publication . Article . Other literature type . 2019

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

Vincent M. Battista; Benjamin S. Arbuckle; Holley Martlew; Melinda A. Zeder; Rebecca Miller; Andrea Zeeb-Lanz; Laurent A. F. Frantz; Laurent A. F. Frantz; Jörg Schibler; Valentin Dumitrascu; ...
Open Access English
  • Published: 27 Aug 2019
  • Publisher: HAL CCSD
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...
Subjects
free text keywords: [SHS]Humanities and Social Sciences, [SHS.ANTHRO-BIO]Humanities and Social Sciences/Biological anthropology, Biological Sciences, Anthropology, domestication, evolution, gene flow, Neolithic, /dk/atira/pure/subjectarea/asjc/1000, General, Animals, DNA, Mitochondrial, Europe, History, Ancient, Middle East, Skin Pigmentation, Swine, DNA, Ancient, Phylogeny, [SDV.GEN]Life Sciences [q-bio]/Genetics, [SHS.ARCHEO]Humanities and Social Sciences/Archaeology and Prehistory, [SDV.EE]Life Sciences [q-bio]/Ecology, environment, [SDV.BBM.BC]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Biomolecules [q-bio.BM], domestication, evolution, gene flow, Neolithic, DOMESTIC PIGS, SPREAD, WILD, INTROGRESSION, HISTORY, BREEDS, LONG, SIZE, DNA, Multidisciplinary, /dk/atira/pure/researchoutput/pubmedpublicationtype/D016428, Journal Article, /dk/atira/pure/researchoutput/pubmedpublicationtype/D016456, Historical Article, /dk/atira/pure/researchoutput/pubmedpublicationtype/D013485, Research Support, Non-U.S. Gov't, /dk/atira/pure/researchoutput/pubmedpublicationtype/D013486, Research Support, U.S. Gov't, Non-P.H.S., Phylogenetics, Coat, Locus (genetics), Zoology, Mitochondrial DNA, Haplotype, Biology
Funded by
NSF| Northern Narratives: Social and Geographical Accounts from Norway, Iceland and Canada
Project
  • Funder: National Science Foundation (NSF)
  • Project Code: 0638897
  • Funding stream: Directorate for Geosciences | Division of Polar Programs
,
NSF| Tephra layers and early warning signals for critical transitions
Project
  • Funder: National Science Foundation (NSF)
  • Project Code: 1249313
  • Funding stream: Directorate for Geosciences | Division of Polar Programs
,
NSF| The Origins of Equid Domestication
Project
  • Funder: National Science Foundation (NSF)
  • Project Code: 1311551
  • Funding stream: Directorate for Social, Behavioral & Economic Sciences | Division of Behavioral and Cognitive Sciences
,
NSF| Conference on Global Long Term Human Ecodyamics
Project
  • Funder: National Science Foundation (NSF)
  • Project Code: 0947862
  • Funding stream: Directorate for Geosciences | Division of Polar Programs
,
NSF| Doctoral Dissertation Improvement Grant: Social Complexity and the Evolution of Sheep and Goat Pastoralism in Central Anatolia
Project
  • Funder: National Science Foundation (NSF)
  • Project Code: 0530699
  • Funding stream: Directorate for Social, Behavioral & Economic Sciences | Division of Behavioral and Cognitive Sciences
Communities
Digital Humanities and Cultural Heritage
71 references, page 1 of 5

This open access article is distributed under Creative Commons Attribution License 4.0 (CC BY).

Data deposition: The reads from both ancient and modern samples have been deposited at the European Nucleotide Archive (ENA) (project no. PRJEB30282).

1L.A.F.F., J.H., and A.T.L. contributed equally to this work.

2To whom correspondence may be addressed. Email: laurent.frantz@qmul.ac.uk or greger.larson@arch.ox.ac.uk.

3Deceased March 20, 2017.

4Deceased January 17, 2019.

This article contains supporting information online at www.pnas.org/lookup/suppl/doi:10.

1073/pnas.1901169116/-/DCSupplemental.

Published online August 12, 2019.

