151
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152
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Díez-del-Molino D, Sánchez-Barreiro F, Barnes I, Gilbert MTP, Dalén L. Quantifying Temporal Genomic Erosion in Endangered Species. Trends Ecol Evol 2018; 33:176-185. [DOI: 10.1016/j.tree.2017.12.002] [Citation(s) in RCA: 59] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2017] [Revised: 11/28/2017] [Accepted: 12/01/2017] [Indexed: 12/30/2022]
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153
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Lipson M, Skoglund P, Spriggs M, Valentin F, Bedford S, Shing R, Buckley H, Phillip I, Ward GK, Mallick S, Rohland N, Broomandkhoshbacht N, Cheronet O, Ferry M, Harper TK, Michel M, Oppenheimer J, Sirak K, Stewardson K, Auckland K, Hill AVS, Maitland K, Oppenheimer SJ, Parks T, Robson K, Williams TN, Kennett DJ, Mentzer AJ, Pinhasi R, Reich D. Population Turnover in Remote Oceania Shortly after Initial Settlement. Curr Biol 2018; 28:1157-1165.e7. [PMID: 29501328 DOI: 10.1016/j.cub.2018.02.051] [Citation(s) in RCA: 51] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2018] [Revised: 02/19/2018] [Accepted: 02/19/2018] [Indexed: 01/08/2023]
Abstract
Ancient DNA from Vanuatu and Tonga dating to about 2,900-2,600 years ago (before present, BP) has revealed that the "First Remote Oceanians" associated with the Lapita archaeological culture were directly descended from the population that, beginning around 5000 BP, spread Austronesian languages from Taiwan to the Philippines, western Melanesia, and eventually Remote Oceania. Thus, ancestors of the First Remote Oceanians must have passed by the Papuan-ancestry populations they encountered in New Guinea, the Bismarck Archipelago, and the Solomon Islands with minimal admixture [1]. However, all present-day populations in Near and Remote Oceania harbor >25% Papuan ancestry, implying that additional eastward migration must have occurred. We generated genome-wide data for 14 ancient individuals from Efate and Epi Islands in Vanuatu from 2900-150 BP, as well as 185 present-day individuals from 18 islands. We find that people of almost entirely Papuan ancestry arrived in Vanuatu by around 2300 BP, most likely reflecting migrations a few hundred years earlier at the end of the Lapita period, when there is also evidence of changes in skeletal morphology and cessation of long-distance trade between Near and Remote Oceania [2, 3]. Papuan ancestry was subsequently diluted through admixture but remains at least 80%-90% in most islands. Through a fine-grained analysis of ancestry profiles, we show that the Papuan ancestry in Vanuatu derives from the Bismarck Archipelago rather than the geographically closer Solomon Islands. However, the Papuan ancestry in Polynesia-the most remote Pacific islands-derives from different sources, documenting a third stream of migration from Near to Remote Oceania.
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Affiliation(s)
- Mark Lipson
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA.
