Ancient pigs reveal a near-complete genomic turnover following their introduction to Europe
Authors: Frantz Laurent A. F. , Haile James , Lin Audrey T. , Scheu Amelie , Geörg Christina , Benecke Norbert , Alexander Michelle , 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 , 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 
Published: August 2019

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.