Becoming pigs: archaeogenomic history of human-boar-pig interactions in northwest Europe

The relationship between humans and pigs has changed dramatically since their domestication in southwest Asia and subsequent human-induced introduction into Europe. Introgression between incoming southwest Asian pigs and European boar resulted in the gradual replacement of southwest Asian ancestry in European pigs. However, we currently lack genomic data required to explore the regional trajectories, nature and extent of contact between European boar and pigs that led to this turnover, and how this process was facilitated by human activity. We addressed this deficit by sequencing 4 Mesolithic boar and 7 Neolithic pig samples from 6 archaeological sites in the Netherlands and Britain ranging from the Mesolithic (5500 BCE) to Neolithic (2500 BCE). Our data shows that despite continuous gene flow with European boar, Neolithic European pigs show varying levels of southwest Asian ancestry. The low and varying southwest Asian ancestry in pigs from the Early Neolithic Dutch settlement Swifterbant indicate a high contribution of wild ancestry. The genetic profile, enriched d15N values, on-site presence and wide size distribution of Swifterbant Sus scrofa suggest a commensal relationship. Runs of homozygosity (ROH) imply that both closed-breeding and free-ranging management occurred in Neolithic communities, where the former showed an extreme burden of long segments of ROH. We further show selection signatures, associated with coat color and behavior, in Neolithic herds despite recurrent wild gene flow. Altogether, our results show distinct husbandry practices through space and time in Neolithic Europe, with heavy reliance on boar recruitment via the commensal pathway in northwest Europe.