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 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 affect 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.具有新表型的隔离种群（isolated populations）为揭示具有生态重要性的适应性演化的遗传基础提供了极具价值的研究契机。基因组扫描（genomic scans）虽常可筛选出与适应性表型直接相关的候选基因，但并非总能达成预期目标。然而，此类种群的建立往往经历了严重的瓶颈效应（severe bottleneck），这会为识别选择靶标带来诸多挑战。本研究模拟了严重瓶颈效应及后续对现存遗传变异（standing variation）的选择作用，以复刻新建小型种群（如岛屿定殖种群或人工选择实验种群）建立后的适应性演化过程。我们基于正选择下的单基因座模拟与种群遗传学理论（population genetics theory），同时采用单位点检测方法与单倍型结构（haplotype structure）分析手段，探究了隔离种群的种群规模与建立时长对选择离群扫描（outlier scans for selection）识别适应性等位基因（adaptive alleles）能力的影响。本研究发现并阐释了适应性演化的最优参数组合：选择强度、适应性等位基因的起始频率与出现时长，我们将该参数区间命名为‘金发姑娘区’（Goldilocks zone）——此时适应性演化易于发生，且适应性变异大概率源自单一祖先（即‘硬’选择扫荡（hard selective sweep））；在此区间内，四种常用统计检验方法可实现高效力的选择检测。本研究还讨论了岛屿定殖与实验演化研究的真实案例，并为开展分化种群的全基因组测序（whole-genome sequencing）前提供了具体的考量要点。