| | - Pontus Skoglund
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA; The Francis Crick Institute, London NW1 1AT, UK
| | - Matthew Spriggs
- School of Archaeology and Anthropology, College of Arts and Social Sciences, The Australian National University, Canberra, ACT 2601, Australia; Vanuatu National Museum, Vanuatu Cultural Centre, P.O. Box 184, Port Vila, Vanuatu
| | - Frederique Valentin
- Maison de l'Archéologie et de l'Ethnologie, CNRS, UMR 7041, 92023 Nanterre, France
| | - Stuart Bedford
- Vanuatu National Museum, Vanuatu Cultural Centre, P.O. Box 184, Port Vila, Vanuatu; Department of Archaeology and Natural History, College of Asia-Pacific, The Australian National University, Canberra, ACT 2601, Australia
| | - Richard Shing
- Vanuatu National Museum, Vanuatu Cultural Centre, P.O. Box 184, Port Vila, Vanuatu
| | - Hallie Buckley
- Department of Anatomy, Otago Global Health Institute, School of Biomedical Sciences, University of Otago, Dunedin 9054, New Zealand
| | - Iarawai Phillip
- Vanuatu National Museum, Vanuatu Cultural Centre, P.O. Box 184, Port Vila, Vanuatu
| | - Graeme K Ward
- Department of Archaeology and Natural History, College of Asia-Pacific, The Australian National University, Canberra, ACT 2601, Australia
| | - Swapan Mallick
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA; Howard Hughes Medical Institute, Boston, MA 02115, USA; Medical and Population Genetics Program, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Nadin Rohland
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
| | - Nasreen Broomandkhoshbacht
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA; Howard Hughes Medical Institute, Boston, MA 02115, USA
| | - Olivia Cheronet
- Department of Anthropology, University of Vienna, Althanstrasse 14, 1090 Vienna, Austria; Earth Institute, University College Dublin, Dublin 4, Ireland
| | - Matthew Ferry
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA; Howard Hughes Medical Institute, Boston, MA 02115, USA
| | - Thomas K Harper
- Department of Anthropology and Institute for Energy and the Environment, The Pennsylvania State University, University Park, PA 16802, USA
| | - Megan Michel
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA; Howard Hughes Medical Institute, Boston, MA 02115, USA
| | - Jonas Oppenheimer
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA; Howard Hughes Medical Institute, Boston, MA 02115, USA
| | - Kendra Sirak
- Earth Institute, University College Dublin, Dublin 4, Ireland; Department of Anthropology, Emory University, Atlanta, GA, USA
| | - Kristin Stewardson
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA; Howard Hughes Medical Institute, Boston, MA 02115, USA
| | - Kathryn Auckland
- Wellcome Centre for Human Genetics, University of Oxford, Oxford OX3 7BN, UK
| | - Adrian V S Hill
- Wellcome Centre for Human Genetics, University of Oxford, Oxford OX3 7BN, UK
| | - Kathryn Maitland
- Department of Paediatrics, Faculty of Medicine, Imperial College, St Mary's Hospital, Norfolk Place, Paddington, London W2 1PG, UK
| | - Stephen J Oppenheimer
- School of Anthropology and Museum Ethnography, University of Oxford, Oxford OX2 6PE, UK
| | - Tom Parks
- Wellcome Centre for Human Genetics, University of Oxford, Oxford OX3 7BN, UK
| | - Kathryn Robson
- MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford OX3 9DS, UK
| | - Thomas N Williams
- Department of Paediatrics, Faculty of Medicine, Imperial College, St Mary's Hospital, Norfolk Place, Paddington, London W2 1PG, UK
| | - Douglas J Kennett
- Department of Anthropology and Institute for Energy and the Environment, The Pennsylvania State University, University Park, PA 16802, USA
| | - Alexander J Mentzer
- Wellcome Centre for Human Genetics, University of Oxford, Oxford OX3 7BN, UK
| | - Ron Pinhasi
- Department of Anthropology, University of Vienna, Althanstrasse 14, 1090 Vienna, Austria; Earth Institute, University College Dublin, Dublin 4, Ireland
| | - David Reich
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA; Howard Hughes Medical Institute, Boston, MA 02115, USA; Medical and Population Genetics Program, Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Max Planck-Harvard Research Center for the Archaeoscience of the Ancient Mediterranean, Cambridge, MA 02138, USA.
