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Kocher A, Papac L, Barquera R, Key FM, Spyrou MA, Hübler R, Rohrlach AB, Aron F, Stahl R, Wissgott A, van Bömmel F, Pfefferkorn M, Mittnik A, Villalba-Mouco V, Neumann GU, Rivollat M, van de Loosdrecht MS, Majander K, Tukhbatova RI, Musralina L, Ghalichi A, Penske S, Sabin S, Michel M, Gretzinger J, Nelson EA, Ferraz T, Nägele K, Parker C, Keller M, Guevara EK, Feldman M, Eisenmann S, Skourtanioti E, Giffin K, Gnecchi-Ruscone GA, Friederich S, Schimmenti V, Khartanovich V, Karapetian MK, Chaplygin MS, Kufterin VV, Khokhlov AA, Chizhevsky AA, Stashenkov DA, Kochkina AF, Tejedor-Rodríguez C, de Lagrán ÍGM, Arcusa-Magallón H, Garrido-Pena R, Royo-Guillén JI, Nováček J, Rottier S, Kacki S, Saintot S, Kaverzneva E, Belinskiy AB, Velemínský P, Limburský P, Kostka M, Loe L, Popescu E, Clarke R, Lyons A, Mortimer R, Sajantila A, de Armas YC, Hernandez Godoy ST, Hernández-Zaragoza DI, Pearson J, Binder D, Lefranc P, Kantorovich AR, Maslov VE, Lai L, Zoledziewska M, Beckett JF, Langová M, Danielisová A, Ingman T, Atiénzar GG, de Miguel Ibáñez MP, Romero A, Sperduti A, Beckett S, Salter SJ, Zilivinskaya ED, Vasil'ev DV, von Heyking K, Burger RL, Salazar LC, Amkreutz L, Navruzbekov M, Rosenstock E, Alonso-Fernández C, Slavchev V, Kalmykov AA, Atabiev BC, Batieva E, Calmet MA, Llamas B, Schultz M, Krauß R, Jiménez-Echevarría J, Francken M, Shnaider S, de Knijff P, Altena E, Van de Vijver K, Fehren-Schmitz L, Tung TA, Lösch S, Dobrovolskaya M, Makarov N, Read C, Van Twest M, Sagona C, Ramsl PC, Akar M, Yener KA, Ballestero EC, Cucca F, Mazzarello V, Utrilla P, Rademaker K, Fernández-Domínguez E, Baird D, Semal P, Márquez-Morfín L, Roksandic M, Steiner H, Salazar-García DC, Shishlina N, Erdal YS, Hallgren F, Boyadzhiev Y, Boyadzhiev K, Küßner M, Sayer D, Onkamo P, Skeates R, Rojo-Guerra M, Buzhilova A, Khussainova E, Djansugurova LB, Beisenov AZ, Samashev Z, Massy K, Mannino M, Moiseyev V, Mannermaa K, Balanovsky O, Deguilloux MF, Reinhold S, Hansen S, Kitov EP, Dobeš M, Ernée M, Meller H, Alt KW, Prüfer K, Warinner C, Schiffels S, Stockhammer PW, Bos K, Posth C, Herbig A, Haak W, Krause J, Kühnert D. Ten millennia of hepatitis B virus evolution. Science 2021; 374:182-188. [PMID: 34618559 DOI: 10.1126/science.abi5658] [Citation(s) in RCA: 38] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
[Figure: see text].
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Affiliation(s)
- Arthur Kocher
- Transmission, Infection, Diversification and Evolution Group, Max Planck Institute for the Science of Human History, 07745 Jena, Germany.,Department of Archaeogenetics, Max Planck Institute for the Science of Human History, 07745 Jena, Germany.,Department of Archaeogenetics, Max Planck Institute for Evolutionary Anthropology, 04103 Leipzig, Germany
| | - Luka Papac
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, 07745 Jena, Germany.,Department of Archaeogenetics, Max Planck Institute for Evolutionary Anthropology, 04103 Leipzig, Germany
| | - Rodrigo Barquera
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, 07745 Jena, Germany.,Department of Archaeogenetics, Max Planck Institute for Evolutionary Anthropology, 04103 Leipzig, Germany
| | - Felix M Key
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, 07745 Jena, Germany.,Max Planck Institute for Infection Biology, 10117 Berlin, Germany
| | - Maria A Spyrou
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, 07745 Jena, Germany.,Department of Archaeogenetics, Max Planck Institute for Evolutionary Anthropology, 04103 Leipzig, Germany.,Archaeo- and Palaeogenetics group, Institute for Archaeological Sciences, Eberhard Karls University Tübingen, 72070 Tübingen, Germany
| | - Ron Hübler
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, 07745 Jena, Germany
| | - Adam B Rohrlach
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, 07745 Jena, Germany.,Department of Archaeogenetics, Max Planck Institute for Evolutionary Anthropology, 04103 Leipzig, Germany.,ARC Centre of Excellence for Mathematical and Statistical Frontiers, School of Mathematical Sciences, University of Adelaide, Adelaide, SA 5005, Australia
| | - Franziska Aron
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, 07745 Jena, Germany
| | - Raphaela Stahl
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, 07745 Jena, Germany
| | - Antje Wissgott
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, 07745 Jena, Germany
| | - Florian van Bömmel
- Division of Hepatology, Department of Medicine II, Leipzig University Medical Center, Leipzig, Germany
| | - Maria Pfefferkorn
- Division of Hepatology, Department of Medicine II, Leipzig University Medical Center, Leipzig, Germany
| | - Alissa Mittnik
