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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Martiniano R, Haber M, Almarri MA, Mattiangeli V, Kuijpers MCM, Chamel B, Breslin EM, Littleton J, Almahari S, Aloraifi F, Bradley DG, Lombard P, Durbin R. Ancient genomes illuminate Eastern Arabian population history and adaptation against malaria. Cell Genom 2024; 4:100507. [PMID: 38417441 PMCID: PMC10943591 DOI: 10.1016/j.xgen.2024.100507] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [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: 08/04/2023] [Revised: 11/01/2023] [Accepted: 01/31/2024] [Indexed: 03/01/2024]
Abstract
The harsh climate of Arabia has posed challenges in generating ancient DNA from the region, hindering the direct examination of ancient genomes for understanding the demographic processes that shaped Arabian populations. In this study, we report whole-genome sequence data obtained from four Tylos-period individuals from Bahrain. Their genetic ancestry can be modeled as a mixture of sources from ancient Anatolia, Levant, and Iran/Caucasus, with variation between individuals suggesting population heterogeneity in Bahrain before the onset of Islam. We identify the G6PD Mediterranean mutation associated with malaria resistance in three out of four ancient Bahraini samples and estimate that it rose in frequency in Eastern Arabia from 5 to 6 kya onward, around the time agriculture appeared in the region. Our study characterizes the genetic composition of ancient Arabians, shedding light on the population history of Bahrain and demonstrating the feasibility of studies of ancient DNA in the region.
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Affiliation(s)
- Rui Martiniano
- School of Biological and Environmental Sciences, Liverpool John Moores University, L3 3AF Liverpool, UK.
| | - Marc Haber
- Institute of Cancer and Genomic Sciences, University of Birmingham Dubai, Dubai, United Arab Emirates
| | - Mohamed A Almarri
- Department of Forensic Science and Criminology, Dubai Police GHQ, Dubai, United Arab Emirates; College of Medicine, Mohammed Bin Rashid University of Medicine and Health Sciences, Dubai, United Arab Emirates
| | | | - Mirte C M Kuijpers
- Department of Ecology, Behavior and Evolution, School of Biological Sciences, University of California, San Diego, La Jolla, CA, USA
| | - Berenice Chamel
- Institut Français du Proche-Orient (MEAE/CNRS), Beirut, Lebanon
| | - Emily M Breslin
- Smurfit Institute of Genetics, Trinity College Dublin, Dublin 2, Ireland
| | - Judith Littleton
- School of Social Sciences, University of Auckland, Auckland, New Zealand
| | - Salman Almahari
- Bahrain Authority for Culture and Antiquities, Manama, Kingdom of Bahrain
| | - Fatima Aloraifi
- Mersey and West Lancashire Teaching Hospitals NHS Trust, Whiston Hospital, Warrington Road, Prescot, L35 5DR Liverpool, UK
| | - Daniel G Bradley
- Smurfit Institute of Genetics, Trinity College Dublin, Dublin 2, Ireland
| | - Pierre Lombard
- Bahrain Authority for Culture and Antiquities, Manama, Kingdom of Bahrain; Archéorient UMR 5133, CNRS, Université Lyon 2, Maison de l'Orient et de la Méditerranée - Jean Pouilloux, Lyon, France
| | - Richard Durbin
- Department of Genetics, University of Cambridge, CB2 3EH Cambridge, UK.
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3
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Cooke NP, Mattiangeli V, Cassidy LM, Okazaki K, Kasai K, Bradley DG, Gakuhari T, Nakagome S. Genomic insights into a tripartite ancestry in the Southern Ryukyu Islands. Evol Hum Sci 2023; 5:e23. [PMID: 37587935 PMCID: PMC10426068 DOI: 10.1017/ehs.2023.18] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2022] [Revised: 06/21/2023] [Accepted: 06/22/2023] [Indexed: 08/18/2023] Open
Abstract
A tripartite structure for the genetic origin of Japanese populations states that present-day populations are descended from three main ancestors: (1) the indigenous Jomon hunter-gatherers; (2) a Northeast Asian component that arrived during the agrarian Yayoi period; and (3) a major influx of East Asian ancestry in the imperial Kofun period. However, the genetic heterogeneity observed in different regions of the Japanese archipelago highlights the need to assess the applicability and suitability of this model. Here, we analyse historic genomes from the southern Ryukyu Islands, which have unique cultural and historical backgrounds compared with other parts of Japan. Our analysis supports the tripartite structure as the best fit in this region, with significantly higher estimated proportions of Jomon ancestry than mainland Japanese. Unlike the main islands, where each continental ancestor was directly brought by immigrants from the continent, those who already possessed the tripartite ancestor migrated to the southern Ryukyu Islands and admixed with the prehistoric people around the eleventh century AD, coinciding with the emergence of the Gusuku period. These results reaffirm the tripartite model in the southernmost extremes of the Japanese archipelago and show variability in how the structure emerged in diverse geographic regions.
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Affiliation(s)
- Niall P. Cooke
- School of Medicine, Trinity College Dublin, Dublin, Ireland
| | | | - Lara M. Cassidy
- Smurfit Institute of Genetics, Trinity College Dublin, Dublin, Ireland
| | - Kenji Okazaki
- Department of Anatomy, Faculty of Medicine, Tottori University, Japan
| | - Kenji Kasai
- Toyama Prefectural Center for Archaeological Operations, Toyama, Japan
| | - Daniel G. Bradley
- Smurfit Institute of Genetics, Trinity College Dublin, Dublin, Ireland
| | - Takashi Gakuhari
- Institute for the Study of Ancient Civilizations and Cultural Resources, College of Human and Social Sciences, Kanazawa University, Kanazawa, Japan
| | - Shigeki Nakagome
- School of Medicine, Trinity College Dublin, Dublin, Ireland
- Institute for the Study of Ancient Civilizations and Cultural Resources, College of Human and Social Sciences, Kanazawa University, Kanazawa, Japan
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4
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Jackson I, Mattiangeli V, Cassidy LM, Murphy E, Bradley DG. Millennium-old pathogenic Mendelian mutation discovery for multiple osteochondromas from a Gaelic Medieval graveyard. Eur J Hum Genet 2023; 31:248-251. [PMID: 36443465 PMCID: PMC9905557 DOI: 10.1038/s41431-022-01219-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2022] [Revised: 07/18/2022] [Accepted: 10/14/2022] [Indexed: 11/29/2022] Open
Abstract
Only a limited number of genetic diseases are diagnosable in archaeological individuals and none have had causal mutations identified in genome-wide screens. Two individuals from the Gaelic Irish Medieval burial ground of Ballyhanna, Co. Donegal, showed evidence of bone tumours consistent with the autosomal dominant condition multiple osteochondromas. Genome sequencing of the earlier individual uncovered a missense mutation in the second exon of EXT1, a specific lesion that has been identified in several modern patients. The later individual lacked this but displayed a novel frameshift mutation leading to a premature stop codon and loss of function in the same gene. These molecular confirmations of a paleopathological diagnosis within a single rural ancient context are surprisingly disjunct, given the observation of clusters of this disease in modern isolated populations and a de novo mutation rate of only 10%.
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Affiliation(s)
- Iseult Jackson
- Smurfit Institute of Genetics, Trinity College Dublin, Dublin 2, Ireland
- The SFI Centre for Research Training in Genomics Data Science, NUI Galway, Galway, Ireland
| | | | - Lara M Cassidy
- Smurfit Institute of Genetics, Trinity College Dublin, Dublin 2, Ireland
| | - Eileen Murphy
- Archaeology and Palaeoecology, School of Natural and Built Environment, Queen's University Belfast, Belfast, Northern Ireland.
| | - Daniel G Bradley
- Smurfit Institute of Genetics, Trinity College Dublin, Dublin 2, Ireland.
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5
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Daly KG, Arbuckle BS, Rossi C, Mattiangeli V, Lawlor PA, Mashkour M, Sauer E, Lesur J, Atici L, Erek CM, Bradley DG. A novel lineage of the Capra genus discovered in the Taurus Mountains of Turkey using ancient genomics. eLife 2022; 11:82984. [PMID: 36190761 PMCID: PMC9529249 DOI: 10.7554/elife.82984] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2022] [Accepted: 09/09/2022] [Indexed: 11/13/2022] Open
Abstract
Direkli Cave, located in the Taurus Mountains of southern Turkey, was occupied by Late Epipaleolithic hunters-gatherers for the seasonal hunting and processing of game including large numbers of wild goats. We report genomic data from new and published Capra specimens from Direkli Cave and, supplemented with historic genomes from multiple Capra species, find a novel lineage best represented by a ~14,000 year old 2.59 X genome sequenced from specimen Direkli4. This newly discovered Capra lineage is a sister clade to the Caucasian tur species (Capra cylindricornis and Capra caucasica), both now limited to the Caucasus region. We identify genomic regions introgressed in domestic goats with high affinity to Direkli4, and find that West Eurasian domestic goats in the past, but not those today, appear enriched for Direkli4-specific alleles at a genome-wide level. This forgotten ‘Taurasian tur’ likely survived Late Pleistocene climatic change in a Taurus Mountain refuge and its genomic fate is unknown.
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Affiliation(s)
- Kevin G Daly
- Smurfit Institute of Genetics, Trinity College Dublin, Dublin, Ireland
| | - Benjamin S Arbuckle
- Department of Anthropology, University of North Carolina at Chapel Hill, Chapel Hill, United States
| | - Conor Rossi
- Smurfit Institute of Genetics, Trinity College Dublin, Dublin, Ireland
| | | | - Phoebe A Lawlor
- Smurfit Institute of Genetics, Trinity College Dublin, Dublin, Ireland
| | - Marjan Mashkour
- Centre National de Recherche Scientifique / Muséum national d'Histoire naturelle, Archéozoologie, Archéobotanique, Paris, France.,University of Tehran, Bioarchaeology Laboratory, (Central Laboratory), Archaeozoology section, Tehran, Islamic Republic of Iran
| | - Eberhard Sauer
- School of History, Classics and Archaeology, University of Edinburgh, Edinburgh, United Kingdom
| | - Joséphine Lesur
- Centre National de Recherche Scientifique / Muséum national d'Histoire naturelle, Archéozoologie, Archéobotanique, Paris, France
| | - Levent Atici
- Department of Anthropology, University of Nevada, Las Vegas, Las Vegas, United States
| | - Cevdet Merih Erek
- Department of Archeology, Department of Prehistoric Archeology, Faculty of Letters, Ankara Hacı Bayram Veli University, Ankara, Turkey
| | - Daniel G Bradley
- Smurfit Institute of Genetics, Trinity College Dublin, Dublin, Ireland
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6
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Todd ET, Tonasso-Calvière L, Chauvey L, Schiavinato S, Fages A, Seguin-Orlando A, Clavel P, Khan N, Pérez Pardal L, Patterson Rosa L, Librado P, Ringbauer H, Verdugo M, Southon J, Aury JM, Perdereau A, Vila E, Marzullo M, Prato O, Tecchiati U, Bagnasco Gianni G, Tagliacozzo A, Tinè V, Alhaique F, Cardoso JL, Valente MJ, Telles Antunes M, Frantz L, Shapiro B, Bradley DG, Boulbes N, Gardeisen A, Horwitz LK, Öztan A, Arbuckle BS, Onar V, Clavel B, Lepetz S, Vahdati AA, Davoudi H, Mohaseb A, Mashkour M, Bouchez O, Donnadieu C, Wincker P, Brooks SA, Beja-Pereira A, Wu DD, Orlando L. The genomic history and global expansion of domestic donkeys. Science 2022; 377:1172-1180. [PMID: 36074859 DOI: 10.1126/science.abo3503] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
Abstract
Donkeys transformed human history as essential beasts of burden for long-distance movement, especially across semi-arid and upland environments. They remain insufficiently studied despite globally expanding and providing key support to low- to middle-income communities. To elucidate their domestication history, we constructed a comprehensive genome panel of 207 modern and 31 ancient donkeys, as well as 15 wild equids. We found a strong phylogeographic structure in modern donkeys that supports a single domestication in Africa ~5000 BCE, followed by further expansions in this continent and Eurasia and ultimately returning to Africa. We uncover a previously unknown genetic lineage in the Levant ~200 BCE, which contributed increasing ancestry toward Asia. Donkey management involved inbreeding and the production of giant bloodlines at a time when mules were essential to the Roman economy and military.
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Affiliation(s)
- Evelyn T Todd
- Centre d'Anthropobiologie et de Génomique de Toulouse (CAGT), CNRS UMR 5288, Université Paul Sabatier, Toulouse 31000, France
| | - Laure Tonasso-Calvière
- Centre d'Anthropobiologie et de Génomique de Toulouse (CAGT), CNRS UMR 5288, Université Paul Sabatier, Toulouse 31000, France
| | - Loreleï Chauvey
- Centre d'Anthropobiologie et de Génomique de Toulouse (CAGT), CNRS UMR 5288, Université Paul Sabatier, Toulouse 31000, France
| | - Stéphanie Schiavinato
- Centre d'Anthropobiologie et de Génomique de Toulouse (CAGT), CNRS UMR 5288, Université Paul Sabatier, Toulouse 31000, France
| | - Antoine Fages
- Centre d'Anthropobiologie et de Génomique de Toulouse (CAGT), CNRS UMR 5288, Université Paul Sabatier, Toulouse 31000, France
| | - Andaine Seguin-Orlando
- Centre d'Anthropobiologie et de Génomique de Toulouse (CAGT), CNRS UMR 5288, Université Paul Sabatier, Toulouse 31000, France
| | - Pierre Clavel
- Centre d'Anthropobiologie et de Génomique de Toulouse (CAGT), CNRS UMR 5288, Université Paul Sabatier, Toulouse 31000, France
| | - Naveed Khan
- Centre d'Anthropobiologie et de Génomique de Toulouse (CAGT), CNRS UMR 5288, Université Paul Sabatier, Toulouse 31000, France.,Department of Biotechnology, Abdul Wali Khan University, Mardan 23200, Pakistan
| | - Lucía Pérez Pardal
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Campus de Vairão, Universidade do Porto, Vairão 4485-661, Portugal.,BIOPOLIS Program in Genomics, Biodiversity and Land Planning, Campus de Vairão, Universidade do Porto, Vairão 4485-661, Portugal
| | | | - Pablo Librado
- Centre d'Anthropobiologie et de Génomique de Toulouse (CAGT), CNRS UMR 5288, Université Paul Sabatier, Toulouse 31000, France
| | - Harald Ringbauer
- Department of Archaeogenetics, Max Planck Institute for Evolutionary Anthropology, Leipzig 04103, Germany
| | - Marta Verdugo
- Smurfit Institute of Genetics, Trinity College Dublin, Dublin D02 PN40, Ireland
| | - John Southon
- Earth System Science Department, University of California, Irvine, CA 92697, USA
| | - Jean-Marc Aury
- Genoscope, Institut de biologie François Jacob, CEA, Université d'Evry, Université Paris-Saclay, Evry 91042, France
| | - Aude Perdereau
- Genoscope, Institut de biologie François Jacob, CEA, Université d'Evry, Université Paris-Saclay, Evry 91042, France
| | - Emmanuelle Vila
- Laboratoire Archéorient, Université Lyon 2, Lyon 69007, France
| | - Matilde Marzullo
- Dipartimento di Beni Culturali e Ambientali, Università degli Studi di Milano, Milan 20122, Italy
| | - Ornella Prato
- Dipartimento di Beni Culturali e Ambientali, Università degli Studi di Milano, Milan 20122, Italy
| | - Umberto Tecchiati
- Dipartimento di Beni Culturali e Ambientali, Università degli Studi di Milano, Milan 20122, Italy
| | - Giovanna Bagnasco Gianni
- Dipartimento di Beni Culturali e Ambientali, Università degli Studi di Milano, Milan 20122, Italy
| | | | - Vincenzo Tinè
- Soprintendenza archeologia belle arti e paesaggio per le province di Verona, Rovigo e Vicenza, Verona 37121, Italy
| | | | - João Luís Cardoso
- ICArEHB, Campus de Gambelas, University of Algarve, Faro 8005-139, Portugal.,Universidade Aberta, Lisbon 1269-001, Portugal
| | - Maria João Valente
- Faculdade de Ciências Humanas e Sociais, Centro de Estudos de Arqueologia, Artes e Ciências do Património, Universidade do Algarve, Faro 8000-117, Portugal
| | - Miguel Telles Antunes
- Centre for Research on Science and Geological Engineering, Universidade NOVA de Lisboa, Lisbon 1099-085, Portugal
| | - Laurent Frantz
- Palaeogenomics Group, Department of Veterinary Sciences, Ludwig Maximilian University, Munich 80539, Germany.,School of Biological and Behavioural Sciences, Queen Mary University of London, London E1 4DQ, United Kingdom
| | - Beth Shapiro
- Department of Ecology and Evolutionary Biology, University of California, Santa Cruz, CA 95064, USA.,Howard Hughes Medical Institute, University of California, Santa Cruz, CA 95064, USA
| | - Daniel G Bradley
- Smurfit Institute of Genetics, Trinity College Dublin, Dublin D02 PN40, Ireland
| | - Nicolas Boulbes
- Institut de Paléontologie Humaine, Fondation Albert Ier, Paris / UMR 7194 HNHP, MNHN-CNRS-UPVD / EPCC Centre Européen de Recherche Préhistorique, Tautavel 66720, France
| | - Armelle Gardeisen
- Archéologie des Sociétés Méditéranéennes, Université Paul Valéry - Site Saint-Charles 2, Montpellier 34090, France
| | - Liora Kolska Horwitz
- National Natural History Collections, Edmond J. Safra Campus, Givat Ram, The Hebrew University, Jerusalem 9190401, Israel
| | - Aliye Öztan
- Archaeology Department, Ankara University, Ankara 06100, Turkey
| | - Benjamin S Arbuckle
- Department of Anthropology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Vedat Onar
- Osteoarchaeology Practice and Research Center and Department of Anatomy, Faculty of Veterinary Medicine, Istanbul University-Cerrahpaşa, Istanbul 34320, Turkey
| | - Benoît Clavel
- Archéozoologie, Archéobotanique, Sociétés, Pratiques et Environnements, Muséum National d'Histoire Naturelle, Paris 75005, France
| | - Sébastien Lepetz
- Archéozoologie, Archéobotanique, Sociétés, Pratiques et Environnements, Muséum National d'Histoire Naturelle, Paris 75005, France
| | - Ali Akbar Vahdati
- Provincial Office of the Iranian Center for Cultural Heritage, Handicrafts and Tourism Organisation, North Khorassan, Bojnord 9416745775, Iran
| | - Hossein Davoudi
- Archaezoology section, Bioarchaeology Laboratory of the Central Laboratory, University of Tehran, Tehran CP1417634934, Iran
| | - Azadeh Mohaseb
- Archéozoologie, Archéobotanique, Sociétés, Pratiques et Environnements, Muséum National d'Histoire Naturelle, Paris 75005, France.,Archaezoology section, Bioarchaeology Laboratory of the Central Laboratory, University of Tehran, Tehran CP1417634934, Iran
| | - Marjan Mashkour
- Archéozoologie, Archéobotanique, Sociétés, Pratiques et Environnements, Muséum National d'Histoire Naturelle, Paris 75005, France.,Archaezoology section, Bioarchaeology Laboratory of the Central Laboratory, University of Tehran, Tehran CP1417634934, Iran.,Department of Osteology, National Museum of Iran, Tehran 1136918111, Iran
| | - Olivier Bouchez
- GeT-PlaGe - Génome et Transcriptome - Plateforme Génomique, GET - Plateforme Génome & Transcriptome, Institut National de Recherche pour l'Agriculture, l'Alimentation et l'Environnement, Castaneet-Tolosan Cedex 31326, France
| | - Cécile Donnadieu
- GeT-PlaGe - Génome et Transcriptome - Plateforme Génomique, GET - Plateforme Génome & Transcriptome, Institut National de Recherche pour l'Agriculture, l'Alimentation et l'Environnement, Castaneet-Tolosan Cedex 31326, France
| | - Patrick Wincker
- Genoscope, Institut de biologie François Jacob, CEA, Université d'Evry, Université Paris-Saclay, Evry 91042, France
| | - Samantha A Brooks
- Department of Animal Science, UF Genetics Institute, University of Florida, Gainesville, FL 32610, USA
| | - Albano Beja-Pereira
- CIBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO Laboratório Associado, Campus de Vairão, Universidade do Porto, Vairão 4485-661, Portugal.,BIOPOLIS Program in Genomics, Biodiversity and Land Planning, Campus de Vairão, Universidade do Porto, Vairão 4485-661, Portugal.,DGAOT, Faculty of Sciences, Universidade do Porto, Porto 4169-007, Portugal.,Sustainable Agrifood Production Research Centre (GreenUPorto), Universidade do Porto, Vairão 4485-646, Portugal
| | - Dong-Dong Wu
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan 650201, China.,Kunming Natural History Museum of Zoology, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan 650223, China
| | - Ludovic Orlando
- Centre d'Anthropobiologie et de Génomique de Toulouse (CAGT), CNRS UMR 5288, Université Paul Sabatier, Toulouse 31000, France
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7
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Consortium VG, Nijman IJ, Rosen BD, Bardou P, Faraut T, Cumer T, Daly KG, Zheng Z, Cai Y, Asadollahpour H, Kul BÇ, Zhang WY, Guangxin E, Ayin A, Baird H, Bakhtin M, Bâlteanu VA, Barfield D, Berger B, Blichfeldt T, Boink G, Bugiwati SRA, Cai Z, Carolan S, Clark E, Cubric-Curik V, Dagong MIA, Dorji T, Drew L, Guo J, Hallsson J, Horvat S, Kantanen J, Kawaguchi F, Kazymbet P, Khayatzadeh N, Kim N, Shah MK, Liao Y, Martínez A, Masangkay JS, Masaoka M, Mazza R, McEwan J, Milanesi M, Faruque MO, Nomura Y, Ouchene-Khelifi NA, Pereira F, Sahana G, Salavati M, Sasazaki S, Da Silva A, Simčič M, Sölkner J, Sutherland A, Tigchelaar J, Zhang H, Consortium E, Ajmone-Marsan P, Bradley DG, Colli L, Drögemüller C, Jiang Y, Lei C, Mannen H, Pompanon F, Tosser-Klopp G, Lenstra JA. Geographical contrasts of Y-chromosomal haplogroups from wild and domestic goats reveal ancient migrations and recent introgressions. Mol Ecol 2022; 31:4364-4380. [PMID: 35751552 DOI: 10.1111/mec.16579] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [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: 03/07/2022] [Revised: 06/12/2022] [Accepted: 06/20/2022] [Indexed: 11/29/2022]
Abstract
By their paternal transmission, Y-chromosomal haplotypes are sensitive markers of population history and male-mediated introgression. Previous studies identified biallelic single-nucleotide variants in the SRY, ZFY, DDX3Y genes, which in domestic goats identified four major Y-chromosomal haplotypes Y1A, Y1B, Y2A and Y2B with a marked geographic partitioning. Here, we extracted goat Y-chromosomal variants from whole-genome sequences of 386 domestic goats (75 breeds) and 7 wild goat species, which were generated by the VarGoats goat genome project. Phylogenetic analyses indicated domestic haplogroups corresponding to Y1B, Y2A and Y2B, respectively, whereas Y1A is split into Y1AA and Y1AB. All five haplogroups were detected in 26 ancient DNA samples from southeast Europe or Asia. Haplotypes from present-day bezoars are not shared with domestic goats and are attached to deep nodes of the trees and networks. Haplogroup distributions for 186 domestic breeds indicate ancient paternal population bottlenecks and expansions during the migrations into northern Europe, eastern and southern Asia and Africa south of the Sahara. In addition, sharing of haplogroups indicates male-mediated introgressions, most notably an early gene flow from Asian goats into Madagascar and the crossbreeding that in the 19th century resulted in the popular Boer and Anglo-Nubian breeds. More recent introgressions are those from European goats into the native Korean goat population and from Boer goat into Uganda, Kenya, Tanzania, Malawi and Zimbabwe. This study illustrates the power of the Y-chromosomal variants for reconstructing the history of domestic species with a wide geographic range.
