Hoban Sean, Kelley Joanna L, Lotterhos Katie E, Antolin Michael F, Bradburd Gideon, Lowry David B, Poss Mary L, Reed Laura K, Storfer Andrew, Whitlock Michael C
Am Nat. 2016 Oct;188(4):379-97. doi: 10.1086/688018. Epub 2016 Aug 15.
Uncovering the genetic and evolutionary basis of local adaptation is a major focus of evolutionary biology. The recent development of cost-effective methods for obtaining high-quality genome-scale data makes it possible to identify some of the loci responsible for adaptive differences among populations. Two basic approaches for identifying putatively locally adaptive loci have been developed and are broadly used: one that identifies loci with unusually high genetic differentiation among populations (differentiation outlier methods) and one that searches for correlations between local population allele frequencies and local environments (genetic-environment association methods). Here, we review the promises and challenges of these genome scan methods, including correcting for the confounding influence of a species' demographic history, biases caused by missing aspects of the genome, matching scales of environmental data with population structure, and other statistical considerations. In each case, we make suggestions for best practices for maximizing the accuracy and efficiency of genome scans to detect the underlying genetic basis of local adaptation. With attention to their current limitations, genome scan methods can be an important tool in finding the genetic basis of adaptive evolutionary change.
揭示局部适应性的遗传和进化基础是进化生物学的一个主要研究重点。近期，获取高质量基因组规模数据的低成本方法的发展，使得识别一些导致种群间适应性差异的基因座成为可能。目前已经开发并广泛应用了两种识别假定的局部适应性基因座的基本方法：一种是识别种群间具有异常高遗传分化的基因座（分化异常值方法），另一种是寻找当地种群等位基因频率与当地环境之间的相关性（遗传-环境关联方法）。在这里，我们回顾了这些基因组扫描方法的前景和挑战，包括校正物种种群历史的混杂影响、基因组缺失部分导致的偏差、环境数据与种群结构的尺度匹配以及其他统计考量。在每种情况下，我们都针对如何最大化基因组扫描的准确性和效率以检测局部适应性的潜在遗传基础提出了最佳实践建议。鉴于其当前的局限性，基因组扫描方法可以成为寻找适应性进化变化遗传基础的重要工具。
