Data from: A new method to scan genomes for introgression in a secondary contact model

Secondary contact between divergent populations or incipient species may result in the exchange and introgression of genomic material. We develop a simple DNA sequence measure, called Gmin, which is designed to identify genomic regions experiencing introgression in a secondary contact model. Gmin is defined as the ratio of the minimum between-population number of nucleotide differences in a genomic window to the average number of between-population differences. Although it is conceptually simple, one advantage of Gmin is that it is computationally inexpensive relative to model-based methods for detecting gene flow and it scales easily to the level of whole-genome analysis. We compare the sensitivity and specificity of Gmin to those of the widely used index of population differentiation, FST, and suggest a simple statistical test for identifying genomic outliers. Extensive computer simulations demonstrate that Gmin has both greater sensitivity and specificity for detecting recent introgression than does FST. Furthermore, we find that the sensitivity of Gmin is robust with respect to both the population mutation and recombination rates. Finally, a scan of Gmin across the X chromosome of Drosophila melanogaster identifies candidate regions of introgression between sub-Saharan African and cosmopolitan populations that were previously missed by other methods. These results show that Gmin is a biologically straightforward, yet powerful, alternative to FST, as well as to more computationally intensive model-based methods for detecting gene flow.分化种群或初期物种之间的二次接触（secondary contact）可能导致基因组物质的交流与基因渐渗（introgression）。我们开发了一种名为Gmin的简易DNA序列度量方法，旨在在二次接触模型中识别发生基因渐渗的基因组区域。Gmin的定义为：基因组窗口内群体间最小核苷酸差异数与群体间平均差异数的比值。尽管该方法在概念上较为简单，但其相较于检测基因流的基于模型的方法而言计算成本低廉，且易于扩展至全基因组分析层面。我们将Gmin的灵敏度与特异性与当前广泛使用的群体分化指标FST进行了对比，并提出了一种用于识别基因组异常值的简易统计检验方法。大量计算机模拟实验表明，相较于FST，Gmin在检测近期基因渐渗事件时具备更高的灵敏度与特异性。此外，我们发现Gmin的灵敏度对于群体突变率与重组率均具有鲁棒性。最后，通过对黑腹果蝇（Drosophila melanogaster）X染色体的Gmin扫描，我们识别出了撒哈拉以南非洲种群与广布种群之间的基因渐渗候选区域，而此类区域此前未被其他方法检出。上述研究结果表明，Gmin是一种生物学原理简明但功能强大的替代方法，可用于替代FST以及计算成本更高的基于模型的基因流检测方法。