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Affiliation(s)
| | - Isaäc J Nijman
- Utrecht Univ., Netherlands.,Univ. Medical Center Utrecht, Utrecht Univ, The Netherlands
| | | | - Philippe Bardou
- GenPhySE, Univ. Toulouse, INRA, INPT, ENVT, Castanet Tolosan, France
| | - Thomas Faraut
- GenPhySE, Univ. Toulouse, INRA, INPT, ENVT, Castanet Tolosan, France
| | - Tristan Cumer
- Université Grenoble Alpes, Université Savoie Mont Blanc, CNRS, LECA, Grenoble, France
| | | | - Zhuqing Zheng
- College of Animal Science & Technology, Northwest A&F Univ., Yangling, China
| | - Yudong Cai
- College of Animal Science & Technology, Northwest A&F Univ., Yangling, China
| | | | | | | | | | | | - Hayley Baird
- AgResearch, Invermay Agricultural Centre, Mosgiel, New Zealand
| | | | - Valentin A Bâlteanu
- Inst. of Life SciencesUniv. Agricultural Sciences and Veterinary Medicine of Cluj-Napoca, Cluj-Napoca, Romania
| | | | - Beate Berger
- Univ. Natural Resources and Life Sciences Vienna (BOKU)
| | - Thor Blichfeldt
- Norwegian Association of Sheep and Goat Breeders, Aas, Norway
| | - Geert Boink
- Stichting Zeldzame Huisdierrassen, Wageningen, The Netherlands
| | | | | | | | | | | | | | - Tashi Dorji
- International Centre for Integrated Mountain Development, Kathmandu, Nepal
| | | | | | | | - Simon Horvat
- Univ. Ljubljana, Biotechnical Faculty, Ljubljana, Slovenia
| | - Juha Kantanen
- Natural Resources Institute Finland (Luke), Jokioinen, Finland
| | | | | | | | - Namshin Kim
- Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon, South Korea
| | | | - Yuying Liao
- Guangxi Key Laboratory of Livestock Genetic Improvement, Guangxi, China
| | | | | | | | - Raffaele Mazza
- Laboratorio Genetica e Servizi, Agrotis srl, Cremona, Italy
| | - John McEwan
- AgResearch, Invermay Agricultural Centre, Mosgiel, New Zealand
| | | | | | | | | | - Filipe Pereira
- IDENTIFICA Genetic Testing Maia & Centre for Functional Ecology, Porto, Portugal
| | | | | | | | | | - Mojca Simčič
- Univ. Ljubljana, Biotechnical Faculty, Ljubljana, Slovenia
| | | | | | | | | | | | - Paolo Ajmone-Marsan
- Univ. Cattolica del S. Cuore di Piacenza and BioDNA Biodiversity and Ancient DNA Res. Centre, Piacenza, Italy.,UCSC PRONUTRIGEN Nutrigenomics Res. Centre, Piacenza, Italy
| | | | - Licia Colli
- Univ. Cattolica del S. Cuore di Piacenza and BioDNA Biodiversity and Ancient DNA Res. Centre, Piacenza, Italy.,UCSC BioDNA Biodiversity and Ancient DNA Res. Centre, Piacenza, Italy
| | | | - Yu Jiang
- College of Animal Science & Technology, Northwest A&F Univ., Yangling, China
| | - Chuzhao Lei
- College of Animal Science & Technology, Northwest A&F Univ., Yangling, China
| | | | - François Pompanon
- Université Grenoble Alpes, Université Savoie Mont Blanc, CNRS, LECA, Grenoble, France
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8
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Ariano B, Mattiangeli V, Breslin EM, Parkinson EW, McLaughlin TR, Thompson JE, Power RK, Stock JT, Mercieca-Spiteri B, Stoddart S, Malone C, Gopalakrishnan S, Cassidy LM, Bradley DG. Ancient Maltese genomes and the genetic geography of Neolithic Europe. Curr Biol 2022; 32:2668-2680.e6. [PMID: 35588742 PMCID: PMC9245899 DOI: 10.1016/j.cub.2022.04.069] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2021] [Revised: 02/07/2022] [Accepted: 04/22/2022] [Indexed: 12/14/2022]
Abstract
Archaeological consideration of maritime connectivity has ranged from a biogeographical perspective that considers the sea as a barrier to a view of seaways as ancient highways that facilitate exchange. Our results illustrate the former. We report three Late Neolithic human genomes from the Mediterranean island of Malta that are markedly enriched for runs of homozygosity, indicating inbreeding in their ancestry and an effective population size of only hundreds, a striking illustration of maritime isolation in this agricultural society. In the Late Neolithic, communities across mainland Europe experienced a resurgence of hunter-gatherer ancestry, pointing toward the persistence of different ancestral strands that subsequently admixed. This is absent in the Maltese genomes, giving a further indication of their genomic insularity. Imputation of genome-wide genotypes in our new and 258 published ancient individuals allowed shared identity-by-descent segment analysis, giving a fine-grained genetic geography of Neolithic Europe. This highlights the differentiating effects of seafaring Mediterranean expansion and also island colonization, including that of Ireland, Britain, and Orkney. These maritime effects contrast profoundly with a lack of migratory barriers in the establishment of Central European farming populations from Anatolia and the Balkans.
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Affiliation(s)
- Bruno Ariano
- Smurfit Institute of Genetics, Trinity College Dublin, Dublin 2, Ireland
| | | | - Emily M Breslin
- Smurfit Institute of Genetics, Trinity College Dublin, Dublin 2, Ireland
| | - Eóin W Parkinson
- Department of Classics and Archaeology, University of Malta, Msida 2080, Malta
| | - T Rowan McLaughlin
- Department of Scientific Research, The British Museum, Great Russell Street, London WC1B 3DG, UK
| | - Jess E Thompson
- McDonald Institute for Archaeological Research, University of Cambridge, Downing Street, Cambridge CB2 3EJ, UK
| | - Ronika K Power
- Department of History and Archaeology, Macquarie University, 25B Wally's Walk, Sydney, NSW, Australia
| | - Jay T Stock
- Department of Anthropology, Western University, 1151 Richmond St, London, ON N6G 2V4, Canada
| | | | - Simon Stoddart
- McDonald Institute for Archaeological Research, University of Cambridge, Downing Street, Cambridge CB2 3EJ, UK
| | - Caroline Malone
- School of Natural and Built Environment, Queen's University Belfast, Elmwood Avenue, Belfast, UK
| | - Shyam Gopalakrishnan
- GLOBE Institute, University of Copenhagen, Øster Farimagsgade 5, 1353 København K, Denmark.
| | - Lara M Cassidy
- Smurfit Institute of Genetics, Trinity College Dublin, Dublin 2, Ireland.
| | - Daniel G Bradley
- Smurfit Institute of Genetics, Trinity College Dublin, Dublin 2, Ireland.
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9
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10
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Sinding MHS, Ciucani MM, Ramos-Madrigal J, Carmagnini A, Rasmussen JA, Feng S, Chen G, Vieira FG, Mattiangeli V, Ganjoo RK, Larson G, Sicheritz-Pontén T, Petersen B, Frantz L, Gilbert MTP, Bradley DG. Kouprey ( Bos sauveli) genomes unveil polytomic origin of wild Asian Bos. iScience 2021; 24:103226. [PMID: 34712923 PMCID: PMC8531564 DOI: 10.1016/j.isci.2021.103226] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2021] [Revised: 08/11/2021] [Accepted: 10/01/2021] [Indexed: 12/30/2022] Open
Abstract
The evolution of the genera Bos and Bison, and the nature of gene flow between wild and domestic species, is poorly understood, with genomic data of wild species being limited. We generated two genomes from the likely extinct kouprey (Bos sauveli) and analyzed them alongside other Bos and Bison genomes. We found that B. sauveli possessed genomic signatures characteristic of an independent species closely related to Bos javanicus and Bos gaurus. We found evidence for extensive incomplete lineage sorting across the three species, consistent with a polytomic diversification of the major ancestry in the group, potentially followed by secondary gene flow. Finally, we detected significant gene flow from an unsampled Asian Bos-like source into East Asian zebu cattle, demonstrating both that the full genomic diversity and evolutionary history of the Bos complex has yet to be elucidated and that museum specimens and ancient DNA are valuable resources to do so. We generated two genomes from the likely extinct kouprey (Bos sauveli) Extensive mt and nuclear-genome-wide incomplete lineage sorting across wild Asian Bos Initial polytomic diversification of the wild Asian Bos—kouprey, banteng, and gaur
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Affiliation(s)
| | | | | | - Alberto Carmagnini
- School of Biological and Chemical Sciences, Queen Mary University of London, London, UK
| | - Jacob Agerbo Rasmussen
- Globe Institute, University of Copenhagen, Copenhagen, Denmark
- Laboratory of Genomics and Molecular Medicine, Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Shaohong Feng
- BGI-Shenzhen, Beishan Industrial Zone, Shenzhen, China
| | - Guangji Chen
- BGI-Shenzhen, Beishan Industrial Zone, Shenzhen, China
- University of Chinese Academy of Sciences, Beijing, China
| | | | | | | | - Greger Larson
- The Palaeogenomics and Bio-Archaeology Research Network, Research Laboratory for Archaeology and History of Art, University of Oxford, Oxford, UK
| | - Thomas Sicheritz-Pontén
- Globe Institute, University of Copenhagen, Copenhagen, Denmark
- Centre of Excellence for Omics-Driven Computational Biodiscovery (COMBio), Faculty of Applied Sciences, AIMST University, Kedah, Malaysia
| | - Bent Petersen
- Globe Institute, University of Copenhagen, Copenhagen, Denmark
- Centre of Excellence for Omics-Driven Computational Biodiscovery (COMBio), Faculty of Applied Sciences, AIMST University, Kedah, Malaysia
| | - Laurent Frantz
- School of Biological and Chemical Sciences, Queen Mary University of London, London, UK
- Palaeogenomics Group, Department of Veterinary Sciences, Ludwig Maximilian University, Munich, Germany
| | - M. Thomas P. Gilbert
- Globe Institute, University of Copenhagen, Copenhagen, Denmark
- Center for Evolutionary Hologenomics, University of Copenhagen, Copenhagen, Denmark
- Norwegian University of Science and Technology, University Museum, Trondheim, Norway
| | - Daniel G. Bradley
- Smurfit Institute of Genetics, Trinity College Dublin, Dublin, Ireland
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11
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Cooke NP, Mattiangeli V, Cassidy LM, Okazaki K, Stokes CA, Onbe S, Hatakeyama S, Machida K, Kasai K, Tomioka N, Matsumoto A, Ito M, Kojima Y, Bradley DG, Gakuhari T, Nakagome S. Ancient genomics reveals tripartite origins of Japanese populations. Sci Adv 2021; 7:eabh2419. [PMID: 34533991 PMCID: PMC8448447 DOI: 10.1126/sciadv.abh2419] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/25/2021] [Accepted: 07/29/2021] [Indexed: 06/13/2023]
Abstract
Prehistoric Japan underwent rapid transformations in the past 3000 years, first from foraging to wet rice farming and then to state formation. A long-standing hypothesis posits that mainland Japanese populations derive dual ancestry from indigenous Jomon hunter-gatherer-fishers and succeeding Yayoi farmers. However, the genomic impact of agricultural migration and subsequent sociocultural changes remains unclear. We report 12 ancient Japanese genomes from pre- and postfarming periods. Our analysis finds that the Jomon maintained a small effective population size of ~1000 over several millennia, with a deep divergence from continental populations dated to 20,000 to 15,000 years ago, a period that saw the insularization of Japan through rising sea levels. Rice cultivation was introduced by people with Northeast Asian ancestry. Unexpectedly, we identify a later influx of East Asian ancestry during the imperial Kofun period. These three ancestral components continue to characterize present-day populations, supporting a tripartite model of Japanese genomic origins.
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Affiliation(s)
- Niall P. Cooke
- School of Medicine, Trinity College Dublin, Dublin, Ireland
| | | | - Lara M. Cassidy
- Smurfit Institute of Genetics, Trinity College Dublin, Dublin, Ireland
| | - Kenji Okazaki
- Department of Anatomy, Faculty of Medicine, Tottori University, Japan
| | | | - Shin Onbe
- Kumakogen Board of Education, Kumakogen, Japan
| | | | - Kenichi Machida
- Toyama Prefectural Research Office for Archaeological Heritage, Toyama, Japan
| | - Kenji Kasai
- Toyama Prefectural Center for Archaeological Operations, Toyama, Japan
| | | | | | - Masafumi Ito
- Foundation of Ishikawa Archaeological Artifacts Center, Kanazawa, Japan
| | - Yoshitaka Kojima
- Center for the Study of Ancient Civilizations and Cultural Resources, College of Human and Social Sciences, Kanazawa University, Kanazawa, Japan
| | - Daniel G. Bradley
- Smurfit Institute of Genetics, Trinity College Dublin, Dublin, Ireland
| | - Takashi Gakuhari
- Center for the Study of Ancient Civilizations and Cultural Resources, College of Human and Social Sciences, Kanazawa University, Kanazawa, Japan
| | - Shigeki Nakagome
- School of Medicine, Trinity College Dublin, Dublin, Ireland
- Center for the Study of Ancient Civilizations and Cultural Resources, College of Human and Social Sciences, Kanazawa University, Kanazawa, Japan
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12
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Rey-Iglesia A, Lister AM, Campos PF, Brace S, Mattiangeli V, Daly KG, Teasdale MD, Bradley DG, Barnes I, Hansen AJ. Exploring the phylogeography and population dynamics of the giant deer ( Megaloceros giganteus) using Late Quaternary mitogenomes. Proc Biol Sci 2021; 288:20201864. [PMID: 33977786 DOI: 10.1098/rspb.2020.1864] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Late Quaternary climatic fluctuations in the Northern Hemisphere had drastic effects on large mammal species, leading to the extinction of a substantial number of them. The giant deer (Megaloceros giganteus) was one of the species that became extinct in the Holocene, around 7660 calendar years before present. In the Late Pleistocene, the species ranged from western Europe to central Asia. However, during the Holocene, its range contracted to eastern Europe and western Siberia, where the last populations of the species occurred. Here, we generated 35 Late Pleistocene and Holocene giant deer mitogenomes to explore the genetics of the demise of this iconic species. Bayesian phylogenetic analyses of the mitogenomes suggested five main clades for the species: three pre-Last Glacial Maximum clades that did not appear in the post-Last Glacial Maximum genetic pool, and two clades that showed continuity into the Holocene. Our study also identified a decrease in genetic diversity starting in Marine Isotope Stage 3 and accelerating during the Last Glacial Maximum. This reduction in genetic diversity during the Last Glacial Maximum, coupled with a major contraction of fossil occurrences, suggests that climate was a major driver in the dynamics of the giant deer.
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Affiliation(s)
- Alba Rey-Iglesia
- Centre for Geogenetics, Natural History Museum Denmark, University of Copenhagen, Østervoldgade 5-7, 1350 Copenhagen, Denmark
| | - Adrian M Lister
- Earth Sciences Department, Natural History Museum, Cromwell Road, London SW7 5BD, UK
| | - Paula F Campos
- Centre for Geogenetics, Natural History Museum Denmark, University of Copenhagen, Østervoldgade 5-7, 1350 Copenhagen, Denmark.,CIIMAR, Interdisciplinary Centre of Marine and Environmental Research, University of Porto, Avenida General Norton de Matos, 4450-208 Matosinhos, Portugal
| | - Selina Brace
- Earth Sciences Department, Natural History Museum, Cromwell Road, London SW7 5BD, UK
| | - Valeria Mattiangeli
- Smurfit Institute of Genetics, Trinity College Dublin, Dublin Dublin 2, Ireland
| | - Kevin G Daly
- Smurfit Institute of Genetics, Trinity College Dublin, Dublin Dublin 2, Ireland
| | - Matthew D Teasdale
- Smurfit Institute of Genetics, Trinity College Dublin, Dublin Dublin 2, Ireland.,McDonald Institute for Archaeological Research, Department of Archaeology, University of Cambridge, Cambridge, UK
| | - Daniel G Bradley
- Smurfit Institute of Genetics, Trinity College Dublin, Dublin Dublin 2, Ireland
| | - Ian Barnes
- Earth Sciences Department, Natural History Museum, Cromwell Road, London SW7 5BD, UK
| | - Anders J Hansen
- Centre for Geogenetics, Natural History Museum Denmark, University of Copenhagen, Østervoldgade 5-7, 1350 Copenhagen, Denmark
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13
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Margaryan A, Lawson DJ, Sikora M, Racimo F, Rasmussen S, Moltke I, Cassidy LM, Jørsboe E, Ingason A, Pedersen MW, Korneliussen T, Wilhelmson H, Buś MM, de Barros Damgaard P, Martiniano R, Renaud G, Bhérer C, Moreno-Mayar JV, Fotakis AK, Allen M, Allmäe R, Molak M, Cappellini E, Scorrano G, McColl H, Buzhilova A, Fox A, Albrechtsen A, Schütz B, Skar B, Arcini C, Falys C, Jonson CH, Błaszczyk D, Pezhemsky D, Turner-Walker G, Gestsdóttir H, Lundstrøm I, Gustin I, Mainland I, Potekhina I, Muntoni IM, Cheng J, Stenderup J, Ma J, Gibson J, Peets J, Gustafsson J, Iversen KH, Simpson L, Strand L, Loe L, Sikora M, Florek M, Vretemark M, Redknap M, Bajka M, Pushkina T, Søvsø M, Grigoreva N, Christensen T, Kastholm O, Uldum O, Favia P, Holck P, Sten S, Arge SV, Ellingvåg S, Moiseyev V, Bogdanowicz W, Magnusson Y, Orlando L, Pentz P, Jessen MD, Pedersen A, Collard M, Bradley DG, Jørkov ML, Arneborg J, Lynnerup N, Price N, Gilbert MTP, Allentoft ME, Bill J, Sindbæk SM, Hedeager L, Kristiansen K, Nielsen R, Werge T, Willerslev E. Population genomics of the Viking world. Nature 2020. [PMID: 32939067 DOI: 10.1038/s41586-020–2688-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
The maritime expansion of Scandinavian populations during the Viking Age (about AD 750-1050) was a far-flung transformation in world history1,2. Here we sequenced the genomes of 442 humans from archaeological sites across Europe and Greenland (to a median depth of about 1×) to understand the global influence of this expansion. We find the Viking period involved gene flow into Scandinavia from the south and east. We observe genetic structure within Scandinavia, with diversity hotspots in the south and restricted gene flow within Scandinavia. We find evidence for a major influx of Danish ancestry into England; a Swedish influx into the Baltic; and Norwegian influx into Ireland, Iceland and Greenland. Additionally, we see substantial ancestry from elsewhere in Europe entering Scandinavia during the Viking Age. Our ancient DNA analysis also revealed that a Viking expedition included close family members. By comparing with modern populations, we find that pigmentation-associated loci have undergone strong population differentiation during the past millennium, and trace positively selected loci-including the lactase-persistence allele of LCT and alleles of ANKA that are associated with the immune response-in detail. We conclude that the Viking diaspora was characterized by substantial transregional engagement: distinct populations influenced the genomic makeup of different regions of Europe, and Scandinavia experienced increased contact with the rest of the continent.
