A New Method to Scan Genomes for Introgression in a Secondary Contact Model

<div><p>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 <i>G</i>_min, which is designed to identify genomic regions experiencing introgression in a secondary contact model. <i>G</i>_min 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 <i>G</i>_min 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 <i>G</i>_min to those of the widely used index of population differentiation, <i>F</i>_ST, and suggest a simple statistical test for identifying genomic outliers. Extensive computer simulations demonstrate that <i>G</i>_min has both greater sensitivity and specificity for detecting recent introgression than does <i>F</i>_ST. Furthermore, we find that the sensitivity of <i>G</i>_min is robust with respect to both the population mutation and recombination rates. Finally, a scan of <i>G</i>_min across the X chromosome of <i>Drosophila melanogaster</i> identifies candidate regions of introgression between sub-Saharan African and cosmopolitan populations that were previously missed by other methods. These results show that <i>G</i>_min is a biologically straightforward, yet powerful, alternative to <i>F</i>_ST, as well as to more computationally intensive model-based methods for detecting gene flow.</p>