ACKNOWLEDGMENTS. We thank L. Orlando and J. Schraiber for their valuable comments and R. Redding, A. Dinu, A. Devault, A. Mahforozi, A. Hammon, A. McMahon, B. Wilkens, C. Commenge, C. Minniti, D. Kennet, D. Mol, D. Binder, E. Vika, G. Bayle, H.-J. Döhle, I. Dubset, I. Fiore, J. de Grossi Mazzorin, J. Enk, J. Glimmerveen, J. Courtin, J. L. Arsuaga, J. Lev-Tov, K. Aaris-Sørensen, K. Post, M. Özdo g˘an, M. Özbas¸aran, P. Miracle, R. Portela-Miguez, R. Meadow, S. Davis, S. Bréhard, S. Hanik, U. Albarella, T. O'Connor, S. Hansen, M. Toderas, P. Bogucki, D. Lo Vetro, R. Andreescu, P. Mirea, D. Popovici, C. Micu, I. M. Chicideanu, P. Damian, C. Becker, R. Gleser, S. Hansen, R. Hofmann, R. Krauss, M. Lichardus-Itten, N. Müller-Scheessel, B. Weninger, and I. Österholm for providing material and support. We also thank the team working at the site of As¸ıklı Höyük: M. Özbas¸aran, H. Buitenhuis, N. Munro, N. Pöllath, and M. Stiner. For the Iranian material, we thank Eberhard Sauer, Jebreil Nokandeh (Iranian Cultural Heritage Handicraft and Tourism Organization) and European Research Council (ERC) Persia and Neighbours (ERC-2011-ADG_20110406). We also thank the staff of the Danish National High-Throughput Sequencing Centre for assistance in data generation. We acknowledge the University of Oxford Advanced Research Computing facility for providing computing time. L.A.F.F. was supported by the Wellcome Trust (Grant 210119/Z/18/Z) and by Wolfson College (University of Oxford).

L.A.F.F., J.H., A. Linderholm, K.D., and G.L. were supported by the ERC (Grant ERC-2013-StG-337574-UNDEAD), Natural Environmental Research Council (Grants NE/K005243/1 and NE/K003259/1), or both. M.T.P.G. was supported by the ERC (Grant ERC-2015-CoG-681396-Extinction Genomics). D.B., V.E.M., and K.D. were supported by the ERC (Grant 295729-CodeX). A. Ba˘ l a˘s¸escu and V. Dumitrascu (Romanian archaeozoological research) were supported by the Romanian National Authority for Scientific Research (Project PN‐III-P4‐ID‐PCE‐2016‐0676) T.M.

was supported by the National Geographic Society, Icelandic Centre for Research (RANNÍS), and US National Science Foundation (NSF) (Grants 0732327, 1140106, 1119354, 1203823, 1203268, 1202692, 1249313, 0527732, 0638897, 0629500, 0947862, and 1446308). J.P. was supported by the General Directorate of Antiquities in Turkey and the Deutsche Forschungsgemeinschaft (Grant PE 424/10,1-3).

C.V. and J.-M.C. were supported by the Atapuerca Project (CGL2015-65387-C3-2-P MINECO-FEDER, Ministerio de Economía y Competitividad, Spain), the Junta de Castilla y León, and the Fundación Atapuerca. L.d.P. was supported by the ERC (Grant ERC-2013-CoG-614725-PATHPHYLODYN). M.C. was supported by the NSF (Grants 0732327 and 1202692). M.G. was supported by a grant from the Romanian National Authority for Scientific Research (Project PN-II-RU-TE-2012-3-0461).

V. Dimitrijevic was supported by the Ministry of Culture and Information and the Ministry of Education and Science of the Republic of Serbia (Project III 47001). B.A.

was supported by the NSF (Grants BCS-0530699 and BCS-1311551), the National Geographic Society, and the American Research Institute in Turkey. C.D. was supported by the Fundação para a Ciência e Tecnologia (Grant SFRH/BPD/ 108326/2015). A.S. and C.G. were supported by the German Archaeological Institute, Berlin (Research Cluster 1, Project: Genetische Studien zur Zucht- und Nutzungsgeschichte der ältesten Wirtschaftshaustiere). L.G.-F. was supported by the British Academy and Leverhulme Trust (Grant SG143331). A.M. was supported by the National Science Centre, Poland (Grant 2017/25/B/HS3/01242). N. Boivin, R. Crassard, M. Petraglia, Eds. (Cambridge University Press, 2017), pp. 261-303.

