Geneva Anthony J, Muirhead Christina A, Kingan Sarah B, Garrigan Daniel
Department of Biology, University of Rochester, Rochester, New York, United States of America.
Department of Biology, University of Rochester, Rochester, New York, United States of America; Ronin Institute, Montclair, New Jersey, United States of America.
PLoS One. 2015 Apr 14;10(4):e0118621. doi: 10.1371/journal.pone.0118621. eCollection 2015.
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.
分化种群或初始物种之间的二次接触可能导致基因组物质的交换和渗入。我们开发了一种简单的DNA序列度量方法，称为Gmin，旨在识别在二次接触模型中经历渗入的基因组区域。Gmin被定义为基因组窗口中种群间核苷酸差异的最小数量与种群间差异平均数量的比值。尽管Gmin在概念上很简单，但其一个优点是相对于基于模型的检测基因流的方法，它的计算成本较低，并且很容易扩展到全基因组分析水平。我们将Gmin的敏感性和特异性与广泛使用的种群分化指数FST的敏感性和特异性进行了比较，并提出了一种用于识别基因组异常值的简单统计检验方法。大量的计算机模拟表明，与FST相比，Gmin在检测近期渗入方面具有更高的敏感性和特异性。此外，我们发现Gmin的敏感性在种群突变率和重组率方面都很稳健。最后，对黑腹果蝇X染色体上的Gmin进行扫描，确定了撒哈拉以南非洲种群和世界性种群之间以前被其他方法遗漏的渗入候选区域。这些结果表明，Gmin是一种生物学上简单但功能强大的替代FST的方法，也是替代用于检测基因流的计算量更大的基于模型的方法的方法。