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Affiliation(s)
- Ashot Margaryan
- Lundbeck Foundation GeoGenetics Centre, GLOBE Institute, University of Copenhagen, Copenhagen, Denmark.,Institute of Molecular Biology, National Academy of Sciences, Yerevan, Armenia.,Section for Evolutionary Genomics, GLOBE Institute, University of Copenhagen, Copenhagen, Denmark
| | - Daniel J Lawson
- MRC Integrative Epidemiology Unit, University of Bristol, Bristol, UK.,School of Statistical Sciences, University of Bristol, Bristol, UK
| | - Martin Sikora
- Lundbeck Foundation GeoGenetics Centre, GLOBE Institute, University of Copenhagen, Copenhagen, Denmark
| | - Fernando Racimo
- Lundbeck Foundation GeoGenetics Centre, GLOBE Institute, University of Copenhagen, Copenhagen, Denmark
| | - Simon Rasmussen
- Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Ida Moltke
- The Bioinformatics Centre, Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Lara M Cassidy
- Smurfit Institute of Genetics, Trinity College Dublin, Dublin, Ireland
| | - Emil Jørsboe
- The Bioinformatics Centre, Department of Biology, University of Copenhagen, Copenhagen, Denmark.,Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Andrés Ingason
- Lundbeck Foundation GeoGenetics Centre, GLOBE Institute, University of Copenhagen, Copenhagen, Denmark.,Department of Clinical Medicine, University of Copenhagen, Copenhagen, Denmark.,Institute of Biological Psychiatry, Mental Health Services Copenhagen, Copenhagen, Denmark
| | - Mikkel W Pedersen
- Lundbeck Foundation GeoGenetics Centre, GLOBE Institute, University of Copenhagen, Copenhagen, Denmark
| | - Thorfinn Korneliussen
- Lundbeck Foundation GeoGenetics Centre, GLOBE Institute, University of Copenhagen, Copenhagen, Denmark.,HSE University, Russian Federation National Research University Higher School of Economics, Moscow, Russia
| | - Helene Wilhelmson
- Department of Archaeology and Ancient History, Lund University, Lund, Sweden.,Sydsvensk Arkeologi AB, Kristianstad, Sweden
| | - Magdalena M Buś
- Department of Immunology, Genetics and Pathology, Uppsala University, Uppsala, Sweden
| | - Peter de Barros Damgaard
- Lundbeck Foundation GeoGenetics Centre, GLOBE Institute, University of Copenhagen, Copenhagen, Denmark
| | - Rui Martiniano
- Department of Genetics, University of Cambridge, Cambridge, UK
| | - Gabriel Renaud
- Lundbeck Foundation GeoGenetics Centre, GLOBE Institute, University of Copenhagen, Copenhagen, Denmark.,Department of Health Technology, Section for Bioinformatics, Technical University of Denmark (DTU), Copenhagen, Denmark
| | - Claude Bhérer
- Department of Human Genetics, McGill University, Montréal, Quebec, Canada
| | - J Víctor Moreno-Mayar
- Lundbeck Foundation GeoGenetics Centre, GLOBE Institute, University of Copenhagen, Copenhagen, Denmark.,National Institute of Genomic Medicine (INMEGEN), Mexico City, Mexico
| | - Anna K Fotakis
- Section for Evolutionary Genomics, GLOBE Institute, University of Copenhagen, Copenhagen, Denmark
| | - Marie Allen
- Department of Immunology, Genetics and Pathology, Uppsala University, Uppsala, Sweden
| | - Raili Allmäe
- Archaeological Research Collection, Tallinn University, Tallinn, Estonia
| | - Martyna Molak
- Museum and Institute of Zoology, Polish Academy of Sciences, Warsaw, Poland
| | - Enrico Cappellini
- Section for Evolutionary Genomics, GLOBE Institute, University of Copenhagen, Copenhagen, Denmark
| | - Gabriele Scorrano
- Section for Evolutionary Genomics, GLOBE Institute, University of Copenhagen, Copenhagen, Denmark
| | - Hugh McColl
- Lundbeck Foundation GeoGenetics Centre, GLOBE Institute, University of Copenhagen, Copenhagen, Denmark
| | - Alexandra Buzhilova
- Anuchin Research Institute and Museum of Anthropology, Moscow State University, Moscow, Russia
| | - Allison Fox
- Manx National Heritage, Douglas, Isle of Man
| | - Anders Albrechtsen
- The Bioinformatics Centre, Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | | | - Birgitte Skar
- NTNU University Museum, Department of Archaeology and Cultural History, Trondheim, Norway
| | - Caroline Arcini
- The Archaeologists, National Historical Museums, Stockholm, Sweden
| | - Ceri Falys
- Thames Valley Archaeological Services (TVAS), Reading, UK
| | | | | | - Denis Pezhemsky
- Anuchin Research Institute and Museum of Anthropology, Moscow State University, Moscow, Russia
| | - Gordon Turner-Walker
- Department of Cultural Heritage Conservation, National Yunlin University of Science and Technology, Douliou, Taiwan
| | | | - Inge Lundstrøm
- Section for Evolutionary Genomics, GLOBE Institute, University of Copenhagen, Copenhagen, Denmark
| | - Ingrid Gustin
- Department of Archaeology and Ancient History, Lund University, Lund, Sweden
| | - Ingrid Mainland
- UHI Archaeology Institute, University of the Highlands and Islands, Kirkwall, UK
| | - Inna Potekhina
- Department of Bioarchaeology, Institute of Archaeology of National Academy of Sciences of Ukraine, Kiev, Ukraine
| | - Italo M Muntoni
- Soprintendenza Archeologia, Belle Arti e Paesaggio per le Province di Barletta, Andria, Trani e Foggia, Foggia, Italy
| | - Jade Cheng
- Lundbeck Foundation GeoGenetics Centre, GLOBE Institute, University of Copenhagen, Copenhagen, Denmark
| | - Jesper Stenderup
- Lundbeck Foundation GeoGenetics Centre, GLOBE Institute, University of Copenhagen, Copenhagen, Denmark
| | - Jilong Ma
- Lundbeck Foundation GeoGenetics Centre, GLOBE Institute, University of Copenhagen, Copenhagen, Denmark
| | - Julie Gibson
- UHI Archaeology Institute, University of the Highlands and Islands, Kirkwall, UK
| | - Jüri Peets
- Archaeological Research Collection, Tallinn University, Tallinn, Estonia
| | | | - Katrine H Iversen
- Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark.,Department of Health Technology, Section for Bioinformatics, Technical University of Denmark (DTU), Copenhagen, Denmark
| | | | - Lisa Strand
- NTNU University Museum, Department of Archaeology and Cultural History, Trondheim, Norway
| | - Louise Loe
- Heritage Burial Services, Oxford Archaeology, Oxford, UK
| | | | - Marek Florek
- Institute of Archaeology, Maria Curie-Sklodowska University in Lublin, Lublin, Poland
| | | | - Mark Redknap
- Department of History and Archaeology, Amgueddfa Cymru-National Museum Wales, Cardiff, UK
| | - Monika Bajka
- Trzy Epoki Archaeological Service, Klimontów, Poland
| | | | | | - Natalia Grigoreva
- Department of Slavic-Finnish Archaeology, Institute for the History of Material Culture, Russian Academy of Sciences, Saint Petersburg, Russia
| | | | - Ole Kastholm
- Department of Research and Heritage, Roskilde Museum, Roskilde, Denmark
| | | | - Pasquale Favia
- Department of Humanities, University of Foggia, Foggia, Italy
| | - Per Holck
- Department of Molecular Medicine, Faculty of Medicine, University of Oslo, Oslo, Norway
| | - Sabine Sten
- Department of Archaeology and Ancient History, Uppsala University Campus Gotland, Visby, Sweden
| | - Símun V Arge
- Tjóðsavnið - Faroe Islands National Museum, Tórshavn, Faroe Islands
| | - Sturla Ellingvåg
- Lundbeck Foundation GeoGenetics Centre, GLOBE Institute, University of Copenhagen, Copenhagen, Denmark
| | - Vayacheslav Moiseyev
- Peter the Great Museum of Anthropology and Ethnography (Kunstkamera), Russian Academy of Science, St Petersburg, Russia
| | | | | | - Ludovic Orlando
- Laboratoire d'Anthropobiologie Moléculaire et d'Imagerie de Synthèse, CNRS UMR 5288, Université de Toulouse, Université Paul Sabatier, Toulouse, France
| | - Peter Pentz
- National Museum of Denmark, Copenhagen, Denmark
| | | | | | - Mark Collard
- Department of Archaeology, Simon Fraser University, Burnaby, British Colombia, Canada
| | - Daniel G Bradley
- Smurfit Institute of Genetics, Trinity College Dublin, Dublin, Ireland
| | - Marie Louise Jørkov
- Department of Forensic Medicine, University of Copenhagen, Copenhagen, Denmark
| | - Jette Arneborg
- National Museum of Denmark, Copenhagen, Denmark.,School of GeoSciences, University of Edinburgh, Edinburgh, UK
| | - Niels Lynnerup
- Department of Forensic Medicine, University of Copenhagen, Copenhagen, Denmark
| | - Neil Price
- Department of Archaeology and Ancient History, Uppsala University, Uppsala, Sweden
| | - M Thomas P Gilbert
- Section for Evolutionary Genomics, GLOBE Institute, University of Copenhagen, Copenhagen, Denmark.,Department of Natural History, Norwegian University of Science and Technology (NTNU), Trondheim, Norway
| | - Morten E Allentoft
- Lundbeck Foundation GeoGenetics Centre, GLOBE Institute, University of Copenhagen, Copenhagen, Denmark.,Trace and Environmental DNA (TrEnD) Laboratory, School of Molecular and Life Sciences, Curtin University, Perth, Western Australia, Australia
| | - Jan Bill
- Museum of Cultural History, University of Oslo, Oslo, Norway
| | - Søren M Sindbæk
- Centre for Urban Network Evolutions (UrbNet), School of Culture and Society, Aarhus University, Højbjerg, Denmark
| | - Lotte Hedeager
- Institute of Archaeology, Conservation and History, Oslo, Norway
| | | | - Rasmus Nielsen
- Lundbeck Foundation GeoGenetics Centre, GLOBE Institute, University of Copenhagen, Copenhagen, Denmark. .,Department of Integrative Biology, UC Berkeley, Berkeley, CA, USA. .,Department of Statistics, UC Berkeley, Berkeley, CA, USA.
| | - Thomas Werge
- Lundbeck Foundation GeoGenetics Centre, GLOBE Institute, University of Copenhagen, Copenhagen, Denmark. .,Department of Clinical Medicine, University of Copenhagen, Copenhagen, Denmark. .,Institute of Biological Psychiatry, Mental Health Services Copenhagen, Copenhagen, Denmark. .,The Lundbeck Foundation Initiative for Integrative Psychiatric Research, iPSYCH, Copenhagen, Denmark.
| | - Eske Willerslev
- Lundbeck Foundation GeoGenetics Centre, GLOBE Institute, University of Copenhagen, Copenhagen, Denmark. .,Department of Zoology, University of Cambridge, Cambridge, UK. .,The Danish Institute for Advanced Study, University of Southern Denmark, Odense, Denmark. .,The Wellcome Trust Sanger Institute, Cambridge, UK.
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14
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Margaryan A, Lawson DJ, Sikora M, Racimo F, Rasmussen S, Moltke I, Cassidy LM, Jørsboe E, Ingason A, Pedersen MW, Korneliussen T, Wilhelmson H, Buś MM, de Barros Damgaard P, Martiniano R, Renaud G, Bhérer C, Moreno-Mayar JV, Fotakis AK, Allen M, Allmäe R, Molak M, Cappellini E, Scorrano G, McColl H, Buzhilova A, Fox A, Albrechtsen A, Schütz B, Skar B, Arcini C, Falys C, Jonson CH, Błaszczyk D, Pezhemsky D, Turner-Walker G, Gestsdóttir H, Lundstrøm I, Gustin I, Mainland I, Potekhina I, Muntoni IM, Cheng J, Stenderup J, Ma J, Gibson J, Peets J, Gustafsson J, Iversen KH, Simpson L, Strand L, Loe L, Sikora M, Florek M, Vretemark M, Redknap M, Bajka M, Pushkina T, Søvsø M, Grigoreva N, Christensen T, Kastholm O, Uldum O, Favia P, Holck P, Sten S, Arge SV, Ellingvåg S, Moiseyev V, Bogdanowicz W, Magnusson Y, Orlando L, Pentz P, Jessen MD, Pedersen A, Collard M, Bradley DG, Jørkov ML, Arneborg J, Lynnerup N, Price N, Gilbert MTP, Allentoft ME, Bill J, Sindbæk SM, Hedeager L, Kristiansen K, Nielsen R, Werge T, Willerslev E. Population genomics of the Viking world. Nature 2020; 585:390-396. [PMID: 32939067 DOI: 10.1038/s41586-020-2688-8] [Citation(s) in RCA: 72] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2019] [Accepted: 05/21/2020] [Indexed: 12/24/2022]
Abstract
The maritime expansion of Scandinavian populations during the Viking Age (about AD 750-1050) was a far-flung transformation in world history1,2. Here we sequenced the genomes of 442 humans from archaeological sites across Europe and Greenland (to a median depth of about 1×) to understand the global influence of this expansion. We find the Viking period involved gene flow into Scandinavia from the south and east. We observe genetic structure within Scandinavia, with diversity hotspots in the south and restricted gene flow within Scandinavia. We find evidence for a major influx of Danish ancestry into England; a Swedish influx into the Baltic; and Norwegian influx into Ireland, Iceland and Greenland. Additionally, we see substantial ancestry from elsewhere in Europe entering Scandinavia during the Viking Age. Our ancient DNA analysis also revealed that a Viking expedition included close family members. By comparing with modern populations, we find that pigmentation-associated loci have undergone strong population differentiation during the past millennium, and trace positively selected loci-including the lactase-persistence allele of LCT and alleles of ANKA that are associated with the immune response-in detail. We conclude that the Viking diaspora was characterized by substantial transregional engagement: distinct populations influenced the genomic makeup of different regions of Europe, and Scandinavia experienced increased contact with the rest of the continent.
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Affiliation(s)
- Ashot Margaryan
- Lundbeck Foundation GeoGenetics Centre, GLOBE Institute, University of Copenhagen, Copenhagen, Denmark.,Institute of Molecular Biology, National Academy of Sciences, Yerevan, Armenia.,Section for Evolutionary Genomics, GLOBE Institute, University of Copenhagen, Copenhagen, Denmark
| | - Daniel J Lawson
- MRC Integrative Epidemiology Unit, University of Bristol, Bristol, UK.,School of Statistical Sciences, University of Bristol, Bristol, UK
| | - Martin Sikora
- Lundbeck Foundation GeoGenetics Centre, GLOBE Institute, University of Copenhagen, Copenhagen, Denmark
| | - Fernando Racimo
- Lundbeck Foundation GeoGenetics Centre, GLOBE Institute, University of Copenhagen, Copenhagen, Denmark
| | - Simon Rasmussen
- Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Ida Moltke
- The Bioinformatics Centre, Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Lara M Cassidy
- Smurfit Institute of Genetics, Trinity College Dublin, Dublin, Ireland
| | - Emil Jørsboe
- The Bioinformatics Centre, Department of Biology, University of Copenhagen, Copenhagen, Denmark.,Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Andrés Ingason
- Lundbeck Foundation GeoGenetics Centre, GLOBE Institute, University of Copenhagen, Copenhagen, Denmark.,Department of Clinical Medicine, University of Copenhagen, Copenhagen, Denmark.,Institute of Biological Psychiatry, Mental Health Services Copenhagen, Copenhagen, Denmark
| | - Mikkel W Pedersen
- Lundbeck Foundation GeoGenetics Centre, GLOBE Institute, University of Copenhagen, Copenhagen, Denmark
| | - Thorfinn Korneliussen
- Lundbeck Foundation GeoGenetics Centre, GLOBE Institute, University of Copenhagen, Copenhagen, Denmark.,HSE University, Russian Federation National Research University Higher School of Economics, Moscow, Russia
| | - Helene Wilhelmson
- Department of Archaeology and Ancient History, Lund University, Lund, Sweden.,Sydsvensk Arkeologi AB, Kristianstad, Sweden
| | - Magdalena M Buś
- Department of Immunology, Genetics and Pathology, Uppsala University, Uppsala, Sweden
| | - Peter de Barros Damgaard
- Lundbeck Foundation GeoGenetics Centre, GLOBE Institute, University of Copenhagen, Copenhagen, Denmark
| | - Rui Martiniano
- Department of Genetics, University of Cambridge, Cambridge, UK
| | - Gabriel Renaud
- Lundbeck Foundation GeoGenetics Centre, GLOBE Institute, University of Copenhagen, Copenhagen, Denmark.,Department of Health Technology, Section for Bioinformatics, Technical University of Denmark (DTU), Copenhagen, Denmark
| | - Claude Bhérer
- Department of Human Genetics, McGill University, Montréal, Quebec, Canada
| | - J Víctor Moreno-Mayar
- Lundbeck Foundation GeoGenetics Centre, GLOBE Institute, University of Copenhagen, Copenhagen, Denmark.,National Institute of Genomic Medicine (INMEGEN), Mexico City, Mexico
| | - Anna K Fotakis
- Section for Evolutionary Genomics, GLOBE Institute, University of Copenhagen, Copenhagen, Denmark
| | - Marie Allen
- Department of Immunology, Genetics and Pathology, Uppsala University, Uppsala, Sweden
| | - Raili Allmäe
- Archaeological Research Collection, Tallinn University, Tallinn, Estonia
| | - Martyna Molak
- Museum and Institute of Zoology, Polish Academy of Sciences, Warsaw, Poland
| | - Enrico Cappellini
- Section for Evolutionary Genomics, GLOBE Institute, University of Copenhagen, Copenhagen, Denmark
| | - Gabriele Scorrano
- Section for Evolutionary Genomics, GLOBE Institute, University of Copenhagen, Copenhagen, Denmark
| | - Hugh McColl
- Lundbeck Foundation GeoGenetics Centre, GLOBE Institute, University of Copenhagen, Copenhagen, Denmark
| | - Alexandra Buzhilova
- Anuchin Research Institute and Museum of Anthropology, Moscow State University, Moscow, Russia
| | - Allison Fox
- Manx National Heritage, Douglas, Isle of Man
| | - Anders Albrechtsen
- The Bioinformatics Centre, Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | | | - Birgitte Skar
- NTNU University Museum, Department of Archaeology and Cultural History, Trondheim, Norway
| | - Caroline Arcini
- The Archaeologists, National Historical Museums, Stockholm, Sweden
| | - Ceri Falys
- Thames Valley Archaeological Services (TVAS), Reading, UK
| | | | | | - Denis Pezhemsky
- Anuchin Research Institute and Museum of Anthropology, Moscow State University, Moscow, Russia
| | - Gordon Turner-Walker
- Department of Cultural Heritage Conservation, National Yunlin University of Science and Technology, Douliou, Taiwan
| | | | - Inge Lundstrøm
- Section for Evolutionary Genomics, GLOBE Institute, University of Copenhagen, Copenhagen, Denmark
| | - Ingrid Gustin
- Department of Archaeology and Ancient History, Lund University, Lund, Sweden
| | - Ingrid Mainland
- UHI Archaeology Institute, University of the Highlands and Islands, Kirkwall, UK
| | - Inna Potekhina
- Department of Bioarchaeology, Institute of Archaeology of National Academy of Sciences of Ukraine, Kiev, Ukraine
| | - Italo M Muntoni
- Soprintendenza Archeologia, Belle Arti e Paesaggio per le Province di Barletta, Andria, Trani e Foggia, Foggia, Italy
| | - Jade Cheng
- Lundbeck Foundation GeoGenetics Centre, GLOBE Institute, University of Copenhagen, Copenhagen, Denmark
| | - Jesper Stenderup
- Lundbeck Foundation GeoGenetics Centre, GLOBE Institute, University of Copenhagen, Copenhagen, Denmark
| | - Jilong Ma
- Lundbeck Foundation GeoGenetics Centre, GLOBE Institute, University of Copenhagen, Copenhagen, Denmark
| | - Julie Gibson
- UHI Archaeology Institute, University of the Highlands and Islands, Kirkwall, UK
| | - Jüri Peets
- Archaeological Research Collection, Tallinn University, Tallinn, Estonia
| | | | - Katrine H Iversen
- Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark.,Department of Health Technology, Section for Bioinformatics, Technical University of Denmark (DTU), Copenhagen, Denmark
| | | | - Lisa Strand
- NTNU University Museum, Department of Archaeology and Cultural History, Trondheim, Norway
| | - Louise Loe
- Heritage Burial Services, Oxford Archaeology, Oxford, UK
| | | | - Marek Florek
- Institute of Archaeology, Maria Curie-Sklodowska University in Lublin, Lublin, Poland
| | | | - Mark Redknap
- Department of History and Archaeology, Amgueddfa Cymru-National Museum Wales, Cardiff, UK
| | - Monika Bajka
- Trzy Epoki Archaeological Service, Klimontów, Poland
| | | | | | - Natalia Grigoreva
- Department of Slavic-Finnish Archaeology, Institute for the History of Material Culture, Russian Academy of Sciences, Saint Petersburg, Russia
| | | | - Ole Kastholm
- Department of Research and Heritage, Roskilde Museum, Roskilde, Denmark
| | | | - Pasquale Favia
- Department of Humanities, University of Foggia, Foggia, Italy
| | - Per Holck
- Department of Molecular Medicine, Faculty of Medicine, University of Oslo, Oslo, Norway
| | - Sabine Sten
- Department of Archaeology and Ancient History, Uppsala University Campus Gotland, Visby, Sweden
| | - Símun V Arge
- Tjóðsavnið - Faroe Islands National Museum, Tórshavn, Faroe Islands
| | - Sturla Ellingvåg
- Lundbeck Foundation GeoGenetics Centre, GLOBE Institute, University of Copenhagen, Copenhagen, Denmark
| | - Vayacheslav Moiseyev
- Peter the Great Museum of Anthropology and Ethnography (Kunstkamera), Russian Academy of Science, St Petersburg, Russia
| | | | | | - Ludovic Orlando
- Laboratoire d'Anthropobiologie Moléculaire et d'Imagerie de Synthèse, CNRS UMR 5288, Université de Toulouse, Université Paul Sabatier, Toulouse, France
| | - Peter Pentz
- National Museum of Denmark, Copenhagen, Denmark
| | | | | | - Mark Collard
- Department of Archaeology, Simon Fraser University, Burnaby, British Colombia, Canada
| | - Daniel G Bradley
- Smurfit Institute of Genetics, Trinity College Dublin, Dublin, Ireland
| | - Marie Louise Jørkov
- Department of Forensic Medicine, University of Copenhagen, Copenhagen, Denmark
| | - Jette Arneborg
- National Museum of Denmark, Copenhagen, Denmark.,School of GeoSciences, University of Edinburgh, Edinburgh, UK
| | - Niels Lynnerup
- Department of Forensic Medicine, University of Copenhagen, Copenhagen, Denmark
| | - Neil Price
- Department of Archaeology and Ancient History, Uppsala University, Uppsala, Sweden
| | - M Thomas P Gilbert
- Section for Evolutionary Genomics, GLOBE Institute, University of Copenhagen, Copenhagen, Denmark.,Department of Natural History, Norwegian University of Science and Technology (NTNU), Trondheim, Norway
| | - Morten E Allentoft
- Lundbeck Foundation GeoGenetics Centre, GLOBE Institute, University of Copenhagen, Copenhagen, Denmark.,Trace and Environmental DNA (TrEnD) Laboratory, School of Molecular and Life Sciences, Curtin University, Perth, Western Australia, Australia
| | - Jan Bill
- Museum of Cultural History, University of Oslo, Oslo, Norway
| | - Søren M Sindbæk
- Centre for Urban Network Evolutions (UrbNet), School of Culture and Society, Aarhus University, Højbjerg, Denmark
| | - Lotte Hedeager
- Institute of Archaeology, Conservation and History, Oslo, Norway
| | | | - Rasmus Nielsen
- Lundbeck Foundation GeoGenetics Centre, GLOBE Institute, University of Copenhagen, Copenhagen, Denmark. .,Department of Integrative Biology, UC Berkeley, Berkeley, CA, USA. .,Department of Statistics, UC Berkeley, Berkeley, CA, USA.
