1
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Sandoval-Castellanos E, Hare AJ, Lin AT, Dimopoulos EA, Daly KG, Geiger S, Mullin VE, Wiechmann I, Mattiangeli V, Lühken G, Zinovieva NA, Zidarov P, Çakırlar C, Stoddart S, Orton D, Bulatović J, Mashkour M, Sauer EW, Horwitz LK, Horejs B, Atici L, Özkaya V, Mullville J, Parker Pearson M, Mainland I, Card N, Brown L, Sharples N, Griffiths D, Allen D, Arbuckle B, Abell JT, Duru G, Mentzer SM, Munro ND, Uzdurum M, Gülçur S, Buitenhuis H, Gladyr E, Stiner MC, Pöllath N, Özbaşaran M, Krebs S, Burger J, Frantz L, Medugorac I, Bradley DG, Peters J. Ancient mitogenomes from Pre-Pottery Neolithic Central Anatolia and the effects of a Late Neolithic bottleneck in sheep ( Ovis aries). Sci Adv 2024; 10:eadj0954. [PMID: 38608027 PMCID: PMC11014441 DOI: 10.1126/sciadv.adj0954] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/06/2023] [Accepted: 03/11/2024] [Indexed: 04/14/2024]
Abstract
Occupied between ~10,300 and 9300 years ago, the Pre-Pottery Neolithic site of Aşıklı Höyük in Central Anatolia went through early phases of sheep domestication. Analysis of 629 mitochondrial genomes from this and numerous sites in Anatolia, southwest Asia, Europe, and Africa produced a phylogenetic tree with excessive coalescences (nodes) around the Neolithic, a potential signature of a domestication bottleneck. This is consistent with archeological evidence of sheep management at Aşıklı Höyük which transitioned from residential stabling to open pasturing over a millennium of site occupation. However, unexpectedly, we detected high genetic diversity throughout Aşıklı Höyük's occupation rather than a bottleneck. Instead, we detected a tenfold demographic bottleneck later in the Neolithic, which caused the fixation of mitochondrial haplogroup B in southwestern Anatolia. The mitochondrial genetic makeup that emerged was carried from the core region of early Neolithic sheep management into Europe and dominates the matrilineal diversity of both its ancient and the billion-strong modern sheep populations.
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Affiliation(s)
- Edson Sandoval-Castellanos
- Population Genomics Group, Department of Veterinary Sciences, LMU Munich, 82152 Martinsried, Germany
- Institute of Palaeoanatomy, Domestication Research and the History of Veterinary Medicine, LMU Munich, 80539 Munich, Germany
| | - Andrew J. Hare
- Smurfit Institute of Genetics, Trinity College Dublin, Dublin D02 PN40, Ireland
| | - Audrey T. Lin
- The Palaeogenomics and Bio-archaeology Research Network, Research Laboratory for Archaeology and History of Art, University of Oxford, Oxford, UK
- Department of Anthropology, National Museum of Natural History, Smithsonian Institution, Washington, DC, 20560 USA
| | - Evangelos A. Dimopoulos
- The Palaeogenomics and Bio-archaeology Research Network, Research Laboratory for Archaeology and History of Art, University of Oxford, Oxford, UK
- Department of Veterinary Medicine, University of Cambridge, Cambridge, UK
| | - Kevin G. Daly
- Smurfit Institute of Genetics, Trinity College Dublin, Dublin D02 PN40, Ireland
- School of Agriculture and Food Science, University College Dublin, Dublin, Ireland
| | - Sheila Geiger
- Institute of Palaeoanatomy, Domestication Research and the History of Veterinary Medicine, LMU Munich, 80539 Munich, Germany
| | - Victoria E. Mullin
- Smurfit Institute of Genetics, Trinity College Dublin, Dublin D02 PN40, Ireland
| | - Ingrid Wiechmann
- Institute of Palaeoanatomy, Domestication Research and the History of Veterinary Medicine, LMU Munich, 80539 Munich, Germany
| | - Valeria Mattiangeli
- Smurfit Institute of Genetics, Trinity College Dublin, Dublin D02 PN40, Ireland
| | - Gesine Lühken
- Institute of Animal Breeding and Genetics, Justus Liebig University of Gießen, Ludwigstr. 21, 35390 Gießen, Germany
| | - Natalia A. Zinovieva
- L.K. Ernst Federal Research Centre for Animal Husbandry, Dubrovitsy, Podolsk, Moscow Region, Russia
| | - Petar Zidarov
- Institute of Prehistory, Early History and Medieval Archaeology, Tübingen University, Tübingen, Germany
| | - Canan Çakırlar
- Institute of Archaeology, University of Groningen, 9712 ER Groningen, Netherlands
| | - Simon Stoddart
- Magdalene College, University of Cambridge, Cambridge CB3 0AG, UK
| | - David Orton
- BioArCh, Department of Archaeology, University of York, York YO10 5NG, UK
| | - Jelena Bulatović
- Department of Historical Studies, University of Gothenburg, BOX 200, 40530 Gothenburg, Sweden
| | - Marjan Mashkour
- Unité Archéozoologie, Archéobotanique, Sociétés Pratiques et Environnements (AASPE), CNRS, Muséum National d’Histoire Naturelle, 75020 Paris, France
| | - Eberhard W. Sauer
- School of History, Classics and Archaeology, University of Edinburgh, Old Medical School, Teviot Place, Edinburgh EH8 9AG, UK
| | - Liora Kolska Horwitz
- National Natural History Collections, Faculty of Life Sciences, The Hebrew University, Jerusalem, Israel
| | - Barbara Horejs
- OeAI, Austrian Academy of Sciences and HEAS, University of Vienna, Vienna, Austria
| | - Levent Atici
- Department of Anthropology, University of Nevada, Las Vegas, NV 89154, USA
| | - Vecihi Özkaya
- Department of Archaeology, Dicle University, Diyarbakir, Türkiye
| | - Jacqui Mullville
- School of History, Archaeology and Religion, Cardiff University, Cardiff CF10 3EU, UK
| | | | - Ingrid Mainland
- The University of the Highlands and Islands Orkney, Kirkwall, UK
| | - Nick Card
- The University of the Highlands and Islands Orkney, Kirkwall, UK
| | | | - Niall Sharples
- School of History, Archaeology and Religion, Cardiff University, Cardiff CF10 3EU, UK
| | - David Griffiths
- University of Oxford, OUDCE, Rewley House, Oxford OX1 2JA, UK
| | - David Allen
- Hampshire Cultural Trust, Chilcomb House, Winchester, SO23 8RB, UK
| | - Benjamin Arbuckle
- Department of Anthropology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Jordan T. Abell
- Department of Geosciences, University of Arizona, Tucson, AZ 85721, USA
| | - Güneş Duru
- Department of Archaeology, Mimar Sinan Fine Arts University, 34381 Şişli/İstanbul, Türkiye
| | - Susan M. Mentzer
- Senckenberg Centre for Human Evolution and Palaeoenvironment, Institute for Archaeological Sciences, Department of Geosciences, Tübingen University, 72074 Tübingen, Germany
| | - Natalie D. Munro
- Department of Anthropology, University of Connecticut, Storrs, CT 06269, USA
| | - Melis Uzdurum
- Department of Archaeology, Ondokuz Mayıs University, 55270 Atakum/Samsun, Türkiye
| | - Sevil Gülçur
- Prehistory Department, Faculty of Letters, Istanbul University, 34134 Istanbul, Türkiye
| | | | - Elena Gladyr
- L.K. Ernst Federal Research Centre for Animal Husbandry, Dubrovitsy, Podolsk, Moscow Region, Russia
| | - Mary C. Stiner
- School of Anthropology, University of Arizona, Tucson, AZ 85721, USA
| | - Nadja Pöllath
- Bavarian Natural History Collections, State Collection of Palaeoanatomy Munich, 80333 Munich, Germany
- ArchaeoBioCenter, LMU Munich, 80539 Munich, Germany
| | - Mihriban Özbaşaran
- Prehistory Department, Faculty of Letters, Istanbul University, 34134 Istanbul, Türkiye
| | - Stefan Krebs
- Laboratory for Functional Genome Analysis (LAFUGA), Gene Center, LMU Munich, Feodor-Lynen-Straße 25, 81377 Munich, Germany
| | - Joachim Burger
- Institute of Organismic and Molecular Evolution (iomE), Johannes Gutenberg University Mainz, 55128 Mainz, Germany
