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

Laurent Frantz; James Haile; Audrey Lin; Amelie Scheu; Christina Geörg; Norbert Benecke; Michelle Alexander; Anna Linderholm; Victoria Mullin; Kevin P Daly; Vincent Battista; Max Price; Kurt Gron; Panoraia Alexandri; Rose-Marie Arbogast; Benjamin Arbuckle; Adrian Bӑlӑşescu; Ross Barnett; László Bartosiewicz; Gennady Baryshnikov; Clive Bonsall; Dušan Borić; Adina Boroneanţ; Jelena Bulatović; Canan Çakirlar; José-Miguel Carretero; John Chapman; Mike Church; Richard Crooijmans; Bea de Cupere; Cleia Detry; Vesna Dimitrijevic; Valentin Dumitraşcu; Louis Du Plessis; Ceiridwen Edwards; Cevdet Merih Erek; Asli Erim-Özdoğan; Anton Ervynck; Domenico Fulgione; Mihai Gligor; Anders Gotherstrom; Lionel Gourichon; Martien A.M. Groenen; Daniel Helmer; Hitomi Hongo; Liora Horwitz; Evan Irving-Pease; Ophélie Lebrasseur; Joséphine Lesur; Caroline Malone; Ninna Manaseryan; Arkadiusz Marciniak; Holley Martlew; Marjan Mashkour; Roger Matthews; Giedre Motuzaite Matuzeviciute; Sepideh Maziar; Erik Meijaard; Tom Mcgovern; Hendrik-Jan Megens; Rebecca M Miller; Azadeh Fatemeh Mohaseb; Jörg Orschiedt; David Orton; Anastasia Papathanasiou; Mike Parker Pearson; Ron Pinhasi; Darko Radmanović; François-Xavier Ricaut; Mike Richards; Richard Sabin; Lucia Sarti; Wolfram Schier; Shiva Sheikhi; Elisabeth Stephan; John Stewart; Simon Stoddart; Antonio Tagliacozzo; Nenad Tasić; Katerina Trantalidou; Anne Tresset; Cristina Valdiosera; Youri van den Hurk; Sophie van Poucke; Jean-Denis Vigne; Alexander Yanevich; Andrea Zeeb-Lanz; Alexandros Triantafyllidis; M. Thomas P. Gilbert; Jörg Schibler; Peter Rowley-Conwy; Melinda Zeder; Joris Peters; Thomas Cucchi; Daniel Bradley; Keith Dobney; Joachim Burger; Allowen Evin; Linus Girdland-Flink; Greger Larson

doi:10.1073/pnas.1901169116

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

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

Laurent Frantz, James Haile, Audrey Lin, Amelie Scheu, Christina Geörg, Norbert Benecke, Michelle Alexander, Anna Linderholm, Victoria Mullin, Kevin P Daly, …

Proceedings of the National Academy of Sciences of the United States of America, Vol.116(35), pp.17231-17238

27/08/2019

DOI: https://doi.org/10.1073/pnas.1901169116

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 Euro-pean 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. domestication | evolution | gene flow | Neolithic