| | - Thomas Werge
- Lundbeck Foundation GeoGenetics Centre, GLOBE Institute, University of Copenhagen, Copenhagen, Denmark. .,Department of Clinical Medicine, University of Copenhagen, Copenhagen, Denmark. .,Institute of Biological Psychiatry, Mental Health Services Copenhagen, Copenhagen, Denmark. .,The Lundbeck Foundation Initiative for Integrative Psychiatric Research, iPSYCH, Copenhagen, Denmark.
| | - Eske Willerslev
- Lundbeck Foundation GeoGenetics Centre, GLOBE Institute, University of Copenhagen, Copenhagen, Denmark. .,Department of Zoology, University of Cambridge, Cambridge, UK. .,The Danish Institute for Advanced Study, University of Southern Denmark, Odense, Denmark. .,The Wellcome Trust Sanger Institute, Cambridge, UK.
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15
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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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16
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Zheng Z, Wang X, Li M, Li Y, Yang Z, Wang X, Pan X, Gong M, Zhang Y, Guo Y, Wang Y, Liu J, Cai Y, Chen Q, Okpeku M, Colli L, Cai D, Wang K, Huang S, Sonstegard TS, Esmailizadeh A, Zhang W, Zhang T, Xu Y, Xu N, Yang Y, Han J, Chen L, Lesur J, Daly KG, Bradley DG, Heller R, Zhang G, Wang W, Chen Y, Jiang Y. The origin of domestication genes in goats. Sci Adv 2020; 6:eaaz5216. [PMID: 32671210 PMCID: PMC7314551 DOI: 10.1126/sciadv.aaz5216] [Citation(s) in RCA: 62] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/16/2019] [Accepted: 03/06/2020] [Indexed: 05/22/2023]
Abstract
Goat domestication was critical for agriculture and civilization, but its underlying genetic changes and selection regimes remain unclear. Here, we analyze the genomes of worldwide domestic goats, wild caprid species, and historical remains, providing evidence of an ancient introgression event from a West Caucasian tur-like species to the ancestor of domestic goats. One introgressed locus with a strong signature of selection harbors the MUC6 gene, which encodes a gastrointestinally secreted mucin. Experiments revealed that the nearly fixed introgressed haplotype confers enhanced immune resistance to gastrointestinal pathogens. Another locus with a strong signal of selection may be related to behavior. The selected alleles at these two loci emerged in domestic goats at least 7200 and 8100 years ago, respectively, and increased to high frequencies concurrent with the expansion of the ubiquitous modern mitochondrial haplogroup A. Tracking these archaeologically cryptic evolutionary transformations provides new insights into the mechanisms of animal domestication.
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Affiliation(s)
- Zhuqing Zheng
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling 712100, China
| | - Xihong Wang
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling 712100, China
| | - Ming Li
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling 712100, China
| | - Yunjia Li
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling 712100, China
| | - Zhirui Yang
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling 712100, China
| | - Xiaolong Wang
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling 712100, China
| | - Xiangyu Pan
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling 712100, China
| | - Mian Gong
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling 712100, China
| | - Yu Zhang
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling 712100, China
| | - Yingwei Guo
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling 712100, China
| | - Yu Wang
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling 712100, China
| | - Jing Liu
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling 712100, China
| | - Yudong Cai
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling 712100, China
| | - Qiuming Chen
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling 712100, China
| | - Moses Okpeku
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, China
- Discipline of Genetics, School of Life Science, University of Kwazulu-Natal, Durban 4000, South Africa
| | - Licia Colli
- Dipartimento di Scienze Animali, della Nutrizione e degli Alimenti, Facoltà di Scienze Agrarie, Alimentari e Ambientali, Università Cattolica del S. Cuore, via Emilia Parmense n. 84, 29122, Piacenza (PC), Italy
- BioDNA–Centro di Ricerca sulla Biodiversità e sul DNA Antico, Facoltà di Scienze Agrarie, Alimentari e Ambientali, Università Cattolica del S. Cuore, via Emilia Parmense n. 84, 29122, Piacenza (PC), Italy
| | - Dawei Cai
- Research Center for Chinese Frontier Archaeology, Jilin University, Changchun 130012, China
| | - Kun Wang
- Center for Ecological and Environmental Sciences, Northwestern Polytechnical University, Xi’an 710072, China
| | - Shisheng Huang
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling 712100, China
| | | | - Ali Esmailizadeh
- Department of Animal Science, Faculty of Agriculture, Shahid Bahonar University of Kerman, Kerman, PB 76169-133, Iran
| | - Wenguang Zhang
- College of Animal Science, Inner Mongolia Agricultural University, Hohhot 010018, China
| | - Tingting Zhang
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling 712100, China
| | - Yangbin Xu
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling 712100, China
| | - Naiyi Xu
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling 712100, China
| | - Yi Yang
- Institute of Preventive Veterinary Medicine, Zhejiang Provincial Key Laboratory of Preventive Veterinary Medicine, College of Animal Sciences, Zhejiang University, Hangzhou 310058, China
| | - Jianlin Han
- CAAS-ILRI Joint Laboratory on Livestock and Forage Genetic Resources, Institute of Animal Science, Chinese Academy of Agriculture Sciences (CAAS), Beijing 100193, China
- International Livestock Research Institute (ILRI), Nairobi 00100, Kenya
| | - Lei Chen
- Center for Ecological and Environmental Sciences, Northwestern Polytechnical University, Xi’an 710072, China
| | | | - Kevin G. Daly
- Smurfit Institute of Genetics, Trinity College Dublin, Dublin 2, Ireland
| | - Daniel G. Bradley
- Smurfit Institute of Genetics, Trinity College Dublin, Dublin 2, Ireland
| | - Rasmus Heller
- Section for Computational and RNA Biology, Department of Biology, University of Copenhagen, Copenhagen N 2200, Denmark
| | - Guojie Zhang
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, China
- China National GeneBank, BGI-Shenzhen, Shenzhen 518083, China
- Section for Ecology and Evolution, Department of Biology, University of Copenhagen, DK-2100 Copenhagen, Denmark
- Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming 650223, China
| | - Wen Wang
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, China
- Center for Ecological and Environmental Sciences, Northwestern Polytechnical University, Xi’an 710072, China
- Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming 650223, China
| | - Yulin Chen
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling 712100, China
| | - Yu Jiang
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling 712100, China
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17
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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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18
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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: 69] [Impact Index Per Article: 11.5] [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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19
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Maixner F, Turaev D, Cazenave-Gassiot A, Janko M, Krause-Kyora B, Hoopmann MR, Kusebauch U, Sartain M, Guerriero G, O'Sullivan N, Teasdale M, Cipollini G, Paladin A, Mattiangeli V, Samadelli M, Tecchiati U, Putzer A, Palazoglu M, Meissen J, Lösch S, Rausch P, Baines JF, Kim BJ, An HJ, Gostner P, Egarter-Vigl E, Malfertheiner P, Keller A, Stark RW, Wenk M, Bishop D, Bradley DG, Fiehn O, Engstrand L, Moritz RL, Doble P, Franke A, Nebel A, Oeggl K, Rattei T, Grimm R, Zink A. The Iceman's Last Meal Consisted of Fat, Wild Meat, and Cereals. Curr Biol 2018; 28:2348-2355.e9. [PMID: 30017480 PMCID: PMC6065529 DOI: 10.1016/j.cub.2018.05.067] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2018] [Revised: 05/15/2018] [Accepted: 05/23/2018] [Indexed: 12/21/2022]
Abstract
The history of humankind is marked by the constant adoption of new dietary habits affecting human physiology, metabolism, and even the development of nutrition-related disorders. Despite clear archaeological evidence for the shift from hunter-gatherer lifestyle to agriculture in Neolithic Europe [1], very little information exists on the daily dietary habits of our ancestors. By undertaking a complementary -omics approach combined with microscopy, we analyzed the stomach content of the Iceman, a 5,300-year-old European glacier mummy [2, 3]. He seems to have had a remarkably high proportion of fat in his diet, supplemented with fresh or dried wild meat, cereals, and traces of toxic bracken. Our multipronged approach provides unprecedented analytical depth, deciphering the nutritional habit, meal composition, and food-processing methods of this Copper Age individual.
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Affiliation(s)
- Frank Maixner
- Eurac Research - Institute for Mummy Studies, Viale Druso 1, 39100 Bolzano, Italy.
| | - Dmitrij Turaev
- CUBE - Division of Computational Systems Biology, Department of Microbiology and Ecosystem Science, University of Vienna, Althanstrasse 14, 1090 Vienna, Austria
| | - Amaury Cazenave-Gassiot
- SLING, Life Sciences Institute, National University of Singapore, Singapore; Department of Biochemistry, National University of Singapore, Singapore
| | - Marek Janko
- Institute of Materials Science, Physics of Surfaces, Technische Universität Darmstadt, Alarich-Weiss-Str. 2, 64287 Darmstadt, Germany; Center of Smart Interfaces, Technische Universität Darmstadt, Alarich-Weiss-Str. 10, 64287 Darmstadt, Germany
| | - Ben Krause-Kyora
- Institute of Clinical Molecular Biology, Kiel University, Rosalind-Franklin-Str. 12, 24105 Kiel, Germany
| | - Michael R Hoopmann
- Institute for Systems Biology, 401 Terry Avenue North, Seattle, WA 98109, USA
| | - Ulrike Kusebauch
- Institute for Systems Biology, 401 Terry Avenue North, Seattle, WA 98109, USA
| | - Mark Sartain
- Institute for Systems Biology, 401 Terry Avenue North, Seattle, WA 98109, USA
| | - Gea Guerriero
- Environmental Research and Innovation (ERIN), Luxembourg Institute of Science and Technology (LIST), Esch/Alzette, Luxembourg
| | - Niall O'Sullivan
- Eurac Research - Institute for Mummy Studies, Viale Druso 1, 39100 Bolzano, Italy
| | - Matthew Teasdale
- Smurfit Institute of Genetics, University of Dublin, Trinity College, Dublin 2, Ireland
| | - Giovanna Cipollini
- Eurac Research - Institute for Mummy Studies, Viale Druso 1, 39100 Bolzano, Italy
| | - Alice Paladin
- Eurac Research - Institute for Mummy Studies, Viale Druso 1, 39100 Bolzano, Italy
| | - Valeria Mattiangeli
- Smurfit Institute of Genetics, University of Dublin, Trinity College, Dublin 2, Ireland
| | - Marco Samadelli
- Eurac Research - Institute for Mummy Studies, Viale Druso 1, 39100 Bolzano, Italy
| | - Umberto Tecchiati
- Responsabile del Laboratorio di Archeozoologia della Soprintendenza Provinciale ai Beni culturali di Bolzano - Alto Adige, Ufficio Beni archeologica, 39100 Bolzano, Italy
| | - Andreas Putzer
- South Tyrol Museum of Archaeology, Museumstrasse 43, 39100 Bolzano, Italy
| | - Mine Palazoglu
- Department of Molecular and Cellular Biology & Genome Center, University of California, Davis, Davis, CA, USA
| | - John Meissen
- Department of Molecular and Cellular Biology & Genome Center, University of California, Davis, Davis, CA, USA
| | - Sandra Lösch
- Department of Physical Anthropology, Institute of Forensic Medicine, University of Bern, Sulgenauweg 40, 3007 Bern, Switzerland
| | - Philipp Rausch
- Max Planck Institute for Evolutionary Biology, August-Thienemann-Strasse 2, D-24306, Plön, Germany
| | - John F Baines
- Max Planck Institute for Evolutionary Biology, August-Thienemann-Strasse 2, D-24306, Plön, Germany
| | - Bum Jin Kim
- Cancer Research Institute & Graduate School of Analytical Science and Technology, Chungnam National University, Daejeon, Korea
| | - Hyun-Joo An
- Cancer Research Institute & Graduate School of Analytical Science and Technology, Chungnam National University, Daejeon, Korea
| | - Paul Gostner
- Department of Radiodiagnostics, Central Hospital Bolzano, Bolzano, Italy
| | - Eduard Egarter-Vigl
- Scuola Superiore Sanitaria Provinciale "Claudiana," Via Lorenz Böhler 13, 39100 Bolzano, Italy
| | - Peter Malfertheiner
- Department of Gastroenterology, Hepatology, and Infectious Diseases, Otto-von-Guericke University, Leipziger Strasse 44, 39120 Magdeburg, Germany
| | - Andreas Keller
- Chair for Clinical Bioinformatics, Saarland University, Medical Faculty, Saarbrücken, Germany
| | - Robert W Stark
- Institute of Materials Science, Physics of Surfaces, Technische Universität Darmstadt, Alarich-Weiss-Str. 2, 64287 Darmstadt, Germany; Center of Smart Interfaces, Technische Universität Darmstadt, Alarich-Weiss-Str. 10, 64287 Darmstadt, Germany
| | - Markus Wenk
- SLING, Life Sciences Institute, National University of Singapore, Singapore; Department of Biochemistry, National University of Singapore, Singapore
| | - David Bishop
- Elemental Bio-imaging Facility, University of Technology Sydney, Broadway, New South Wales, 2007, Australia
| | - Daniel G Bradley
- Smurfit Institute of Genetics, University of Dublin, Trinity College, Dublin 2, Ireland
| | - Oliver Fiehn
- Department of Molecular and Cellular Biology & Genome Center, University of California, Davis, Davis, CA, USA
| | - Lars Engstrand
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, 141 83 Stockholm, Sweden
| | - Robert L Moritz
- Institute for Systems Biology, 401 Terry Avenue North, Seattle, WA 98109, USA
| | - Philip Doble
- Elemental Bio-imaging Facility, University of Technology Sydney, Broadway, New South Wales, 2007, Australia
| | - Andre Franke
- Institute of Clinical Molecular Biology, Kiel University, Rosalind-Franklin-Str. 12, 24105 Kiel, Germany
| | - Almut Nebel
- Institute of Clinical Molecular Biology, Kiel University, Rosalind-Franklin-Str. 12, 24105 Kiel, Germany
| | - Klaus Oeggl
- Institute of Botany, Sternwartestrasse 15, University of Innsbruck, 6020 Innsbruck, Austria
| | - Thomas Rattei
- CUBE - Division of Computational Systems Biology, Department of Microbiology and Ecosystem Science, University of Vienna, Althanstrasse 14, 1090 Vienna, Austria
| | - Rudolf Grimm
- Agilent Technologies, 5301 Stevens Creek Blvd, Santa Clara, CA 95051, USA
| | - Albert Zink
- Eurac Research - Institute for Mummy Studies, Viale Druso 1, 39100 Bolzano, Italy.
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20
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Byrne RP, Martiniano R, Cassidy LM, Carrigan M, Hellenthal G, Hardiman O, Bradley DG, McLaughlin RL. Insular Celtic population structure and genomic footprints of migration. PLoS Genet 2018; 14:e1007152. [PMID: 29370172 PMCID: PMC5784891 DOI: 10.1371/journal.pgen.1007152] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [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: 09/14/2017] [Accepted: 12/13/2017] [Indexed: 12/14/2022] Open
Abstract
Previous studies of the genetic landscape of Ireland have suggested homogeneity, with population substructure undetectable using single-marker methods. Here we have harnessed the haplotype-based method fineSTRUCTURE in an Irish genome-wide SNP dataset, identifying 23 discrete genetic clusters which segregate with geographical provenance. Cluster diversity is pronounced in the west of Ireland but reduced in the east where older structure has been eroded by historical migrations. Accordingly, when populations from the neighbouring island of Britain are included, a west-east cline of Celtic-British ancestry is revealed along with a particularly striking correlation between haplotypes and geography across both islands. A strong relationship is revealed between subsets of Northern Irish and Scottish populations, where discordant genetic and geographic affinities reflect major migrations in recent centuries. Additionally, Irish genetic proximity of all Scottish samples likely reflects older strata of communication across the narrowest inter-island crossing. Using GLOBETROTTER we detected Irish admixture signals from Britain and Europe and estimated dates for events consistent with the historical migrations of the Norse-Vikings, the Anglo-Normans and the British Plantations. The influence of the former is greater than previously estimated from Y chromosome haplotypes. In all, we paint a new picture of the genetic landscape of Ireland, revealing structure which should be considered in the design of studies examining rare genetic variation and its association with traits. A recent genetic study of the UK (People of the British Isles; PoBI) expanded our understanding of population history of the islands, using newly-developed, powerful techniques that harness the rich information embedded in chunks of genetic code called haplotypes. These methods revealed subtle regional diversity across the UK, and, using genetic data alone, timed key migration events into southeast England and Orkney. We have extended these methods to Ireland, identifying regional differences in genetics across the island that adhere to geography at a resolution not previously reported. Our study reveals relative western diversity and eastern homogeneity in Ireland owing to a history of settlement concentrated on the east coast and longstanding Celtic diversity in the west. We show that Irish Celtic diversity enriches the findings of PoBI; haplotypes mirror geography across Britain and Ireland, with relic Celtic populations contributing greatly to haplotypic diversity. Finally, we used genetic information to date migrations into Ireland from Europe and Britain consistent with historical records of Viking and Norman invasions, demonstrating the signatures of these migrations the on modern Irish genome. Our findings demonstrate that genetic structure exists in even small isolated populations, which has important implications for population-based genetic association studies.