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, 07745 Jena, Germany.,Department of Genetics, Harvard Medical School, Boston, MA, USA.,Department of Human Evolutionary Biology, Harvard University, Cambridge, MA 02138, USA
| | - Vanessa Villalba-Mouco
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, 07745 Jena, Germany.,Institute of Evolutionary Biology, CSIC-Universitat Pompeu Fabra, Barcelona, Spain
| | - Gunnar U Neumann
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, 07745 Jena, Germany.,Department of Archaeogenetics, Max Planck Institute for Evolutionary Anthropology, 04103 Leipzig, Germany
| | - Maïté Rivollat
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, 07745 Jena, Germany.,Université de Bordeaux, CNRS, PACEA UMR 5199, Pessac, France
| | | | - Kerttu Majander
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, 07745 Jena, Germany.,Institute of Evolutionary Medicine (IEM), University of Zürich, 8057 Zürich, Switzerland
| | - Rezeda I Tukhbatova
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, 07745 Jena, Germany.,Laboratory of Structural Biology, Kazan Federal University, Kazan, Russia
| | - Lyazzat Musralina
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, 07745 Jena, Germany.,Department of Archaeogenetics, Max Planck Institute for Evolutionary Anthropology, 04103 Leipzig, Germany.,Al-Farabi Kazakh National University, Almaty, Kazakhstan.,Institute of Genetics and Physiology, 050060 Almaty, Kazakhstan
| | - Ayshin Ghalichi
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, 07745 Jena, Germany.,Department of Archaeogenetics, Max Planck Institute for Evolutionary Anthropology, 04103 Leipzig, Germany
| | - Sandra Penske
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, 07745 Jena, Germany.,Department of Archaeogenetics, Max Planck Institute for Evolutionary Anthropology, 04103 Leipzig, Germany
| | - Susanna Sabin
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, 07745 Jena, Germany
| | - Megan Michel
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, 07745 Jena, Germany.,Department of Archaeogenetics, Max Planck Institute for Evolutionary Anthropology, 04103 Leipzig, Germany.,Department of Human Evolutionary Biology, Harvard University, Cambridge, MA 02138, USA
| | - Joscha Gretzinger
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, 07745 Jena, Germany.,Department of Archaeogenetics, Max Planck Institute for Evolutionary Anthropology, 04103 Leipzig, Germany
| | - Elizabeth A Nelson
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, 07745 Jena, Germany
| | - Tiago Ferraz
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, 07745 Jena, Germany.,Departmento de Genética e Biologia Evolutiva, Instituto de Biociências, Universidade de São Paulo, São Paulo, SP, Brazil
| | - Kathrin Nägele
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, 07745 Jena, Germany.,Department of Archaeogenetics, Max Planck Institute for Evolutionary Anthropology, 04103 Leipzig, Germany
| | - Cody Parker
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, 07745 Jena, Germany.,Arizona State University School of Human Evolution and Social Change, Tempe Arizona, USA
| | - Marcel Keller
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, 07745 Jena, Germany.,Estonian Biocentre, Institute of Genomics, University of Tartu, Tartu, Estonia
| | - Evelyn K Guevara
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, 07745 Jena, Germany.,Department of Forensic Medicine, University of Helsinki, Helsinki, Finland
| | - Michal Feldman
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, 07745 Jena, Germany.,Archaeo- and Palaeogenetics group, Institute for Archaeological Sciences, Eberhard Karls University Tübingen, 72070 Tübingen, Germany
| | - Stefanie Eisenmann
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, 07745 Jena, Germany.,Department of Archaeogenetics, Max Planck Institute for Evolutionary Anthropology, 04103 Leipzig, Germany
| | - Eirini Skourtanioti
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, 07745 Jena, Germany.,Department of Archaeogenetics, Max Planck Institute for Evolutionary Anthropology, 04103 Leipzig, Germany
| | - Karen Giffin
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, 07745 Jena, Germany.,Department of Archaeogenetics, Max Planck Institute for Evolutionary Anthropology, 04103 Leipzig, Germany
| | - Guido Alberto Gnecchi-Ruscone
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, 07745 Jena, Germany.,Department of Archaeogenetics, Max Planck Institute for Evolutionary Anthropology, 04103 Leipzig, Germany
| | - Susanne Friederich
- State Office for Heritage Management and Archaeology Saxony-Anhalt and State Museum of Prehistory, D-06114 Halle, Germany
| | | | - Valery Khartanovich
- Peter the Great Museum of Anthropology and Ethnography (Kunstkamera) RAS, 199034 St. Petersburg, Russia
