roe deer mtDNA, suggesting that the present widespread introgression is evolutionarily neutral.渐渗杂交（introgressive hybridization）为研究作用于线粒体基因组（mitogenome）的自然选择分子基础提供了独特的研究平台。绝大多数线粒体DNA（mtDNA）蛋白编码基因具有高度保守性，但部分观测到的变异可能具有适应性意义。本研究旨在探究受广泛线粒体DNA渐渗影响的狍属近缘物种的线粒体DNA演化，究竟遵循中性演化模式还是适应性演化模式。我们对欧洲狍（Capreolus capreolus）与西伯利亚狍（C. pygargus）的16条完整线粒体基因组进行了表征与比较，其中4条源自渐渗进入欧洲狍的西伯利亚狍线粒体基因组。物种特异性支系的平均序列分化度经估算为2.8%，且该分化度在不同基因类别间存在差异。在蛋白编码基因中鉴定出的315个固定差异位点中，仅有21个为非同义突变。其中仅3个非同义突变被确定为自两种狍属动物的最近共同祖先时间（time to the most recent common ancestor, TMRCA）以来，在西伯利亚狍支系中产生的变异，这反映出演化速率的减缓。欧洲狍支系的dN/dS（同义替换速率与非同义替换速率比值）几乎高出4倍，但该比值受到整体纯化选择的约束，在ND4与ND5基因中尤为显著。我们推测，分化程度极高的欧洲狍支系，或许仍保留了对西伯利亚狍体内保存完好、近乎祖先型线粒体基因组的基因组整合能力。本研究的分析未发现西伯利亚狍线粒体DNA存在正向选择的迹象，表明当前广泛存在的线粒体DNA渐渗在演化上属于中性过程。