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Affiliation(s)
- Ross P. Byrne
- Complex Trait Genomics Laboratory, Smurfit Institute of Genetics, School of Genetics and Microbiology, Trinity College Dublin, College Green, Dublin, Republic of Ireland
- * E-mail: (RPB); (RLM)
| | - Rui Martiniano
- Population Genetics Laboratory, Smurfit Institute of Genetics, School of Genetics and Microbiology, Trinity College Dublin, College Green, Dublin, Republic of Ireland
- Wellcome Trust Sanger Institute, Cambridge, United Kingdom
| | - Lara M. Cassidy
- Population Genetics Laboratory, Smurfit Institute of Genetics, School of Genetics and Microbiology, Trinity College Dublin, College Green, Dublin, Republic of Ireland
| | - Matthew Carrigan
- Ocular Genetics Unit, Smurfit Institute of Genetics, School of Genetics and Microbiology, Trinity College Dublin, College Green, Dublin, Republic of Ireland
| | - Garrett Hellenthal
- UCL Genetics Institute, Department of Genetics, Evolution and Environment, University College London, London, United Kingdom
| | - Orla Hardiman
- Academic Unit of Neurology, Trinity Biomedical Sciences Institute, Trinity College Dublin, Dublin, Republic of Ireland
| | - Daniel G. Bradley
- Population Genetics Laboratory, Smurfit Institute of Genetics, School of Genetics and Microbiology, Trinity College Dublin, College Green, Dublin, Republic of Ireland
| | - Russell L. McLaughlin
- Complex Trait Genomics Laboratory, Smurfit Institute of Genetics, School of Genetics and Microbiology, Trinity College Dublin, College Green, Dublin, Republic of Ireland
- * E-mail: (RPB); (RLM)
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21
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Cassidy LM, Teasdale MD, Carolan S, Enright R, Werner R, Bradley DG, Finlay EK, Mattiangeli V. Capturing goats: documenting two hundred years of mitochondrial DNA diversity among goat populations from Britain and Ireland. Biol Lett 2017; 13:rsbl.2016.0876. [PMID: 28250207 DOI: 10.1098/rsbl.2016.0876] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [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: 11/07/2016] [Accepted: 02/07/2017] [Indexed: 11/12/2022] Open
Abstract
The domestic goat (Capra hircus) plays a key role in global agriculture, being especially prized in regions of marginal pasture. However, the advent of industrialized breeding has seen a dramatic reduction in genetic diversity within commercial populations, while high extinction rates among feral herds have further depleted the reservoir of genetic variation available. Here, we present the first survey of whole mitochondrial genomic variation among the modern and historical goat populations of Britain and Ireland using a combination of mtDNA enrichment and high throughput sequencing. Fifteen historical taxidermy samples, representing the indigenous 'Old Goat' populations of the islands, were sequenced alongside five modern Irish dairy goats and four feral samples from endangered populations in western Ireland. Phylogenetic and network analyses of European mitochondrial variation revealed distinct groupings dominated by historical British and Irish samples, which demonstrate a degree of maternal genetic structure between the goats of insular and continental Europe. Several Irish modern feral samples also fall within these clusters, suggesting continuity between these dwindling populations and the ancestral 'Old Goats' of Ireland and Britain.
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Affiliation(s)
- Lara M Cassidy
- Smurfit Institute of Genetics, Trinity College Dublin, Ireland
| | | | | | - Ruth Enright
- School of Biological, Earth and Environmental Sciences, University College Cork, Cork, Ireland
| | | | | | - Emma K Finlay
- School of Biotechnology, Dublin City University, Dublin, Ireland
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22
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Teasdale MD, Fiddyment S, Vnouček J, Mattiangeli V, Speller C, Binois A, Carver M, Dand C, Newfield TP, Webb CC, Bradley DG, Collins MJ. The York Gospels: a 1000-year biological palimpsest. R Soc Open Sci 2017. [PMID: 29134095 DOI: 10.5061/dryad.1p390] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 05/13/2023]
Abstract
Medieval manuscripts, carefully curated and conserved, represent not only an irreplaceable documentary record but also a remarkable reservoir of biological information. Palaeographic and codicological investigation can often locate and date these documents with remarkable precision. The York Gospels (York Minster Ms. Add. 1) is one such codex, one of only a small collection of pre-conquest Gospel books to have survived the Reformation. By extending the non-invasive triboelectric (eraser-based) sampling technique eZooMS, to include the analysis of DNA, we report a cost-effective and simple-to-use biomolecular sampling technique for parchment. We apply this combined methodology to document for the first time a rich palimpsest of biological information contained within the York Gospels, which has accumulated over the 1000-year lifespan of this cherished object that remains an active participant in the life of York Minster. These biological data provide insights into the decisions made in the selection of materials, the construction of the codex and the use history of the object.
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Affiliation(s)
- Matthew D Teasdale
- Smurfit Institute of Genetics, Trinity College Dublin, Dublin 2, Ireland
| | | | - Jiří Vnouček
- BioArCh, University of York, York YO10 5DD, UK
- Department of Preservation, The Royal Library, København K DK-1016, Denmark
| | | | | | - Annelise Binois
- Department of Archaeology, University of Paris 1 Panthéon-Sorbonne, 3 rue Michelet, 75006 Paris, France
| | - Martin Carver
- Department of Archaeology, University of York, York YO10 5DD, UK
| | - Catherine Dand
- Borthwick Institute for Archives, University of York, York YO10 5DD, UK
| | - Timothy P Newfield
- Departments of History and Biology, Georgetown University, 37th and O Streets NW, ICC 600, Washington, DC 20057, USA
| | | | - Daniel G Bradley
- Smurfit Institute of Genetics, Trinity College Dublin, Dublin 2, Ireland
| | - Matthew J Collins
- BioArCh, University of York, York YO10 5DD, UK
- Museum of Natural History, University of Copenhagen, Copenhagen, Denmark
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23
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Teasdale MD, Fiddyment S, Vnouček J, Mattiangeli V, Speller C, Binois A, Carver M, Dand C, Newfield TP, Webb CC, Bradley DG, Collins MJ. The York Gospels: a 1000-year biological palimpsest. R Soc Open Sci 2017; 4:170988. [PMID: 29134095 PMCID: PMC5666278 DOI: 10.1098/rsos.170988] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/27/2017] [Accepted: 09/22/2017] [Indexed: 05/10/2023]
Abstract
Medieval manuscripts, carefully curated and conserved, represent not only an irreplaceable documentary record but also a remarkable reservoir of biological information. Palaeographic and codicological investigation can often locate and date these documents with remarkable precision. The York Gospels (York Minster Ms. Add. 1) is one such codex, one of only a small collection of pre-conquest Gospel books to have survived the Reformation. By extending the non-invasive triboelectric (eraser-based) sampling technique eZooMS, to include the analysis of DNA, we report a cost-effective and simple-to-use biomolecular sampling technique for parchment. We apply this combined methodology to document for the first time a rich palimpsest of biological information contained within the York Gospels, which has accumulated over the 1000-year lifespan of this cherished object that remains an active participant in the life of York Minster. These biological data provide insights into the decisions made in the selection of materials, the construction of the codex and the use history of the object.
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Affiliation(s)
- Matthew D. Teasdale
- Smurfit Institute of Genetics, Trinity College Dublin, Dublin 2, Ireland
- Authors for correspondence: Matthew D. Teasdale e-mail: ;
| | - Sarah Fiddyment
- BioArCh, University of York, York YO10 5DD, UK
- Authors for correspondence: Sarah Fiddyment e-mail:
| | - Jiří Vnouček
- BioArCh, University of York, York YO10 5DD, UK
- Department of Preservation, The Royal Library, København K DK-1016, Denmark
| | | | | | - Annelise Binois
- Department of Archaeology, University of Paris 1 Panthéon-Sorbonne, 3 rue Michelet, 75006 Paris, France
| | - Martin Carver
- Department of Archaeology, University of York, York YO10 5DD, UK
| | - Catherine Dand
- Borthwick Institute for Archives, University of York, York YO10 5DD, UK
| | - Timothy P. Newfield
- Departments of History and Biology, Georgetown University, 37th and O Streets NW, ICC 600, Washington, DC 20057, USA
| | | | - Daniel G. Bradley
- Smurfit Institute of Genetics, Trinity College Dublin, Dublin 2, Ireland
| | - Matthew J. Collins
- BioArCh, University of York, York YO10 5DD, UK
- Museum of Natural History, University of Copenhagen, Copenhagen, Denmark
- Authors for correspondence: Matthew J. Collins e-mail:
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24
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Martiniano R, Cassidy LM, Ó'Maoldúin R, McLaughlin R, Silva NM, Manco L, Fidalgo D, Pereira T, Coelho MJ, Serra M, Burger J, Parreira R, Moran E, Valera AC, Porfirio E, Boaventura R, Silva AM, Bradley DG. The population genomics of archaeological transition in west Iberia: Investigation of ancient substructure using imputation and haplotype-based methods. PLoS Genet 2017; 13:e1006852. [PMID: 28749934 PMCID: PMC5531429 DOI: 10.1371/journal.pgen.1006852] [Citation(s) in RCA: 77] [Impact Index Per Article: 11.0] [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: 02/22/2017] [Accepted: 06/02/2017] [Indexed: 11/18/2022] Open
Abstract
We analyse new genomic data (0.05–2.95x) from 14 ancient individuals from Portugal distributed from the Middle Neolithic (4200–3500 BC) to the Middle Bronze Age (1740–1430 BC) and impute genomewide diploid genotypes in these together with published ancient Eurasians. While discontinuity is evident in the transition to agriculture across the region, sensitive haplotype-based analyses suggest a significant degree of local hunter-gatherer contribution to later Iberian Neolithic populations. A more subtle genetic influx is also apparent in the Bronze Age, detectable from analyses including haplotype sharing with both ancient and modern genomes, D-statistics and Y-chromosome lineages. However, the limited nature of this introgression contrasts with the major Steppe migration turnovers within third Millennium northern Europe and echoes the survival of non-Indo-European language in Iberia. Changes in genomic estimates of individual height across Europe are also associated with these major cultural transitions, and ancestral components continue to correlate with modern differences in stature. Recent ancient DNA work has demonstrated the significant genetic impact of mass migrations from the Steppe into Central and Northern Europe during the transition from the Neolithic to the Bronze Age. In Iberia, archaeological change at the level of material culture and funerary rituals has been reported during this period, however, the genetic impact associated with this cultural transformation has not yet been estimated. In order to investigate this, we sequence Neolithic and Bronze Age samples from Portugal, which we compare to other ancient and present-day individuals. Genome-wide imputation of a large dataset of ancient samples enabled sensitive methods for detecting population structure and selection in ancient samples. We revealed subtle genetic differentiation between the Portuguese Neolithic and Bronze Age samples suggesting a markedly reduced influx in Iberia compared to other European regions. Furthermore, we predict individual height in ancients, suggesting that stature was reduced in the Neolithic and affected by subsequent admixtures. Lastly, we examine signatures of strong selection in important traits and the timing of their origins.
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Affiliation(s)
- Rui Martiniano
- Smurfit Institute of Genetics, School of Genetics and Microbiology, Trinity College Dublin, Dublin, Ireland
- Research Centre for Anthropology and Health, Department of Life Sciences, University of Coimbra, Coimbra, Portugal
- * E-mail: (DGB); (RM)
| | - Lara M. Cassidy
- Smurfit Institute of Genetics, School of Genetics and Microbiology, Trinity College Dublin, Dublin, Ireland
| | - Ros Ó'Maoldúin
- Smurfit Institute of Genetics, School of Genetics and Microbiology, Trinity College Dublin, Dublin, Ireland
- The Irish Fieldschool of Prehistoric Archaeology, Department of Archaeology, NUI Galway, Galway, Ireland
| | - Russell McLaughlin
- Smurfit Institute of Genetics, School of Genetics and Microbiology, Trinity College Dublin, Dublin, Ireland
| | - Nuno M. Silva
- Department of Genetics & Evolution - Anthropology Unit, University of Geneva, Switzerland
| | - Licinio Manco
- Research Centre for Anthropology and Health, Department of Life Sciences, University of Coimbra, Coimbra, Portugal
| | - Daniel Fidalgo
- Research Centre for Anthropology and Health, Department of Life Sciences, University of Coimbra, Coimbra, Portugal
| | - Tania Pereira
- Research Centre for Anthropology and Health, Department of Life Sciences, University of Coimbra, Coimbra, Portugal
| | - Maria J. Coelho
- Research Centre for Anthropology and Health, Department of Life Sciences, University of Coimbra, Coimbra, Portugal
| | - Miguel Serra
- Palimpsesto - Estudo e Preservação do Património Cultural Lda., Coimbra, Portugal
| | - Joachim Burger
- Palaeogenetics Group, Johannes Gutenberg University, Mainz, Germany
| | - Rui Parreira
- Workgroup on Ancient Peasant Societies, University of Lisbon Archaeological Center, Lisboa, Portugal
| | - Elena Moran
- Workgroup on Ancient Peasant Societies, University of Lisbon Archaeological Center, Lisboa, Portugal
| | - Antonio C. Valera
- Nucleo de Investigação Arqueologica - ERA Arqueologia, Cruz Quebrada, Portugal
- Interdisciplinary Center for Archaeology and Evolution of Human Behavior – University of Algarve, Faro, Portugal
| | - Eduardo Porfirio
- Palimpsesto - Estudo e Preservação do Património Cultural Lda., Coimbra, Portugal
| | - Rui Boaventura
- Workgroup on Ancient Peasant Societies, University of Lisbon Archaeological Center, Lisboa, Portugal
| | - Ana M. Silva
- Research Centre for Anthropology and Health, Department of Life Sciences, University of Coimbra, Coimbra, Portugal
- Workgroup on Ancient Peasant Societies, University of Lisbon Archaeological Center, Lisboa, Portugal
- Laboratory of Forensic Anthropology, Centre for Functional Ecology, Department of Life Sciences, University of Coimbra, Calçada Martim de Freitas, Coimbra, Portugal
| | - Daniel G. Bradley
- Smurfit Institute of Genetics, School of Genetics and Microbiology, Trinity College Dublin, Dublin, Ireland
- * E-mail: (DGB); (RM)
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25
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McLaughlin RL, Schijven D, van Rheenen W, van Eijk KR, O'Brien M, Kahn RS, Ophoff RA, Goris A, Bradley DG, Al-Chalabi A, van den Berg LH, Luykx JJ, Hardiman O, Veldink JH. Genetic correlation between amyotrophic lateral sclerosis and schizophrenia. Nat Commun 2017; 8:14774. [PMID: 28322246 PMCID: PMC5364411 DOI: 10.1038/ncomms14774] [Citation(s) in RCA: 85] [Impact Index Per Article: 12.1] [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: 07/06/2016] [Accepted: 02/03/2017] [Indexed: 12/11/2022] Open
Abstract
We have previously shown higher-than-expected rates of schizophrenia in relatives of patients with amyotrophic lateral sclerosis (ALS), suggesting an aetiological relationship between the diseases. Here, we investigate the genetic relationship between ALS and schizophrenia using genome-wide association study data from over 100,000 unique individuals. Using linkage disequilibrium score regression, we estimate the genetic correlation between ALS and schizophrenia to be 14.3% (7.05-21.6; P=1 × 10-4) with schizophrenia polygenic risk scores explaining up to 0.12% of the variance in ALS (P=8.4 × 10-7). A modest increase in comorbidity of ALS and schizophrenia is expected given these findings (odds ratio 1.08-1.26) but this would require very large studies to observe epidemiologically. We identify five potential novel ALS-associated loci using conditional false discovery rate analysis. It is likely that shared neurobiological mechanisms between these two disorders will engender novel hypotheses in future preclinical and clinical studies.
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Affiliation(s)
- Russell L. McLaughlin
- Academic Unit of Neurology, Trinity Biomedical Sciences Institute, Trinity College Dublin, Dublin DO2 DK07, Republic of Ireland
- Smurfit Institute of Genetics, Trinity College Dublin, Dublin D02 DK07, Republic of Ireland
| | - Dick Schijven
- Department of Neurology and Neurosurgery, Brain Center Rudolf Magnus, University Medical Center Utrecht, Utrecht 3584 CX, The Netherlands
- Department of Psychiatry, Brain Center Rudolf Magnus, University Medical Center Utrecht, Utrecht 3584 CX, The Netherlands
| | - Wouter van Rheenen
- Department of Neurology and Neurosurgery, Brain Center Rudolf Magnus, University Medical Center Utrecht, Utrecht 3584 CX, The Netherlands
| | - Kristel R. van Eijk
- Department of Neurology and Neurosurgery, Brain Center Rudolf Magnus, University Medical Center Utrecht, Utrecht 3584 CX, The Netherlands
| | - Margaret O'Brien
- Academic Unit of Neurology, Trinity Biomedical Sciences Institute, Trinity College Dublin, Dublin DO2 DK07, Republic of Ireland
| | - René S. Kahn
- Department of Psychiatry, Brain Center Rudolf Magnus, University Medical Center Utrecht, Utrecht 3584 CX, The Netherlands
| | - Roel A. Ophoff
- Department of Psychiatry, Brain Center Rudolf Magnus, University Medical Center Utrecht, Utrecht 3584 CX, The Netherlands
- Department of Human Genetics, David Geffen School of Medicine, University of California, Los Angeles, California 90095, USA
- Center for Neurobehavioral Genetics, Semel Institute for Neuroscience and Human Behavior, University of California, Los Angeles, California 90095, USA
| | - An Goris
- Department of Neurosciences, Experimental Neurology and Leuven Research Institute for Neuroscience and Disease (LIND), KU Leuven—University of Leuven, Leuven B-3000, Belgium
| | - Daniel G. Bradley
- Smurfit Institute of Genetics, Trinity College Dublin, Dublin D02 DK07, Republic of Ireland
| | - Ammar Al-Chalabi
- Department of Basic and Clinical Neuroscience, Maurice Wohl Clinical Neuroscience Institute, King's College London, London WC2R 2LS, UK
| | - Leonard H. van den Berg
- Department of Neurology and Neurosurgery, Brain Center Rudolf Magnus, University Medical Center Utrecht, Utrecht 3584 CX, The Netherlands
| | - Jurjen J. Luykx
- Department of Neurology and Neurosurgery, Brain Center Rudolf Magnus, University Medical Center Utrecht, Utrecht 3584 CX, The Netherlands
- Department of Psychiatry, Brain Center Rudolf Magnus, University Medical Center Utrecht, Utrecht 3584 CX, The Netherlands
- Department of Psychiatry, Hospital Network Antwerp (ZNA) Stuivenberg and Sint Erasmus, Antwerp 2020, Belgium
| | - Orla Hardiman
- Smurfit Institute of Genetics, Trinity College Dublin, Dublin D02 DK07, Republic of Ireland
| | - Jan H. Veldink
- Department of Neurology and Neurosurgery, Brain Center Rudolf Magnus, University Medical Center Utrecht, Utrecht 3584 CX, The Netherlands
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26
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Jones ER, Zarina G, Moiseyev V, Lightfoot E, Nigst PR, Manica A, Pinhasi R, Bradley DG. The Neolithic Transition in the Baltic Was Not Driven by Admixture with Early European Farmers. Curr Biol 2017; 27:576-582. [PMID: 28162894 PMCID: PMC5321670 DOI: 10.1016/j.cub.2016.12.060] [Citation(s) in RCA: 83] [Impact Index Per Article: 11.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2016] [Revised: 11/10/2016] [Accepted: 12/29/2016] [Indexed: 12/04/2022]
Abstract
The Neolithic transition was a dynamic time in European prehistory of cultural, social, and technological change. Although this period has been well explored in central Europe using ancient nuclear DNA [1, 2], its genetic impact on northern and eastern parts of this continent has not been as extensively studied. To broaden our understanding of the Neolithic transition across Europe, we analyzed eight ancient genomes: six samples (four to ∼1- to 4-fold coverage) from a 3,500 year temporal transect (∼8,300–4,800 calibrated years before present) through the Baltic region dating from the Mesolithic to the Late Neolithic and two samples spanning the Mesolithic-Neolithic boundary from the Dnieper Rapids region of Ukraine. We find evidence that some hunter-gatherer ancestry persisted across the Neolithic transition in both regions. However, we also find signals consistent with influxes of non-local people, most likely from northern Eurasia and the Pontic Steppe. During the Late Neolithic, this Steppe-related impact coincides with the proposed emergence of Indo-European languages in the Baltic region [3, 4]. These influences are distinct from the early farmer admixture that transformed the genetic landscape of central Europe, suggesting that changes associated with the Neolithic package in the Baltic were not driven by the same Anatolian-sourced genetic exchange. A degree of genetic continuity from the Mesolithic to the Neolithic in the Baltic Steppe-related genetic influences found in the Baltic during the Neolithic No Anatolian farmer-related genetic admixture in Neolithic Baltic samples Steppe ancestry in Latvia at the time of the emergence of Balto-Slavic languages
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Affiliation(s)
- Eppie R Jones
- Smurfit Institute of Genetics, Trinity College Dublin, Dublin 2, Ireland; Department of Zoology, University of Cambridge, Downing Street, Cambridge CB2 3EJ, UK.
| | - Gunita Zarina
- Institute of Latvian History, University of Latvia, Kalpaka Bulvāris 4, Rīga 1050, Latvia
| | - Vyacheslav Moiseyev
- Peter the Great Museum of Anthropology and Ethnography (Kunstkamera) RAS, 199034 St. Petersburg, Russia
| | - Emma Lightfoot
- McDonald Institute for Archaeological Research, University of Cambridge, Downing Street, Cambridge CB2 3ER, UK
| | - Philip R Nigst
- Division of Archaeology, Department of Archaeology and Anthropology, University of Cambridge, Downing Street, Cambridge CB2 3DZ, UK
| | - Andrea Manica
- Department of Zoology, University of Cambridge, Downing Street, Cambridge CB2 3EJ, UK.
| | - Ron Pinhasi
- School of Archaeology and Earth Institute, Belfield, University College Dublin, Dublin 4, Ireland.
| | - Daniel G Bradley
- Smurfit Institute of Genetics, Trinity College Dublin, Dublin 2, Ireland.
