Divergence-based introgression polarization

Abstract

Introgressive hybridization results in the transfer of genetic material between species, often with fitness implications for the recipient species. The development of statistical methods for detecting the signatures of historical introgression (IG) in whole-genome data has been a major area of focus. While existing techniques are able to identify the taxa that exchanged genes during IG using a four-taxon system, most methods do not explicitly distinguish which taxon served as donor and which as recipient during IG (i.e. polarization of IG directionality). The existing methods that do polarize IG are only able to do so when there is a fifth taxon available and that taxon is sister to one of the taxa involved in IG. Here, we present Divergence-based Introgression Polarization (DIP), a method for polarizing IG using patterns of sequence divergence across whole genomes, which operates in a four-taxon context. Thus, DIP can be applied to infer the directionality of IG when additional taxa are not available. We use simulations to show that DIP can polarize IG and identify potential sources of bias in the assignment of directionality, and we apply DIP to a well-described hominin IG event.