71 references, page 1 of 5
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...
Subjects
free text keywords: [SHS]Humanities and Social Sciences, [SHS.ANTHRO-BIO]Humanities and Social Sciences/Biological anthropology, Biological Sciences, Anthropology, domestication, evolution, gene flow, Neolithic, /dk/atira/pure/subjectarea/asjc/1000, General, Animals, DNA, Mitochondrial, Europe, History, Ancient, Middle East, Skin Pigmentation, Swine, DNA, Ancient, Phylogeny, [SDV.GEN]Life Sciences [q-bio]/Genetics, [SHS.ARCHEO]Humanities and Social Sciences/Archaeology and Prehistory, [SDV.EE]Life Sciences [q-bio]/Ecology, environment, [SDV.BBM.BC]Life Sciences [q-bio]/Biochemistry, Molecular Biology/Biomolecules [q-bio.BM], domestication, evolution, gene flow, Neolithic, DOMESTIC PIGS, SPREAD, WILD, INTROGRESSION, HISTORY, BREEDS, LONG, SIZE, DNA, Multidisciplinary, /dk/atira/pure/researchoutput/pubmedpublicationtype/D016428, Journal Article, /dk/atira/pure/researchoutput/pubmedpublicationtype/D016456, Historical Article, /dk/atira/pure/researchoutput/pubmedpublicationtype/D013485, Research Support, Non-U.S. Gov't, /dk/atira/pure/researchoutput/pubmedpublicationtype/D013486, Research Support, U.S. Gov't, Non-P.H.S., Phylogenetics, Coat, Locus (genetics), Zoology, Mitochondrial DNA, Haplotype, Biology
Funded by
NSF| Northern Narratives: Social and Geographical Accounts from Norway, Iceland and Canada
Project
  • Funder: National Science Foundation (NSF)
  • Project Code: 0638897
  • Funding stream: Directorate for Geosciences | Division of Polar Programs
,
NSF| Tephra layers and early warning signals for critical transitions
Project
  • Funder: National Science Foundation (NSF)
  • Project Code: 1249313
  • Funding stream: Directorate for Geosciences | Division of Polar Programs
,
NSF| The Origins of Equid Domestication
Project
  • Funder: National Science Foundation (NSF)
  • Project Code: 1311551
  • Funding stream: Directorate for Social, Behavioral & Economic Sciences | Division of Behavioral and Cognitive Sciences
,
NSF| Conference on Global Long Term Human Ecodyamics
Project
  • Funder: National Science Foundation (NSF)
  • Project Code: 0947862
  • Funding stream: Directorate for Geosciences | Division of Polar Programs
,
NSF| Doctoral Dissertation Improvement Grant: Social Complexity and the Evolution of Sheep and Goat Pastoralism in Central Anatolia
Project
  • Funder: National Science Foundation (NSF)
  • Project Code: 0530699
  • Funding stream: Directorate for Social, Behavioral & Economic Sciences | Division of Behavioral and Cognitive Sciences
Communities
Digital Humanities and Cultural Heritage
71 references, page 1 of 5

This open access article is distributed under Creative Commons Attribution License 4.0 (CC BY).

Data deposition: The reads from both ancient and modern samples have been deposited at the European Nucleotide Archive (ENA) (project no. PRJEB30282).

1L.A.F.F., J.H., and A.T.L. contributed equally to this work.

2To whom correspondence may be addressed. Email: laurent.frantz@qmul.ac.uk or greger.larson@arch.ox.ac.uk.

3Deceased March 20, 2017.

4Deceased January 17, 2019.

This article contains supporting information online at www.pnas.org/lookup/suppl/doi:10.

1073/pnas.1901169116/-/DCSupplemental.

Published online August 12, 2019.

