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

Frantz, LAF; Haile, J; Lin, AT; Scheu, A; Geoerg, C; Benecke, N; Alexander, M; ... Larson, G; + view all (2019) Ancient pigs reveal a near-complete genomic turnover following their introduction to Europe. Proceedings of the National Academy of Sciences of the United States of America , 116 (35) pp. 17231-17238. 10.1073/pnas.1901169116. Green open access

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Abstract

Archaeological evidence indicates that pig domestication had begun by ∼10,500 y before the present (BP) in the Near East, and mitochondrial DNA (mtDNA) suggests that pigs arrived in Europe alongside farmers ∼8,500 y BP. A few thousand years after the introduction of Near Eastern pigs into 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 flow from local European wild boars, although it is also possible that European wild boars were domesticated independently without any genetic contribution from the Near East. To test these hypotheses, we obtained mtDNA sequences from 2,099 modern and ancient pig samples and 63 nuclear ancient genomes from Near Eastern and European pigs. Our analyses revealed that European domestic pigs dating from 7,100 to 6,000 y BP possessed both Near Eastern and European nuclear ancestry, while later pigs possessed no more than 4% Near Eastern ancestry, indicating that gene flow from European wild boars resulted 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 pigs were 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.

Type: Article
Title: Ancient pigs reveal a near-complete genomic turnover following their introduction to Europe
Open access status: An open access version is available from UCL Discovery
DOI: 10.1073/pnas.1901169116
Publisher version: https://doi.org/10.1073/pnas.1901169116
Language: Czech
Additional information: © 2019 the Author(s). Published by PNAS. This open access article is distributed under Creative Commons Attribution License 4.0 (https://creativecommons.org/licenses/by/4.0/).
Keywords: domestication, evolution, gene flow, Neolithic
UCL classification: UCL
UCL > Provost and Vice Provost Offices > UCL SLASH
UCL > Provost and Vice Provost Offices > UCL SLASH > Faculty of S&HS
UCL > Provost and Vice Provost Offices > UCL SLASH > Faculty of S&HS > Institute of Archaeology
UCL > Provost and Vice Provost Offices > UCL SLASH > Faculty of S&HS > Institute of Archaeology > Institute of Archaeology Gordon Square
URI: https://discovery.ucl.ac.uk/id/eprint/10088659
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