| | - Laurent Frantz
- Palaeogenomics Group, Institute of Palaeoanatomy, Domestication Research and the History of Veterinary Medicine, LMU Munich, 80539 Munich, Germany
- School of Biological and Behavioural Sciences, Queen Mary University of London, London, UK
| | - Ivica Medugorac
- Population Genomics Group, Department of Veterinary Sciences, LMU Munich, 82152 Martinsried, Germany
- ArchaeoBioCenter, LMU Munich, 80539 Munich, Germany
| | - Daniel G. Bradley
- Smurfit Institute of Genetics, Trinity College Dublin, Dublin D02 PN40, Ireland
| | - Joris Peters
- Institute of Palaeoanatomy, Domestication Research and the History of Veterinary Medicine, LMU Munich, 80539 Munich, Germany
- Bavarian Natural History Collections, State Collection of Palaeoanatomy Munich, 80333 Munich, Germany
- ArchaeoBioCenter, LMU Munich, 80539 Munich, Germany
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2
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Arce AN, Cantwell-Jones A, Tansley M, Barnes I, Brace S, Mullin VE, Notton D, Ollerton J, Eatough E, Rhodes MW, Bian X, Hogan J, Hunter T, Jackson S, Whiffin A, Blagoderov V, Broad G, Judd S, Kokkini P, Livermore L, Dixit MK, Pearse WD, Gill RJ. Signatures of increasing environmental stress in bumblebee wings over the past century: Insights from museum specimens. J Anim Ecol 2023; 92:297-309. [PMID: 35978494 PMCID: PMC10086799 DOI: 10.1111/1365-2656.13788] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2021] [Accepted: 06/22/2022] [Indexed: 11/27/2022]
Abstract
Determining when animal populations have experienced stress in the past is fundamental to understanding how risk factors drive contemporary and future species' responses to environmental change. For insects, quantifying stress and associating it with environmental factors has been challenging due to a paucity of time-series data and because detectable population-level responses can show varying lag effects. One solution is to leverage historic entomological specimens to detect morphological proxies of stress experienced at the time stressors emerged, allowing us to more accurately determine population responses. Here we studied specimens of four bumblebee species, an invaluable group of insect pollinators, from five museums collected across Britain over the 20th century. We calculated the degree of fluctuating asymmetry (FA; random deviations from bilateral symmetry) between the right and left forewings as a potential proxy of developmental stress. We: (a) investigated whether baseline FA levels vary between species, and how this compares between the first and second half of the century; (b) determined the extent of FA change over the century in the four bumblebee species, and whether this followed a linear or nonlinear trend; (c) tested which annual climatic conditions correlated with increased FA in bumblebees. Species differed in their baseline FA, with FA being higher in the two species that have recently expanded their ranges in Britain. Overall, FA significantly increased over the century but followed a nonlinear trend, with the increase starting c. 1925. We found relatively warm and wet years were associated with higher FA. Collectively our findings show that FA in bumblebees increased over the 20th century and under weather conditions that will likely increase in frequency with climate change. By plotting FA trends and quantifying the contribution of annual climate conditions on past populations, we provide an important step towards improving our understanding of how environmental factors could impact future populations of wild beneficial insects.
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Affiliation(s)
- Andres N Arce
- Georgina Mace Centre for The Living Planet, Department of Life Sciences, Silwood Park, Imperial College London, Ascot, UK.,School of Engineering, Arts, Science & Technology, University of Suffolk, Ipswich, UK
| | - Aoife Cantwell-Jones
- Georgina Mace Centre for The Living Planet, Department of Life Sciences, Silwood Park, Imperial College London, Ascot, UK
| | - Michael Tansley
- Georgina Mace Centre for The Living Planet, Department of Life Sciences, Silwood Park, Imperial College London, Ascot, UK.,Department of Zoology, University of Oxford, Oxford, UK
| | - Ian Barnes
- Department of Earth Sciences, Natural History Museum, London, UK
| | - Selina Brace
- Department of Earth Sciences, Natural History Museum, London, UK
| | - Victoria E Mullin
- Department of Earth Sciences, Natural History Museum, London, UK.,Smurfit Institute of Genetics, Trinity College Dublin, Dublin, Ireland
| | - David Notton
- Department of Earth Sciences, Natural History Museum, London, UK.,National Museum Scotland, Edinburgh, UK
| | - Jeff Ollerton
- Faculty of Arts, Science and Technology, University of Northampton, Northampton, UK
| | - Emma Eatough
- Georgina Mace Centre for The Living Planet, Department of Life Sciences, Silwood Park, Imperial College London, Ascot, UK
| | - Marcus W Rhodes
- Georgina Mace Centre for The Living Planet, Department of Life Sciences, Silwood Park, Imperial College London, Ascot, UK
| | - Xueni Bian
- Georgina Mace Centre for The Living Planet, Department of Life Sciences, Silwood Park, Imperial College London, Ascot, UK.,Department of Earth Sciences, Natural History Museum, London, UK
| | - James Hogan
- Oxford University Museum of Natural History, Oxford, UK
| | | | - Simon Jackson
- Tullie House Museum and Art Gallery Trust, Cumbria, UK.,Ipswich Museum (Colchester and Ipswich Museums), Ipswich, UK
| | | | | | - Gavin Broad
- Department of Earth Sciences, Natural History Museum, London, UK
| | | | - Phaedra Kokkini
- Department of Earth Sciences, Natural History Museum, London, UK
| | | | - Mahika K Dixit
- Georgina Mace Centre for The Living Planet, Department of Life Sciences, Silwood Park, Imperial College London, Ascot, UK
| | - William D Pearse
- Georgina Mace Centre for The Living Planet, Department of Life Sciences, Silwood Park, Imperial College London, Ascot, UK
| | - Richard J Gill
- Georgina Mace Centre for The Living Planet, Department of Life Sciences, Silwood Park, Imperial College London, Ascot, UK
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3
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Mullin VE, Stephen W, Arce AN, Nash W, Raine C, Notton DG, Whiffin A, Blagderov V, Gharbi K, Hogan J, Hunter T, Irish N, Jackson S, Judd S, Watkins C, Haerty W, Ollerton J, Brace S, Gill RJ, Barnes I. First large‐scale quantification study of DNA preservation in insects from natural history collections using genome‐wide sequencing. Methods Ecol Evol 2022. [DOI: 10.1111/2041-210x.13945] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Victoria E. Mullin
- Department of Earth Sciences The Natural History Museum London UK
- Smurfit Institute of Genetics Trinity College Dublin Dublin Ireland
| | - William Stephen
- Department of Earth Sciences The Natural History Museum London UK
| | - Andres N. Arce
- Georgina Mace Centre for The Living Planet Department of Life Sciences, Silwood Park, Imperial College London Berks UK
- School of Engineering, Arts, Science & Technology University of Suffolk Ipswich UK
| | - Will Nash
- The Earlham Institute Norwich Research Park, Colney Lane Norwich UK
| | - Calum Raine
- The Earlham Institute Norwich Research Park, Colney Lane Norwich UK
