Ancient pigs reveal a near-complete genomic turnover following their introduction to Europe

Archaeological evidence indicates that pigdomestication had begun by ∼10,500 y before the present (BP) in the Near East, and mitochondrial DNA (mtDNA) suggests that pigsarrived in Europe alongside farmers ∼8,500 y BP. A few thousand years after the introduction of Near Eastern pigsinto Europe, however, their characteristic mtDNA signature disappeared and was replaced by haplotypes associated with European wild boars. This turnover could be accounted for by substantial gene flowfrom local European wild boars, although it is also possible that European wild boarswere domesticated independently without any genetic contribution from the Near East. To test these hypotheses, we obtained mtDNA sequences from 2,099 modern and ancient pigsamples and 63 nuclear ancient genomes from Near Eastern and European pigs. Our analyses revealed that European domestic pigsdating from 7,100 to 6,000 y BP possessed both Near Eastern and Europeannuclear ancestry, while later pigspossessed no more than 4% Near Eastern ancestry, indicating that gene flowfrom European wild boarsresulted in a near-complete disappearance of Near East ancestry. In addition, we demonstrate that a variant at a locus encoding black coat color likely originated in the Near East and persisted in European pigs. Altogether, our results indicate that while pigswere not independently domesticated in Europe, the vast majority of human-mediated selection over the past 5,000 y focused on the genomic fraction derived from the European wild boars, and not on the fraction that was selected by early Neolithic farmers over the first 2,500 y of the domestication process.