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 data sets 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.

Whole-genome alignment of A. arabiensis and A. quadriannulatus pop. samplesThe data are supplied in the Multisample Variant Format (Pease and Rosenzweig, 2015). A complete suite of tools for processing MVF files is available on github at https://github.com/jbpease/mvftools. Each file contains a full-chromosome alignment of computationally phased haplotypes for 23 samples of A. arabiensis, A. quadriannulatus, and A. christyi (outgroup); haplotypes are identified by ".A" or ".B" appended to the sample ID. The sample key (SampleCode.txt) is also included.AarAqu_align.tar.gz