Data from: The demographic history of populations experiencing asymmetric gene flow: combining simulated and empirical data.

Population structure can significantly affect genetic-based demographic inferences, generating spurious bottleneck-like signals. Previous studies have typically assumed island or stepping-stone models, which are characterized by symmetric gene flow. However, many organisms are characterized by asymmetric gene flow. Here, we combined simulated and empirical data to test whether asymmetric gene flow affects the inference of past demographic changes. Through the analysis of simulated genetic data with three methods (i.e. bottleneck, M-ratio and msvar), we demonstrated that asymmetric gene flow biases past demographic changes. Most biases were towards spurious signals of expansion, albeit their strength depended on values of effective population size and migration rate. It is noteworthy that the spurious signals of demographic changes also depended on the statistical approach underlying each of the three methods. For one of the three methods, biases induced by asymmetric gene flow were confirmed in an empirical multispecific data set involving four freshwater fish species (Squalius cephalus, Leuciscus burdigalensis, Gobio gobio and Phoxinus phoxinus). However, for the two other methods, strong signals of bottlenecks were detected for all species and across two rivers. This suggests that, although potentially biased by asymmetric gene flow, some of these methods were able to bypass this bias when a bottleneck actually occurred. Our results show that population structure and dispersal patterns have to be considered for proper inference of demographic changes from genetic data.

种群结构可显著影响基于遗传标记的种群历史推断，进而催生虚假的类瓶颈信号。既往研究多采用具备对称基因流特征的岛屿模型或踏脚石模型作为假设前提，但绝大多数生物的基因流实则呈不对称分布特征。本研究结合模拟数据与实证数据，旨在检验不对称基因流是否会干扰种群历史变化的遗传推断。通过采用bottleneck、M-ratio及msvar三种方法对模拟遗传数据进行分析，本研究证实不对称基因流会对种群历史变化的推断产生偏倚，此类偏倚多指向虚假的种群扩张信号，但其强度受有效种群大小与迁移率的取值影响。值得关注的是，种群历史变化的虚假信号还取决于三种方法各自依托的统计框架。针对其中一种方法，我们在涵盖4种淡水鱼类（欧鳊Squalius cephalus、布尔丹鱥Leuciscus burdigalensis、麦穗鱼Gobio gobio及欧洲鱥Phoxinus phoxinus）的多物种实证数据集中，验证了不对称基因流诱导的偏倚效应。但针对另外两种方法，我们在两条河流的所有受试物种中均检测到了显著的瓶颈信号。这表明，尽管这些方法可能受不对称基因流干扰产生偏倚，但当真实存在种群瓶颈时，部分方法能够规避此类偏差。本研究结果显示，若要从遗传数据中准确推断种群历史变化，必须将种群结构与扩散模式纳入考量范畴。