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154
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Gaunitz C, Fages A, Hanghøj K, Albrechtsen A, Khan N, Schubert M, Seguin-Orlando A, Owens IJ, Felkel S, Bignon-Lau O, de Barros Damgaard P, Mittnik A, Mohaseb AF, Davoudi H, Alquraishi S, Alfarhan AH, Al-Rasheid KAS, Crubézy E, Benecke N, Olsen S, Brown D, Anthony D, Massy K, Pitulko V, Kasparov A, Brem G, Hofreiter M, Mukhtarova G, Baimukhanov N, Lõugas L, Onar V, Stockhammer PW, Krause J, Boldgiv B, Undrakhbold S, Erdenebaatar D, Lepetz S, Mashkour M, Ludwig A, Wallner B, Merz V, Merz I, Zaibert V, Willerslev E, Librado P, Outram AK, Orlando L. Ancient genomes revisit the ancestry of domestic and Przewalski’s horses. Science 2018; 360:111-114. [DOI: 10.1126/science.aao3297] [Citation(s) in RCA: 176] [Impact Index Per Article: 29.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2017] [Accepted: 01/31/2018] [Indexed: 12/28/2022]
Abstract
The Eneolithic Botai culture of the Central Asian steppes provides the earliest archaeological evidence for horse husbandry, ~5500 years ago, but the exact nature of early horse domestication remains controversial. We generated 42 ancient-horse genomes, including 20 from Botai. Compared to 46 published ancient- and modern-horse genomes, our data indicate that Przewalski’s horses are the feral descendants of horses herded at Botai and not truly wild horses. All domestic horses dated from ~4000 years ago to present only show ~2.7% of Botai-related ancestry. This indicates that a massive genomic turnover underpins the expansion of the horse stock that gave rise to modern domesticates, which coincides with large-scale human population expansions during the Early Bronze Age.
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155
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Mathieson I, Alpaslan-Roodenberg S, Posth C, Szécsényi-Nagy A, Rohland N, Mallick S, Olalde I, Broomandkhoshbacht N, Candilio F, Cheronet O, Fernandes D, Ferry M, Gamarra B, Fortes GG, Haak W, Harney E, Jones E, Keating D, Krause-Kyora B, Kucukkalipci I, Michel M, Mittnik A, Nägele K, Novak M, Oppenheimer J, Patterson N, Pfrengle S, Sirak K, Stewardson K, Vai S, Alexandrov S, Alt KW, Andreescu R, Antonović D, Ash A, Atanassova N, Bacvarov K, Gusztáv MB, Bocherens H, Bolus M, Boroneanţ A, Boyadzhiev Y, Budnik A, Burmaz J, Chohadzhiev S, Conard NJ, Cottiaux R, Čuka M, Cupillard C, Drucker DG, Elenski N, Francken M, Galabova B, Ganetsovski G, Gély B, Hajdu T, Handzhyiska V, Harvati K, Higham T, Iliev S, Janković I, Karavanić I, Kennett DJ, Komšo D, Kozak A, Labuda D, Lari M, Lazar C, Leppek M, Leshtakov K, Vetro DL, Los D, Lozanov I, Malina M, Martini F, McSweeney K, Meller H, Menđušić M, Mirea P, Moiseyev V, Petrova V, Price TD, Simalcsik A, Sineo L, Šlaus M, Slavchev V, Stanev P, Starović A, Szeniczey T, Talamo S, Teschler-Nicola M, Thevenet C, Valchev I, Valentin F, Vasilyev S, Veljanovska F, Venelinova S, Veselovskaya E, Viola B, Virag C, Zaninović J, Zäuner S, Stockhammer PW, Catalano G, Krauß R, Caramelli D, Zariņa G, Gaydarska B, Lillie M, Nikitin AG, Potekhina I, Papathanasiou A, Borić D, Bonsall C, Krause J, Pinhasi R, Reich D. The genomic history of southeastern Europe. Nature 2018; 555:197-203. [PMID: 29466330 PMCID: PMC6091220 DOI: 10.1038/nature25778] [Citation(s) in RCA: 283] [Impact Index Per Article: 47.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2017] [Accepted: 01/16/2018] [Indexed: 12/22/2022]
Abstract
Farming was first introduced to Europe in the mid-7th millennium BCE–associated with migrants from Anatolia who settled in the Southeast before spreading throughout Europe. To understand the dynamics of this process, we analyzed genome-wide ancient DNA data from 225 individuals who lived in southeastern Europe and surrounding regions between 12,000 and 500 BCE. We document a West-East cline of ancestry in indigenous hunter-gatherers and–in far-eastern Europe–early stages in the formation of Bronze Age Steppe ancestry. We show that the first farmers of northern and western Europe passed through southeastern Europe with limited hunter-gatherer admixture, but that some groups that remained mixed extensively, without the male-biased hunter-gatherer admixture that prevailed later in the North and West. Southeastern Europe continued to be a nexus between East and West, with intermittent genetic contact with the Steppe up to 2000 years before the migrations that replaced much of northern Europe’s population.
