Powerful methods for detecting introgressed regions from population genomic data

Abstract

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.

Comparative analysis examining patterns of genomic differentiation across multiple episodes of population divergence in birds

“…; Rosenzweig et al. ). Accordingly, much of the pattern we documented may be related solely to variation in mutation rates.…”

Hybridization in Plants: Old Ideas, New Techniques

“…Although tests to detect hybridization do not require the identification of exchanged genes, similar analyses have been adapted to detect the targets of introgression (Rosenzweig et al, 2016). For instance the f statistic, an expansion of Patterson's D, is used to search for genomic regions with increased proportions of shared derived variants, likely exchanged by recent gene flow (Green et al, 2010;Durand et al, 2011).…”

Genomics of hybridization and its evolutionary consequences

“…In this issue, Rosenzweig et al . () have developed a new statistical test for introgression. Their approach builds upon established methods that use patterns of sequence divergence between species to detect introgression (Joly et al .…”

“…As a proof of principle, Rosenzweig et al . () apply this test to phased genome data from two sister species of mosquito and identify three novel candidate regions for introgression one of which is located on the X‐chromosome, but outside an inversion that distinguishes the two species.…”