| | - Marina K Karapetian
- Anuchin Research Institute and Museum of Anthropology, Lomonosov Moscow State University, Moscow, Russia
| | | | - Vladimir V Kufterin
- Institute of Ethnology and Anthropology, Russian Academy of Sciences, Moscow, Russia
| | | | - Andrey A Chizhevsky
- Institute of Archaeology named after A. Kh. Khalikov, Tatarstan Academy of Sciences, Kazan, Russia
| | - Dmitry A Stashenkov
- Samara Museum for Historical and Regional Studies named after P. V. Alabin, Samara, Russia
| | - Anna F Kochkina
- Samara Museum for Historical and Regional Studies named after P. V. Alabin, Samara, Russia
| | - Cristina Tejedor-Rodríguez
- Department of Prehistory and Archaeology, Faculty of Philosophy and Letters, University of Valladolid, Spain
| | | | | | - Rafael Garrido-Pena
- Department of Prehistory and Archaeology, Faculty of Philosophy and Letters, Autonomous University of Madrid, Spain
| | | | - Jan Nováček
- Thuringian State Office for Heritage Management and Archaeology, 99423 Weimar, Germany.,University Medical School Göttingen, Institute of Anatomy and Cell Biology, 37075 Göttingen, Germany
| | | | - Sacha Kacki
- Université de Bordeaux, CNRS, PACEA UMR 5199, Pessac, France.,Department of Archaeology, Durham University, South Road, Durham. DH1 3LE. UK
| | - Sylvie Saintot
- INRAP, ARAR UMR 5138, Maison de l'Orient et de la Méditerranée, Lyon, France
| | | | | | - Petr Velemínský
- Department of Anthropology, The National Museum, Prague, Czech Republic
| | - Petr Limburský
- Institute of Archaeology of the Czech Academy of Sciences, Prague, Czech Republic
| | | | - Louise Loe
- Oxford Archaeology South, Janus House, Osney Mead, Oxford, OX2 0ES, UK
| | | | - Rachel Clarke
- Oxford Archaeology East, Bar Hill, Cambridge, CB23 8SQ, UK
| | - Alice Lyons
- Oxford Archaeology East, Bar Hill, Cambridge, CB23 8SQ, UK
| | | | - Antti Sajantila
- Department of Forensic Medicine, University of Helsinki, Helsinki, Finland.,Forensic Medicine Unit, Finnish Institute of Health and Welfare, Helsinki, Finland
| | | | - Silvia Teresita Hernandez Godoy
- Grupo de Investigación y Desarrollo, Dirección Provincial de Cultura, Matanzas, Cuba.,Universidad de Matanzas, Matanzas, Cuba
| | - Diana I Hernández-Zaragoza
- Molecular Genetics Laboratory, Escuela Nacional de Antropología e Historia (ENAH), Mexico City, Mexico.,Immunogenetics Unit, Técnicas Genéticas Aplicadas a la Clínica (TGAC), Mexico City, Mexico
| | - Jessica Pearson
- Department of Archaeology, Classics and Egyptology, University of Liverpool, Liverpool L69 7WZ, UK
| | - Didier Binder
- Université Côte d'Azur, CNRS, CEPAM UMR 7264, Nice, France
| | - Philippe Lefranc
- Université de Strasbourg, CNRS, Archimède UMR 7044, Strasbourg, France
| | - Anatoly R Kantorovich
- Department of Archaeology, Faculty of History, Lomonosov Moscow State University, 119192 Moscow, Russia
| | - Vladimir E Maslov
- Institute of Archaeology, Russian Academy of Sciences, , Moscow 117292, Russia
| | - Luca Lai
- Department of Anthropology, University of South Florida, Tampa, FL, USA.,Department of Anthropology, University of North Carolina at Charlotte, Charlotte, NC, USA
| | | | | | - Michaela Langová
- Institute of Archaeology of the Czech Academy of Sciences, Prague, Czech Republic
| | - Alžběta Danielisová
- Institute of Archaeology of the Czech Academy of Sciences, Prague, Czech Republic
| | - Tara Ingman
- Koç University, Research Center for Anatolian Civilizations, Istanbul 34433, Turkey
| | - Gabriel García Atiénzar
- Institute for Research in Archaeology and Historical Heritage (INAPH), University of Alicante, 03690, Alicante, Spain
| | - Maria Paz de Miguel Ibáñez
- Institute for Research in Archaeology and Historical Heritage (INAPH), University of Alicante, 03690, Alicante, Spain
| | - Alejandro Romero
- Institute for Research in Archaeology and Historical Heritage (INAPH), University of Alicante, 03690, Alicante, Spain.,Departamento de Biotecnología, Facultad de Ciencias, Universidad de Alicante, 03690, Alicante, Spain
| | - Alessandra Sperduti
- Bioarchaeology Service, Museum of Civilizations, Rome, Italy.,Dipartimento Asia Africa e Mediterraneo, Università di Napoli L'Orientale, Napoli, Italy
| | - Sophie Beckett
- Sedgeford Historical and Archaeological Research Project, Old Village Hall, Sedgeford, Hunstanton PE36 5LS, UK.,Melbourne Dental School, University of Melbourne, Victoria 3010 Australia.,Cranfield Forensic Institute, Cranfield Defence and Security, Cranfield University, College Road, Cranfield, MK43 0AL, UK
| | - Susannah J Salter
- Sedgeford Historical and Archaeological Research Project, Old Village Hall, Sedgeford, Hunstanton PE36 5LS, UK.,Department of Veterinary Medicine, University of Cambridge, Cambridge CB3 0ES, UK
| | - Emma D Zilivinskaya