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27
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Siska V, Jones ER, Jeon S, Bhak Y, Kim HM, Cho YS, Kim H, Lee K, Veselovskaya E, Balueva T, Gallego-Llorente M, Hofreiter M, Bradley DG, Eriksson A, Pinhasi R, Bhak J, Manica A. Genome-wide data from two early Neolithic East Asian individuals dating to 7700 years ago. Sci Adv 2017; 3:e1601877. [PMID: 28164156 PMCID: PMC5287702 DOI: 10.1126/sciadv.1601877] [Citation(s) in RCA: 58] [Impact Index Per Article: 8.3] [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: 08/10/2016] [Accepted: 12/21/2016] [Indexed: 05/06/2023]
Abstract
Ancient genomes have revolutionized our understanding of Holocene prehistory and, particularly, the Neolithic transition in western Eurasia. In contrast, East Asia has so far received little attention, despite representing a core region at which the Neolithic transition took place independently ~3 millennia after its onset in the Near East. We report genome-wide data from two hunter-gatherers from Devil's Gate, an early Neolithic cave site (dated to ~7.7 thousand years ago) located in East Asia, on the border between Russia and Korea. Both of these individuals are genetically most similar to geographically close modern populations from the Amur Basin, all speaking Tungusic languages, and, in particular, to the Ulchi. The similarity to nearby modern populations and the low levels of additional genetic material in the Ulchi imply a high level of genetic continuity in this region during the Holocene, a pattern that markedly contrasts with that reported for Europe.
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Affiliation(s)
- Veronika Siska
- Department of Zoology, University of Cambridge, Downing Street, Cambridge CB23EJ, U.K
- Corresponding author. (V.S.); (R.P.); (J.B.); (A.M.)
| | - Eppie Ruth Jones
- Department of Zoology, University of Cambridge, Downing Street, Cambridge CB23EJ, U.K
- Smurfit Institute of Genetics, Trinity College Dublin, Dublin, Ireland
| | - Sungwon Jeon
- The Genomics Institute, Ulsan National Institute of Science and Technology, Ulsan 44919, Republic of Korea
| | - Youngjune Bhak
- The Genomics Institute, Ulsan National Institute of Science and Technology, Ulsan 44919, Republic of Korea
| | - Hak-Min Kim
- The Genomics Institute, Ulsan National Institute of Science and Technology, Ulsan 44919, Republic of Korea
| | - Yun Sung Cho
- The Genomics Institute, Ulsan National Institute of Science and Technology, Ulsan 44919, Republic of Korea
| | - Hyunho Kim
- Geromics, Ulsan 44919, Republic of Korea
| | - Kyusang Lee
- Clinomics Inc., Ulsan 4919, Republic of Korea
| | | | - Tatiana Balueva
- Institute of Ethnology and Anthropology, Russian Academy of Sciences, Moscow, Russia
| | | | - Michael Hofreiter
- Institute for Biochemistry and Biology, Faculty for Mathematics and Natural Sciences, University of Potsdam, Karl-Liebknecht-Str. 24-25, 14476 Potsdam-Golm, Germany
| | - Daniel G. Bradley
- Smurfit Institute of Genetics, Trinity College Dublin, Dublin, Ireland
| | - Anders Eriksson
- Department of Zoology, University of Cambridge, Downing Street, Cambridge CB23EJ, U.K
| | - Ron Pinhasi
- School of Archaeology and Earth Institute, University College Dublin, Dublin, Ireland
- Corresponding author. (V.S.); (R.P.); (J.B.); (A.M.)
| | - Jong Bhak
- The Genomics Institute, Ulsan National Institute of Science and Technology, Ulsan 44919, Republic of Korea
- Geromics, Ulsan 44919, Republic of Korea
- Corresponding author. (V.S.); (R.P.); (J.B.); (A.M.)
| | - Andrea Manica
- Department of Zoology, University of Cambridge, Downing Street, Cambridge CB23EJ, U.K
- Corresponding author. (V.S.); (R.P.); (J.B.); (A.M.)
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28
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O'Sullivan NJ, Teasdale MD, Mattiangeli V, Maixner F, Pinhasi R, Bradley DG, Zink A. A whole mitochondria analysis of the Tyrolean Iceman's leather provides insights into the animal sources of Copper Age clothing. Sci Rep 2016; 6:31279. [PMID: 27537861 PMCID: PMC4989873 DOI: 10.1038/srep31279] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2016] [Accepted: 07/15/2016] [Indexed: 02/07/2023] Open
Abstract
The attire of the Tyrolean Iceman, a 5,300-year-old natural mummy from the Ötzal Italian Alps, provides a surviving example of ancient manufacturing technologies. Research into his garments has however, been limited by ambiguity surrounding their source species. Here we present a targeted enrichment and sequencing of full mitochondrial genomes sampled from his clothes and quiver, which elucidates the species of production for nine fragments. Results indicate that the majority of the samples originate from domestic ungulate species (cattle, sheep and goat), whose recovered haplogroups are now at high frequency in today’s domestic populations. Intriguingly, the hat and quiver samples were produced from wild species, brown bear and roe deer respectively. Combined, these results suggest that Copper Age populations made considered choices of clothing material from both the wild and domestic populations available to them. Moreover, these results show the potential for the recovery of complete mitochondrial genomes from degraded prehistoric artefacts.
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Affiliation(s)
- Niall J O'Sullivan
- Institute for Mummies and the Iceman, EURAC research, 39100 Bolzano, Italy.,School of Archaeology and Earth Institute, University College Dublin, Belfield, Dublin 4, Ireland
| | - Matthew D Teasdale
- Smurfit Institute of Genetics, University of Dublin, Trinity College, Dublin 2, Ireland
| | - Valeria Mattiangeli
- Smurfit Institute of Genetics, University of Dublin, Trinity College, Dublin 2, Ireland
| | - Frank Maixner
- Institute for Mummies and the Iceman, EURAC research, 39100 Bolzano, Italy
| | - Ron Pinhasi
- School of Archaeology and Earth Institute, University College Dublin, Belfield, Dublin 4, Ireland
| | - Daniel G Bradley
- Smurfit Institute of Genetics, University of Dublin, Trinity College, Dublin 2, Ireland
| | - Albert Zink
- Institute for Mummies and the Iceman, EURAC research, 39100 Bolzano, Italy
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29
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Broushaki F, Thomas MG, Link V, López S, van Dorp L, Kirsanow K, Hofmanová Z, Diekmann Y, Cassidy LM, Díez-Del-Molino D, Kousathanas A, Sell C, Robson HK, Martiniano R, Blöcher J, Scheu A, Kreutzer S, Bollongino R, Bobo D, Davudi H, Munoz O, Currat M, Abdi K, Biglari F, Craig OE, Bradley DG, Shennan S, Veeramah K, Mashkour M, Wegmann D, Hellenthal G, Burger J. Early Neolithic genomes from the eastern Fertile Crescent. Science 2016; 353:499-503. [PMID: 27417496 DOI: 10.1126/science.aaf7943] [Citation(s) in RCA: 138] [Impact Index Per Article: 17.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2016] [Accepted: 07/05/2016] [Indexed: 01/06/2023]
Abstract
We sequenced Early Neolithic genomes from the Zagros region of Iran (eastern Fertile Crescent), where some of the earliest evidence for farming is found, and identify a previously uncharacterized population that is neither ancestral to the first European farmers nor has contributed substantially to the ancestry of modern Europeans. These people are estimated to have separated from Early Neolithic farmers in Anatolia some 46,000 to 77,000 years ago and show affinities to modern-day Pakistani and Afghan populations, but particularly to Iranian Zoroastrians. We conclude that multiple, genetically differentiated hunter-gatherer populations adopted farming in southwestern Asia, that components of pre-Neolithic population structure were preserved as farming spread into neighboring regions, and that the Zagros region was the cradle of eastward expansion.
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Affiliation(s)
- Farnaz Broushaki
- Palaeogenetics Group, Johannes Gutenberg University Mainz, 55099 Mainz, Germany
| | - Mark G Thomas
- Department of Genetics, Evolution and Environment, University College London, London WC1E 6BT, UK
| | - Vivian Link
- Department of Biology, University of Fribourg, 1700 Fribourg, Switzerland.,Swiss Institute of Bioinformatics, 1015 Lausanne, Switzerland
| | - Saioa López
- Department of Genetics, Evolution and Environment, University College London, London WC1E 6BT, UK
| | - Lucy van Dorp
- Department of Genetics, Evolution and Environment, University College London, London WC1E 6BT, UK
| | - Karola Kirsanow
- Palaeogenetics Group, Johannes Gutenberg University Mainz, 55099 Mainz, Germany
| | - Zuzana Hofmanová
- Palaeogenetics Group, Johannes Gutenberg University Mainz, 55099 Mainz, Germany
| | - Yoan Diekmann
- Department of Genetics, Evolution and Environment, University College London, London WC1E 6BT, UK
| | - Lara M Cassidy
- Smurfit Institute of Genetics, Trinity College Dublin, Dublin 2, Ireland
| | - David Díez-Del-Molino
- Department of Genetics, Evolution and Environment, University College London, London WC1E 6BT, UK.,Department of Bioinformatics and Genetics, Swedish Museum of Natural History, SE-10405, Stockholm, Sweden
| | - Athanasios Kousathanas
- Department of Biology, University of Fribourg, 1700 Fribourg, Switzerland.,Swiss Institute of Bioinformatics, 1015 Lausanne, Switzerland.,Unit of Human Evolutionary Genetics, Institut Pasteur, 75015 Paris, France
| | - Christian Sell
- Palaeogenetics Group, Johannes Gutenberg University Mainz, 55099 Mainz, Germany
| | - Harry K Robson
- BioArCh, Department of Archaeology, University of York, York, YO10 5YW, UK
| | - Rui Martiniano
- Smurfit Institute of Genetics, Trinity College Dublin, Dublin 2, Ireland
| | - Jens Blöcher
- Palaeogenetics Group, Johannes Gutenberg University Mainz, 55099 Mainz, Germany
| | - Amelie Scheu
- Palaeogenetics Group, Johannes Gutenberg University Mainz, 55099 Mainz, Germany
| | - Susanne Kreutzer
- Palaeogenetics Group, Johannes Gutenberg University Mainz, 55099 Mainz, Germany
| | - Ruth Bollongino
- Palaeogenetics Group, Johannes Gutenberg University Mainz, 55099 Mainz, Germany
| | - Dean Bobo
- Department of Ecology and Evolution, Stony Brook University, Stony Brook, New York, 11794- 5245, USA
| | - Hossein Davudi
- Department of Archaeology, Faculty of Humanities, Tarbiat Modares University, Tehran, Iran
| | - Olivia Munoz
- UMR 7041 ArScAn -VEPMO, Maison de l'Archéologie et de l'Ethnologie, 21 allée de l'Université, 92023 Nanterre, France
| | - Mathias Currat
- Department of Genetics & Evolution-Anthropology Unit, University of Geneva, 1211 Geneva, Switzerland
| | - Kamyar Abdi
- Samuel Jordan Center for Persian Studies and Culture, University of California-lrvine, Irvine, CA 92697-3370, USA
| | - Fereidoun Biglari
- Paleolithic Department, National Museum of Iran, 113617111, Tehran, Iran
| | - Oliver E Craig
- BioArCh, Department of Archaeology, University of York, York, YO10 5YW, UK
| | - Daniel G Bradley
- Smurfit Institute of Genetics, Trinity College Dublin, Dublin 2, Ireland
| | - Stephen Shennan
- Institute of Archaeology, University College London, London WC1H 0PY, UK
| | - Krishna Veeramah
- Department of Ecology and Evolution, Stony Brook University, Stony Brook, New York, 11794- 5245, USA
| | - Marjan Mashkour
- CNRS/MNHN/SUs - UMR 7209, Archéozoologie et Archéobotanique, Sociétés, Pratiques et Environnements, Département Ecologie et Gestion de la Biodiversité, 55 rue Buffon, 75005 Paris, France
| | - Daniel Wegmann
- Department of Biology, University of Fribourg, 1700 Fribourg, Switzerland.,Swiss Institute of Bioinformatics, 1015 Lausanne, Switzerland
| | - Garrett Hellenthal
- Department of Genetics, Evolution and Environment, University College London, London WC1E 6BT, UK
| | - Joachim Burger
- Palaeogenetics Group, Johannes Gutenberg University Mainz, 55099 Mainz, Germany
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30
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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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31
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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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32
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Richardson IW, Berry DP, Wiencko HL, Higgins IM, More SJ, McClure J, Lynn DJ, Bradley DG. A genome-wide association study for genetic susceptibility to Mycobacterium bovis infection in dairy cattle identifies a susceptibility QTL on chromosome 23. Genet Sel Evol 2016; 48:19. [PMID: 26960806 PMCID: PMC4784436 DOI: 10.1186/s12711-016-0197-x] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2015] [Accepted: 02/29/2016] [Indexed: 01/08/2023] Open
Abstract
Background Bovine tuberculosis (bTB) infection in cattle is a significant economic concern in many countries, with annual costs to the UK and Irish governments of approximately €190 million and €63 million, respectively, for bTB control. The existence of host additive and non-additive genetic components to bTB susceptibility has been established. Methods Two approaches i.e. single-SNP (single nucleotide polymorphism) regression and a Bayesian method were applied to genome-wide association studies (GWAS) using high-density SNP genotypes (n = 597,144 SNPs) from 841 dairy artificial insemination (AI) sires. Deregressed estimated breeding values for bTB susceptibility were used as the quantitative dependent variable. Network analysis was performed using the quantitative trait loci (QTL) that were identified as significant in the single-SNP regression and Bayesian analyses separately. In addition, an identity-by-descent analysis was performed on a subset of the most prolific sires in the dataset that showed contrasting prevalences of bTB infection in daughters. Results A significant QTL region was identified on BTA23 (P value >1 × 10−5, Bayes factor >10) across all analyses. Sires with the minor allele (minor allele frequency = 0.136) for this QTL on BTA23 had estimated breeding values that conferred a greater susceptibility to bTB infection than those that were homozygous for the major allele. Imputation of the regions that flank this QTL on BTA23 to full sequence indicated that the most significant associations were located within introns of the FKBP5 gene. Conclusions A genomic region on BTA23 that is strongly associated with host susceptibility to bTB infection was identified. This region contained FKBP5, a gene involved in the TNFα/NFκ-B signalling pathway, which is a major biological pathway associated with immune response. Although there is no study that validates this region in the literature, our approach represents one of the most powerful studies for the analysis of bTB susceptibility to
date. Electronic supplementary material The online version of this article (doi:10.1186/s12711-016-0197-x) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Ian W Richardson
- Smurfit Institute of Genetics, University of Dublin, Trinity College, Dublin 2, Ireland. .,Animal and Grassland Research and Innovation Centre, Teagasc, Moorepark, Fermoy, Co. Cork, Ireland.
| | - Donagh P Berry
- Animal and Grassland Research and Innovation Centre, Teagasc, Moorepark, Fermoy, Co. Cork, Ireland.
| | - Heather L Wiencko
- Animal and Bioscience Research Department, Animal and Grassland Research and Innovation Centre, Teagasc, Grange, Co. Meath, Ireland.
| | - Isabella M Higgins
- UCD Centre for Veterinary Epidemiology and Risk Analysis, UCD School of Veterinary Medicine, University College Dublin, Belfield, Dublin 4, Ireland.
| | - Simon J More
- UCD Centre for Veterinary Epidemiology and Risk Analysis, UCD School of Veterinary Medicine, University College Dublin, Belfield, Dublin 4, Ireland.
| | | | - David J Lynn
- Animal and Bioscience Research Department, Animal and Grassland Research and Innovation Centre, Teagasc, Grange, Co. Meath, Ireland. .,South Australian Health and Medical Research Institute, North Terrace, Adelaide, SA, 5000, Australia. .,School of Medicine, Flinders University, Bedford Park, SA, 5042, Australia.
| | - Daniel G Bradley
- Smurfit Institute of Genetics, University of Dublin, Trinity College, Dublin 2, Ireland.
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33
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Martiniano R, Caffell A, Holst M, Hunter-Mann K, Montgomery J, Müldner G, McLaughlin RL, Teasdale MD, van Rheenen W, Veldink JH, van den Berg LH, Hardiman O, Carroll M, Roskams S, Oxley J, Morgan C, Thomas MG, Barnes I, McDonnell C, Collins MJ, Bradley DG. Genomic signals of migration and continuity in Britain before the Anglo-Saxons. Nat Commun 2016; 7:10326. [PMID: 26783717 PMCID: PMC4735653 DOI: 10.1038/ncomms10326] [Citation(s) in RCA: 65] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2015] [Accepted: 11/25/2015] [Indexed: 11/09/2022] Open
Abstract
The purported migrations that have formed the peoples of Britain have been the focus of generations of scholarly controversy. However, this has not benefited from direct analyses of ancient genomes. Here we report nine ancient genomes (∼ 1 ×) of individuals from northern Britain: seven from a Roman era York cemetery, bookended by earlier Iron-Age and later Anglo-Saxon burials. Six of the Roman genomes show affinity with modern British Celtic populations, particularly Welsh, but significantly diverge from populations from Yorkshire and other eastern English samples. They also show similarity with the earlier Iron-Age genome, suggesting population continuity, but differ from the later Anglo-Saxon genome. This pattern concords with profound impact of migrations in the Anglo-Saxon period. Strikingly, one Roman skeleton shows a clear signal of exogenous origin, with affinities pointing towards the Middle East, confirming the cosmopolitan character of the Empire, even at its northernmost fringes.