| | | | | | | | - Karim Gharbi
- The Earlham Institute Norwich Research Park, Colney Lane Norwich UK
| | - James Hogan
- Oxford University Museum of Natural History Oxford UK
| | | | - Naomi Irish
- The Earlham Institute Norwich Research Park, Colney Lane Norwich UK
| | - Simon Jackson
- Tullie House Museum and Art Gallery Trust Carlisle UK
- Ipswich Museum (Colchester and Ipswich Museums) Ipswich UK
| | | | - Chris Watkins
- The Earlham Institute Norwich Research Park, Colney Lane Norwich UK
| | - Wilfried Haerty
- The Earlham Institute Norwich Research Park, Colney Lane Norwich UK
| | - Jeff Ollerton
- Faculty of Arts, Science and Technology University of Northampton Northampton UK
| | - Selina Brace
- Department of Earth Sciences The Natural History Museum London UK
| | - Richard J. Gill
- Georgina Mace Centre for The Living Planet Department of Life Sciences, Silwood Park, Imperial College London Berks UK
| | - Ian Barnes
- Department of Earth Sciences The Natural History Museum London UK
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4
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Chen N, Ren L, Du L, Hou J, Mullin VE, Wu D, Zhao X, Li C, Huang J, Qi X, Capodiferro MR, Achilli A, Lei C, Chen F, Su B, Dong G, Zhang X. Ancient genomes reveal tropical bovid species in the Tibetan Plateau contributed to the prevalence of hunting game until the late Neolithic. Proc Natl Acad Sci U S A 2020; 117:28150-28159. [PMID: 33077602 PMCID: PMC7668038 DOI: 10.1073/pnas.2011696117] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
Local wild bovids have been determined to be important prey on the northeastern Tibetan Plateau (NETP), where hunting game was a major subsistence strategy until the late Neolithic, when farming lifestyles dominated in the neighboring Loess Plateau. However, the species affiliation and population ecology of these prehistoric wild bovids in the prehistoric NETP remain unknown. Ancient DNA (aDNA) analysis is highly informative in decoding this puzzle. Here, we applied aDNA analysis to fragmented bovid and rhinoceros specimens dating ∼5,200 y B.P. from the Neolithic site of Shannashuzha located in the marginal area of the NETP. Utilizing both whole genomes and mitochondrial DNA, our results demonstrate that the range of the present-day tropical gaur (Bos gaurus) extended as far north as the margins of the NETP during the late Neolithic from ∼29°N to ∼34°N. Furthermore, comparative analysis with zooarchaeological and paleoclimatic evidence indicated that a high summer temperature in the late Neolithic might have facilitated the northward expansion of tropical animals (at least gaur and Sumatran-like rhinoceros) to the NETP. This enriched the diversity of wildlife, thus providing abundant hunting resources for humans and facilitating the exploration of the Tibetan Plateau as one of the last habitats for hunting game in East Asia.
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Affiliation(s)
- Ningbo Chen
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences (CAS), 650223 Kunming, China
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, 712100 Yangling, China
| | - Lele Ren
- School of History and Culture, Lanzhou University, 730000 Lanzhou, China
| | - Linyao Du
- College of Earth and Environmental Sciences, Lanzhou University, 730000 Lanzhou, China
| | - Jiawen Hou
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, 712100 Yangling, China
| | - Victoria E Mullin
- Department of Earth Sciences, Natural History Museum, London SW7 5BD, United Kingdom
| | - Duo Wu
- College of Earth and Environmental Sciences, Lanzhou University, 730000 Lanzhou, China
| | - Xueye Zhao
- Gansu Provincial Institute of Cultural Relics and Archaeology, 730000 Lanzhou, China
| | - Chunmei Li
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences (CAS), 650223 Kunming, China
- Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, 650223 Kunming, China
| | - Jiahui Huang
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences (CAS), 650223 Kunming, China
- Kunming College of Life Science, University of Chinese Academy of Sciences, 100049 Beijing, China
| | - Xuebin Qi
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences (CAS), 650223 Kunming, China
- Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, 650223 Kunming, China
| | | | - Alessandro Achilli
- Dipartimento di Biologia e Biotecnologie "L. Spallanzani," Università di Pavia, 27100 Pavia, Italy
| | - Chuzhao Lei
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, 712100 Yangling, China
| | - Fahu Chen
- CAS Center for Excellence in Tibetan Plateau Earth Sciences, Institute of Tibetan Plateau Research, Chinese Academy of Sciences, 100101 Beijing, China
| | - Bing Su
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences (CAS), 650223 Kunming, China;
- Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, 650223 Kunming, China
| | - Guanghui Dong
- College of Earth and Environmental Sciences, Lanzhou University, 730000 Lanzhou, China;
- CAS Center for Excellence in Tibetan Plateau Earth Sciences, Institute of Tibetan Plateau Research, Chinese Academy of Sciences, 100101 Beijing, China
| | - Xiaoming Zhang
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences (CAS), 650223 Kunming, China;
- Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, 650223 Kunming, China
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5
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Kontopoulos I, Penkman K, Mullin VE, Winkelbach L, Unterländer M, Scheu A, Kreutzer S, Hansen HB, Margaryan A, Teasdale MD, Gehlen B, Street M, Lynnerup N, Liritzis I, Sampson A, Papageorgopoulou C, Allentoft ME, Burger J, Bradley DG, Collins MJ. Screening archaeological bone for palaeogenetic and palaeoproteomic studies. PLoS One 2020; 15:e0235146. [PMID: 32584871 PMCID: PMC7316274 DOI: 10.1371/journal.pone.0235146] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2020] [Accepted: 06/09/2020] [Indexed: 11/18/2022] Open
Abstract
The recovery and analysis of ancient DNA and protein from archaeological bone is time-consuming and expensive to carry out, while it involves the partial or complete destruction of valuable or rare specimens. The fields of palaeogenetic and palaeoproteomic research would benefit greatly from techniques that can assess the molecular quality prior to sampling. To be relevant, such screening methods should be effective, minimally-destructive, and rapid. This study reports results based on spectroscopic (Fourier-transform infrared spectroscopy in attenuated total reflectance [FTIR-ATR]; n = 266), palaeoproteomic (collagen content; n = 226), and palaeogenetic (endogenous DNA content; n = 88) techniques. We establish thresholds for three different FTIR indices, a) the infrared splitting factor [IRSF] that assesses relative changes in bioapatite crystals’ size and homogeneity; b) the carbonate-to-phosphate [C/P] ratio as a relative measure of carbonate content in bioapatite crystals; and c) the amide-to-phosphate ratio [Am/P] for assessing the relative organic content preserved in bone. These thresholds are both extremely reliable and easy to apply for the successful and rapid distinction between well- and poorly-preserved specimens. This is a milestone for choosing appropriate samples prior to genomic and collagen analyses, with important implications for biomolecular archaeology and palaeontology.