- Institute of Ethnology and Anthropology, Russian Academy of Sciences, Moscow, Russia
| | | | - Kristin von Heyking
- SNSB, State Collection for Anthropology and Palaeoanatomy, 80333 Munich, Germany
| | - Richard L Burger
- Department of Anthropology, Yale University, New Haven, CT 06511, USA
| | - Lucy C Salazar
- Department of Anthropology, Yale University, New Haven, CT 06511, USA
| | - Luc Amkreutz
- National Museum of Antiquities, 2301 EC Leiden, Netherlands
| | | | - Eva Rosenstock
- Freie Universität Berlin, Einstein Center Chronoi, 14195 Berlin, Germany
| | | | | | | | - Biaslan Ch Atabiev
- Institute for Caucasus Archaeology, 361401 Nalchik, Republic Kabardino-Balkaria, Russia
| | - Elena Batieva
- Azov History, Archaeology and Palaeontology Museum-Reserve, Azov 346780, Russia
| | | | - Bastien Llamas
- Australian Centre for Ancient DNA, School of Biological Sciences and The Environment Institute, Adelaide University, Adelaide, SA 5005, Australia.,Centre of Excellence for Australian Biodiversity and Heritage (CABAH), University of Adelaide, Adelaide, SA 5005, Australia.,National Centre for Indigenous Genomics, Australian National University, Canberra, ACT 0200, Australia
| | - Michael Schultz
- University Medical School Göttingen, Institute of Anatomy and Embryology, 37075 Göttingen, Germany.,Institute of Biology, University of Hildeshein, Germany
| | - Raiko Krauß
- Institute for Prehistory, Early History and Medieval Archaeology, University of Tübingen, 72070 Tübingen, Germany
| | | | - Michael Francken
- State Office for Cultural Heritage Baden-Württemberg, 78467 Konstanz, Germany
| | - Svetlana Shnaider
- ArchaeoZoology in Siberia and Central Asia-ZooSCAn, CNRS-IAET SB RAS International Research Laboratory, IRL 2013, Novosibirsk, Russia
| | - Peter de Knijff
- Department of Human Genetics, Leiden University Medical Center, Leiden, 2333 ZC, Netherlands
| | - Eveline Altena
- Department of Human Genetics, Leiden University Medical Center, Leiden, 2333 ZC, Netherlands
| | - Katrien Van de Vijver
- Royal Belgian Institute of Natural Sciences, Brussels, Belgium.,Center for Archaeological Sciences, University of Leuven, Belgium.,Dienst Archeologie-Stad Mechelen, Belgium
| | - Lars Fehren-Schmitz
- UCSC Paleogenomics Laboratory, Department of Anthropology, University of California at Santa Cruz, Santa Cruz, CA 95064, USA.,UCSC Genomics Institute, University of California at Santa Cruz, Santa Cruz, CA 95064, USA
| | - Tiffiny A Tung
- Department of Anthropology, Vanderbilt University, Nashville, TN 37235, USA
| | - Sandra Lösch
- Department of Physical Anthropology, Institute of Forensic Medicine, University of Bern, Bern, Switzerland
| | - Maria Dobrovolskaya
- Institute of Archaeology, Russian Academy of Sciences, , Moscow 117292, Russia
| | - Nikolaj Makarov
- Institute of Archaeology, Russian Academy of Sciences, , Moscow 117292, Russia
| | - Chris Read
- Applied Archaeology School of Science, Institute of Technology Sligo, Ireland
| | - Melanie Van Twest
- Sedgeford Historical and Archaeological Research Project, Old Village Hall, Sedgeford, Hunstanton PE36 5LS, UK
| | - Claudia Sagona
- School of Historical and Philosophical Studies, University of Melbourne, Victoria 3010, Australia
| | - Peter C Ramsl
- Institute of Prehistoric and Historical Archaeology, University of Vienna, Austria
| | - Murat Akar
- Department of Archaeology, Hatay Mustafa Kemal University, Alahan-Antakya, Hatay 31060, Turkey
| | - K Aslihan Yener
- Institute for the Study of the Ancient World (ISAW), New York University, New York, NY 10028, USA
| | - Eduardo Carmona Ballestero
- Territorial Service of Culture and Tourism from Valladolid, Castilla y León Regional Government, C/ San Lorenzo, 5, 47001, Valladolid, Spain.,Department of History, Geography and Comunication, University of Burgos, Paseo de Comendadores, s/n 09001 Burgos (Burgos), Spain
| | - Francesco Cucca
- Istituto di Ricerca Genetica e Biomedica-CNR, Monserrato, Italy.,Dipartimento di Scienze Biomediche, Università di Sassari, Sassari, Italy
| | | | - Pilar Utrilla
- Área de Prehistoria, P3A DGA Research Group, IPH, University of Zaragoza, C/ Pedro Cerbuna 12, 50009, Zaragoza, Spain
| | - Kurt Rademaker
- Department of Anthropology, Michigan State University, East Lansing, MI 48824, USA
| | | | - Douglas Baird
- Department of Archaeology, Classics and Egyptology, University of Liverpool, Liverpool L69 7WZ, UK
| | - Patrick Semal
- Royal Belgian Institute of Natural Sciences, Brussels, Belgium
| | - Lourdes Márquez-Morfín
- Osteology Laboratory, Post Graduate Studies Division, Escuela Nacional de Antropología e Historia (ENAH), Mexico City, Mexico
| | - Mirjana Roksandic