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Affiliation(s)
- Iain Mathieson
- Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA
| | | | - Cosimo Posth
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, 07745 Jena, Germany.,Institute for Archaeological Sciences, University of Tübingen, Tübingen, Germany
| | - Anna Szécsényi-Nagy
- Laboratory of Archaeogenetics, Institute of Archaeology, Research Centre for the Humanities, Hungarian Academy of Sciences, H-1097 Budapest, Hungary
| | - Nadin Rohland
- Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Swapan Mallick
- Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA.,Howard Hughes Medical Institute, Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Iñigo Olalde
- Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Nasreen Broomandkhoshbacht
- Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA.,Howard Hughes Medical Institute, Harvard Medical School, Boston, Massachusetts 02115, USA
| | | | - Olivia Cheronet
- Earth Institute, University College Dublin, Belfield, Dublin 4, Ireland.,Department of Anthropology, University of Vienna, 1090 Vienna, Austria
| | - Daniel Fernandes
- Earth Institute, University College Dublin, Belfield, Dublin 4, Ireland.,CIAS, Department of Life Sciences, University of Coimbra, 3000-456 Coimbra, Portugal
| | - Matthew Ferry
- Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA.,Howard Hughes Medical Institute, Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Beatriz Gamarra
- Earth Institute, University College Dublin, Belfield, Dublin 4, Ireland
| | - Gloria González Fortes
- Department of Life Sciences and Biotechnology, University of Ferrara, Ferrara 44100, Italy
| | - Wolfgang Haak
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, 07745 Jena, Germany.,Australian Centre for Ancient DNA, School of Biological Sciences, The University of Adelaide, SA-5005 Adelaide, South Australia, Australia
| | - Eadaoin Harney
- Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA.,Howard Hughes Medical Institute, Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Eppie Jones
- Smurfit Institute of Genetics, Trinity College Dublin, Dublin 2, Ireland.,Department of Zoology, University of Cambridge, Cambridge CB2 3EJ, UK
| | - Denise Keating
- Earth Institute, University College Dublin, Belfield, Dublin 4, Ireland
| | - Ben Krause-Kyora
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, 07745 Jena, Germany
| | - Isil Kucukkalipci
- Institute for Archaeological Sciences, University of Tübingen, Tübingen, Germany
| | - Megan Michel
- Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA.,Howard Hughes Medical Institute, Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Alissa Mittnik
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, 07745 Jena, Germany.,Institute for Archaeological Sciences, University of Tübingen, Tübingen, Germany
| | - Kathrin Nägele
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, 07745 Jena, Germany
| | - Mario Novak
- Earth Institute, University College Dublin, Belfield, Dublin 4, Ireland.,Institute for Anthropological Research, 10000 Zagreb, Croatia
| | - Jonas Oppenheimer
- Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA.,Howard Hughes Medical Institute, Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Nick Patterson
- Broad Institute of Harvard and MIT, Cambridge, Massachusetts 02142, USA
| | - Saskia Pfrengle
- Institute for Archaeological Sciences, University of Tübingen, Tübingen, Germany
| | - Kendra Sirak
- Earth Institute, University College Dublin, Belfield, Dublin 4, Ireland.,Department of Anthropology, Emory University, Atlanta, Georgia 30322, USA
| | - Kristin Stewardson
- Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA.,Howard Hughes Medical Institute, Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Stefania Vai
- Dipartimento di Biologia, Università di Firenze, 50122 Florence, Italy
| | - Stefan Alexandrov
- National Institute of Archaeology and Museum, Bulgarian Academy of Sciences, BG-1000 Sofia, Bulgaria
| | - Kurt W Alt
- Danube Private University, A-3500 Krems, Austria.,Department of Biomedical Engineering and Integrative Prehistory and Archaeological Science, CH-4123 Basel-Allschwil, Switzerland.,State Office for Heritage Management and Archaeology Saxony-Anhalt and State Museum of Prehistory, 06114 Halle, Germany
| | | | | | - Abigail Ash
- Earth Institute, University College Dublin, Belfield, Dublin 4, Ireland
| | - Nadezhda Atanassova
- Institute of Experimental Morphology, Pathology and Anthropology with Museum, Bulgarian Academy of Sciences, 1113 Sofia, Bulgaria
| | - Krum Bacvarov
- National Institute of Archaeology and Museum, Bulgarian Academy of Sciences, BG-1000 Sofia, Bulgaria
| | - Mende Balázs Gusztáv
- Laboratory of Archaeogenetics, Institute of Archaeology, Research Centre for the Humanities, Hungarian Academy of Sciences, H-1097 Budapest, Hungary
| | - Hervé Bocherens
- Department of Geosciences, Biogeology, Universität Tübingen, 72074 Tübingen, Germany.,Senckenberg Centre for Human Evolution and Palaeoenvironment at the University of Tübingen, 72076 Tübingen, Germany
| | - Michael Bolus
- ROCEEH Research Center, Heidelberg Academy of Sciences and Humanities, University of Tübingen, 72070 Tübingen, Germany
| | - Adina Boroneanţ
- Vasile Pârvan Institute of Archaeology, Romanian Academy, 010667 Bucharest, Romania
| | - Yavor Boyadzhiev
- National Institute of Archaeology and Museum, Bulgarian Academy of Sciences, BG-1000 Sofia, Bulgaria
| | - Alicja Budnik
- Human Biology Department, Cardinal Stefan Wyszyński University, 01-938 Warsaw, Poland
| | | | | | - Nicholas J Conard
- Senckenberg Centre for Human Evolution and Palaeoenvironment at the University of Tübingen, 72076 Tübingen, Germany.,Department of Early Prehistory and Quaternary Ecology, University of Tübingen, 72070 Tübingen, Germany
| | | | - Maja Čuka
- Archaeological Museum of Istria, 52100 Pula, Croatia
| | - Christophe Cupillard
- Service Régional de l'Archéologie de Bourgogne-Franche-Comté, 25043 Besançon Cedex, France.,Laboratoire Chronoenvironnement, UMR 6249 du CNRS, UFR des Sciences et Techniques, 25030 Besançon Cedex, France
| | - Dorothée G Drucker
- Senckenberg Centre for Human Evolution and Palaeoenvironment at the University of Tübingen, 72076 Tübingen, Germany
| | - Nedko Elenski
- Regional Museum of History Veliko Tarnovo, 5000 Veliko Tarnovo, Bulgaria
| | - Michael Francken
- Institute for Archaeological Sciences, Paleoanthropology, University of Tübingen, 72070 Tübingen, Germany
| | | | | | - Bernard Gély
- DRAC Auvergne - Rhône Alpes, Ministère de la Culture, Lyon Cedex 01, France
| | - Tamás Hajdu
- Eötvös Loránd University, Faculty of Science, Institute of Biology, Department of Biological Anthropology, H-1117 Budapest, Hungary
| | - Veneta Handzhyiska
- Department of Archaeology, Sofia University St. Kliment Ohridski, 1504 Sofia, Bulgaria
| | - Katerina Harvati
- Senckenberg Centre for Human Evolution and Palaeoenvironment at the University of Tübingen, 72076 Tübingen, Germany.,Institute for Archaeological Sciences, Paleoanthropology, University of Tübingen, 72070 Tübingen, Germany
| | - Thomas Higham
- Oxford Radiocarbon Accelerator Unit, Research Laboratory for Archaeology and the History of Art, University of Oxford, Dyson Perrins Building, Oxford OX1 3QY, UK
