Nearly Neutral Evolution across the Drosophila melanogaster Genome
Nearly Neutral Evolution across the Drosophila melanogaster Genome
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DOI：
10.1093/molbev/msy164
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发表时间：
2018-11-01
影响因子：
10.7
通讯作者：
Eyre-Walker, Adam
中科院分区：
文献类型：
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作者：
Castellano, David;James, Jennifer;Eyre-Walker, Adam
根据分子进化的近中性理论，有效中性突变的比例预计取决于有效种群规模（N-e）。在这里，我们利用北美和非洲品系的多态性数据来研究黑腹果蝇基因组中是否存在这种情况。我们发现，即使考虑了非独立性，非同义多态性和同义多态性的数量之比与同义多态性的数量呈负相关。这种关系使得当 N-e 减半时，有效中性非同义突变的比例增加了大约 45%。然而，我们还表明，根据站点频谱对适应度效应分布的独立估计，这种关系比预期的更陡峭。我们对此进行了一些可能的解释，并通过模拟表明，这与遗传搭便车模型是一致的：遗传搭便车会抑制中性和弱选择位点的多样性，但对强选择位点的多样性几乎没有影响。
Under the nearly neutral theory of molecular evolution, the proportion of effectively neutral mutations is expected to depend upon the effective population size (N-e). Here, we investigate whether this is the case across the genome of Drosophila melanogaster using polymorphism data from North American and African lines. We show that the ratio of the number of nonsynonymous and synonymous polymorphisms is negatively correlated to the number of synonymous polymorphisms, even when the nonindependence is accounted for. The relationship is such that the proportion of effectively neutral nonsynonymous mutations increases by similar to 45% as N-e is halved. However, we also show that this relationship is steeper than expected from an independent estimate of the distribution of fitness effects from the site frequency spectrum. We investigate a number of potential explanations for this and show, using simulation, that this is consistent with a model of genetic hitchhiking: Genetic hitchhiking depresses diversity at neutral and weakly selected sites, but has little effect on the diversity of strongly selected sites.