Data from: Adaptation in isolated populations: when does it happen and when can we tell?

Isolated populations with novel phenotypes present an exciting opportunity to uncover the genetic basis of ecologically significant adaptation, and genomic scans for positive selection in such populations have often, but not always, led to candidate genes directly related to an adaptive phenotype. However, in many cases these populations were established by a severe bottleneck, which can make identifying targets of selection problematic. Here we simulate severe bottlenecks and subsequent selection on standing variation, mimicking adaptation after establishment of a new small population, such as an island or an artificial selection experiment. Using simulations of single loci under positive selection and population genetics theory, we examine how population size and age of the population isolate affects the ability of outlier scans for selection to identify adaptive alleles using both single site measures and haplotype structure. We find and explain an optimal combination of selection strength, starting frequency, and age of the adaptive allele, which we refer to as a Goldilocks zone, where adaptation is likely to occur, and yet the adaptive variants are most likely to derive from a single ancestor (a "hard" selective sweep); in this zone, four commonly used statistics detect selection with high power. Real-world examples of both island colonization and experimental evolution studies are discussed. Our study provides concrete considerations to be made before embarking on whole genome sequencing of differentiated populations.携带新颖表型的隔离种群，为解析具有生态重要性的适应性演化的遗传基础提供了宝贵研究契机。针对此类种群开展的正向选择基因组扫描研究，虽常能获得与适应性表型直接相关的候选基因，但并非总能如愿。然而，多数此类隔离种群均由严重种群瓶颈事件奠基建立，这会为识别选择靶标带来诸多挑战。本研究通过模拟严重种群瓶颈事件及后续对现存遗传变异的选择过程，复刻了新小型种群奠基后的适应性演化场景，例如岛屿殖民或人工选择实验情境。本研究基于正向选择下单基因座的模拟实验与群体遗传学理论，分别借助单位点检测手段与单倍型结构分析，探究隔离种群的种群规模与建立时长如何影响选择异常值扫描识别适应性等位基因的效能。我们发现并阐释了适应性等位基因的选择强度、初始频率与建立时长的最优组合区间——我们将其称为“金发姑娘区”（Goldilocks zone）：在此区间内，适应性演化既易于发生，且适应性变异更大概率源自单一祖先个体（即“硬”选择性清除）；该区间内，四种常用统计量均可获得较高检验效能以检测正向选择信号。本研究还讨论了岛屿殖民与实验演化研究的真实案例。本研究为后续开展分化种群的全基因组测序工作提供了具体的参考依据。