Causes and Consequences of Rapidly Evolving mtDNA in a Plant Lineage.
Causes and Consequences of Rapidly Evolving mtDNA in a Plant Lineage.
复制标题
植物谱系中 mtDNA 快速进化的原因和后果。
DOI：
10.1093/gbe/evx010
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发表时间：
2017-02-01
影响因子：
3.3
通讯作者：
Sloan DB
中科院分区：
文献类型：
--
作者：
Havird JC;Trapp P;Miller CM;Bazos I;Sloan DB
理解核基因组和线粒体基因组之间的协同进化机制是真核生物遗传学中的一个决定性挑战。被子植物蝇子草属是研究mt突变率变化的原因和后果的自然系统，因为密切相关的物种具有高度的分歧率。在具有快速进化mtDNA的蝇子草属物种中，编码神经靶向蛋白质的核基因（N-mt基因）也在快速进化。这种相关性可能表明正选择补偿mt突变，但也可能是最近放松选择的结果。为了区分这些解释，我们使用系统发育和群体遗传学方法来测试三类N-mt基因（氧化磷酸化基因，核糖体基因和参与mtDNA重组，复制和修复的“RRR”基因）的正选择和宽松选择。在所有三个类别中，我们发现具有快速进化mtDNA的物种具有：1）升高的dN/dS，2）相对于种内多态性水平的非同义分歧过多，这是正选择的标志，3）没有明确的放松选择信号。“对照”基因表现出相对较少的正选择迹象。这些结果表明，高mt突变率可以创建选择N-mt基因和宽松的选择是一个不太可能的原因，最近加速进化的N-mt基因。由于mt-RRR基因被发现是在积极的选择，这是不太可能的MT突变率升高，在Silene是由这些mt-RRR基因的失活。因此，被子植物mt突变率极端增加的原因仍然不确定。
Understanding mechanisms of coevolution between nuclear and mitochondrial (mt) genomes is a defining challenge in eukaryotic genetics. The angiosperm genus Silene is a natural system to investigate the causes and consequences of mt mutation rate variation because closely related species have highly divergent rates. In Silene species with fast-evolving mtDNA, nuclear genes that encode mitochondrially targeted proteins (N-mt genes) are also fast-evolving. This correlation could indicate positive selection to compensate for mt mutations, but might also result from a recent relaxation of selection. To differentiate between these interpretations, we used phylogenetic and population-genetic methods to test for positive and relaxed selection in three classes of N-mt genes (oxidative phosphorylation genes, ribosomal genes, and “RRR” genes involved in mtDNA recombination, replication, and repair). In all three classes, we found that species with fast-evolving mtDNA had: 1) elevated dN/dS, 2) an excess of nonsynonymous divergence relative to levels of intraspecific polymorphism, which is a signature of positive selection, and 3) no clear signals of relaxed selection. “Control” genes exhibited comparatively few signs of positive selection. These results suggest that high mt mutation rates can create selection on N-mt genes and that relaxed selection is an unlikely cause of recent accelerations in the evolution of N-mt genes. Because mt-RRR genes were found to be under positive selection, it is unlikely that elevated mt mutation rates in Silene were caused by inactivation of these mt-RRR genes. Therefore, the causes of extreme increases in angiosperm mt mutation rates remain uncertain.