Data from: The relative power of genome scans to detect local adaptation depends on sampling design and statistical method

Although genome scans have become a popular approach toward understanding the genetic basis of local adaptation, the field still does not have a firm grasp on how sampling design and demographic history affect the performance of genome scans on complex landscapes. To explore these issues, we compared 20 different sampling designs in equilibrium (i.e., island model and isolation by distance) and non-equilibrium (i.e., range expansion from one or two refugia) demographies in spatially heterogeneous environments. We simulated spatially complex landscapes, which allowed us to exploit local maxima and minima in the environment in “pair” and “transect” sampling strategies. We compared Fst outlier and genetic-environment association (GEA) methods for each of two approaches that control for population structure: with a covariance matrix or with latent factors. We show that while the relative power of two methods in the same category (Fst or GEA) depended largely on the number of individuals sampled, overall GEA tests had higher power in the island model and Fst had higher power under isolation by distance. In the refugia models, however, these methods varied in their power to detect local adaptation at weakly selected loci. At weakly selected loci, paired sampling designs had equal or higher power than transect or random designs to detect local adaptation. Our results can inform sampling designs for studies of local adaptation, and have important implications for the interpretation of genome scans based on landscape data.尽管基因组扫描（genome scans）已成为解析局部适应遗传基础的主流研究手段，但当前学界尚未明确采样设计与种群历史如何影响复杂景观背景下基因组扫描的检测性能。为探究该科学问题，本研究在空间异质环境中，针对平衡态（含岛屿模型与距离隔离模型）与非平衡态（含单、双避难所种群范围扩张）场景下的20种不同采样设计开展对比分析。我们模拟了空间复杂景观，借此可在‘配对’与‘样带’两类采样策略中利用环境的局部极值特征。针对两种控制种群结构的分析框架（基于协方差矩阵或潜在因子），我们分别对比了Fst异常值法与遗传-环境关联（GEA，genetic-environment association）两类分析手段。研究结果表明，同一类别（Fst法或GEA法）内的两种方法的相对检验功效，主要取决于采样个体数量；整体而言，GEA检验在岛屿模型中展现出更高的检验效力，而Fst法在距离隔离模型下表现更优。但在避难所种群模型中，两类方法对弱选择位点局部适应的检测功效存在差异。在弱选择位点上，配对采样策略的检测功效等于或优于样带采样与随机采样设计。本研究结果可为局部适应相关研究的采样设计提供科学参考，并对基于景观数据的基因组扫描结果解读具有重要启示意义。