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Journal Articles Proceedings of the National Academy of Sciences of the United States of America Year : 2019

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

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Laurent Frantz
James Haile
Audrey Lin
Amelie Scheu
  • Function : Author
Christina Geörg
  • Function : Author
Michelle Alexander
  • Function : Author
Victoria Mullin
  • Function : Author
Vincent Battista
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Max Price
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Kurt Gron
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Panoraia Alexandri
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Adrian Bӑlӑşescu
  • Function : Author
Gennady Baryshnikov
  • Function : Author
Clive Bonsall
  • Function : Author
Jelena Bulatović
  • Function : Author
Canan Çakirlar
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José-Miguel Carretero
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John Chapman
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Mike Church
  • Function : Author
Bea de Cupere
Cleia Detry
  • Function : Author
Vesna Dimitrijevic
  • Function : Author
Valentin Dumitraşcu
  • Function : Author
Louis Du Plessis
Ceiridwen Edwards
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Cevdet Merih Erek
  • Function : Author
Asli Erim-Özdoğan
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Anton Ervynck
  • Function : Author
Mihai Gligor
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Hitomi Hongo
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Liora Horwitz
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Evan Irving-Pease
  • Function : Author
Ophélie Lebrasseur
Caroline Malone
  • Function : Author
Ninna Manaseryan
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Arkadiusz Marciniak
  • Function : Author
Holley Martlew
  • Function : Author
Roger Matthews
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Giedre Motuzaite Matuzeviciute
  • Function : Author
Erik Meijaard
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Tom Mcgovern
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Hendrik-Jan Megens
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Azadeh Fatemeh Mohaseb
Jörg Orschiedt
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Anastasia Papathanasiou
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Mike Parker Pearson
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Darko Radmanović
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Mike Richards
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Richard Sabin
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Lucia Sarti
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Wolfram Schier
  • Function : Author
Shiva Sheikhi
  • Function : Author
Elisabeth Stephan
  • Function : Author
Nenad Tasić
  • Function : Author
Katerina Trantalidou
  • Function : Author
Cristina Valdiosera
  • Function : Author
Sophie van Poucke
  • Function : Author
Alexander Yanevich
  • Function : Author
Andrea Zeeb-Lanz
  • Function : Author
Alexandros Triantafyllidis
  • Function : Author
Peter Rowley-Conwy
  • Function : Author
Melinda Zeder
  • Function : Author
Daniel Bradley
Joachim Burger
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Linus Girdland-Flink
  • Function : Author
Greger Larson

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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Dates and versions

hal-02322137 , version 1 (21-10-2019)

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Laurent Frantz, James Haile, Audrey Lin, Amelie Scheu, Christina Geörg, et al.. 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, 2019, 116 (35), pp.17231-17238. ⟨10.1073/pnas.1901169116⟩. ⟨hal-02322137⟩
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