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

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.

Metadata

Item Type:	Article
Authors/Creators:	Frantz, Laurent A F Haile, James Lin, Audrey T Scheu, Amelie Geörg, Christina Benecke, Norbert Alexander, Michelle https://orcid.org/0000-0001-8000-3639 Linderholm, Anna Mullin, Victoria E Daly, Kevin G Battista, Vincent M Price, Max Gron, Kurt J Alexandri, Panoraia Arbogast, Rose-Marie Arbuckle, Benjamin Bӑlӑşescu, Adrian Barnett, Ross Bartosiewicz, László Baryshnikov, Gennady Bonsall, Clive Borić, Dušan Boroneanţ, Adina Bulatović, Jelena Çakirlar, Canan Carretero, José-Miguel Chapman, John Church, Mike Crooijmans, Richard De Cupere, Bea Detry, Cleia Dimitrijevic, Vesna Dumitraşcu, Valentin du Plessis, Louis Edwards, Ceiridwen J Erek, Cevdet Merih Erim-Özdoğan, Aslı Ervynck, Anton Fulgione, Domenico Gligor, Mihai Götherström, Anders Gourichon, Lionel Groenen, Martien A M Helmer, Daniel Hongo, Hitomi Horwitz, Liora K Irving-Pease, Evan K Lebrasseur, Ophélie Lesur, Joséphine Malone, Caroline Manaseryan, Ninna Marciniak, Arkadiusz Martlew, Holley Mashkour, Marjan Matthews, Roger Matuzeviciute, Giedre Motuzaite Maziar, Sepideh Meijaard, Erik McGovern, Tom Megens, Hendrik-Jan Miller, Rebecca Mohaseb, Azadeh Fatemeh Orschiedt, Jörg Orton, David https://orcid.org/0000-0003-4069-8004 Papathanasiou, Anastasia Pearson, Mike Parker Pinhasi, Ron Radmanović, Darko Ricaut, François-Xavier Richards, Mike Sabin, Richard Sarti, Lucia Schier, Wolfram Sheikhi, Shiva Stephan, Elisabeth Stewart, John R Stoddart, Simon Tagliacozzo, Antonio Tasić, Nenad Trantalidou, Katerina Tresset, Anne Valdiosera, Cristina van den Hurk, Youri Van Poucke, Sophie Vigne, Jean-Denis Yanevich, Alexander Zeeb-Lanz, Andrea Triantafyllidis, Alexandros Gilbert, M Thomas P Schibler, Jörg Rowley-Conwy, Peter Zeder, Melinda Peters, Joris Cucchi, Thomas Bradley, Daniel G Dobney, Keith Burger, Joachim Evin, Allowen Girdland-Flink, Linus Larson, Greger
Copyright, Publisher and Additional Information:	Copyright © 2019 the Author(s). Published by PNAS.
Dates:	Accepted: 21 June 2019 Published (online): 12 August 2019 Published: 27 August 2019
Institution:	The University of York
Academic Units:	The University of York > Faculty of Arts and Humanities (York) > Archaeology (York)
Depositing User:	Pure (York)
Date Deposited:	10 Sep 2019 08:40
Last Modified:	10 Apr 2025 23:22
Published Version:	https://doi.org/10.1073/pnas.1901169116
Status:	Published
Refereed:	Yes
Identification Number:	10.1073/pnas.1901169116
Open Archives Initiative ID (OAI ID):	oai:eprints.whiterose.ac.uk:150689