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.

分化种群或新成种（incipient species）之间的二次接触（secondary contact）可能会引发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序列检测指标，旨在识别二次接触模型中发生基因渐渗的基因组区域。Gmin的定义为：某基因组窗口（genomic window）内种群间最小核苷酸差异数与种群间平均核苷酸差异数的比值。尽管Gmin在概念上十分简洁，但其相较于检测基因流（gene flow）的基于模型的方法而言，计算成本更低，且可轻松扩展至全基因组分析规模。我们将Gmin的灵敏度与特异性与当前广泛使用的种群分化指标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时具有更高的灵敏度与特异性。此外，我们发现Gmin的灵敏度对于种群突变率与重组率均具有良好的稳健性。最后，我们对黑腹果蝇（Drosophila melanogaster）X染色体开展的Gmin扫描，成功识别出了撒哈拉以南非洲种群与全球广布种群之间的基因渐渗候选区域——这类区域此前被其他方法所遗漏。上述研究结果证明，Gmin是一种生物学逻辑简洁且功能强大的替代工具，可替代FST以及其他计算成本高昂的基于模型的基因流检测方法。