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 1 Michelle Alexander Anna Linderholm 2 Victoria Mullin Kevin Daly 3 Vincent Battista Max Price Kurt Gron Panoraia Alexandri Rose-Marie Arbogast 4 Benjamin Arbuckle 5 Adrian Bӑlӑşescu Ross Barnett 6 László Bartosiewicz 7 Gennady Baryshnikov Clive Bonsall Dušan Borić 8 Adina Boroneanţ 9 Jelena Bulatović Canan Çakirlar José-Miguel Carretero John Chapman Mike Church Richard Crooijmans 10 Bea de Cupere Cleia Detry 11 Vesna Dimitrijevic Valentin Dumitraşcu Louis Du Plessis Ceiridwen Edwards Cevdet Merih Erek Aslı Erim-Özdoğan Anton Ervynck Domenico Fulgione 12 Mihai Gligor Anders Gotherstrom 13 Lionel Gourichon 14 Martien A.M. Groenen 15 Daniel Helmer 16 Hitomi Hongo Liora Horwitz Evan Irving-Pease Ophélie Lebrasseur 17 Joséphine Lesur 18 Caroline Malone Ninna Manaseryan Arkadiusz Marciniak Holley Martlew Marjan Mashkour 18 Roger Matthews Giedre Motuzaite Matuzeviciute Sepideh Maziar 19 Erik Meijaard Tom Mcgovern Hendrik-Jan Megens Rebecca Miller 20 Azadeh Fatemeh Mohaseb Jörg Orschiedt David Orton 21 Anastasia Papathanasiou Mike Parker Pearson Ron Pinhasi 22 Darko Radmanović François-Xavier Ricaut 23 Mike Richards 24 Richard Sabin Lucia Sarti Wolfram Schier Shiva Sheikhi Elisabeth Stephan John Stewart 25 Simon Stoddart 26 Antonio Tagliacozzo 27 Nenad Tasić Katerina Trantalidou Anne Tresset 18 Cristina Valdiosera Youri van den Hurk 28 Sophie van Poucke Jean-Denis Vigne 18 Alexander Yanevich Andrea Zeeb-Lanz Alexandros Triantafyllidis M. Thomas P. Gilbert 29 Jörg Schibler 30 Peter Rowley-Conwy Melinda Zeder Joris Peters 31 Thomas Cucchi 18 Daniel Bradley Keith Dobney 32 Joachim Burger Allowen Evin 33 Linus Girdland-Flink Greger Larson 17
CEPAM - Culture et Environnements, Préhistoire, Antiquité, Moyen-Age
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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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 , National Academy of Sciences, 2019, 116 (35), pp.17231-17238. ⟨10.1073/pnas.1901169116⟩. ⟨hal-02322137⟩



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