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Affiliation(s)
- Rui Martiniano
- Smurfit Institute of Genetics, School of Genetics and Microbiology, Trinity College Dublin, Dublin 2, Ireland
| | - Anwen Caffell
- York Osteoarchaeology Ltd, 75 Main Street, Bishop Wilton, York YO42 1SR, UK.,Department of Archaeology, Dawson Building, Durham University, South Road, Durham DH1 3LE, UK
| | - Malin Holst
- York Osteoarchaeology Ltd, 75 Main Street, Bishop Wilton, York YO42 1SR, UK.,BioArCh, Biology, S Block, Wentworth Way, York YO10 5DD, UK
| | - Kurt Hunter-Mann
- York Archaeological Trust for Excavation and Research Limited, 47 Aldwark, York YO1 7BX, UK
| | - Janet Montgomery
- Department of Archaeology, Dawson Building, Durham University, South Road, Durham DH1 3LE, UK
| | - Gundula Müldner
- Department of Archaeology, University of Reading, Whiteknights PO Box 227, Reading RG6 6AB, UK
| | - Russell L McLaughlin
- Smurfit Institute of Genetics, School of Genetics and Microbiology, Trinity College Dublin, Dublin 2, Ireland
| | - Matthew D Teasdale
- Smurfit Institute of Genetics, School of Genetics and Microbiology, Trinity College Dublin, Dublin 2, Ireland
| | - Wouter van Rheenen
- Department of Neurology and Neurosurgery, Brain Center Rudolf Magnus, University Medical Center Utrecht, Heidelberglaan 100, 3584 CX Utrecht, The Netherlands
| | - Jan H Veldink
- Department of Neurology and Neurosurgery, Brain Center Rudolf Magnus, University Medical Center Utrecht, Heidelberglaan 100, 3584 CX Utrecht, The Netherlands
| | - Leonard H van den Berg
- Department of Neurology and Neurosurgery, Brain Center Rudolf Magnus, University Medical Center Utrecht, Heidelberglaan 100, 3584 CX Utrecht, The Netherlands
| | - Orla Hardiman
- Academic Unit of Neurology, Trinity Biomedical Sciences Institute, Trinity College Dublin, Pearse Street, Dublin 2, Ireland
| | - Maureen Carroll
- Department of Archaeology, University of Sheffield Northgate House, West Street, Sheffield S1 4ET, UK
| | - Steve Roskams
- BioArCh, Biology, S Block, Wentworth Way, York YO10 5DD, UK
| | | | - Colleen Morgan
- BioArCh, Biology, S Block, Wentworth Way, York YO10 5DD, UK
| | - Mark G Thomas
- Research Department of Genetics, Evolution and Environment, University College London, Gower Street, London WC1E 6BT, UK
| | - Ian Barnes
- Department of Earth Sciences, Natural History Museum, Cromwell Road, London SW7 5BD, UK
| | - Christine McDonnell
- York Archaeological Trust for Excavation and Research Limited, 47 Aldwark, York YO1 7BX, UK
| | | | - Daniel G Bradley
- Smurfit Institute of Genetics, School of Genetics and Microbiology, Trinity College Dublin, Dublin 2, Ireland
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Park SDE, Magee DA, McGettigan PA, Teasdale MD, Edwards CJ, Lohan AJ, Murphy A, Braud M, Donoghue MT, Liu Y, Chamberlain AT, Rue-Albrecht K, Schroeder S, Spillane C, Tai S, Bradley DG, Sonstegard TS, Loftus BJ, MacHugh DE. Genome sequencing of the extinct Eurasian wild aurochs, Bos primigenius, illuminates the phylogeography and evolution of cattle. Genome Biol 2015; 16:234. [PMID: 26498365 PMCID: PMC4620651 DOI: 10.1186/s13059-015-0790-2] [Citation(s) in RCA: 104] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2015] [Accepted: 09/25/2015] [Indexed: 11/10/2022] Open
Abstract
Background Domestication of the now-extinct wild aurochs, Bos primigenius, gave rise to the two major domestic extant cattle taxa, B. taurus and B. indicus. While previous genetic studies have shed some light on the evolutionary relationships between European aurochs and modern cattle, important questions remain unanswered, including the phylogenetic status of aurochs, whether gene flow from aurochs into early domestic populations occurred, and which genomic regions were subject to selection processes during and after domestication. Here, we address these questions using whole-genome sequencing data generated from an approximately 6,750-year-old British aurochs bone and genome sequence data from 81 additional cattle plus genome-wide single nucleotide polymorphism data from a diverse panel of 1,225 modern animals. Results Phylogenomic analyses place the aurochs as a distinct outgroup to the domestic B. taurus lineage, supporting the predominant Near Eastern origin of European cattle. Conversely, traditional British and Irish breeds share more genetic variants with this aurochs specimen than other European populations, supporting localized gene flow from aurochs into the ancestors of modern British and Irish cattle, perhaps through purposeful restocking by early herders in Britain. Finally, the functions of genes showing evidence for positive selection in B. taurus are enriched for neurobiology, growth, metabolism and immunobiology, suggesting that these biological processes have been important in the domestication of cattle. Conclusions This work provides important new information regarding the origins and functional evolution of modern cattle, revealing that the interface between early European domestic populations and wild aurochs was significantly more complex than previously thought. Electronic supplementary material The online version of this article (doi:10.1186/s13059-015-0790-2) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Stephen D E Park
- IdentiGEN Ltd, Unit 2, Trinity Enterprise Centre, Pearse Street, Dublin 2, Ireland.
| | - David A Magee
- Animal Genomics Laboratory, UCD School of Agriculture and Food Science, University College Dublin, Belfield, Dublin 4, Ireland. .,Department of Animal Science, University of Connecticut, Storrs, CT, 06029, USA.
| | - Paul A McGettigan
- Animal Genomics Laboratory, UCD School of Agriculture and Food Science, University College Dublin, Belfield, Dublin 4, Ireland.
| | | | - Ceiridwen J Edwards
- Research Laboratory for Archaeology and the History of Art, Dyson Perrins Building, South Parks Rd, Oxford, OX1 3QY, UK.
| | - Amanda J Lohan
- UCD Conway Institute of Biomolecular and Biomedical Research, University College Dublin, Dublin 4, Ireland.
| | - Alison Murphy
- UCD Conway Institute of Biomolecular and Biomedical Research, University College Dublin, Dublin 4, Ireland.
| | - Martin Braud
- Genetics and Biotechnology Laboratory, Plant and AgriBiosciences Research Centre (PABC), School of Natural Sciences, National University of Ireland Galway, University Road, Galway, Ireland.
| | - Mark T Donoghue
- Genetics and Biotechnology Laboratory, Plant and AgriBiosciences Research Centre (PABC), School of Natural Sciences, National University of Ireland Galway, University Road, Galway, Ireland.
| | - Yuan Liu
- BGI Shenzhen, Beishan Industrial Zone, Yantian District, Shenzhen, 518083, China.
| | - Andrew T Chamberlain
- Faculty of Life Sciences, University of Manchester, Oxford Road, Manchester, M13 9PT, UK.
| | - Kévin Rue-Albrecht
- Animal Genomics Laboratory, UCD School of Agriculture and Food Science, University College Dublin, Belfield, Dublin 4, Ireland.
| | - Steven Schroeder
- Animal Genomics and Improvement Laboratory, Agricultural Research Service, USDA, Beltsville, MD, 20705-2350, USA.
| | - Charles Spillane
- Genetics and Biotechnology Laboratory, Plant and AgriBiosciences Research Centre (PABC), School of Natural Sciences, National University of Ireland Galway, University Road, Galway, Ireland.
| | - Shuaishuai Tai
- BGI Shenzhen, Beishan Industrial Zone, Yantian District, Shenzhen, 518083, China.
| | - Daniel G Bradley
- Smurfit Institute of Genetics, Trinity College, Dublin 2, Ireland.
| | - Tad S Sonstegard
- Animal Genomics and Improvement Laboratory, Agricultural Research Service, USDA, Beltsville, MD, 20705-2350, USA. .,Recombinetics Inc., St. Paul, MN, 55104, USA.
| | - Brendan J Loftus
- UCD Conway Institute of Biomolecular and Biomedical Research, University College Dublin, Dublin 4, Ireland. .,UCD School of Medicine, University College Dublin, Belfield, Dublin 4, Ireland.
| | - David E MacHugh
- Animal Genomics Laboratory, UCD School of Agriculture and Food Science, University College Dublin, Belfield, Dublin 4, Ireland. .,UCD Conway Institute of Biomolecular and Biomedical Research, University College Dublin, Dublin 4, Ireland.
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Vegh P, Magee DA, Nalpas NC, Bryan K, McCabe MS, Browne JA, Conlon KM, Gordon SV, Bradley DG, MacHugh DE, Lynn DJ. MicroRNA profiling of the bovine alveolar macrophage response to Mycobacterium bovis infection suggests pathogen survival is enhanced by microRNA regulation of endocytosis and lysosome trafficking. Tuberculosis (Edinb) 2015; 95:60-7. [PMID: 25692199 DOI: 10.1016/j.tube.2014.10.011] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
Mycobacterium bovis, the causative agent of bovine tuberculosis, a major problem for global agriculture, spreads via an airborne route and is taken up by alveolar macrophages (AM) in the lung. Here, we describe the first next-generation sequencing (RNA-seq) approach to temporally profile miRNA expression in primary bovine AMs post-infection with M. bovis. One, six, and forty miRNAs were identified as significantly differentially expressed at 2, 24 and 48 h post-infection, respectively. The differential expression of three miRNAs (bta-miR-142-5p, bta-miR-146a, and bta-miR-423-3p) was confirmed by RT-qPCR. Pathway analysis of the predicted mRNA targets of differentially expressed miRNAs suggests that these miRNAs preferentially target several pathways that are functionally relevant for mycobacterial pathogenesis, including endocytosis and lysosome trafficking, IL-1 signalling and the TGF-β pathway. Over-expression studies using a bovine macrophage cell-line (Bomac) reveal the targeting of two key genes in the innate immune response to M. bovis, IL-1 receptor-associated kinase 1 (IRAK1) and TGF-β receptor 2 (TGFBR2), by miR-146. Taken together, our study suggests that miRNAs play a key role in tuning the complex interplay between M. bovis survival strategies and the host immune response.
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Teasdale MD, van Doorn NL, Fiddyment S, Webb CC, O'Connor T, Hofreiter M, Collins MJ, Bradley DG. Paging through history: parchment as a reservoir of ancient DNA for next generation sequencing. Philos Trans R Soc Lond B Biol Sci 2015; 370:20130379. [PMID: 25487331 PMCID: PMC4275887 DOI: 10.1098/rstb.2013.0379] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
Parchment represents an invaluable cultural reservoir. Retrieving an additional layer of information from these abundant, dated livestock-skins via the use of ancient DNA (aDNA) sequencing has been mooted by a number of researchers. However, prior PCR-based work has indicated that this may be challenged by cross-individual and cross-species contamination, perhaps from the bulk parchment preparation process. Here we apply next generation sequencing to two parchments of seventeenth and eighteenth century northern English provenance. Following alignment to the published sheep, goat, cow and human genomes, it is clear that the only genome displaying substantial unique homology is sheep and this species identification is confirmed by collagen peptide mass spectrometry. Only 4% of sequence reads align preferentially to a different species indicating low contamination across species. Moreover, mitochondrial DNA sequences suggest an upper bound of contamination at 5%. Over 45% of reads aligned to the sheep genome, and even this limited sequencing exercise yield 9 and 7% of each sampled sheep genome post filtering, allowing the mapping of genetic affinity to modern British sheep breeds. We conclude that parchment represents an excellent substrate for genomic analyses of historical livestock.
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Affiliation(s)
- M D Teasdale
- Smurfit Institute of Genetics, University of Dublin, Trinity College, Dublin 2, Ireland
| | | | - S Fiddyment
- BioArCh, University of York, York YO10 5DD, UK
| | - C C Webb
- Borthwick Institute for Archives, University of York, York YO10 5DD, UK
| | - T O'Connor
- BioArCh, University of York, York YO10 5DD, UK
| | - M Hofreiter
- BioArCh, University of York, York YO10 5DD, UK Institute for Biochemistry and Biology, Faculty of Natural Sciences, University of Potsdam, Karl-Liebknecht-Str. 24-25, Potsdam 14476, Germany
| | - M J Collins
- BioArCh, University of York, York YO10 5DD, UK
| | - D G Bradley
- Smurfit Institute of Genetics, University of Dublin, Trinity College, Dublin 2, Ireland
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Aloraifi F, McDevitt T, Martiniano R, McGreevy J, McLaughlin R, Egan CM, Cody N, Meany M, Kenny E, Green AJ, Bradley DG, Geraghty JG, Bracken AP. Detection of novel germline mutations for breast cancer in non-BRCA1/2 families. FEBS J 2015; 282:3424-37. [PMID: 26094658 DOI: 10.1111/febs.13352] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.8] [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: 05/08/2015] [Revised: 06/12/2015] [Accepted: 06/17/2015] [Indexed: 01/22/2023]
Abstract
The identification of the breast cancer susceptibility genes BRCA1 and BRCA2 enhanced clinicians' ability to select high-risk individuals for aggressive surveillance and prevention, and led to the development of targeted therapies. However, BRCA1/2 mutations account for only 25% of familial breast cancer cases. To systematically identify rare, probably pathogenic variants in familial cases of breast cancer without BRCA1/2 mutations, we developed a list of 312 genes, and performed targeted DNA enrichment coupled to multiplex next-generation sequencing on 104 'BRCAx' patients and 101 geographically matched controls in Ireland. As expected, this strategy allowed us to identify mutations in several well-known high-susceptibility and moderate-susceptibility genes, including ATM (~ 5%), RAD50 (~ 3%), CHEK2 (~ 2%), TP53 (~ 1%), PALB2 (~ 1%), and MRE11A (~ 1%). However, we also identified novel pathogenic variants in 30 other genes, which, when taken together, potentially explain the etiology of the missing heritability in up to 35% of BRCAx patients. These included novel potential pathogenic mutations in MAP3K1, CASP8, RAD51B, ZNF217, CDKN2B-AS1, and ERBB2, including a splice site mutation, which we predict would generate a constitutively active HER2 protein. Taken together, this work extends our understanding of the genetics of familial breast cancer, and supports the need to implement hereditary multigene panel testing to more appropriately orientate clinical management.
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Affiliation(s)
- Fatima Aloraifi
- Smurfit Institute of Genetics, Trinity College Dublin, Ireland
| | - Trudi McDevitt
- National Centre for Medical Genetics, Our Lady's Hospital, Crumlin, Dublin 12, Ireland
| | - Rui Martiniano
- Smurfit Institute of Genetics, Trinity College Dublin, Ireland
| | - Jonah McGreevy
- Smurfit Institute of Genetics, Trinity College Dublin, Ireland
| | | | - Chris M Egan
- Smurfit Institute of Genetics, Trinity College Dublin, Ireland
| | - Nuala Cody
- National Centre for Medical Genetics, Our Lady's Hospital, Crumlin, Dublin 12, Ireland
| | - Marie Meany
- National Centre for Medical Genetics, Our Lady's Hospital, Crumlin, Dublin 12, Ireland
| | | | - Andrew J Green
- National Centre for Medical Genetics, Our Lady's Hospital, Crumlin, Dublin 12, Ireland
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Kassahun Y, Mattiangeli V, Ameni G, Hailu E, Aseffa A, Young DB, Hewinson RG, Vordermeier HM, Bradley DG. Admixture mapping of tuberculosis and pigmentation-related traits in an African-European hybrid cattle population. Front Genet 2015; 6:210. [PMID: 26124773 PMCID: PMC4467177 DOI: 10.3389/fgene.2015.00210] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2015] [Accepted: 05/30/2015] [Indexed: 12/03/2022] Open
Abstract
Admixture mapping affords a powerful approach to genetic mapping of complex traits and may be particularly suited to investigation in cattle where many breeds and populations are hybrids of the two divergent ancestral genomes, derived from Bos taurus and Bos indicus. Here we design a minimal genome wide SNP panel for tracking ancestry in recent hybrids of Holstein–Friesian and local Arsi zebu in a field sample from a region of high bovine tuberculosis (BTB) endemicity in the central Ethiopian highlands. We first demonstrate the utility of this approach by mapping the red coat color phenotype, uncovering a highly significant peak over the MC1R gene and a second peak with no previously known candidate gene. Secondly, we exploit the described differential susceptibility to BTB between the ancestral strains to identify a region in which Bos taurus ancestry associates, at suggestive significance, with skin test positivity. Interestingly, this association peak contains the toll-like receptor gene cluster on chromosome 6. With this work we have shown the potential of admixture mapping in hybrid domestic animals with divergent ancestral genomes, a recurring condition in domesticated species.
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Affiliation(s)
- Yonas Kassahun
- Smurfit Institute of Genetics, Trinity College Dublin Dublin, Ireland
| | | | - Gobena Ameni
- Aklilu Lemma Institute of Pathobiology, Addis Ababa University Addis Ababa, Ethiopia ; Armauer Hansen Research Institute Addis Ababa, Ethiopia
| | - Elena Hailu
- Armauer Hansen Research Institute Addis Ababa, Ethiopia
| | | | - Douglas B Young
- Centre for Molecular Microbiology and Infection, Imperial College London London, UK
| | - R Glyn Hewinson
- TB Research Group, Animal and Plant Health Agency Addlestone, UK
| | | | - Daniel G Bradley
- Smurfit Institute of Genetics, Trinity College Dublin Dublin, Ireland
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39
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Purfield DC, Bradley DG, Evans RD, Kearney FJ, Berry DP. Genome-wide association study for calving performance using high-density genotypes in dairy and beef cattle. Genet Sel Evol 2015; 47:47. [PMID: 26065883 PMCID: PMC4464877 DOI: 10.1186/s12711-015-0126-4] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2014] [Accepted: 05/18/2015] [Indexed: 12/02/2022] Open
Abstract
Background Calving difficulty and perinatal mortality are prevalent in modern-day cattle production systems. It is well-established that there is a genetic component to both traits, yet little is known about their underlying genomic architecture, particularly in beef breeds. Therefore, we performed a genome-wide association study using high-density genotypes to elucidate the genomic architecture of these traits and to identify regions of the bovine genome associated with them. Results Genomic regions associated with calving difficulty (direct and maternal) and perinatal mortality were detected using two statistical approaches: (1) single-SNP (single nucleotide polymorphism) regression and (2) a Bayesian approach. Data included high-density genotypes on 770 Holstein-Friesian, 927 Charolais and 963 Limousin bulls. Several novel or previously identified genomic regions were detected but associations differed by breed. For example, two genomic associations, one each on chromosomes 18 and 2 explained 2.49 % and 3.13 % of the genetic variance in direct calving difficulty in the Holstein-Friesian and Charolais populations, respectively. Imputed Holstein-Friesian sequence data was used to refine the genomic regions responsible for significant associations. Several candidate genes on chromosome 18 were identified and four highly significant missense variants were detected within three of these genes (SIGLEC12, CTU1, and ZNF615). Nevertheless, only CTU1 contained a missense variant with a putative impact on direct calving difficulty based on SIFT (0.06) and Polyphen (0.95) scores. Using imputed sequence data, we refined a genomic region on chromosome 4 associated with maternal calving difficulty in the Holstein-Friesian population and found the strongest association with an intronic variant in the PCLO gene. A meta-analysis was performed across the three breeds for each calving performance trait to identify common variants associated with these traits in the three breeds. Our results suggest that a portion of the genetic variation in calving performance is common to all three breeds. Conclusion The genomic architecture of calving performance is complex and mainly influenced by many polymorphisms of small effect. We identified several associations of moderate effect size but the majority were breed-specific, indicating that breed-specific alleles exist for calving performance or that the linkage phase between genotyped allele and causal mutation varies between breeds. Electronic supplementary material The online version of this article (doi:10.1186/s12711-015-0126-4) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Deirdre C Purfield
- Smurfit Institute of Genetics, University of Dublin, Trinity College, Dublin 2, Ireland. .,Animal & Grassland Research and Innovation Center, Teagasc, Moorepark, Fermoy, Co. Cork, Ireland.
| | - Daniel G Bradley
- Smurfit Institute of Genetics, University of Dublin, Trinity College, Dublin 2, Ireland.
| | - Ross D Evans
- Irish Cattle Breeding Federation, Bandon, Co. Cork, Ireland.
| | | | - Donagh P Berry
- Animal & Grassland Research and Innovation Center, Teagasc, Moorepark, Fermoy, Co. Cork, Ireland.
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McLaughlin RL, Kenna KP, Vajda A, Heverin M, Byrne S, Donaghy CG, Cronin S, Bradley DG, Hardiman O. Homozygosity mapping in an Irish ALS case–control cohort describes local demographic phenomena and points towards potential recessive risk loci. Genomics 2015; 105:237-41. [DOI: 10.1016/j.ygeno.2015.01.002] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2014] [Revised: 01/07/2015] [Accepted: 01/16/2015] [Indexed: 12/19/2022]
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Bede P, Elamin M, Byrne S, McLaughlin RL, Kenna K, Vajda A, Fagan A, Bradley DG, Hardiman O. Patterns of cerebral and cerebellar white matter degeneration in ALS. J Neurol Neurosurg Psychiatry 2015; 86:468-70. [PMID: 25053771 PMCID: PMC4392231 DOI: 10.1136/jnnp-2014-308172] [Citation(s) in RCA: 56] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
- P Bede
- Biomedical Sciences Institute, Trinity College Dublin, Dublin, Ireland
| | - M Elamin
- Biomedical Sciences Institute, Trinity College Dublin, Dublin, Ireland
| | - S Byrne
- Biomedical Sciences Institute, Trinity College Dublin, Dublin, Ireland
| | - R L McLaughlin
- Smurfit Institute of Genetics, Trinity College Dublin, Dublin, Ireland
| | - K Kenna
- Smurfit Institute of Genetics, Trinity College Dublin, Dublin, Ireland
| | - A Vajda
- Biomedical Sciences Institute, Trinity College Dublin, Dublin, Ireland
| | - A Fagan
- Centre for Advanced Medical Imaging, St James's Hospital and Trinity College Dublin, Dublin, Ireland
| | - D G Bradley
- Smurfit Institute of Genetics, Trinity College Dublin, Dublin, Ireland
| | - O Hardiman
- Biomedical Sciences Institute, Trinity College Dublin, Dublin, Ireland
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Sanderson ND, Norman PJ, Guethlein LA, Ellis SA, Williams C, Breen M, Park SDE, Magee DA, Babrzadeh F, Warry A, Watson M, Bradley DG, MacHugh DE, Parham P, Hammond JA. Definition of the cattle killer cell Ig-like receptor gene family: comparison with aurochs and human counterparts. J Immunol 2014; 193:6016-30. [PMID: 25398326 PMCID: PMC4258407 DOI: 10.4049/jimmunol.1401980] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
Under selection pressure from pathogens, variable NK cell receptors that recognize polymorphic MHC class I evolved convergently in different species of placental mammal. Unexpectedly, diversified killer cell Ig-like receptors (KIRs) are shared by simian primates, including humans, and cattle, but not by other species. Whereas much is known of human KIR genetics and genomics, knowledge of cattle KIR is limited to nine cDNA sequences. To facilitate comparison of the cattle and human KIR gene families, we determined the genomic location, structure, and sequence of two cattle KIR haplotypes and defined KIR sequences of aurochs, the extinct wild ancestor of domestic cattle. Larger than its human counterpart, the cattle KIR locus evolved through successive duplications of a block containing ancestral KIR3DL and KIR3DX genes that existed before placental mammals. Comparison of two cattle KIR haplotypes and aurochs KIR show the KIR are polymorphic and the gene organization and content appear conserved. Of 18 genes, 8 are functional and 10 were inactivated by point mutation. Selective inactivation of KIR3DL and activating receptor genes leaves a functional cohort of one inhibitory KIR3DL, one activating KIR3DX, and six inhibitory KIR3DX. Functional KIR diversity evolved from KIR3DX in cattle and from KIR3DL in simian primates. Although independently evolved, cattle and human KIR gene families share important function-related properties, indicating that cattle KIR are NK cell receptors for cattle MHC class I. Combinations of KIR and MHC class I are the major genetic factors associated with human disease and merit investigation in cattle.