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Affiliation(s)
- Ioannis Kontopoulos
- Department of Archaeology, BioArCh, University of York, York, United Kingdom
- * E-mail:
| | - Kirsty Penkman
- Department of Chemistry, BioArCh, University of York, York, United Kingdom
| | - Victoria E. Mullin
- Smurfit Institute of Genetics, Trinity College Dublin, Dublin, Ireland
- Department of Earth Sciences, Natural History Museum, London, United Kingdom
| | - Laura Winkelbach
- Palaeogenetics Group, Institute of Organismic and Molecular Evolution (iomE), Johannes Gutenberg-University Mainz, Mainz, Germany
| | - Martina Unterländer
- Palaeogenetics Group, Institute of Organismic and Molecular Evolution (iomE), Johannes Gutenberg-University Mainz, Mainz, Germany
- Laboratory of Physical Anthropology, Department of History and Ethnology, Democritus University of Thrace, Komotini, Greece
- German Federal Criminal Police Office, Wiesbaden, Germany
| | - Amelie Scheu
- Palaeogenetics Group, Institute of Organismic and Molecular Evolution (iomE), Johannes Gutenberg-University Mainz, Mainz, Germany
| | - Susanne Kreutzer
- Palaeogenetics Group, Institute of Organismic and Molecular Evolution (iomE), Johannes Gutenberg-University Mainz, Mainz, Germany
| | - Henrik B. Hansen
- Centre for GeoGenetics, GLOBE Institute, University of Copenhagen, Copenhagen, Denmark
| | - Ashot Margaryan
- Centre for GeoGenetics, GLOBE Institute, University of Copenhagen, Copenhagen, Denmark
| | - Matthew D. Teasdale
- Smurfit Institute of Genetics, Trinity College Dublin, Dublin, Ireland
- Department of Archaeology, McDonald Institute for Archaeological Research, University of Cambridge, Cambridge, United Kingdom
| | - Birgit Gehlen
- Collaborative Research Centre, project D4, Cologne University, Cologne, Germany
| | - Martin Street
- MONREPOS Archaeological Research Centre and Museum for Human Behavioural Evolution, RGZM Leibniz Research Institute for Archaeology, Neuwied, Germany
| | - Niels Lynnerup
- Unit of Forensic Anthropology, Department of Forensic Medicine, University of Copenhagen, Copenhagen, Denmark
| | - Ioannis Liritzis
- Laboratory of Archaeometry, Department of Mediterranean Studies, University of the Aegean, Rhodes, Greece
- Center on Yellow River Civilization of Henan Province, Key Research Institute of Yellow River Civilization and Sustainable Development and Collaborative Innovation, Henan University, Kaifeng, China
| | - Adamantios Sampson
- Department of Mediterranean Studies, University of the Aegean, Rhodes, Greece
| | - Christina Papageorgopoulou
- Laboratory of Physical Anthropology, Department of History and Ethnology, Democritus University of Thrace, Komotini, Greece
| | - Morten E. Allentoft
- Centre for GeoGenetics, GLOBE Institute, University of Copenhagen, Copenhagen, Denmark
| | - Joachim Burger
- Palaeogenetics Group, Institute of Organismic and Molecular Evolution (iomE), Johannes Gutenberg-University Mainz, Mainz, Germany
| | - Daniel G. Bradley
- Smurfit Institute of Genetics, Trinity College Dublin, Dublin, Ireland
| | - Matthew J. Collins
- Department of Archaeology, McDonald Institute for Archaeological Research, University of Cambridge, Cambridge, United Kingdom
- Centre for Evogenomics, Globe Institute, University of Copenhagen, Copenhagen, Denmark
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6
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Verdugo MP, Mullin VE, Scheu A, Mattiangeli V, Daly KG, Maisano Delser P, Hare AJ, Burger J, Collins MJ, Kehati R, Hesse P, Fulton D, Sauer EW, Mohaseb FA, Davoudi H, Khazaeli R, Lhuillier J, Rapin C, Ebrahimi S, Khasanov M, Vahidi SMF, MacHugh DE, Ertuğrul O, Koukouli-Chrysanthaki C, Sampson A, Kazantzis G, Kontopoulos I, Bulatovic J, Stojanović I, Mikdad A, Benecke N, Linstädter J, Sablin M, Bendrey R, Gourichon L, Arbuckle BS, Mashkour M, Orton D, Horwitz LK, Teasdale MD, Bradley DG. Ancient cattle genomics, origins, and rapid turnover in the Fertile Crescent. Science 2020; 365:173-176. [PMID: 31296769 DOI: 10.1126/science.aav1002] [Citation(s) in RCA: 75] [Impact Index Per Article: 18.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Subscribe] [Scholar Register] [Received: 08/28/2018] [Accepted: 06/14/2019] [Indexed: 11/02/2022]
Abstract
Genome-wide analysis of 67 ancient Near Eastern cattle, Bos taurus, remains reveals regional variation that has since been obscured by admixture in modern populations. Comparisons of genomes of early domestic cattle to their aurochs progenitors identify diverse origins with separate introgressions of wild stock. A later region-wide Bronze Age shift indicates rapid and widespread introgression of zebu, Bos indicus, from the Indus Valley. This process was likely stimulated at the onset of the current geological age, ~4.2 thousand years ago, by a widespread multicentury drought. In contrast to genome-wide admixture, mitochondrial DNA stasis supports that this introgression was male-driven, suggesting that selection of arid-adapted zebu bulls enhanced herd survival. This human-mediated migration of zebu-derived genetics has continued through millennia, altering tropical herding on each continent.
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Affiliation(s)
| | - Victoria E Mullin
- Smurfit Institute of Genetics, Trinity College Dublin, Dublin D02 PN40, Ireland.,Department of Earth Sciences, Natural History Museum, London SW7 5BD, UK
| | - Amelie Scheu
- Smurfit Institute of Genetics, Trinity College Dublin, Dublin D02 PN40, Ireland.,Palaeogenetics Group, Institute of Organismic and Molecular Evolution (iOME), Johannes Gutenberg-University Mainz, 55099 Mainz, Germany
| | - Valeria Mattiangeli
- Smurfit Institute of Genetics, Trinity College Dublin, Dublin D02 PN40, Ireland
| | - Kevin G Daly
- Smurfit Institute of Genetics, Trinity College Dublin, Dublin D02 PN40, Ireland
| | - Pierpaolo Maisano Delser
- Smurfit Institute of Genetics, Trinity College Dublin, Dublin D02 PN40, Ireland.,Department of Zoology, University of Cambridge, Cambridge CB2 3EJ, UK
| | - Andrew J Hare
- Smurfit Institute of Genetics, Trinity College Dublin, Dublin D02 PN40, Ireland
| | - Joachim Burger
- Palaeogenetics Group, Institute of Organismic and Molecular Evolution (iOME), Johannes Gutenberg-University Mainz, 55099 Mainz, Germany
| | - Matthew J Collins
- BioArCh, University of York, York YO10 5DD, UK.,Museum of Natural History, University of Copenhagen, Copenhagen, Denmark
| | - Ron Kehati
- 448 Shvil Hachalav Street, Nir Banim 7952500, Israel
| | - Paula Hesse
- Jewish Studies Program, Department of Classics and Ancient Mediterranean Studies, The Pennsylvania State University, University Park, PA 16802, USA
| | - Deirdre Fulton
- Department of Religion, Baylor University, Waco, TX 76798, USA
| | - Eberhard W Sauer
- School of History, Classics and Archaeology, University of Edinburgh, Edinburgh EH8 9AG, UK
| | - Fatemeh A Mohaseb
- Archéozoologie et Archéobotanique (UMR 7209), CNRS, MNHN, UPMC, Sorbonne Universités, Paris, France.,Bioarchaeology Laboratory, Central Laboratory, University of Tehran, 1417634934 Tehran, Iran
| | - Hossein Davoudi
- Bioarchaeology Laboratory, Central Laboratory, University of Tehran, 1417634934 Tehran, Iran.,Osteology Department, National Museum of Iran, 1136918111 Tehran, Iran.,Department of Archaeology, Faculty of Humanities, Tarbiat Modares University, 111-14115 Tehran, Iran
| | - Roya Khazaeli
- Bioarchaeology Laboratory, Central Laboratory, University of Tehran, 1417634934 Tehran, Iran
| | - Johanna Lhuillier
- Archéorient Université Lyon 2, CNRS UMR 5133, Maison de l'Orient et de la Méditerranée, 69365 Lyon, France
| | - Claude Rapin
