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.
| Original language | English |
|---|---|
| Pages (from-to) | 17231-17238 |
| Number of pages | 8 |
| Journal | Proceedings of the National Academy of Sciences of the United States of America |
| Volume | 116 |
| Issue number | 35 |
| DOIs | |
| Publication status | Published - 27 Aug 2019 |
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Ancient pigs reveal a near-complete genomic turnover following their introduction to Europe. / 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; Bǎlǎşescu, 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-Özdoǧan, Asli; 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.
In: Proceedings of the National Academy of Sciences of the United States of America, Vol. 116, No. 35, 27.08.2019, p. 17231-17238.Research output: Contribution to journal › Article
TY - JOUR
T1 - Ancient pigs reveal a near-complete genomic turnover following their introduction to Europe
AU - Frantz, Laurent A.F.
AU - Haile, James
AU - Lin, Audrey T.
AU - Scheu, Amelie
AU - Geörg, Christina
AU - Benecke, Norbert
AU - Alexander, Michelle
AU - Linderholm, Anna
AU - Mullin, Victoria E.
AU - Daly, Kevin G.
AU - Battista, Vincent M.
AU - Price, Max
AU - Gron, Kurt J.
AU - Alexandri, Panoraia
AU - Arbogast, Rose Marie
AU - Arbuckle, Benjamin
AU - Bǎlǎşescu, Adrian
AU - Barnett, Ross
AU - Bartosiewicz, László
AU - Baryshnikov, Gennady
AU - Bonsall, Clive
AU - Borić, Dušan
AU - Boroneanţ, Adina
AU - Bulatović, Jelena
AU - Çakirlar, Canan
AU - Carretero, José Miguel
AU - Chapman, John
AU - Church, Mike
AU - Crooijmans, Richard
AU - De Cupere, Bea
AU - Detry, Cleia
AU - Dimitrijevic, Vesna
AU - Dumitraşcu, Valentin
AU - Du Plessis, Louis
AU - Edwards, Ceiridwen J.
AU - Erek, Cevdet Merih
AU - Erim-Özdoǧan, Asli
AU - Ervynck, Anton
AU - Fulgione, Domenico
AU - Gligor, Mihai
AU - Götherström, Anders
AU - Gourichon, Lionel
AU - Groenen, Martien A.M.
AU - Helmer, Daniel
AU - Hongo, Hitomi
AU - Horwitz, Liora K.
AU - Irving-Pease, Evan K.
AU - Lebrasseur, Ophélie
AU - Lesur, Joséphine
AU - Malone, Caroline
AU - Manaseryan, Ninna
AU - Marciniak, Arkadiusz
AU - Martlew, Holley
AU - Mashkour, Marjan
AU - Matthews, Roger
AU - Matuzeviciute, Giedre Motuzaite
AU - Maziar, Sepideh
AU - Meijaard, Erik
AU - McGovern, Tom
AU - Megens, Hendrik Jan
AU - Miller, Rebecca
AU - Mohaseb, Azadeh Fatemeh
AU - Orschiedt, Jörg
AU - Orton, David
AU - Papathanasiou, Anastasia
AU - Pearson, Mike Parker
AU - Pinhasi, Ron
AU - Radmanović, Darko
AU - Ricaut, François Xavier
AU - Richards, Mike
AU - Sabin, Richard
AU - Sarti, Lucia
AU - Schier, Wolfram
AU - Sheikhi, Shiva
AU - Stephan, Elisabeth
AU - Stewart, John R.
AU - Stoddart, Simon
AU - Tagliacozzo, Antonio
AU - Tasić, Nenad
AU - Trantalidou, Katerina
AU - Tresset, Anne
AU - Valdiosera, Cristina
AU - Van Den Hurk, Youri
AU - Van Poucke, Sophie
AU - Vigne, Jean Denis
AU - Yanevich, Alexander
AU - Zeeb-Lanz, Andrea
AU - Triantafyllidis, Alexandros
AU - Gilbert, M. Thomas P.
AU - Schibler, Jörg
AU - Rowley-Conwy, Peter
AU - Zeder, Melinda
AU - Peters, Joris
AU - Cucchi, Thomas
AU - Bradley, Daniel G.
AU - Dobney, Keith
AU - Burger, Joachim
AU - Evin, Allowen
AU - Girdland-Flink, Linus
AU - Larson, Greger
PY - 2019/8/27
Y1 - 2019/8/27
N2 - 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.
AB - 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.
KW - Domestication
KW - Evolution
KW - Gene flow
KW - Neolithic
UR - http://www.scopus.com/inward/record.url?scp=85071714237&partnerID=8YFLogxK
U2 - 10.1073/pnas.1901169116
DO - 10.1073/pnas.1901169116
M3 - Article
VL - 116
SP - 17231
EP - 17238
JO - Proceedings of the National Academy of Sciences of the United States of America
JF - Proceedings of the National Academy of Sciences of the United States of America
SN - 0027-8424
IS - 35
ER -