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 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.