- Department of Anthropology, University of Winnipeg, Winnipeg, MB, Canada.,Caribbean Research Institute, Univeristy of Winnipeg, Winnipeg, MB, Canada.,DFG Center for Advanced Studies "Words, Bones, Genes, Tools," University of Tübingen, Tübingen, Germany
| | - Hubert Steiner
- South Tyrol Provincial Heritage Service, South Tyrol, Italy
| | - Domingo Carlos Salazar-García
- Grupo de Investigación en Prehistoria IT-1223-19 (UPV-EHU)/IKERBASQUE-Basque Foundation for Science, Vitoria, Spain.,Departament de Prehistòria, Arqueologia i Història Antiga, Universitat de València, València, Spain.,Department of Geological Sciences, University of Cape Town, Cape Town, South Africa
| | - Natalia Shishlina
- Peter the Great Museum of Anthropology and Ethnography (Kunstkamera) RAS, 199034 St. Petersburg, Russia.,State Historical Museum, Moscow, Russia
| | - Yilmaz Selim Erdal
- Human_G Laboratory, Department of Anthropology, Hacettepe University, Ankara 06800, Turkey
| | | | - Yavor Boyadzhiev
- National Archaeological Institute with Museum at the Bulgarian Academy of Sciences, Sofia 1000, Bulgaria
| | - Kamen Boyadzhiev
- National Archaeological Institute with Museum at the Bulgarian Academy of Sciences, Sofia 1000, Bulgaria
| | - Mario Küßner
- Thuringian State Office for Heritage Management and Archaeology, 99423 Weimar, Germany
| | - Duncan Sayer
- School of Natural Sciences, University of Central Lancashire, Preston, UK
| | - Päivi Onkamo
- Department of Biosciences, University of Helsinki, 00014 Helsinki, Finland.,Department of Biology, University of Turku, 20500 Turku, Finland
| | - Robin Skeates
- Department of Archaeology, Durham University, South Road, Durham. DH1 3LE. UK
| | - Manuel Rojo-Guerra
- Department of Prehistory and Archaeology, Faculty of Philosophy and Letters, University of Valladolid, Spain
| | - Alexandra Buzhilova
- Anuchin Research Institute and Museum of Anthropology, Lomonosov Moscow State University, Moscow, Russia
| | | | | | - Arman Z Beisenov
- Institute of archaeology named after A. Kh. Margulan, 44 Almaty, Kazakhstan
| | - Zainolla Samashev
- Branch of Institute of Archaeology named after A.Kh. Margulan, 24 of 511 Nur-Sultan, Kazakhstan.,State Historical and Cultural Museum-Reserve "Berel," Katon-Karagay district, East Kazakhstan region, Kazakhstan
| | - Ken Massy
- Institut für Vor- und Frühgeschichtliche Archäologie und Provinzialrömische Archäologie, Ludwig-Maximilians-Universität München, 80539 Munich, Germany
| | - Marcello Mannino
- Department of Archeology and Heritage Studies, Aarhus University, 8270 Højbjerg, Denmark.,Department of Human Evolution, Max Planck Institute for Evolutionary Anthropology, 04103 Leipzig Germany
| | - Vyacheslav Moiseyev
- Peter the Great Museum of Anthropology and Ethnography (Kunstkamera) RAS, 199034 St. Petersburg, Russia
| | | | - Oleg Balanovsky
- Research Centre for Medical Genetics, Moscow, Russia.,Biobank of North Eurasia, Moscow, Russia.,Vavilov Institute of General Genetics, Moscow, Russia
| | | | - Sabine Reinhold
- Eurasia Department, German Archaeological Institute, Berlin, Germany
| | - Svend Hansen
- Eurasia Department, German Archaeological Institute, Berlin, Germany
| | - Egor P Kitov
- Institute of Ethnology and Anthropology, Russian Academy of Sciences, Moscow, Russia.,Institute of archaeology named after A. Kh. Margulan, 44 Almaty, Kazakhstan
| | - Miroslav Dobeš
- Institute of Archaeology of the Czech Academy of Sciences, Prague, Czech Republic
| | - Michal Ernée
- Institute of Archaeology of the Czech Academy of Sciences, Prague, Czech Republic
| | - Harald Meller
- State Office for Heritage Management and Archaeology Saxony-Anhalt and State Museum of Prehistory, D-06114 Halle, Germany
| | - Kurt W Alt
- Danube Private University, Center of Natural and Cultural Human History, A - 3500 Krems-Stein, Austria.,Integrative Prehistory and Archaeological Science, Spalenring 145, CH-4055 Basel, Switzerland.,Department of Biomedical Engineering (DBE), Universitätsspital Basel (HFZ), CH-4123 Allschwil, Switzerland
| | - Kay Prüfer
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, 07745 Jena, Germany.,Department of Archaeogenetics, Max Planck Institute for Evolutionary Anthropology, 04103 Leipzig, Germany
| | - Christina Warinner
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, 07745 Jena, Germany.,Department of Archaeogenetics, Max Planck Institute for Evolutionary Anthropology, 04103 Leipzig, Germany.,Department of Anthropology, Harvard University, Cambridge, MA 02138, USA
| | - Stephan Schiffels
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, 07745 Jena, Germany.,Department of Archaeogenetics, Max Planck Institute for Evolutionary Anthropology, 04103 Leipzig, Germany
| | - Philipp W Stockhammer