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Affiliation(s)
| | - Paul J Norman
- Department of Structural Biology, Stanford University, Stanford, CA 94035; Department of Microbiology and Immunology, Stanford University, Stanford, CA 94035
| | - Lisbeth A Guethlein
- Department of Structural Biology, Stanford University, Stanford, CA 94035; Department of Microbiology and Immunology, Stanford University, Stanford, CA 94035
| | - Shirley A Ellis
- The Pirbright Institute, Pirbright, Woking, Surrey GU24 0NF, United Kingdom
| | - Christina Williams
- Department of Molecular Biomedical Sciences, College of Veterinary Medicine, North Carolina State University, Raleigh, NC 27695
| | - Matthew Breen
- Department of Molecular Biomedical Sciences, College of Veterinary Medicine, North Carolina State University, Raleigh, NC 27695; Center for Comparative Medicine and Translational Research, Raleigh, NC 27539; Lineberger Comprehensive Cancer Center, Chapel Hill, NC 27599
| | - Steven D E Park
- Animal Genomics Laboratory, School of Agriculture and Food Science, College of Agriculture, Food Science and Veterinary Medicine, University College Dublin, Belfield, Dublin 4, Ireland
| | - David A Magee
- Animal Genomics Laboratory, School of Agriculture and Food Science, College of Agriculture, Food Science and Veterinary Medicine, University College Dublin, Belfield, Dublin 4, Ireland
| | | | - Andrew Warry
- Bioscience Information Technology Services, Biotechnology and Biological Sciences Research Council, Swindon SN2 1UH, United Kingdom
| | - Mick Watson
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Easter Bush Campus, Midlothian EH25 9RG, United Kingdom
| | - Daniel G Bradley
- Smurfit Institute of Genetics, Trinity College, Dublin 2, Ireland; and
| | - David E MacHugh
- Animal Genomics Laboratory, School of Agriculture and Food Science, College of Agriculture, Food Science and Veterinary Medicine, University College Dublin, Belfield, Dublin 4, Ireland; Conway Institute of Biomolecular and Biomedical Research, University College Dublin, Belfield, Dublin 4, Ireland
| | - Peter Parham
- Department of Structural Biology, Stanford University, Stanford, CA 94035; Department of Microbiology and Immunology, Stanford University, Stanford, CA 94035
| | - John A Hammond
- The Pirbright Institute, Pirbright, Woking, Surrey GU24 0NF, United Kingdom;
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McLaughlin RL, Kenna KP, Vajda A, Bede P, Elamin M, Cronin S, Donaghy CG, Bradley DG, Hardiman O. Second-generation Irish genome-wide association study for amyotrophic lateral sclerosis. Neurobiol Aging 2014; 36:1221.e7-13. [PMID: 25442119 DOI: 10.1016/j.neurobiolaging.2014.08.030] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [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: 05/15/2014] [Revised: 08/22/2014] [Accepted: 08/28/2014] [Indexed: 12/12/2022]
Abstract
Amyotrophic lateral sclerosis (ALS) is a heritable neurological disease for which the underlying genetic etiology is only partially understood. In Ireland, 83%-90% of cases are currently unexplained. Through large international collaborations, genome-wide association studies (GWASs) have succeeded in identifying a number of genomic loci that contribute toward ALS risk and age at onset. However, for the large proportion of risk that remains unexplained, population specificity of pathogenic variants could interfere with the detection of disease-associated loci. Single-population studies are therefore an important complement to larger international collaborations. In this study, we conduct a GWAS for ALS risk and age at onset in a large Irish ALS case-control cohort, using genome-wide imputation to increase marker density. Despite being adequately powered to detect associations of modest effect size, the study did not identify any locus associated with ALS risk or age at onset above the genome-wide significance threshold. Several speculative associations were, however, identified at loci that have been previously implicated in ALS. The lack of any clear association supports the conclusion that ALS is likely to be caused by multiple rare genetic risk factors. The findings of the present study highlight the importance of ongoing genetic research into the cause of ALS and its likely future challenges.
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Affiliation(s)
- Russell L McLaughlin
- Population Genetics Laboratory, Smurfit Institute of Genetics, Trinity College Dublin, College Green, Dublin, Republic of Ireland.
| | - Kevin P Kenna
- Population Genetics Laboratory, Smurfit Institute of Genetics, Trinity College Dublin, College Green, Dublin, Republic of Ireland
| | - Alice Vajda
- Academic Unit of Neurology, Trinity Biomedical Sciences Institute, Trinity College Dublin, Dublin, Republic of Ireland
| | - Peter Bede
- Academic Unit of Neurology, Trinity Biomedical Sciences Institute, Trinity College Dublin, Dublin, Republic of Ireland
| | - Marwa Elamin
- Academic Unit of Neurology, Trinity Biomedical Sciences Institute, Trinity College Dublin, Dublin, Republic of Ireland
| | - Simon Cronin
- Beaumont Hospital, Dublin, Republic of Ireland; Cork University Hospital, Cork, Republic of Ireland
| | - Colette G Donaghy
- Department of Neurology, Royal Victoria Hospital, Belfast, Northern Ireland
| | - Daniel G Bradley
- Population Genetics Laboratory, Smurfit Institute of Genetics, Trinity College Dublin, College Green, Dublin, Republic of Ireland
| | - Orla Hardiman
- Academic Unit of Neurology, Trinity Biomedical Sciences Institute, Trinity College Dublin, Dublin, Republic of Ireland
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Martiniano R, Coelho C, Ferreira MT, Neves MJ, Pinhasi R, Bradley DG. Genetic evidence of African slavery at the beginning of the trans-Atlantic slave trade. Sci Rep 2014; 4:5994. [PMID: 25104065 PMCID: PMC4125989 DOI: 10.1038/srep05994] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2014] [Accepted: 07/10/2014] [Indexed: 12/04/2022] Open
Abstract
An archaeological excavation in Valle da Gafaria (Lagos, Portugal), revealed two contiguous burial places outside the medieval city walls, dating from the 15(th)-17(th) centuries AD: one was interpreted as a Leprosarium cemetery and the second as an urban discard deposit, where signs of violent, unceremonious burials suggested that these remains may belong to slaves captured in Africa by the Portuguese. We obtained random short autosomal sequence reads from seven individuals: two from the latter site and five from the Leprosarium and used these to call SNP identities and estimate ancestral affinities with modern reference data. The Leprosarium site samples were less preserved but gave some probability of both African and European ancestry. The two discard deposit burials each gave African affinity signals, which were further refined toward modern West African or Bantu genotyped samples. These data from distressed burials illustrate an African contribution to a low status stratum of Lagos society at a time when this port became a hub of the European trade in African slaves which formed a precursor to the transatlantic transfer of millions.
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Affiliation(s)
- Rui Martiniano
- Smurfit Institute of Genetics, Trinity College Dublin, Dublin, Ireland
| | - Catarina Coelho
- Life Sciences Department, University of Coimbra, Coimbra, Portugal
| | - Maria Teresa Ferreira
- Life Sciences Department, University of Coimbra, Coimbra, Portugal
- Forensic Sciences Centre, Coimbra, Portugal
- Centro de Investigação em Antropologia e Saúde, Coimbra, Portugal
| | - Maria João Neves
- Life Sciences Department, University of Coimbra, Coimbra, Portugal
- Dryas Arqueologia Lda., Coimbra, Portugal
- Centro de Investigação em Antropologia e Saúde, Coimbra, Portugal
| | - Ron Pinhasi
- School of Archaeology, University College Dublin, Dublin, Ireland
- UCD Conway Institute of Biomolecular and Biomedical Research, University College Dublin, Dublin, Ireland
| | - Daniel G. Bradley
- Smurfit Institute of Genetics, Trinity College Dublin, Dublin, Ireland
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Fahey C, Byrne S, McLaughlin R, Kenna K, Shatunov A, Donohoe G, Gill M, Al-Chalabi A, Bradley DG, Hardiman O, Corvin AP, Morris DW. Analysis of the hexanucleotide repeat expansion and founder haplotype at C9ORF72 in an Irish psychosis case-control sample. Neurobiol Aging 2014; 35:1510.e1-5. [DOI: 10.1016/j.neurobiolaging.2013.12.003] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2013] [Revised: 12/02/2013] [Accepted: 12/05/2013] [Indexed: 12/13/2022]
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Gerbault P, Allaby RG, Boivin N, Rudzinski A, Grimaldi IM, Pires JC, Climer Vigueira C, Dobney K, Gremillion KJ, Barton L, Arroyo-Kalin M, Purugganan MD, Rubio de Casas R, Bollongino R, Burger J, Fuller DQ, Bradley DG, Balding DJ, Richerson PJ, Gilbert MTP, Larson G, Thomas MG. Storytelling and story testing in domestication. Proc Natl Acad Sci U S A 2014; 111:6159-64. [PMID: 24753572 PMCID: PMC4035932 DOI: 10.1073/pnas.1400425111] [Citation(s) in RCA: 62] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The domestication of plants and animals marks one of the most significant transitions in human, and indeed global, history. Traditionally, study of the domestication process was the exclusive domain of archaeologists and agricultural scientists; today it is an increasingly multidisciplinary enterprise that has come to involve the skills of evolutionary biologists and geneticists. Although the application of new information sources and methodologies has dramatically transformed our ability to study and understand domestication, it has also generated increasingly large and complex datasets, the interpretation of which is not straightforward. In particular, challenges of equifinality, evolutionary variance, and emergence of unexpected or counter-intuitive patterns all face researchers attempting to infer past processes directly from patterns in data. We argue that explicit modeling approaches, drawing upon emerging methodologies in statistics and population genetics, provide a powerful means of addressing these limitations. Modeling also offers an approach to analyzing datasets that avoids conclusions steered by implicit biases, and makes possible the formal integration of different data types. Here we outline some of the modeling approaches most relevant to current problems in domestication research, and demonstrate the ways in which simulation modeling is beginning to reshape our understanding of the domestication process.
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Affiliation(s)
| | - Robin G. Allaby
- School of Life Sciences, Gibbet Hill Campus, University of Warwick, Coventry CV4 7AL, United Kingdom
| | - Nicole Boivin
- Research Laboratory for Archaeology and the History of Art, School of Archaeology, Oxford OX1 3QY, United Kingdom
| | - Anna Rudzinski
- Research Department of Genetics, Evolution, and Environment and
| | - Ilaria M. Grimaldi
- Research Laboratory for Archaeology and the History of Art, School of Archaeology, Oxford OX1 3QY, United Kingdom
| | - J. Chris Pires
- Division of Biological Sciences, University of Missouri, Columbia, MO 65211
| | | | - Keith Dobney
- Department of Archaeology, University of Aberdeen, Aberdeen AB24 3UF, United Kingdom
| | | | - Loukas Barton
- Department of Anthropology, Center for Comparative Archaeology, University of Pittsburgh, Pittsburgh, PA 15260
| | - Manuel Arroyo-Kalin
- Institute of Archaeology, University College London, London WC1H 0PY, United Kingdom
| | - Michael D. Purugganan
- Department of Biology, New York University, New York, NY 10003-6688
- Center for Genomics and Systems Biology, New York University Abu Dhabi Research Institute, Abu Dhabi, United Arab Emirates
| | | | - Ruth Bollongino
- Institute of Anthropology, Johannes Gutenberg University, D-55099 Mainz, Germany
| | - Joachim Burger
- Institute of Anthropology, Johannes Gutenberg University, D-55099 Mainz, Germany
| | - Dorian Q. Fuller
- Institute of Archaeology, University College London, London WC1H 0PY, United Kingdom
| | | | - David J. Balding
- University College London Genetics Institute, University College London, London WC1E 6BT, United Kingdom
| | - Peter J. Richerson
- Department of Environmental Science and Policy, University of California, Davis, CA 95616
| | - M. Thomas P. Gilbert
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, 1350 Copenhagen, Denmark; and
| | - Greger Larson
- Durham Evolution and Ancient DNA, Department of Archaeology, Durham University, Durham DH1 3LE, United Kingdom
| | - Mark G. Thomas
- Research Department of Genetics, Evolution, and Environment and
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Affiliation(s)
- Greger Larson
- Durham Evolution and Ancient DNA, Department of Archaeology, University of Durham, Durham, United Kingdom
| | - Daniel G. Bradley
- Smurfit Institute of Genetics, Trinity College Dublin, Dublin, Ireland
- * E-mail:
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Meredith BK, Berry DP, Kearney F, Finlay EK, Fahey AG, Bradley DG, Lynn DJ. A genome-wide association study for somatic cell score using the Illumina high-density bovine beadchip identifies several novel QTL potentially related to mastitis susceptibility. Front Genet 2013; 4:229. [PMID: 24223582 PMCID: PMC3818585 DOI: 10.3389/fgene.2013.00229] [Citation(s) in RCA: 45] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2013] [Accepted: 10/17/2013] [Indexed: 12/19/2022] Open
Abstract
Mastitis is an inflammation-driven disease of the bovine mammary gland that occurs in response to physical damage or infection and is one of the most costly production-related diseases in the dairy industry worldwide. We performed a genome-wide association study (GWAS) to identify genetic loci associated with somatic cell score (SCS), an indicator trait of mammary gland inflammation. A total of 702 Holstein-Friesian bulls were genotyped for 777,962 single nucleotide polymorphisms (SNPs) and associated with SCS phenotypes. The SCS phenotypes were expressed as daughter yield deviations (DYD) based on a large number of progeny performance records. A total of 138 SNPs on 15 different chromosomes reached genome-wide significance (corrected p-value ≤ 0.05) for association with SCS (after correction for multiple testing). We defined 28 distinct QTL regions and a number of candidate genes located in these QTL regions were identified. The most significant association (p-value = 1.70 × 10−7) was observed on chromosome 6. This QTL had no known genes annotated within it, however, the Ensembl Genome Browser predicted the presence of a small non-coding RNA (a Y RNA gene) in this genomic region. This Y RNA gene was 99% identical to human RNY4. Y RNAs are a rare type of non-coding RNA that were originally discovered due to their association with the autoimmune disease, systemic lupus erythematosus. Examining small-RNA sequencing (RNAseq) data being generated by us in multiple different mastitis-pathogen challenged cell-types has revealed that this Y RNA is expressed (but not differentially expressed) in these cells. Other QTL regions identified in this study also encoded strong candidate genes for mastitis susceptibility. A QTL region on chromosome 13, for example, was found to contain a cluster of β-defensin genes, a gene family with known roles in innate immunity. Due to the increased SNP density, this study also refined the boundaries for several known QTL for SCS and mastitis.
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Affiliation(s)
- Brian K Meredith
- Animal and Bioscience Research Department, Teagasc, Animal and Grassland Research and Innovation Centre Grange, Dunsany, Co. Meath, Ireland ; School of Agriculture and Food Science, University College Dublin Dublin 4, Ireland
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Vegh P, Foroushani ABK, Magee DA, McCabe MS, Browne JA, Nalpas NC, Conlon KM, Gordon SV, Bradley DG, MacHugh DE, Lynn DJ. Profiling microRNA expression in bovine alveolar macrophages using RNA-seq. Vet Immunol Immunopathol 2013; 155:238-44. [PMID: 24021155 DOI: 10.1016/j.vetimm.2013.08.004] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2013] [Revised: 08/06/2013] [Accepted: 08/13/2013] [Indexed: 11/17/2022]
Abstract
MicroRNAs (miRNAs) are important regulators of gene expression and are known to play a key role in regulating both adaptive and innate immunity. Bovine alveolar macrophages (BAMs) help maintain lung homeostasis and constitute the front line of host defense against several infectious respiratory diseases, such as bovine tuberculosis. Little is known, however, about the role miRNAs play in these cells. In this study, we used a high-throughput sequencing approach, RNA-seq, to determine the expression levels of known and novel miRNAs in unchallenged BAMs isolated from lung lavages of eight different healthy Holstein-Friesian male calves. Approximately 80 million sequence reads were generated from eight BAM miRNA Illumina sequencing libraries, and 80 miRNAs were identified as being expressed in BAMs at a threshold of at least 100 reads per million (RPM). The expression levels of miRNAs varied over a large dynamic range, with a few miRNAs expressed at very high levels (up to 800,000RPM), and the majority lowly expressed. Notably, many of the most highly expressed miRNAs in BAMs have known roles in regulating immunity in other species (e.g. bta-let-7i, bta-miR-21, bta-miR-27, bta-miR-99b, bta-miR-146, bta-miR-147, bta-miR-155 and bta-miR-223). The most highly expressed miRNA in BAMs was miR-21, which has been shown to regulate the expression of antimicrobial peptides in Mycobacterium leprae-infected human monocytes. Furthermore, the predicted target genes of BAM-expressed miRNAs were found to be statistically enriched for roles in innate immunity. In addition to profiling the expression of known miRNAs, the RNA-seq data was also analysed to identify potentially novel bovine miRNAs. One putatively novel bovine miRNA was identified. To the best of our knowledge, this is the first RNA-seq study to profile miRNA expression in BAMs and provides an important reference dataset for investigating the regulatory roles miRNAs play in this important immune cell type.
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Affiliation(s)
- Peter Vegh
- Animal & Bioscience Research Department, Animal & Grassland Research and Innovation Centre, Teagasc, Grange, Dunsany, Co. Meath, Ireland; Smurfit Institute of Genetics, Trinity College, Dublin 2, Ireland
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Kenna KP, McLaughlin RL, Byrne S, Elamin M, Heverin M, Kenny EM, Cormican P, Morris DW, Donaghy CG, Bradley DG, Hardiman O. Delineating the genetic heterogeneity of ALS using targeted high-throughput sequencing. J Med Genet 2013; 50:776-83. [PMID: 23881933 PMCID: PMC3812897 DOI: 10.1136/jmedgenet-2013-101795] [Citation(s) in RCA: 135] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
BACKGROUND Over 100 genes have been implicated in the aetiology of amyotrophic lateral sclerosis (ALS). A detailed understanding of their independent and cumulative contributions to disease burden may help guide various clinical and research efforts. METHODS Using targeted high-throughput sequencing, we characterised the variation of 10 Mendelian and 23 low penetrance/tentative ALS genes within a population-based cohort of 444 Irish ALS cases (50 fALS, 394 sALS) and 311 age-matched and geographically matched controls. RESULTS Known or potential high-penetrance ALS variants were identified within 17.1% of patients (38% of fALS, 14.5% of sALS). 12.8% carried variants of Mendelian disease genes (C9orf72 8.78%; SETX 2.48%; ALS2 1.58%; FUS 0.45%; TARDBP 0.45%; OPTN 0.23%; VCP 0.23%. ANG, SOD1, VAPB 0%), 4.7% carried variants of low penetrance/tentative ALS genes and 9.7% (30% of fALS, 7.1% of sALS) carried previously described ALS variants (C9orf72 8.78%; FUS 0.45%; TARDBP 0.45%). 1.6% of patients carried multiple known/potential disease variants, including all identified carriers of an established ALS variant (p<0.01); TARDBP:c.859G>A(p.[G287S]) (n=2/2 sALS). Comparison of our results with those from studies of other European populations revealed significant differences in the spectrum of disease variation (p=1.7×10(-4)). CONCLUSIONS Up to 17% of Irish ALS cases may carry high-penetrance variants within the investigated genes. However, the precise nature of genetic susceptibility differs significantly from that reported within other European populations. Certain variants may not cause disease in isolation and concomitant analysis of disease genes may prove highly important.
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Affiliation(s)
- Kevin P Kenna
- Smurfit Institute of Genetics, Trinity College, Dublin, Ireland
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