| | | | - Ivor Janković
- Institute for Anthropological Research, 10000 Zagreb, Croatia.,Department of Anthropology, University of Wyoming, Laramie, Wyoming 82071, USA
| | - Ivor Karavanić
- Department of Anthropology, University of Wyoming, Laramie, Wyoming 82071, USA.,Department of Archaeology, Faculty of Humanities and Social Sciences, University of Zagreb, 10000 Zagreb, Croatia
| | - Douglas J Kennett
- Department of Anthropology and Institutes for Energy and the Environment, Pennsylvania State University, University Park, Pennsylvania 16802, USA
| | - Darko Komšo
- Archaeological Museum of Istria, 52100 Pula, Croatia
| | - Alexandra Kozak
- Department of Bioarchaeology, Institute of Archaeology, National Academy of Sciences of Ukraine, 04210 Kiev, Ukraine
| | - Damian Labuda
- CHU Sainte-Justine Research Center, Pediatric Department, Université de Montréal, Montreal, Québec H3T 1C5, Canada
| | - Martina Lari
- Dipartimento di Biologia, Università di Firenze, 50122 Florence, Italy
| | - Catalin Lazar
- National History Museum of Romania, 030026, Bucharest, Romania.,Department of Ancient History, Archaeology and History of Art, Faculty of History, University of Bucharest, 50107 Bucharest, Romania
| | - Maleen Leppek
- Institute for Pre- and Protohistoric Archaeology and the Archaeology of the Roman Provinces, Ludwig-Maximilians-University, 80799 Munich, Germany
| | - Krassimir Leshtakov
- Department of Archaeology, Sofia University St. Kliment Ohridski, 1504 Sofia, Bulgaria
| | - Domenico Lo Vetro
- Dipartimento SAGAS - Sezione di Archeologia e Antico Oriente, Università degli Studi di Firenze, 50122 Florence, Italy.,Museo e Istituto fiorentino di Preistoria, 50122 Florence, Italy
| | - Dženi Los
- KADUCEJ d.o.o., 21000 Split, Croatia
| | - Ivaylo Lozanov
- Department of Archaeology, Sofia University St. Kliment Ohridski, 1504 Sofia, Bulgaria
| | - Maria Malina
- ROCEEH Research Center, Heidelberg Academy of Sciences and Humanities, University of Tübingen, 72070 Tübingen, Germany
| | - Fabio Martini
- Dipartimento SAGAS - Sezione di Archeologia e Antico Oriente, Università degli Studi di Firenze, 50122 Florence, Italy.,Museo e Istituto fiorentino di Preistoria, 50122 Florence, Italy
| | - Kath McSweeney
- School of History, Classics and Archaeology, University of Edinburgh, Edinburgh EH8 9AG, UK
| | - Harald Meller
- State Office for Heritage Management and Archaeology Saxony-Anhalt and State Museum of Prehistory, 06114 Halle, Germany
| | - Marko Menđušić
- Conservation Department in Šibenik, Ministry of Culture of the Republic of Croatia, 22000 Šibenik, Croatia
| | - Pavel Mirea
- Teleorman County Museum, 140033 Alexandria, Romania
| | - Vyacheslav Moiseyev
- Peter the Great Museum of Anthropology and Ethnography (Kunstkamera) RAS, 199034 St. Petersburg, Russia
| | - Vanya Petrova
- Department of Archaeology, Sofia University St. Kliment Ohridski, 1504 Sofia, Bulgaria
| | - T Douglas Price
- Department of Anthropology, University of Wisconsin, Madison, Wisconsin 53706, USA
| | - Angela Simalcsik
- Olga Necrasov Centre for Anthropological Research, Romanian Academy - Iaşi Branch, 700481 Iaşi, Romania
| | - Luca Sineo
- Dipartimento di Scienze e tecnologie biologiche, chimiche e farmaceutiche, Lab. of Anthropology, Università degli studi di Palermo, 90133 Palermo, Italy
| | - Mario Šlaus
- Anthropological Center, Croatian Academy of Sciences and Arts, 10000 Zagreb, Croatia
| | | | - Petar Stanev
- Regional Museum of History Veliko Tarnovo, 5000 Veliko Tarnovo, Bulgaria
| | | | - Tamás Szeniczey
- Eötvös Loránd University, Faculty of Science, Institute of Biology, Department of Biological Anthropology, H-1117 Budapest, Hungary