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, 07745 Jena, Germany.,Department of Archaeogenetics, Max Planck Institute for Evolutionary Anthropology, 04103 Leipzig, Germany.,Institut für Vor- und Frühgeschichtliche Archäologie und Provinzialrömische Archäologie, Ludwig-Maximilians-Universität München, 80539 Munich, Germany
| | - Kirsten Bos
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, 07745 Jena, Germany.,Department of Archaeogenetics, Max Planck Institute for Evolutionary Anthropology, 04103 Leipzig, Germany
| | - Cosimo Posth
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, 07745 Jena, Germany.,Archaeo- and Palaeogenetics group, Institute for Archaeological Sciences, Eberhard Karls University Tübingen, 72070 Tübingen, Germany
| | - Alexander Herbig
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, 07745 Jena, Germany.,Department of Archaeogenetics, Max Planck Institute for Evolutionary Anthropology, 04103 Leipzig, Germany
| | - Wolfgang Haak
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, 07745 Jena, Germany.,Department of Archaeogenetics, Max Planck Institute for Evolutionary Anthropology, 04103 Leipzig, Germany.,School of Biological Sciences, University of Adelaide, Adelaide, SA, 5005, Australia
| | - Johannes Krause
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, 07745 Jena, Germany.,Department of Archaeogenetics, Max Planck Institute for Evolutionary Anthropology, 04103 Leipzig, Germany
| | - Denise Kühnert
- Transmission, Infection, Diversification and Evolution Group, Max Planck Institute for the Science of Human History, 07745 Jena, Germany.,Department of Archaeogenetics, Max Planck Institute for the Science of Human History, 07745 Jena, Germany.,Department of Archaeogenetics, Max Planck Institute for Evolutionary Anthropology, 04103 Leipzig, Germany.,European Virus Bioinformatics Center (EVBC), Jena, Germany
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Marcus JH, Posth C, Ringbauer H, Lai L, Skeates R, Sidore C, Beckett J, Furtwängler A, Olivieri A, Chiang CWK, Al-Asadi H, Dey K, Joseph TA, Liu CC, Der Sarkissian C, Radzevičiūtė R, Michel M, Gradoli MG, Marongiu P, Rubino S, Mazzarello V, Rovina D, La Fragola A, Serra RM, Bandiera P, Bianucci R, Pompianu E, Murgia C, Guirguis M, Orquin RP, Tuross N, van Dommelen P, Haak W, Reich D, Schlessinger D, Cucca F, Krause J, Novembre J. Genetic history from the Middle Neolithic to present on the Mediterranean island of Sardinia. Nat Commun 2020; 11:939. [PMID: 32094358 PMCID: PMC7039977 DOI: 10.1038/s41467-020-14523-6] [Citation(s) in RCA: 68] [Impact Index Per Article: 17.0] [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: 03/21/2019] [Accepted: 01/08/2020] [Indexed: 11/30/2022] Open
Abstract
The island of Sardinia has been of particular interest to geneticists for decades. The current model for Sardinia's genetic history describes the island as harboring a founder population that was established largely from the Neolithic peoples of southern Europe and remained isolated from later Bronze Age expansions on the mainland. To evaluate this model, we generate genome-wide ancient DNA data for 70 individuals from 21 Sardinian archaeological sites spanning the Middle Neolithic through the Medieval period. The earliest individuals show a strong affinity to western Mediterranean Neolithic populations, followed by an extended period of genetic continuity on the island through the Nuragic period (second millennium BCE). Beginning with individuals from Phoenician/Punic sites (first millennium BCE), we observe spatially-varying signals of admixture with sources principally from the eastern and northern Mediterranean. Overall, our analysis sheds light on the genetic history of Sardinia, revealing how relationships to mainland populations shifted over time.
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MESH Headings
- Archaeology/methods
- Body Remains
- Chromosomes, Human, X/genetics
- Chromosomes, Human, Y/genetics
- DNA, Ancient
- DNA, Mitochondrial/genetics
- Datasets as Topic
- Female
- Genetics, Population/history
- History, 15th Century
- History, 16th Century
- History, 17th Century
- History, 18th Century
- History, 19th Century
- History, 20th Century
- History, 21st Century
- History, Ancient
- History, Medieval
- Human Migration
- Humans
- Italy
- Male
- Models, Genetic
- Sequence Analysis, DNA
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Affiliation(s)
- Joseph H Marcus
- Department of Human Genetics, University of Chicago, Chicago, IL, USA
| | - Cosimo Posth
- Max Planck Institute for the Science of Human History, Jena, Germany
- Institute for Archaeological Sciences, University of Tübingen, Tübingen, Germany
| | - Harald Ringbauer
- Department of Human Genetics, University of Chicago, Chicago, IL, USA
| | - Luca Lai
- Department of Anthropology, University of South Florida, Tampa, FL, USA
