The effect of variation in the effective population size on the rate of adaptive molecular evolution in eukaryotes.
The effect of variation in the effective population size on the rate of adaptive molecular evolution in eukaryotes.
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DOI：
10.1093/gbe/evs027
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发表时间：
2012
影响因子：
3.3
通讯作者：
Eyre-Walker A
中科院分区：
文献类型：
--
作者：
Gossmann TI;Keightley PD;Eyre-Walker A
适应的作用是分子进化中的一个基本问题。理论预测，如果适应受到突变供应的限制，有效种群规模大的物种应该比有效种群规模低的物种经历更高的适应性进化速度。以前的分析似乎支持这一猜测，因为在具有较大Ne的物种中，对适应性进化α固定的非同义替换比例的估计往往更高。然而，α是有利的和有效的中性取代的数量的函数，两者中的任何一个都可能取决于Ne。在这里，我们使用来自13个独立的真核物种对的核苷酸多态和分歧数据，研究了Ne和ωa之间的关系，即适应性进化的速率相对于中性进化的速率。我们发现ωa和Ne之间存在高度显著的正相关。我们还发现一些证据表明，对于给定的NE，不同的有机体群体的适应性进化速度是不同的。ωa和ne之间的相关性似乎不是人口统计学变化或同义密码子使用选择的产物。我们的结果表明，适应在一定程度上受到突变供应的限制，至少部分适应取决于新出现的突变，而不是现有的遗传变异。最后，我们证明了近中性非自适应取代的比例随着Ne的增加而下降。具有较小Ne的物种的低适应性进化速率和有效中性替代的高比例有望结合在一起，使得在具有较小Ne的物种中很难检测适应性分子进化。
The role of adaptation is a fundamental question in molecular evolution. Theory predicts that species with large effective population sizes should undergo a higher rate of adaptive evolution than species with low effective population sizes if adaptation is limited by the supply of mutations. Previous analyses have appeared to support this conjecture because estimates of the proportion of nonsynonymous substitutions fixed by adaptive evolution, α, tend to be higher in species with large Ne. However, α is a function of both the number of advantageous and effectively neutral substitutions, either of which might depend on Ne. Here, we investigate the relationship between Ne and ωa, the rate of adaptive evolution relative to the rate of neutral evolution, using nucleotide polymorphism and divergence data from 13 independent pairs of eukaryotic species. We find a highly significant positive correlation between ωa and Ne. We also find some evidence that the rate of adaptive evolution varies between groups of organisms for a given Ne. The correlation between ωa and Ne does not appear to be an artifact of demographic change or selection on synonymous codon use. Our results suggest that adaptation is to some extent limited by the supply of mutations and that at least some adaptation depends on newly occurring mutations rather than on standing genetic variation. Finally, we show that the proportion of nearly neutral nonadaptive substitutions declines with increasing Ne. The low rate of adaptive evolution and the high proportion of effectively neutral substitution in species with small Ne are expected to combine to make it difficult to detect adaptive molecular evolution in species with small Ne.
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