- Archéologie d'Orient et d'Occident (AOROC, UMR 8546, CNRS ENS), Centre d'archéologie, 75005 Paris, France
| | - Saeed Ebrahimi
- Faculty of Literature and Humanities, Islamic Azad University, 1711734353 Tehran, Iran
| | - Mutalib Khasanov
- Uzbekistan Institute of Archaeology of the Academy of Sciences of the Republic of Uzbekistan, 703051 Samarkand, Uzbekistan
| | - S M Farhad Vahidi
- Agricultural Biotechnology Research Institute of Iran-North branch (ABRII), Agricultural Research, Education and Extension Organization, 4188958883 Rasht, Iran
| | - David E MacHugh
- Animal Genomics Laboratory, UCD School of Agriculture and Food Science, University College Dublin, Dublin D04 V1W8, Ireland.,UCD Conway Institute of Biomolecular and Biomedical Research, University College Dublin, Dublin D04 V1W8, Ireland
| | - Okan Ertuğrul
- Veterinary Faculty, Ankara University, 06110 Ankara, Turkey
| | - Chaido Koukouli-Chrysanthaki
- Hellenic Ministry of Culture and Sports, Department of Prehistoric and Classical Antiquities, and Museums, Serres 62 122, Greece
| | - Adamantios Sampson
- Department of Mediterranean Studies, University of the Aegean, 85132 Rhodes, Greece
| | - George Kazantzis
- Archaeological Museum of Aeani, 500 04, Kozani, Western Macedonia, Greece
| | | | - Jelena Bulatovic
- Laboratory for Bioarchaeology, Department of Archaeology, University of Belgrade, 11000 Belgrade, Serbia
| | | | - Abdesalam Mikdad
- Institut National des Sciences de l'Archéologie et du Patrimoine de Maroc (INSAP) Hay Riad, Madinat al Ifrane, Rabat Instituts, 10000 Rabat, Morocco
| | - Norbert Benecke
- Department of Natural Sciences, German Archaeological Institute, 14195 Berlin, Germany
| | - Jörg Linstädter
- Deutsches Archäologisches Institut, Kommission für Archäologie Außereuropäischer Kulturen (KAAK), 53173 Bonn, Germany
| | - Mikhail Sablin
- Zoological Institute of the Russian Academy of Sciences, 199034 St Petersburg, Russia
| | - Robin Bendrey
- School of History, Classics and Archaeology, University of Edinburgh, Edinburgh EH8 9AG, UK.,Department of Archaeology, University of Reading, Reading RG6 6AB, UK
| | - Lionel Gourichon
- Université Côte d'Azur, CNRS, CEPAM (UMR 7264), 06357 Nice, France
| | - Benjamin S Arbuckle
- Department of Anthropology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Marjan Mashkour
- Archéozoologie et Archéobotanique (UMR 7209), CNRS, MNHN, UPMC, Sorbonne Universités, Paris, France.,Bioarchaeology Laboratory, Central Laboratory, University of Tehran, 1417634934 Tehran, Iran.,Osteology Department, National Museum of Iran, 1136918111 Tehran, Iran
| | - David Orton
- BioArCh, University of York, York YO10 5DD, UK
| | - Liora Kolska Horwitz
- National Natural History Collections, Faculty of Life Sciences, The Hebrew University, 9190401 Jerusalem, Israel
| | - Matthew D Teasdale
- Smurfit Institute of Genetics, Trinity College Dublin, Dublin D02 PN40, Ireland.,BioArCh, University of York, York YO10 5DD, UK
| | - Daniel G Bradley
- Smurfit Institute of Genetics, Trinity College Dublin, Dublin D02 PN40, Ireland.
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7
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Scott MF, Botigué LR, Brace S, Stevens CJ, Mullin VE, Stevenson A, Thomas MG, Fuller DQ, Mott R. A 3,000-year-old Egyptian emmer wheat genome reveals dispersal and domestication history. Nat Plants 2019; 5:1120-1128. [PMID: 31685951 PMCID: PMC6858886 DOI: 10.1038/s41477-019-0534-5] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/29/2019] [Accepted: 09/22/2019] [Indexed: 05/05/2023]
Abstract
Tetraploid emmer wheat (Triticum turgidum ssp. dicoccon) is a progenitor of the world's most widely grown crop, hexaploid bread wheat (Triticum aestivum), as well as the direct ancestor of tetraploid durum wheat (T. turgidum subsp. turgidum). Emmer was one of the first cereals to be domesticated in the old world; it was cultivated from around 9700 BC in the Levant1,2 and subsequently in south-western Asia, northern Africa and Europe with the spread of Neolithic agriculture3,4. Here, we report a whole-genome sequence from a museum specimen of Egyptian emmer wheat chaff, 14C dated to the New Kingdom, 1130-1000 BC. Its genome shares haplotypes with modern domesticated emmer at loci that are associated with shattering, seed size and germination, as well as within other putative domestication loci, suggesting that these traits share a common origin before the introduction of emmer to Egypt. Its genome is otherwise unusual, carrying haplotypes that are absent from modern emmer. Genetic similarity with modern Arabian and Indian emmer landraces connects ancient Egyptian emmer with early south-eastern dispersals, whereas inferred gene flow with wild emmer from the Southern Levant signals a later connection. Our results show the importance of museum collections as sources of genetic data to uncover the history and diversity of ancient cereals.
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Affiliation(s)
- Michael F Scott
- Genetics Institute, Research Department of Genetics, Evolution and Environment, University College London, London, UK.
| | - Laura R Botigué
- Centre for Research in Agricultural Genomics (CRAG), CSIC-IRTA-UAB-UB, Barcelona, Spain
| | - Selina Brace
- Department of Earth Sciences, Natural History Museum, London, UK
| | - Chris J Stevens
- Institute of Archaeology, University College London, London, UK
| | | | - Alice Stevenson
- Institute of Archaeology, University College London, London, UK
| | - Mark G Thomas
- Genetics Institute, Research Department of Genetics, Evolution and Environment, University College London, London, UK
- Research Department of Genetics, Evolution and Environment, University College London, London, UK
| | - Dorian Q Fuller
- Institute of Archaeology, University College London, London, UK
| | - Richard Mott
- Genetics Institute, Research Department of Genetics, Evolution and Environment, University College London, London, UK.
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8
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Daly KG, Maisano Delser P, Mullin VE, Scheu A, Mattiangeli V, Teasdale MD, Hare AJ, Burger J, Verdugo MP, Collins MJ, Kehati R, Erek CM, Bar-Oz G, Pompanon F, Cumer T, Çakırlar C, Mohaseb AF, Decruyenaere D, Davoudi H, Çevik Ö, Rollefson G, Vigne JD, Khazaeli R, Fathi H, Doost SB, Rahimi Sorkhani R, Vahdati AA, Sauer EW, Azizi Kharanaghi H, Maziar S, Gasparian B, Pinhasi R, Martin L, Orton D, Arbuckle BS, Benecke N, Manica A, Horwitz LK, Mashkour M, Bradley DG. Ancient goat genomes reveal mosaic domestication in the Fertile Crescent. Science 2018; 361:85-88. [PMID: 29976826 DOI: 10.1126/science.aas9411] [Citation(s) in RCA: 96] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2018] [Revised: 02/13/2018] [Accepted: 06/04/2018] [Indexed: 12/16/2022]
Abstract
Current genetic data are equivocal as to whether goat domestication occurred multiple times or was a singular process. We generated genomic data from 83 ancient goats (51 with genome-wide coverage) from Paleolithic to Medieval contexts throughout the Near East. Our findings demonstrate that multiple divergent ancient wild goat sources were domesticated in a dispersed process that resulted in genetically and geographically distinct Neolithic goat populations, echoing contemporaneous human divergence across the region. These early goat populations contributed differently to modern goats in Asia, Africa, and Europe. We also detect early selection for pigmentation, stature, reproduction, milking, and response to dietary change, providing 8000-year-old evidence for human agency in molding genome variation within a partner species.