- Department of Anthropology, University of North Carolina at Charlotte, Charlotte, NC, USA
| | - Robin Skeates
- Department of Archaeology, Durham University, Durham, UK
| | - Carlo Sidore
- Istituto di Ricerca Genetica e Biomedica - CNR, Cagliari, Italy
- Dipartimento di Scienze Biomediche, Università di Sassari, Sassari, Italy
| | | | - Anja Furtwängler
- Institute for Archaeological Sciences, University of Tübingen, Tübingen, Germany
| | - Anna Olivieri
- Dipartimento di Biologia e Biotecnologie "L. Spallanzani", Università di Pavia, Pavia, Italy
| | - Charleston W K Chiang
- Center for Genetic Epidemiology, Department of Preventive Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
- Quantitative and Computational Biology Section, Department of Biological Sciences, University of Southern California, Los Angeles, CA, USA
| | - Hussein Al-Asadi
- Department of Statistics, University of Chicago, Chicago, IL, USA
- Committee on Evolutionary Biology, University of Chicago, Chicago, IL, USA
| | - Kushal Dey
- Department of Statistics, University of Chicago, Chicago, IL, USA
- Department of Epidemiology, Harvard School of Public Health, Boston, MA, 02115, USA
| | - Tyler A Joseph
- Department of Computer Science, Columbia University, New York, NY, USA
| | - Chi-Chun Liu
- Department of Human Genetics, University of Chicago, Chicago, IL, USA
| | - Clio Der Sarkissian
- Laboratoire d'Anthropologie Moléculaire et d'Imagerie de Synthèse, CNRS UMR 5288, Université de Toulouse 3, Toulouse, France
| | - Rita Radzevičiūtė
- Max Planck Institute for the Science of Human History, Jena, Germany
| | - Megan Michel
- Max Planck Institute for the Science of Human History, Jena, Germany
- Department of Human Evolutionary Biology, Harvard University, Cambridge, MA, 02138, USA
| | | | - Patrizia Marongiu
- Dipartimento di Scienze Biomediche, Università di Sassari, Sassari, Italy
| | - Salvatore Rubino
- Dipartimento di Scienze Biomediche, Università di Sassari, Sassari, Italy
| | | | - Daniela Rovina
- Soprintendenza Archeologia, belle arti e paesaggio delle province di Sassari e Nuoro, Sassari, Italy
| | - Alessandra La Fragola
- Departamento de Geografía, Historia y Humanidades Escuela Internacional de Doctorado de la Universidad de Almería, Almería, Spain
| | - Rita Maria Serra
- Dipartimento di Scienze Biomediche, Università di Sassari, Sassari, Italy
- Center for Anthropological, Paleopathological and Historical Studies of the Sardinian and Mediterranean Populations, University of Sassari, Sassari, Italy
| | - Pasquale Bandiera
- Dipartimento di Scienze Biomediche, Università di Sassari, Sassari, Italy
- Center for Anthropological, Paleopathological and Historical Studies of the Sardinian and Mediterranean Populations, University of Sassari, Sassari, Italy
| | - Raffaella Bianucci
- Department of Sciences and Technological Innovation, University of Eastern Piedmont, 15121, Alessandria, Italy
- Legal Medicine Section, Department of Public Health and Paediatric Sciences, University of Turin, 10126, Turin, Italy
| | - Elisa Pompianu
- Department of History, Human Sciences and Education, University of Sassari, 07100, Sassari, Italy
| | - Clizia Murgia
- Universitat Autònoma de Barcelona, Departament de Biologia Animal, Biologia Vegetal i Ecologia, 08193, Barcelona, Spain
| | - Michele Guirguis
- Department of History, Human Sciences and Education, University of Sassari, 07100, Sassari, Italy
| | - Rosana Pla Orquin
- Department of History, Human Sciences and Education, University of Sassari, 07100, Sassari, Italy
| | - Noreen Tuross
- Department of Human Evolutionary Biology, Harvard University, Cambridge, MA, 02138, USA
| | - Peter van Dommelen
- Joukowsky Institute for Archaeology and the Ancient World, Brown University, Providence, RI, 02912, USA
| | - Wolfgang Haak
- Max Planck Institute for the Science of Human History, Jena, Germany
| | - David Reich
- Department of Genetics, Harvard Medical School, Boston, MA, 02115, USA
- Broad Institute of Harvard and MIT, Cambridge, MA, USA
- Howard Hughes Medical Institute, Harvard Medical School, Boston, MA, USA
- Max Planck-Harvard Research Center for the Archaeoscience of the Ancient Mediterranean, Munich, Germany
| | | | - Francesco Cucca
- Istituto di Ricerca Genetica e Biomedica - CNR, Cagliari, Italy.
- Dipartimento di Scienze Biomediche, Università di Sassari, Sassari, Italy.
| | - Johannes Krause
- Max Planck Institute for the Science of Human History, Jena, Germany.
- Institute for Archaeological Sciences, University of Tübingen, Tübingen, Germany.
- Max Planck-Harvard Research Center for the Archaeoscience of the Ancient Mediterranean, Munich, Germany.
| | - John Novembre
- Department of Human Genetics, University of Chicago, Chicago, IL, USA.
- Department of Ecology and Evolution, University of Chicago, Chicago, IL, USA.
