Ancient introgression drives wild boar expansion and phenotypic diversification of domestic pigs

Despite the ubiquity of wild boar populations across Eurasia, their origins, routes of dispersal, and phenotypic evolution remain uncertain. Here, using 745 genomes representing populations across Eurasia, we demonstrate that wild boar expanded from South Asia during the Middle Pleistocene. This expansion was preceded by a Pliocene introgression (~3 to 5 million years ago) in South Asia from an archaic Suinae lineage that introduced a ~43 megabase X-chromosomal haplotype into the ancestral wild boar population. This haplotype includes loci associated with increased body size and adaptation to cold climates. During domestication, this region was selected at least three times independently to develop modern large-bodied breeds. Our findings reveal a long-lasting evolutionary legacy of this ancient introgression, which provided genetic material that was later shaped by natural and artificial selection.