| | - Sahra Talamo
- Department of Human Evolution, Max Planck Institute for Evolutionary Anthropology, 04103 Leipzig, Germany
| | - Maria Teschler-Nicola
- Department of Anthropology, University of Vienna, 1090 Vienna, Austria.,Department of Anthropology, Natural History Museum Vienna, 1010 Vienna, Austria
| | | | - Ivan Valchev
- Department of Archaeology, Sofia University St. Kliment Ohridski, 1504 Sofia, Bulgaria
| | | | - Sergey Vasilyev
- Institute of Ethnology and Anthropology, Russian Academy of Sciences, Moscow, 119991, Russia
| | - Fanica Veljanovska
- Archaeological Museum of Macedonia, 1000 Skopje, the former Yugoslav Republic of Macedonia
| | | | - Elizaveta Veselovskaya
- Institute of Ethnology and Anthropology, Russian Academy of Sciences, Moscow, 119991, Russia
| | - Bence Viola
- Department of Anthropology, University of Toronto, Toronto, Ontario, M5S 2S2, Canada.,Institute of Archaeology & Ethnography, Siberian Branch, Russian Academy of Sciences, Novosibirsk 630090, Russia
| | - Cristian Virag
- Satu Mare County Museum Archaeology Department, 440026 Satu Mare, Romania
| | | | - Steve Zäuner
- anthropol - Anthropologieservice, 72379 Hechingen, Germany
| | - Philipp W Stockhammer
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, 07745 Jena, Germany.,Institute for Pre- and Protohistoric Archaeology and the Archaeology of the Roman Provinces, Ludwig-Maximilians-University, 80799 Munich, Germany
| | - Giulio Catalano
- Dipartimento di Scienze e tecnologie biologiche, chimiche e farmaceutiche, Lab. of Anthropology, Università degli studi di Palermo, 90133 Palermo, Italy
| | - Raiko Krauß
- Institute for Prehistory, Early History and Medieval Archaeology, University of Tübingen, 72070 Tübingen, Germany
| | - David Caramelli
- Dipartimento di Biologia, Università di Firenze, 50122 Florence, Italy
| | - Gunita Zariņa
- Institute of Latvian History, University of Latvia, Rı¯ga 1050, Latvia
| | | | - Malcolm Lillie
- School of Environmental Sciences, Geography, University of Hull, Hull HU6 7RX, UK
| | - Alexey G Nikitin
- Department of Biology, Grand Valley State University, Allendale, Michigan 49401, USA
| | - Inna Potekhina
- Department of Bioarchaeology, Institute of Archaeology, National Academy of Sciences of Ukraine, 04210 Kiev, Ukraine
| | | | - Dušan Borić
- The Italian Academy for Advanced Studies in America, Columbia University, New York, New York 10027, USA
| | - Clive Bonsall
- School of History, Classics and Archaeology, University of Edinburgh, Edinburgh EH8 9AG, UK
| | - Johannes Krause
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, 07745 Jena, Germany.,Institute for Archaeological Sciences, University of Tübingen, Tübingen, Germany
| | - Ron Pinhasi
- Earth Institute, University College Dublin, Belfield, Dublin 4, Ireland.,Department of Anthropology, University of Vienna, 1090 Vienna, Austria
| | - David Reich
- Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA.,Howard Hughes Medical Institute, Harvard Medical School, Boston, Massachusetts 02115, USA.,Broad Institute of Harvard and MIT, Cambridge, Massachusetts 02142, USA
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156
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Leonardi M, Librado P, Der Sarkissian C, Schubert M, Alfarhan AH, Alquraishi SA, Al-Rasheid KAS, Gamba C, Willerslev E, Orlando L. Evolutionary Patterns and Processes: Lessons from Ancient DNA. Syst Biol 2018; 66:e1-e29. [PMID: 28173586 PMCID: PMC5410953 DOI: 10.1093/sysbio/syw059] [Citation(s) in RCA: 37] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2016] [Revised: 06/04/2016] [Accepted: 06/06/2016] [Indexed: 12/02/2022] Open