ACKNOWLEDGMENTS. We thank L. Orlando and J. Schraiber for their valuable comments and R. Redding, A. Dinu, A. Devault, A. Mahforozi, A. Hammon, A. McMahon, B. Wilkens, C. Commenge, C. Minniti, D. Kennet, D. Mol, D. Binder, E. Vika, G. Bayle, H.-J. Döhle, I. Dubset, I. Fiore, J. de Grossi Mazzorin, J. Enk, J. Glimmerveen, J. Courtin, J. L. Arsuaga, J. Lev-Tov, K. Aaris-Sørensen, K. Post, M. Özdo g˘an, M. Özbas¸aran, P. Miracle, R. Portela-Miguez, R. Meadow, S. Davis, S. Bréhard, S. Hanik, U. Albarella, T. O'Connor, S. Hansen, M. Toderas, P. Bogucki, D. Lo Vetro, R. Andreescu, P. Mirea, D. Popovici, C. Micu, I. M. Chicideanu, P. Damian, C. Becker, R. Gleser, S. Hansen, R. Hofmann, R. Krauss, M. Lichardus-Itten, N. Müller-Scheessel, B. Weninger, and I. Österholm for providing material and support. We also thank the team working at the site of As¸ıklı Höyük: M. Özbas¸aran, H. Buitenhuis, N. Munro, N. Pöllath, and M. Stiner. For the Iranian material, we thank Eberhard Sauer, Jebreil Nokandeh (Iranian Cultural Heritage Handicraft and Tourism Organization) and European Research Council (ERC) Persia and Neighbours (ERC-2011-ADG_20110406). We also thank the staff of the Danish National High-Throughput Sequencing Centre for assistance in data generation. We acknowledge the University of Oxford Advanced Research Computing facility for providing computing time. L.A.F.F. was supported by the Wellcome Trust (Grant 210119/Z/18/Z) and by Wolfson College (University of Oxford).

L.A.F.F., J.H., A. Linderholm, K.D., and G.L. were supported by the ERC (Grant ERC-2013-StG-337574-UNDEAD), Natural Environmental Research Council (Grants NE/K005243/1 and NE/K003259/1), or both. M.T.P.G. was supported by the ERC (Grant ERC-2015-CoG-681396-Extinction Genomics). D.B., V.E.M., and K.D. were supported by the ERC (Grant 295729-CodeX). A. Ba˘ l a˘s¸escu and V. Dumitrascu (Romanian archaeozoological research) were supported by the Romanian National Authority for Scientific Research (Project PN‐III-P4‐ID‐PCE‐2016‐0676) T.M.

was supported by the National Geographic Society, Icelandic Centre for Research (RANNÍS), and US National Science Foundation (NSF) (Grants 0732327, 1140106, 1119354, 1203823, 1203268, 1202692, 1249313, 0527732, 0638897, 0629500, 0947862, and 1446308). J.P. was supported by the General Directorate of Antiquities in Turkey and the Deutsche Forschungsgemeinschaft (Grant PE 424/10,1-3).

C.V. and J.-M.C. were supported by the Atapuerca Project (CGL2015-65387-C3-2-P MINECO-FEDER, Ministerio de Economía y Competitividad, Spain), the Junta de Castilla y León, and the Fundación Atapuerca. L.d.P. was supported by the ERC (Grant ERC-2013-CoG-614725-PATHPHYLODYN). M.C. was supported by the NSF (Grants 0732327 and 1202692). M.G. was supported by a grant from the Romanian National Authority for Scientific Research (Project PN-II-RU-TE-2012-3-0461).

V. Dimitrijevic was supported by the Ministry of Culture and Information and the Ministry of Education and Science of the Republic of Serbia (Project III 47001). B.A.

was supported by the NSF (Grants BCS-0530699 and BCS-1311551), the National Geographic Society, and the American Research Institute in Turkey. C.D. was supported by the Fundação para a Ciência e Tecnologia (Grant SFRH/BPD/ 108326/2015). A.S. and C.G. were supported by the German Archaeological Institute, Berlin (Research Cluster 1, Project: Genetische Studien zur Zucht- und Nutzungsgeschichte der ältesten Wirtschaftshaustiere). L.G.-F. was supported by the British Academy and Leverhulme Trust (Grant SG143331). A.M. was supported by the National Science Centre, Poland (Grant 2017/25/B/HS3/01242). N. Boivin, R. Crassard, M. Petraglia, Eds. (Cambridge University Press, 2017), pp. 261-303.

71 references, page 1 of 5
Any information missing or wrong?Report an Issue