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4
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Key FM, Posth C, Esquivel-Gomez LR, Hübler R, Spyrou MA, Neumann GU, Furtwängler A, Sabin S, Burri M, Wissgott A, Lankapalli AK, Vågene ÅJ, Meyer M, Nagel S, Tukhbatova R, Khokhlov A, Chizhevsky A, Hansen S, Belinsky AB, Kalmykov A, Kantorovich AR, Maslov VE, Stockhammer PW, Vai S, Zavattaro M, Riga A, Caramelli D, Skeates R, Beckett J, Gradoli MG, Steuri N, Hafner A, Ramstein M, Siebke I, Lösch S, Erdal YS, Alikhan NF, Zhou Z, Achtman M, Bos K, Reinhold S, Haak W, Kühnert D, Herbig A, Krause J. Emergence of human-adapted Salmonella enterica is linked to the Neolithization process. Nat Ecol Evol 2020; 4:324-333. [PMID: 32094538 PMCID: PMC7186082 DOI: 10.1038/s41559-020-1106-9] [Citation(s) in RCA: 48] [Impact Index Per Article: 12.0] [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: 04/12/2019] [Accepted: 01/08/2020] [Indexed: 11/13/2022]
Abstract
It has been hypothesized that the Neolithic transition towards an
agricultural and pastoralist economy facilitated the emergence of human adapted
pathogens. Here, we recovered eight Salmonella enterica subsp.
enterica genomes from human skeletons of transitional
foragers, pastoralists, and agro-pastoralists in western Eurasia that were up to
6,500 years old. Despite the high genetic diversity of S.
enterica all ancient bacterial genomes clustered in a single
previously uncharacterized branch that contains S. enterica
adapted to multiple mammalian species. All ancient bacterial genomes from
prehistoric (agro-)pastoralists fall within a part of this branch that also
includes the human-specific S. enterica Paratyphi C,
illustrating the evolution of a human pathogen over a period of five thousand
years. Bacterial genomic comparisons suggest that the earlier ancient strains
were not host specific, differed in pathogenic potential, and experienced
convergent pseudogenization that accompanied their downstream host adaptation.
These observations support the concept that the emergence of human adapted
S. enterica is linked to human cultural
transformations.
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Affiliation(s)
- Felix M Key
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, Jena, Germany. .,Institute for Medical Engineering and Sciences, Massachusetts Institute of Technology, Cambridge, MA, USA. .,Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA.
| | - Cosimo Posth
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, Jena, Germany
| | - Luis R Esquivel-Gomez
- Transmission, Infection, Diversification & Evolution Group, Max Planck Institute for the Science of Human History, Jena, Germany
| | - Ron Hübler
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, Jena, Germany
| | - Maria A Spyrou
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, Jena, Germany
| | - Gunnar U Neumann
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, Jena, Germany
| | - Anja Furtwängler
- Institute for Archaeological Sciences, Archaeo- and Palaeogenetics, University of Tuebingen, Tuebingen, Germany
| | - Susanna Sabin
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, Jena, Germany
| | - Marta Burri
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, Jena, Germany
| | - Antje Wissgott
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, Jena, Germany
| | - Aditya Kumar Lankapalli
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, Jena, Germany
| | - Åshild J Vågene
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, Jena, Germany
| | - Matthias Meyer
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Sarah Nagel
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Rezeda Tukhbatova
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, Jena, Germany.,Laboratory of Structural Biology, Kazan Federal University, Kazan, Russian Federation
| | - Aleksandr Khokhlov
- Samara State University of Social Sciences and Education, Samara, Russian Federation
| | - Andrey Chizhevsky
- Institute of Archaeology named after A.Kh. Khalikov of the Academy of Sciences of the Republic of Tatarstan, Kazan, Russian Federation
| | - Svend Hansen
- Eurasia Department, German Archaeological Institute, Berlin, Germany
| | | | - Alexey Kalmykov
- 'Nasledie' Cultural Heritage Unit, Stavropol, Russian Federation
| | - Anatoly R Kantorovich
- Department of Archaeology, Faculty of History, Lomonosov Moscow State University, Moscow, Russian Federation
| | | | - Philipp W Stockhammer
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, Jena, Germany.,Institute for Pre- and Protohistoric Archaeology and Archaeology of the Roman Provinces, Ludwig Maximilian University Munich, Munich, Germany
| | - Stefania Vai
- Department of Biology, University of Florence, Florence, Italy
| | - Monica Zavattaro
- Museum of Anthropology and Ethnology, Museum System of the University of Florence, Florence, Italy
| | - Alessandro Riga
- Department of Biology, University of Florence, Florence, Italy
| | - David Caramelli
- Department of Biology, University of Florence, Florence, Italy
| | - Robin Skeates
- Department of Archaeology, Durham University, Durham, UK
| | | | | | - Noah Steuri
- Institute of Archaeological Sciences and Oeschger Centre for Climate Change Research, University of Bern, Bern, Switzerland
| | - Albert Hafner
- Institute of Archaeological Sciences and Oeschger Centre for Climate Change Research, University of Bern, Bern, Switzerland
| | | | - Inga Siebke
- Department of Physical Anthropology Institute of Forensic Medicine, University of Bern, Bern, Switzerland
| | - Sandra Lösch
- Department of Physical Anthropology Institute of Forensic Medicine, University of Bern, Bern, Switzerland
| | | | | | - Zhemin Zhou
- Warwick Medical School, University of Warwick, Coventry, UK
| | - Mark Achtman
- Warwick Medical School, University of Warwick, Coventry, UK
| | - Kirsten Bos
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, Jena, Germany
| | - Sabine Reinhold
- Eurasia Department, German Archaeological Institute, Berlin, Germany
| | - Wolfgang Haak
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, Jena, Germany
| | - Denise Kühnert
- Transmission, Infection, Diversification & Evolution Group, Max Planck Institute for the Science of Human History, Jena, Germany
| | - Alexander Herbig
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, Jena, Germany.
| | - Johannes Krause
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, Jena, Germany.
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