Adaptive Evolution Is Substantially Impeded by Hill-Robertson Interference in Drosophila
Adaptive Evolution Is Substantially Impeded by Hill-Robertson Interference in Drosophila
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DOI：
10.1093/molbev/msv236
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发表时间：
2016-02-01
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;Coronado-Zamora, Marta;Eyre-Walker, Adam
当两个或多个连锁选定位点不能自由分离时，希尔-罗伯逊干扰 (HRi) 预计会降低自然选择的效率，但迄今为止尚未尝试量化 HRi 对任何给定基因组适应性进化速率的总体影响。在这项工作中，我们估计了 HRi 在多大程度上阻碍了果蝇编码基因组的适应性进化速度。我们编译了来自果蝇的 6,141 个常染色体蛋白编码基因的数据集，从中估计了黑腹果蝇的多态性水平以及与 yakuba 果蝇的分歧。适应性进化的速率是使用控制轻微有害突变的麦克唐纳-克雷特曼测试的衍生物来计算的。我们发现基因组给定位置的适应性氨基酸取代率与重组率和突变率正相关，与该区域的基因密度负相关。这些相关性对于相互控制、同义密码子偏倚以及与免疫反应和睾丸相关的基因功能来说是稳健的。我们发现 HRi 使适应性进化的速度降低了大约 27%。有趣的是，嵌入基因贫乏区域的低突变率基因丢失了大约 17% 的适应性替换，而嵌入基因丰富区域的高突变率基因丢失了大约 60%。我们得出的结论是，HRi 阻碍了果蝇的适应性进化速度，并且基因组中重组、突变和基因密度的变化会影响 HRi 效应。
Hill-Robertson interference (HRi) is expected to reduce the efficiency of natural selection when two or more linked selected sites do not segregate freely, but no attempt has been done so far to quantify the overall impact of HRi on the rate of adaptive evolution for any given genome. In this work, we estimate how much HRi impedes the rate of adaptive evolution in the coding genome of Drosophila melanogaster. We compiled a data set of 6,141 autosomal protein-coding genes from Drosophila, from which polymorphism levels in D. melanogaster and divergence out to D. yakuba were estimated. The rate of adaptive evolution was calculated using a derivative of the McDonald-Kreitman test that controls for slightly deleterious mutations. We find that the rate of adaptive amino acid substitution at a given position of the genome is positively correlated to both the rate of recombination and the mutation rate, and negatively correlated to the gene density of the region. These correlations are robust to controlling for each other, for synonymous codon bias and for gene functions related to immune response and testes. We show that HRi diminishes the rate of adaptive evolution by approximately 27%. Interestingly, genes with low mutation rates embedded in gene poor regions lose approximately 17% of their adaptive substitutions whereas genes with high mutation rates embedded in gene rich regions lose approximately 60%. We conclude that HRi hampers the rate of adaptive evolution in Drosophila and that the variation in recombination, mutation, and gene density along the genome affects the HRi effect.