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

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Author(s)

  • Laurent A F Frantz
  • James Haile
  • Audrey T Lin
  • Amelie Scheu
  • Christina Geörg
  • Norbert Benecke
  • Anna Linderholm
  • Victoria E Mullin
  • Kevin G Daly
  • Vincent M Battista
  • Max Price
  • Kurt J 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 J Edwards
  • Cevdet Merih Erek
  • Aslı Erim-Özdoğan
  • Anton Ervynck
  • Domenico Fulgione
  • Mihai Gligor
  • Anders Götherström
  • Lionel Gourichon
  • Martien A M Groenen
  • Daniel Helmer
  • Hitomi Hongo
  • Liora K Horwitz
  • Evan K 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 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 R 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 G Bradley
  • Keith Dobney
  • Joachim Burger
  • Allowen Evin
  • Linus Girdland-Flink
  • Greger Larson

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Publication details

JournalProceedings of the National Academy of Sciences of the United States of America
DateAccepted/In press - 21 Jun 2019
DateE-pub ahead of print - 12 Aug 2019
DatePublished (current) - 27 Aug 2019
Issue number35
Volume116
Number of pages8
Pages (from-to)17231-17238
Early online date12/08/19
Original languageEnglish

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.

Bibliographical note

Copyright © 2019 the Author(s). Published by PNAS.

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