Facilitated introgression from domestic goat into Alpine ibex at immune loci

Abstract

Introgression is expected to be adaptive at loci under balancing selection, for instance at loci relevant for the immune response, but these loci generally also contain ancient polymorphisms. Ancient genomics is a promising tool to detect recent introgression and disentangle it from ancient polymorphisms. Alpine ibex (Capra ibex), a wild goat species native to the European Alps, faced near-extinction two centuries ago, but has recovered thanks to successful restoration programs. Previously, signals of introgression from the domestic goat (Capra aegagrus hircus) into the Alpine ibex genome were found at the major histocompatibility complex. This introgression was suggested to potentially be adaptive since it introduced new diversity at a gene locus important for immunity. But no genome-wide analyses of introgression have been performed to confirm the potential relevance of immune loci. Here we take advantage of two ancient whole genomes of Alpine ibex combined with 29 modern Alpine ibex genomes and 31 genomes representing six related Capra species to investigate genome-wide patterns of introgression. Our complementary analysis of putatively introgressed haplotypes and demographic modelling suggests 2.3% recent domestic goat ancestry among wild Alpine ibex. The introgression was estimated to have happened during the last 300 years coinciding with the time when the species had very small population size. Further analysis suggested an enrichment of immune-related genes, where the adaptive value of alternative alleles may give individuals with otherwise depleted genetic diversity a selective advantage.