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Affiliation(s)
- Kevin G Daly
- Smurfit Institute of Genetics, Trinity College Dublin, Dublin 2, Ireland
| | - Pierpaolo Maisano Delser
- Smurfit Institute of Genetics, Trinity College Dublin, Dublin 2, Ireland.,Department of Zoology, University of Cambridge, Cambridge CB2 3EJ, UK
| | - Victoria E Mullin
- Smurfit Institute of Genetics, Trinity College Dublin, Dublin 2, Ireland.,Department of Earth Sciences, Natural History Museum, London SW7 5BD, UK
| | - Amelie Scheu
- Smurfit Institute of Genetics, Trinity College Dublin, Dublin 2, Ireland.,Palaeogenetics Group, Institute of Organismic and Molecular Evolution (iOME), Johannes Gutenberg University Mainz, 55099 Mainz, Germany
| | | | - Matthew D Teasdale
- Smurfit Institute of Genetics, Trinity College Dublin, Dublin 2, Ireland.,BioArCh, University of York, York YO10 5DD, UK
| | - Andrew J Hare
- Smurfit Institute of Genetics, Trinity College Dublin, Dublin 2, Ireland
| | - Joachim Burger
- Palaeogenetics Group, Institute of Organismic and Molecular Evolution (iOME), Johannes Gutenberg University Mainz, 55099 Mainz, Germany
| | | | - Matthew J Collins
- BioArCh, University of York, York YO10 5DD, UK.,Museum of Natural History, University of Copenhagen, Copenhagen, Denmark
| | - Ron Kehati
- National Natural History Collections, Faculty of Life Sciences, The Hebrew University, Jerusalem, Israel
| | | | - Guy Bar-Oz
- Zinman Institute of Archaeology, University of Haifa, Mount Carmel, Haifa, Israel
| | - François Pompanon
- Université Grenoble Alpes, Univ. Savoie Mont Blanc, CNRS, LECA, F-38000 Grenoble, France
| | - Tristan Cumer
- Université Grenoble Alpes, Univ. Savoie Mont Blanc, CNRS, LECA, F-38000 Grenoble, France
| | - Canan Çakırlar
- Groningen Institute of Archaeology, Groningen University, Groningen, Netherlands
| | - Azadeh Fatemeh Mohaseb
- Archéozoologie, Archéobotanique (UMR 7209), CNRS, MNHN, UPMC, Sorbonne Universités, Paris, France.,Archaeozoology section, Archaeometry Laboratory, University of Tehran, Tehran, Iran
| | - Delphine Decruyenaere
- Archéozoologie, Archéobotanique (UMR 7209), CNRS, MNHN, UPMC, Sorbonne Universités, Paris, France
| | - Hossein Davoudi
- Department of Archaeology, Faculty of Humanities, Tarbiat Modares University, Tehran, Iran.,Osteology Department, National Museum of Iran, Tehran, Iran
| | - Özlem Çevik
- Trakya Universitesi, Edebiyat Fakültesi, Arkeoloi Bölümü, Edirne, Turkey
| | - Gary Rollefson
- Department of Anthropology, Whitman College, Walla Walla, WA 99362, USA
| | - Jean-Denis Vigne
- Archéozoologie, Archéobotanique (UMR 7209), CNRS, MNHN, UPMC, Sorbonne Universités, Paris, France
| | - Roya Khazaeli
- Archaeozoology section, Archaeometry Laboratory, University of Tehran, Tehran, Iran
| | - Homa Fathi
- Archaeozoology section, Archaeometry Laboratory, University of Tehran, Tehran, Iran
| | - Sanaz Beizaee Doost
- Archaeozoology section, Archaeometry Laboratory, University of Tehran, Tehran, Iran
| | | | - Ali Akbar Vahdati
- Provincial Office of the Iranian Center for Cultural Heritage, Handicrafts and Tourism Organisation, North Khorassan, Bojnord, Iran
| | - Eberhard W Sauer
- School of History, Classics and Archaeology, University of Edinburgh, William Robertson Wing, Old Medical School, Edinburgh EH8 9AG, UK
| | | | - Sepideh Maziar
- Institut für Archäologische Wissenschaften, Goethe Universität, Frankfurt am Main, Germany
| | - Boris Gasparian
- Institute of Archaeology and Ethnology, National Academy of Sciences of the Republic of Armenia, Yerevan 0025, Republic of Armenia
| | - Ron Pinhasi
- Department of Anthropology, University of Vienna, 1090 Vienna, Austria
| | - Louise Martin
- Institute of Archeology, University College London, London, UK
| | - David Orton
- BioArCh, University of York, York YO10 5DD, UK
| | - Benjamin S Arbuckle
- Department of Anthropology, University of North Carolina, Chapel Hill, NC, USA
| | - Norbert Benecke
- Department of Natural Sciences, German Archaeological Institute, 14195 Berlin, Germany
| | - Andrea Manica
- Department of Zoology, University of Cambridge, Cambridge CB2 3EJ, UK
| | - Liora Kolska Horwitz
- National Natural History Collections, Faculty of Life Sciences, The Hebrew University, Jerusalem, Israel
| | - Marjan Mashkour
- Archéozoologie, Archéobotanique (UMR 7209), CNRS, MNHN, UPMC, Sorbonne Universités, Paris, France.,Archaeozoology section, Archaeometry Laboratory, University of Tehran, Tehran, Iran.,Osteology Department, National Museum of Iran, Tehran, Iran
| | - Daniel G Bradley
- Smurfit Institute of Genetics, Trinity College Dublin, Dublin 2, Ireland.
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9
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Frantz LAF, Mullin VE, Pionnier-Capitan M, Lebrasseur O, Ollivier M, Perri A, Linderholm A, Mattiangeli V, Teasdale MD, Dimopoulos EA, Tresset A, Duffraisse M, McCormick F, Bartosiewicz L, Gál E, Nyerges ÉA, Sablin MV, Bréhard S, Mashkour M, Bălăşescu A, Gillet B, Hughes S, Chassaing O, Hitte C, Vigne JD, Dobney K, Hänni C, Bradley DG, Larson G. Genomic and archaeological evidence suggest a dual origin of domestic dogs. Science 2016. [PMID: 27257259 DOI: 10.1126/science.aaf316] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/08/2023]
Abstract
The geographic and temporal origins of dogs remain controversial. We generated genetic sequences from 59 ancient dogs and a complete (28x) genome of a late Neolithic dog (dated to ~4800 calendar years before the present) from Ireland. Our analyses revealed a deep split separating modern East Asian and Western Eurasian dogs. Surprisingly, the date of this divergence (~14,000 to 6400 years ago) occurs commensurate with, or several millennia after, the first appearance of dogs in Europe and East Asia. Additional analyses of ancient and modern mitochondrial DNA revealed a sharp discontinuity in haplotype frequencies in Europe. Combined, these results suggest that dogs may have been domesticated independently in Eastern and Western Eurasia from distinct wolf populations. East Eurasian dogs were then possibly transported to Europe with people, where they partially replaced European Paleolithic dogs.
