Center for Population Biology, University of California, Davis, California 95616
Department of Evolution and Ecology, University of California, Davis, California 95616.
Genetics. 2017 Dec;207(4):1591-1619. doi: 10.1534/genetics.117.300417. Epub 2017 Oct 18.
Geographically separated populations can convergently adapt to the same selection pressure. Convergent evolution at the level of a gene may arise via three distinct modes. The selected alleles can (1) have multiple independent mutational origins, (2) be shared due to shared ancestral standing variation, or (3) spread throughout subpopulations via gene flow. We present a model-based, statistical approach that utilizes genomic data to detect cases of convergent adaptation at the genetic level, identify the loci involved and distinguish among these modes. To understand the impact of convergent positive selection on neutral diversity at linked loci, we make use of the fact that hitchhiking can be modeled as an increase in the variance in neutral allele frequencies around a selected site within a population. We build on coalescent theory to show how shared hitchhiking events between subpopulations act to increase covariance in allele frequencies between subpopulations at loci near the selected site, and extend this theory under different models of migration and selection on the same standing variation. We incorporate this hitchhiking effect into a multivariate normal model of allele frequencies that also accounts for population structure. Based on this theory, we present a composite-likelihood-based approach that utilizes genomic data to identify loci involved in convergence, and distinguishes among alternate modes of convergent adaptation. We illustrate our method on genome-wide polymorphism data from two distinct cases of convergent adaptation. First, we investigate the adaptation for copper toxicity tolerance in two populations of the common yellow monkey flower, We show that selection has occurred on an allele that has been standing in these populations prior to the onset of copper mining in this region. Lastly, we apply our method to data from four populations of the killifish, , that show very rapid convergent adaptation for tolerance to industrial pollutants. Here, we identify a single locus at which both independent mutation events and selection on an allele shared via gene flow, either slightly before or during selection, play a role in adaptation across the species' range.
地理隔离的种群可以对相同的选择压力趋同适应。基因水平上的趋同进化可能通过三种不同的模式产生。选择的等位基因可以 (1) 具有多个独立的突变起源，(2) 由于共享的祖先等位基因变异而共享，或 (3) 通过基因流在亚种群中传播。我们提出了一种基于模型的统计方法，该方法利用基因组数据来检测遗传水平上趋同适应的情况，确定涉及的基因座，并区分这些模式。为了了解趋同正选择对连锁基因座中性多样性的影响，我们利用这样一个事实，即漂变可以被建模为群体内选择位点周围中性等位基因频率方差的增加。我们基于合并理论，展示了亚种群之间的共享漂变事件如何增加选择位点附近基因座上亚种群之间等位基因频率的协方差，并在不同的迁移模型和对相同的祖先变异的选择下扩展了这一理论。我们将这种漂变效应纳入到一个多变量正态模型中，该模型还考虑了群体结构。基于这一理论，我们提出了一种基于复合似然的方法，该方法利用基因组数据来识别参与趋同的基因座，并区分趋同适应的替代模式。我们在两个趋同适应的独特案例的全基因组多态性数据上验证了我们的方法。首先，我们研究了两种常见黄猴花种群对铜毒性耐受的适应。我们表明，选择发生在一个等位基因上，该等位基因在该地区铜矿开采之前就已经存在于这些种群中。最后，我们将我们的方法应用于来自四个适应工业污染物能力迅速趋同的食蚊鱼种群的数据。在这里，我们确定了一个单一的基因座，在这个基因座上，独立的突变事件和通过基因流选择的共享等位基因都发挥了作用，无论是在选择之前还是选择期间。
