Evolutionary dynamics of adaptive introgression and balancing selection in domestic and wild Capra species

Abstract Introgression is increasingly documented, yet its detection remains challenging because patterns used to infer gene flow may reflect multiple processes, including the persistence of ancestral polymorphism under balancing selection. Domestic species, like goats, and their wild relatives provide informative models for testing the biological feasibility and genomic consequences of interspecific gene flow. We analyze whole-genome sequences from 164 individuals of the genus Capra , including 36 newly generated, to investigate hybridization and signatures of introgression within the genus. Genomic analyses confirm a goat–ibex hybrid and identify two backcross offspring, providing evidence of male F1 fertility. Further analyses involving domestic goats ( Capra hircus ), their ancestor the bezoar ( C. aegagrus ), and three ibex species ( C. ibex , C. pyrenaica , and C. sibirica ) revealed patterns consistent with both pre- and post-domestication introgression. We identify 8 candidate regions with shared haplotypes consistent with ancient introgression predating domestication and enriched for genes involved in olfaction and immunity. However, some regions show signatures compatible with balancing selection. Overall, our results show that hybridization between domestic and wild Capra is biologically possible, that most shared haplotypes likely predate domestication, and highlight the importance of distinguishing introgression from balancing selection when interpreting shared genomic variation across species.