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

Frantz, Laurent A. F. and Haile, James and Lin, Audrey T. and Scheu, Amelie and Geörg, Christina and Benecke, Norbert and Alexander, Michelle and Linderholm, Anna and Mullin, Victoria E. and Daly, Kevin G. and Battista, Vincent M. and Price, Max and Gron, Kurt J. and Alexandri, Panoraia and Arbogast, Rose-Marie and Arbuckle, Benjamin and Bӑlӑşescu, Adrian and Barnett, Ross and Bartosiewicz, László and Baryshnikov, Gennady and Bonsall, Clive and Borić, Dušan and Boroneanţ, Adina and Bulatović, Jelena and Çakirlar, Canan and Carretero, José-Miguel and Chapman, John and Church, Mike and Crooijmans, Richard and De Cupere, Bea and Detry, Cleia and Dimitrijevic, Vesna and Dumitraşcu, Valentin and du Plessis, Louis and Edwards, Ceiridwen J. and Erek, Cevdet Merih and Erim-Özdoğan, Aslı and Ervynck, Anton and Fulgione, Domenico and Gligor, Mihai and Götherström, Anders and Gourichon, Lionel and Groenen, Martien A.M. and Helmer, Daniel and Hongo, Hitomi and Horwitz, Liora K. and Irving-Pease, Evan K. and Lebrasseur, Ophélie and Lesur, Joséphine and Malone, Caroline and Manaseryan, Ninna and Marciniak, Arkadiusz and Martlew, Holley and Mashkour, Marjan and Matthews, Roger and Matuzeviciute, Giedre Motuzaite and Maziar, Sepideh and Meijaard, Erik and McGovern, Tom and Megens, Hendrik-Jan and Miller, Rebecca and Mohaseb, Azadeh Fatemeh and Orschiedt, Jörg and Orton, David and Papathanasiou, Anastasia and Pearson, Mike Parker and Pinhasi, Ron and Radmanović, Darko and Ricaut, François-Xavier and Richards, Mike and Sabin, Richard and Sarti, Lucia and Schier, Wolfram and Sheikhi, Shiva and Stephan, Elisabeth and Stewart, John R. and Stoddart, Simon and Tagliacozzo, Antonio and Tasić, Nenad and Trantalidou, Katerina and Tresset, Anne and Valdiosera, Cristina and van den Hurk, Youri and Van Poucke, Sophie and Vigne, Jean-Denis and Yanevich, Alexander and Zeeb-Lanz, Andrea and Triantafyllidis, Alexandros and Gilbert, M. Thomas P. and Schibler, Jörg and Rowley-Conwy, Peter and Zeder, Melinda and Peters, Joris and Cucchi, Thomas and Bradley, Daniel G. and Dobney, Keith and Burger, Joachim and Evin, Allowen and Girdland-Flink, Linus and Larson, Greger (2019) 'Ancient pigs reveal a near-complete genomic turnover following their introduction to Europe.', Proceedings of the National Academy of Sciences., 116 (35). pp. 17231-17238.

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.

Item Type:Article
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Status:Peer-reviewed
Publisher Web site:https://doi.org/10.1073/pnas.1901169116
Publisher statement:Copyright © 2019 the Author(s). This open access article is distributed under Creative Commons Attribution License 4.0 (CC BY).
Date accepted:24 June 2019
Date deposited:13 August 2019
Date of first online publication:12 August 2019
Date first made open access:No date available

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