Ancient pigs reveal a near-complete genomic turnover following their introduction to Europe
2019
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.
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