UMR 5554 Institut des Sciences de l'Evolution, CNRS, Université de Montpellier, IRD, EPHE, Montpellier, France.
Department of Evolutionary Biology, Evolutionary Biology Centre, Uppsala University, Uppsala, Sweden.
Mol Biol Evol. 2016 Jun;33(6):1517-27. doi: 10.1093/molbev/msw033. Epub 2016 Mar 4.
The nearly neutral theory of molecular evolution predicts that small populations should accumulate deleterious mutations at a faster rate than large populations. The analysis of nonsynonymous (dN) versus synonymous (dS) substitution rates in birds versus mammals, however, has provided contradictory results, questioning the generality of the nearly neutral theory. Here we analyzed the impact of life history traits, taken as proxies of the effective population size, on molecular evolutionary and population genetic processes in amniotes, including the so far neglected reptiles. We report a strong effect of species body mass, longevity, and age of sexual maturity on genome-wide patterns of polymorphism and divergence across the major groups of amniotes, in agreement with the nearly neutral theory. Our results indicate that the rate of protein evolution in amniotes is determined in the first place by the efficiency of purifying selection against deleterious mutations-and this is true of both radical and conservative amino acid changes. Interestingly, the among-species distribution of dN/dS in birds did not follow this general trend: dN/dS was not higher in large, long-lived than in small, short-lived species of birds. We show that this unexpected pattern is not due to a more narrow range of life history traits, a lack of correlation between traits and Ne, or a peculiar distribution of fitness effects of mutations in birds. Our analysis therefore highlights the bird dN/dS ratio as a molecular evolutionary paradox and a challenge for future research.
分子进化的近中性理论预测，小种群积累有害突变的速度应快于大种群。然而，鸟类与哺乳动物非同义（dN）与同义（dS）替换率的分析得出了相互矛盾的结果，对近中性理论的普遍性提出了质疑。在这里，我们分析了生活史特征（作为有效种群大小的代表）对羊膜动物（包括迄今被忽视的爬行动物）的分子进化和种群遗传过程的影响。我们报告了物种体质量、寿命和性成熟年龄对羊膜动物主要类群的全基因组多态性和分歧模式的强烈影响，这与近中性理论一致。我们的结果表明，羊膜动物的蛋白质进化速率首先由清除有害突变的纯化选择效率决定，这对激进和保守的氨基酸变化都是如此。有趣的是，鸟类中的种间 dN/dS 分布并没有遵循这一总体趋势：与小体型、短寿命的鸟类相比，大型、长寿的鸟类的 dN/dS 并不更高。我们表明，这种出乎意料的模式不是由于生活史特征的范围更窄、特征与 Ne 之间缺乏相关性或鸟类突变适应度效应的独特分布所致。因此，我们的分析突出了鸟类的 dN/dS 比值作为分子进化悖论和未来研究的挑战。
