Graduate Group in Population Biology, University of California, Davis, California 95616 Center for Population Biology, University of California, Davis, California 95616 Department of Evolution and Ecology, University of California, Davis, California 95616
Center for Population Biology, University of California, Davis, California 95616 Department of Evolution and Ecology, University of California, Davis, California 95616
Genetics. 2015 Oct;201(2):707-25. doi: 10.1534/genetics.115.178962. Epub 2015 Aug 25.
The use of genetic polymorphism data to understand the dynamics of adaptation and identify the loci that are involved has become a major pursuit of modern evolutionary genetics. In addition to the classical "hard sweep" hitchhiking model, recent research has drawn attention to the fact that the dynamics of adaptation can play out in a variety of different ways and that the specific signatures left behind in population genetic data may depend somewhat strongly on these dynamics. One particular model for which a large number of empirical examples are already known is that in which a single derived mutation arises and drifts to some low frequency before an environmental change causes the allele to become beneficial and sweeps to fixation. Here, we pursue an analytical investigation of this model, bolstered and extended via simulation study. We use coalescent theory to develop an analytical approximation for the effect of a sweep from standing variation on the genealogy at the locus of the selected allele and sites tightly linked to it. We show that the distribution of haplotypes that the selected allele is present on at the time of the environmental change can be approximated by considering recombinant haplotypes as alleles in the infinite-alleles model. We show that this approximation can be leveraged to make accurate predictions regarding patterns of genetic polymorphism following such a sweep. We then use simulations to highlight which sources of haplotypic information are likely to be most useful in distinguishing this model from neutrality, as well as from other sweep models, such as the classic hard sweep and multiple-mutation soft sweeps. We find that in general, adaptation from a unique standing variant will likely be difficult to detect on the basis of genetic polymorphism data from a single population time point alone, and when it can be detected, it will be difficult to distinguish from other varieties of selective sweeps. Samples from multiple populations and/or time points have the potential to ease this difficulty.
利用遗传多态性数据来理解适应的动态，并确定涉及的基因座，已成为现代进化遗传学的主要追求。除了经典的“硬扫除” hitchhiking 模型外，最近的研究还引起了人们的注意，即适应的动态可以以多种不同的方式发挥作用，而在群体遗传数据中留下的特定特征可能在某种程度上强烈依赖于这些动态。一个已经有大量实证例子的特殊模型是，在这个模型中，一个单一的衍生突变出现并漂移到一个低频率，然后环境变化使等位基因变得有利并扫除到固定。在这里，我们通过模拟研究，对该模型进行了分析研究。我们使用合并理论为从固定变异到选择等位基因和紧密连锁的位点的系谱的扫除效应开发了一个分析近似。我们表明，在环境变化时选择等位基因所在的单倍型的分布可以通过将重组单倍型视为无限等位基因模型中的等位基因来近似。我们表明，这种近似可以用来对这种扫除后遗传多态性的模式进行准确的预测。然后，我们使用模拟来突出哪些单倍型信息来源最有可能用于区分这种模型与中性以及其他扫除模型，如经典的硬扫除和多突变软扫除。我们发现，一般来说，从独特的固定变体进行的适应仅凭单个群体的单个时间点的遗传多态性数据可能很难检测到，而且当可以检测到适应时，它将难以与其他类型的选择扫除区分开来。来自多个群体和/或时间点的样本有可能缓解这种困难。