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Title: Ancient pigs reveal a near-complete genomic turnover following their introduction to Europe
Creators - without role: Laurent Frantz - Queen Mary University of London
James Haile - University of Oxford
Audrey Lin - Oxford Archaeology
Amelie Scheu - Johannes Gutenberg University Mainz
Christina Geörg - Johannes Gutenberg University Mainz
Norbert Benecke - Deutsches Archäologisches Institut, Zentrale
Michelle Alexander - University of York
Anna Linderholm - University of Oxford
Victoria Mullin - Natural History Museum
Kevin P Daly - Transplant Research Program [Boston, MA, USA]
Vincent Battista - University of Michigan–Ann Arbor
Max Price - Massachusetts Institute of Technology
Kurt Gron - Durham University
Panoraia Alexandri - Aristotle University of Thessaloniki
Rose-Marie Arbogast - Archéologie et Histoire Ancienne : Méditerranée – Europe
Benjamin Arbuckle - Baylor University
Adrian Bӑlӑşescu
Ross Barnett - Durham University
László Bartosiewicz - Stockholm University
Gennady Baryshnikov - Zoological Institute
Clive Bonsall - University of Edinburgh
Dušan Borić - Columbia University
Adina Boroneanţ - Romanian Academy
Jelena Bulatović - University of Belgrade
Canan Çakirlar
José-Miguel Carretero - Universidad de Burgos
John Chapman - Durham University
Mike Church - Durham University
Richard Crooijmans - Genomics
Bea de Cupere - Institute of Natural Sciences
Cleia Detry - University of Lisbon
Vesna Dimitrijevic - University of Belgrade
Valentin Dumitraşcu
Louis Du Plessis - University of Oxford
Ceiridwen Edwards - University of Huddersfield
Cevdet Merih Erek - Gazi University
Asli Erim-Özdoğan - Çanakkale Onsekiz Mart Üniversitesi
Anton Ervynck - Agence Wallonne du Patrimoine
Domenico Fulgione - University of Naples Federico II
Mihai Gligor - 1 Decembrie 1918 University
Anders Gotherstrom - Stockholm University
Lionel Gourichon - Université Côte d'Azur
Martien A.M. Groenen - Wageningen University & Research
Daniel Helmer - Archéorient
Hitomi Hongo - The Graduate University for Advanced Studies, SOKENDAI
Liora Horwitz - National Library of Israel
Evan Irving-Pease - Oxford Archaeology
Ophélie Lebrasseur - University of Liverpool
Joséphine Lesur - Archéozoologie et Archéobotanique
Caroline Malone - Queen's University Belfast
Ninna Manaseryan - Scientific Center of Zoology and Hydroecology
Arkadiusz Marciniak - Adam Mickiewicz University in Poznań
Holley Martlew - York Archaeological Trust
Marjan Mashkour - Archéozoologie et Archéobotanique
Roger Matthews - University of Reading
Giedre Motuzaite Matuzeviciute - Vilnius University
Sepideh Maziar - Goethe University Frankfurt
Erik Meijaard - International Union for Conservation of Nature
Tom Mcgovern - Hunter College
Hendrik-Jan Megens
Rebecca M Miller - University of Liège
Azadeh Fatemeh Mohaseb - Centre National de la Recherche Scientifique
Jörg Orschiedt - Deutsches Archäologisches Institut, Zentrale
David Orton - University of York
Anastasia Papathanasiou - Hellenic Ministry of Culture and Sports
Mike Parker Pearson - University College London
Ron Pinhasi - University of Vienna
Darko Radmanović - Klinički centar Vojvodine
François-Xavier Ricaut - Anthropologie Moléculaire et Imagerie de Synthèse
Mike Richards - Department of Human Evolution [Leipzig]
Richard Sabin - Natural History Museum
Lucia Sarti - University of Siena
Wolfram Schier - Deutsches Archäologisches Institut, Zentrale
Shiva Sheikhi - Archéozoologie et Archéobotanique
Elisabeth Stephan - Regierungspräsidium Stuttgart
John Stewart - Bournemouth University
Simon Stoddart - University of Cambridge
Antonio Tagliacozzo - Pigorini National Museum of Prehistory and Ethnography
Nenad Tasić - University of Belgrade
Katerina Trantalidou - Hellenic Ministry of Culture and Sports
Anne Tresset - Archéozoologie et Archéobotanique
Cristina Valdiosera - La Trobe University
Youri van den Hurk - Museum of London Archaeology
Sophie van Poucke - Institute of Natural Sciences
Jean-Denis Vigne - BioArchéologie, Interactions Sociétés Environnements
Alexander Yanevich - National Academy of Sciences of Ukraine
Andrea Zeeb-Lanz - Generaldirektion Kulturelles Erbe Rheinland-Pfalz
Alexandros Triantafyllidis - Aristotle University of Thessaloniki
M. Thomas P. Gilbert - Natural History Museum Aarhus
Jörg Schibler - University of Basel
Peter Rowley-Conwy - Durham University
Melinda Zeder - National Museum of Natural History
Joris Peters - Ludwig-Maximilians-Universität München
Thomas Cucchi - Archéozoologie et Archéobotanique
Daniel Bradley - Trinity College Dublin
Keith Dobney - University of Liverpool
Joachim Burger - Johannes Gutenberg University Mainz
Allowen Evin - Université de Montpellier, Institut des Sciences de l'Evolution - Montpellier - ISEM
Linus Girdland-Flink - Liverpool John Moores University
Greger Larson - Oxford Archaeology
Publication Details: Proceedings of the National Academy of Sciences of the United States of America, Vol.116(35), pp.17231-17238
Identifiers: 9934098709311
Academic Unit: Institut des Sciences de l'Evolution - Montpellier - ISEM
Language: English
Resource Type: Journal article
Local Fields: hal-02322137