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Affiliation(s)
- Laurent A F Frantz
- The Palaeogenomics and Bio-Archaeology Research Network, Research Laboratory for Archaeology and History of Art, University of Oxford, Oxford, UK.
| | - Victoria E Mullin
- Smurfit Institute of Genetics, Trinity College Dublin, Dublin 2, Ireland
| | - Maud Pionnier-Capitan
- CNRS/ENS de Lyon, IGFL, UMR 5242 and French National Platform of Paleogenetics, PALGENE, Ecole Normale Supérieure de Lyon, 46 Allée d'Italie, 69364 Lyon Cedex 07, France/Université Grenoble Alpes, Laboratoire d'Ecologie Alpine (LECA), F-38000 Grenoble, France. CNRS/Muséum National d'Histoire Naturelle/Sorbonne Universités, Archéozoologie, Archéobotanique: Sociétés, Pratiques et Environnement (UMR 7209), CP56, 55 rue Buffon, F-75005 Paris, France
| | - Ophélie Lebrasseur
- The Palaeogenomics and Bio-Archaeology Research Network, Research Laboratory for Archaeology and History of Art, University of Oxford, Oxford, UK
| | - Morgane Ollivier
- CNRS/ENS de Lyon, IGFL, UMR 5242 and French National Platform of Paleogenetics, PALGENE, Ecole Normale Supérieure de Lyon, 46 Allée d'Italie, 69364 Lyon Cedex 07, France/Université Grenoble Alpes, Laboratoire d'Ecologie Alpine (LECA), F-38000 Grenoble, France
| | - Angela Perri
- Department of Human Evolution, Max Planck Institute for Evolutionary Anthropology, 04103 Leipzig, Germany
| | - Anna Linderholm
- The Palaeogenomics and Bio-Archaeology Research Network, Research Laboratory for Archaeology and History of Art, University of Oxford, Oxford, UK. Department of Anthropology, Texas A&M University, College Station, TX 77843-4352, USA
| | | | - Matthew D Teasdale
- Smurfit Institute of Genetics, Trinity College Dublin, Dublin 2, Ireland
| | - Evangelos A Dimopoulos
- The Palaeogenomics and Bio-Archaeology Research Network, Research Laboratory for Archaeology and History of Art, University of Oxford, Oxford, UK. School of Biology, Aristotle University of Thessaloniki, Thessaloniki, Greece
| | - Anne Tresset
- CNRS/Muséum National d'Histoire Naturelle/Sorbonne Universités, Archéozoologie, Archéobotanique: Sociétés, Pratiques et Environnement (UMR 7209), CP56, 55 rue Buffon, F-75005 Paris, France
| | - Marilyne Duffraisse
- CNRS/ENS de Lyon, IGFL, UMR 5242 and French National Platform of Paleogenetics, PALGENE, Ecole Normale Supérieure de Lyon, 46 Allée d'Italie, 69364 Lyon Cedex 07, France/Université Grenoble Alpes, Laboratoire d'Ecologie Alpine (LECA), F-38000 Grenoble, France
| | - Finbar McCormick
- School of Geography, Archaeology and Palaeoecology, Queen's University Belfast, University Road, Belfast, Northern Ireland, UK
| | - László Bartosiewicz
- Osteoarchaeological Research Laboratory, University of Stockholm, Stockholm, Sweden
| | - Erika Gál
- Archaeological Institute, Research Centre for the Humanities, Hungarian Academy of Sciences, Budapest, Hungary
| | - Éva A Nyerges
- Archaeological Institute, Research Centre for the Humanities, Hungarian Academy of Sciences, Budapest, Hungary
| | - Mikhail V Sablin
- Zoological Institute, Russian Academy of Sciences, Universitetskaya Nab. 1, 199034 Saint-Petersburg, Russia
| | - Stéphanie Bréhard
- CNRS/Muséum National d'Histoire Naturelle/Sorbonne Universités, Archéozoologie, Archéobotanique: Sociétés, Pratiques et Environnement (UMR 7209), CP56, 55 rue Buffon, F-75005 Paris, France
| | - Marjan Mashkour
- CNRS/Muséum National d'Histoire Naturelle/Sorbonne Universités, Archéozoologie, Archéobotanique: Sociétés, Pratiques et Environnement (UMR 7209), CP56, 55 rue Buffon, F-75005 Paris, France
| | - Adrian Bălăşescu
- The National Museum of Romanian History, 12 Calea Victoriei, 030026 Bucharest, Romania
| | - Benjamin Gillet
- CNRS/ENS de Lyon, IGFL, UMR 5242 and French National Platform of Paleogenetics, PALGENE, Ecole Normale Supérieure de Lyon, 46 Allée d'Italie, 69364 Lyon Cedex 07, France/Université Grenoble Alpes, Laboratoire d'Ecologie Alpine (LECA), F-38000 Grenoble, France
| | - Sandrine Hughes
- CNRS/ENS de Lyon, IGFL, UMR 5242 and French National Platform of Paleogenetics, PALGENE, Ecole Normale Supérieure de Lyon, 46 Allée d'Italie, 69364 Lyon Cedex 07, France/Université Grenoble Alpes, Laboratoire d'Ecologie Alpine (LECA), F-38000 Grenoble, France
| | - Olivier Chassaing
- CNRS/ENS de Lyon, IGFL, UMR 5242 and French National Platform of Paleogenetics, PALGENE, Ecole Normale Supérieure de Lyon, 46 Allée d'Italie, 69364 Lyon Cedex 07, France/Université Grenoble Alpes, Laboratoire d'Ecologie Alpine (LECA), F-38000 Grenoble, France
| | - Christophe Hitte
- Institut de Génétique et Développement de Rennes, CNRS-UMR6290, Université de Rennes 1, Rennes, France
| | - Jean-Denis Vigne
- CNRS/Muséum National d'Histoire Naturelle/Sorbonne Universités, Archéozoologie, Archéobotanique: Sociétés, Pratiques et Environnement (UMR 7209), CP56, 55 rue Buffon, F-75005 Paris, France
| | - Keith Dobney
- Department of Archaeology, School of Geosciences, University of Aberdeen, St. Mary's, Elphinstone Road, AB24 3UF, UK. Department of Archaeology, Classics and Egyptology, University of Liverpool, 12-14 Abercromby Square, Liverpool L69 7WZ, UK
| | - Catherine Hänni
- CNRS/ENS de Lyon, IGFL, UMR 5242 and French National Platform of Paleogenetics, PALGENE, Ecole Normale Supérieure de Lyon, 46 Allée d'Italie, 69364 Lyon Cedex 07, France/Université Grenoble Alpes, Laboratoire d'Ecologie Alpine (LECA), F-38000 Grenoble, France
| | - Daniel G Bradley
- Smurfit Institute of Genetics, Trinity College Dublin, Dublin 2, Ireland.
| | - Greger Larson
- The Palaeogenomics and Bio-Archaeology Research Network, Research Laboratory for Archaeology and History of Art, University of Oxford, Oxford, UK.
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10
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Frantz LAF, Mullin VE, Pionnier-Capitan M, Lebrasseur O, Ollivier M, Perri A, Linderholm A, Mattiangeli V, Teasdale MD, Dimopoulos EA, Tresset A, Duffraisse M, McCormick F, Bartosiewicz L, Gál E, Nyerges ÉA, Sablin MV, Bréhard S, Mashkour M, Bălăşescu A, Gillet B, Hughes S, Chassaing O, Hitte C, Vigne JD, Dobney K, Hänni C, Bradley DG, Larson G. Genomic and archaeological evidence suggest a dual origin of domestic dogs. Science 2016; 352:1228-31. [PMID: 27257259 DOI: 10.1126/science.aaf3161] [Citation(s) in RCA: 272] [Impact Index Per Article: 34.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2016] [Accepted: 04/25/2016] [Indexed: 01/19/2023]
Abstract
The geographic and temporal origins of dogs remain controversial. We generated genetic sequences from 59 ancient dogs and a complete (28x) genome of a late Neolithic dog (dated to ~4800 calendar years before the present) from Ireland. Our analyses revealed a deep split separating modern East Asian and Western Eurasian dogs. Surprisingly, the date of this divergence (~14,000 to 6400 years ago) occurs commensurate with, or several millennia after, the first appearance of dogs in Europe and East Asia. Additional analyses of ancient and modern mitochondrial DNA revealed a sharp discontinuity in haplotype frequencies in Europe. Combined, these results suggest that dogs may have been domesticated independently in Eastern and Western Eurasia from distinct wolf populations. East Eurasian dogs were then possibly transported to Europe with people, where they partially replaced European Paleolithic dogs.
