Pervasive Linked Selection and Intermediate-Frequency Alleles Are Implicated in an Evolve-and-Resequencing Experiment of Drosophila simulans
Pervasive Linked Selection and Intermediate-Frequency Alleles Are Implicated in an Evolve-and-Resequencing Experiment of Drosophila simulans
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DOI：
10.1534/genetics.118.301824
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发表时间：
2019-03-01
期刊：
影响因子：
3.3
通讯作者：
Hughes, Kimberly A.
中科院分区：
文献类型：
--
作者：
Kelly, John K.;Hughes, Kimberly A.
我们开发了用于进化和重测序实验的分析和模拟工具，并将其应用于模拟果蝇快速进化的新研究。应用于汇总群体测序数据的似然检验统计表明，整个基因组中有 138 个 SNP 平行进化。由于实验设计和统计分析的差异，这个数字比之前的研究（数千或数万）减少了几个数量级。根据果蝇遗传数据集校准的全基因组模拟表明，在具有相应搭便车效应的强定向选择下，全基因组反应的主要特征可以通过少至 30 个基因座来解释。较小的效应位点也可能有反应，但低于实验的检测限。最后，实验中表现出强烈平行进化的SNP在自然群体中的频率为中等（通常为30-70%），表明自然界中存在平衡选择。这些位点在模拟拟螟自然种群中也表现出较高的分化，表明环境异质性是一种潜在的平衡机制。进化和重新测序（E＆R）实验，研究人员允许种群在一个或多个受控环境中进化，然后对所得种群进行全基因组测序，在进化遗传学方法中变得越来越重要。在这里，凯莉...
We develop analytical and simulation tools for evolve-and-resequencing experiments and apply them to a new study of rapid evolution in Drosophila simulans. Likelihood test statistics applied to pooled population sequencing data suggest parallel evolution of 138 SNPs across the genome. This number is reduced by orders of magnitude from previous studies (thousands or tens of thousands), owing to differences in both experimental design and statistical analysis. Whole genome simulations calibrated from Drosophila genetic data sets indicate that major features of the genome-wide response could be explained by as few as 30 loci under strong directional selection with a corresponding hitchhiking effect. Smaller effect loci are likely also responding, but are below the detection limit of the experiment. Finally, SNPs showing strong parallel evolution in the experiment are intermediate in frequency in the natural population (usually 30-70%) indicative of balancing selection in nature. These loci also exhibit elevated differentiation among natural populations of D. simulans, suggesting environmental heterogeneity as a potential balancing mechanism.Evolve-and-Resequence (E&R) experiments, where researchers allow populations to evolve within one or more controlled environments and then whole-genome sequence the resultant populations, are increasingly important in evolutionary genetics methodology. Here, Kelly...