Data from: Powerful methods for detecting introgressed regions from population genomic data

Understanding the types and functions of genes that are able to cross species boundaries—and those that are not—is an important step in understanding the forces maintaining species as largely independent lineages across the remainder of the genome. With large next-generation sequencing datasets we are now able to ask whether introgression has occurred across the genome, and multiple methods have been proposed to detect the signature of such events. Here, we introduce a new summary statistic that can be used to test for introgression, RNDmin, that makes use of the minimum pairwise sequence distance between two population samples relative to divergence to an outgroup. We find that our method offers a modest increase in power over other, related tests, but that all such tests have high power to detect introgressed loci when migration is recent and strong. RNDmin is robust to variation in the mutation rate, and remains reliable even when estimates of the divergence time between sister species are inaccurate. We apply RNDmin to population genomic data from the African mosquitoes Anopheles quadriannulatus and A. arabiensis, identifying three novel candidate regions for introgression. Interestingly, one of the introgressed loci is on the X chromosome, but outside of an inversion separating these two species. Our results suggest that significant, but rare, sharing of alleles is occurring between species that diverged more than 1 million years ago, and that application of these methods to additional systems are likely to reveal similar results.

解析能够跨物种边界（与无法跨物种边界）的基因类型及功能，是探究维持物种在基因组其余区域保持独立谱系的演化动力的关键步骤。借助大规模下一代测序（next-generation sequencing, NGS）数据集，如今我们得以探究全基因组范围内是否发生了基因渐渗（introgression），学界已提出多种方法以检测这类事件的特征信号。本研究介绍一种可用于检测基因渐渗的新型汇总统计量（summary statistic）：RNDmin，该统计量基于两个种群样本间的最小成对序列距离，并相对于外类群（outgroup）的分化水平进行校准。研究发现，相较于其他同类检验方法，本方法的统计效力（power）仅有小幅提升，但当基因流近期且强度较高时，所有这类检验方法均能高效检测到渐渗基因座（locus，复数为loci）。RNDmin对突变率波动具有良好的稳健性，即便姊妹物种（sister species）间的分化时间估算存在偏差，该统计量仍能保持可靠的检测性能。我们将RNDmin应用于非洲按蚊（Anopheles quadriannulatus）与阿拉伯按蚊（A. arabiensis）的群体基因组数据，成功鉴定出三个全新的基因渐渗候选区域。值得注意的是，其中一个渐渗基因座位于X染色体上，却处于区分这两个物种的染色体倒位（inversion）区域之外。本研究结果表明，在分化时长超百万年的物种之间，正发生着显著但罕见的等位基因（allele）共享现象；将这类方法应用于其他研究系统，大概率会得到类似的结论。