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Affiliation(s)
- Laurent A F Frantz
- The Palaeogenomics and Bio-Archaeology Research Network, Research Laboratory for Archaeology and History of Art, University of Oxford, Oxford, UK.
| | - Victoria E Mullin
- Smurfit Institute of Genetics, Trinity College Dublin, Dublin 2, Ireland
| | - Maud Pionnier-Capitan
- CNRS/ENS de Lyon, IGFL, UMR 5242 and French National Platform of Paleogenetics, PALGENE, Ecole Normale Supérieure de Lyon, 46 Allée d'Italie, 69364 Lyon Cedex 07, France/Université Grenoble Alpes, Laboratoire d'Ecologie Alpine (LECA), F-38000 Grenoble, France. CNRS/Muséum National d'Histoire Naturelle/Sorbonne Universités, Archéozoologie, Archéobotanique: Sociétés, Pratiques et Environnement (UMR 7209), CP56, 55 rue Buffon, F-75005 Paris, France
| | - Ophélie Lebrasseur
- The Palaeogenomics and Bio-Archaeology Research Network, Research Laboratory for Archaeology and History of Art, University of Oxford, Oxford, UK
| | - Morgane Ollivier
- CNRS/ENS de Lyon, IGFL, UMR 5242 and French National Platform of Paleogenetics, PALGENE, Ecole Normale Supérieure de Lyon, 46 Allée d'Italie, 69364 Lyon Cedex 07, France/Université Grenoble Alpes, Laboratoire d'Ecologie Alpine (LECA), F-38000 Grenoble, France
| | - Angela Perri
- Department of Human Evolution, Max Planck Institute for Evolutionary Anthropology, 04103 Leipzig, Germany
| | - Anna Linderholm
- The Palaeogenomics and Bio-Archaeology Research Network, Research Laboratory for Archaeology and History of Art, University of Oxford, Oxford, UK. Department of Anthropology, Texas A&M University, College Station, TX 77843-4352, USA
| | | | - Matthew D Teasdale
- Smurfit Institute of Genetics, Trinity College Dublin, Dublin 2, Ireland
| | - Evangelos A Dimopoulos
- The Palaeogenomics and Bio-Archaeology Research Network, Research Laboratory for Archaeology and History of Art, University of Oxford, Oxford, UK. School of Biology, Aristotle University of Thessaloniki, Thessaloniki, Greece
| | - Anne Tresset
- CNRS/Muséum National d'Histoire Naturelle/Sorbonne Universités, Archéozoologie, Archéobotanique: Sociétés, Pratiques et Environnement (UMR 7209), CP56, 55 rue Buffon, F-75005 Paris, France
| | - Marilyne Duffraisse
- CNRS/ENS de Lyon, IGFL, UMR 5242 and French National Platform of Paleogenetics, PALGENE, Ecole Normale Supérieure de Lyon, 46 Allée d'Italie, 69364 Lyon Cedex 07, France/Université Grenoble Alpes, Laboratoire d'Ecologie Alpine (LECA), F-38000 Grenoble, France
| | - Finbar McCormick
- School of Geography, Archaeology and Palaeoecology, Queen's University Belfast, University Road, Belfast, Northern Ireland, UK
| | - László Bartosiewicz
- Osteoarchaeological Research Laboratory, University of Stockholm, Stockholm, Sweden
| | - Erika Gál
- Archaeological Institute, Research Centre for the Humanities, Hungarian Academy of Sciences, Budapest, Hungary
| | - Éva A Nyerges
- Archaeological Institute, Research Centre for the Humanities, Hungarian Academy of Sciences, Budapest, Hungary
| | - Mikhail V Sablin
- Zoological Institute, Russian Academy of Sciences, Universitetskaya Nab. 1, 199034 Saint-Petersburg, Russia
| | - Stéphanie Bréhard
- CNRS/Muséum National d'Histoire Naturelle/Sorbonne Universités, Archéozoologie, Archéobotanique: Sociétés, Pratiques et Environnement (UMR 7209), CP56, 55 rue Buffon, F-75005 Paris, France
| | - Marjan Mashkour
- CNRS/Muséum National d'Histoire Naturelle/Sorbonne Universités, Archéozoologie, Archéobotanique: Sociétés, Pratiques et Environnement (UMR 7209), CP56, 55 rue Buffon, F-75005 Paris, France
| | - Adrian Bălăşescu
- The National Museum of Romanian History, 12 Calea Victoriei, 030026 Bucharest, Romania
| | - Benjamin Gillet
- CNRS/ENS de Lyon, IGFL, UMR 5242 and French National Platform of Paleogenetics, PALGENE, Ecole Normale Supérieure de Lyon, 46 Allée d'Italie, 69364 Lyon Cedex 07, France/Université Grenoble Alpes, Laboratoire d'Ecologie Alpine (LECA), F-38000 Grenoble, France
| | - Sandrine Hughes
- CNRS/ENS de Lyon, IGFL, UMR 5242 and French National Platform of Paleogenetics, PALGENE, Ecole Normale Supérieure de Lyon, 46 Allée d'Italie, 69364 Lyon Cedex 07, France/Université Grenoble Alpes, Laboratoire d'Ecologie Alpine (LECA), F-38000 Grenoble, France
| | - Olivier Chassaing
- CNRS/ENS de Lyon, IGFL, UMR 5242 and French National Platform of Paleogenetics, PALGENE, Ecole Normale Supérieure de Lyon, 46 Allée d'Italie, 69364 Lyon Cedex 07, France/Université Grenoble Alpes, Laboratoire d'Ecologie Alpine (LECA), F-38000 Grenoble, France
| | - Christophe Hitte
- Institut de Génétique et Développement de Rennes, CNRS-UMR6290, Université de Rennes 1, Rennes, France
| | - Jean-Denis Vigne
- CNRS/Muséum National d'Histoire Naturelle/Sorbonne Universités, Archéozoologie, Archéobotanique: Sociétés, Pratiques et Environnement (UMR 7209), CP56, 55 rue Buffon, F-75005 Paris, France
| | - Keith Dobney
- Department of Archaeology, School of Geosciences, University of Aberdeen, St. Mary's, Elphinstone Road, AB24 3UF, UK. Department of Archaeology, Classics and Egyptology, University of Liverpool, 12-14 Abercromby Square, Liverpool L69 7WZ, UK
| | - Catherine Hänni
- CNRS/ENS de Lyon, IGFL, UMR 5242 and French National Platform of Paleogenetics, PALGENE, Ecole Normale Supérieure de Lyon, 46 Allée d'Italie, 69364 Lyon Cedex 07, France/Université Grenoble Alpes, Laboratoire d'Ecologie Alpine (LECA), F-38000 Grenoble, France
| | - Daniel G Bradley
- Smurfit Institute of Genetics, Trinity College Dublin, Dublin 2, Ireland.
| | - Greger Larson
- The Palaeogenomics and Bio-Archaeology Research Network, Research Laboratory for Archaeology and History of Art, University of Oxford, Oxford, UK.
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