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（population structure）可显著影响基于遗传数据的种群人口统计学推断，进而产生类似种群瓶颈的虚假信号。既往研究通常默认采用岛屿模型（island model）或踏脚石模型（stepping-stone model），这类模型以对称基因流（symmetric gene flow）为特征。但多数生物的基因流实则为不对称基因流（asymmetric gene flow）。本研究结合模拟数据与实证数据，探究不对称基因流是否会对过往种群动态变化的推断产生影响。本研究采用瓶颈检测法（bottleneck）、M比率法（M-ratio）以及msvar法三种方法对模拟遗传数据展开分析，结果证实不对称基因流会对过往种群动态变化的推断产生偏倚。多数偏倚会导向虚假的种群扩张信号，不过偏倚的强度取决于有效种群大小（effective population size）与迁移率（migration rate）的取值。值得注意的是，这类虚假的种群动态变化信号还会受三种方法各自依托的统计框架影响。针对三种方法中的一种，研究人员在涵盖4种淡水鱼类的多物种种群实证数据集（分别为*Squalius cephalus*、*Leuciscus burdigalensis*、*Gobio gobio*及*Phoxinus phoxinus*）中证实了不对称基因流所引发的偏倚。但针对另外两种方法，研究人员在两条河流的所有受试鱼类物种中均检测到了显著的种群瓶颈信号。这表明，尽管这些方法可能会受不对称基因流的影响而产生偏倚，但当真实存在种群瓶颈时，部分方法能够规避这类偏倚。本研究结果证实，若要基于遗传数据对种群动态变化做出准确推断，必须将种群结构与扩散模式（dispersal patterns）纳入考量范畴。