Abstract
Ever since its emergence in 1984, the field of ancient DNA has struggled to overcome the challenges related to the decay of DNA molecules in the fossil record. With the recent development of high-throughput DNA sequencing technologies and molecular techniques tailored to ultra-damaged templates, it has now come of age, merging together approaches in phylogenomics, population genomics, epigenomics, and metagenomics. Leveraging on complete temporal sample series, ancient DNA provides direct access to the most important dimension in evolution—time, allowing a wealth of fundamental evolutionary processes to be addressed at unprecedented resolution. This review taps into the most recent findings in ancient DNA research to present analyses of ancient genomic and metagenomic data.
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Affiliation(s)
- Michela Leonardi
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Øster Voldgade, Copenhagen, Denmark
| | - Pablo Librado
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Øster Voldgade, Copenhagen, Denmark
| | - Clio Der Sarkissian
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Øster Voldgade, Copenhagen, Denmark
| | - Mikkel Schubert
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Øster Voldgade, Copenhagen, Denmark
| | - Ahmed H Alfarhan
- Zoology Department, College of Science, King Saud University, Riyadh, Saudi Arabia
| | - Saleh A Alquraishi
- Zoology Department, College of Science, King Saud University, Riyadh, Saudi Arabia
| | | | - Cristina Gamba
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Øster Voldgade, Copenhagen, Denmark
| | - Eske Willerslev
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Øster Voldgade, Copenhagen, Denmark.,Zoology Department, College of Science, King Saud University, Riyadh, Saudi Arabia
| | - Ludovic Orlando
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Øster Voldgade, Copenhagen, Denmark.,Université de Toulouse, University Paul Sabatier (UPS), Laboratoire AMIS, Toulouse, France
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157
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Schröder C, Steimer W. gDNA extraction yield and methylation status of blood samples are affected by long-term storage conditions. PLoS One 2018; 13:e0192414. [PMID: 29415017 PMCID: PMC5802893 DOI: 10.1371/journal.pone.0192414] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2017] [Accepted: 01/22/2018] [Indexed: 12/13/2022] Open
Abstract
Epigenetics is believed to provide great chances for a better understanding of the development and treatment of many diseases where the analysis of genomic DNA has so far failed to provide conclusive answers. Methylcytosine is a frequently used quantitative marker of epigenetic studies. Since immediate analysis of sampled material is in most cases not possible, storage time and conditions are critical aspects regarding the quality of genomic DNA and reliability of analysis. Blood is frequently used for such analyses. We, therefore, collected blood samples of ten volunteers and stored them under various conditions for ten months: -70°C, -20°C, 2-8°C and room temperature. An additional aliquot was frozen at -70°C and thawed once a week at room temperature. We then compared the DNA extraction yields and methylation status in relation to storage time and conditions. We found significantly lower DNA extraction yields (up to -97.45%; p ≤ 0.001) as well as significantly higher methylation levels after ten months of storage (up to +42.0%; p ≤ 0.001). These results suggest that storage time has an important influence on DNA analyses of blood samples for all storage conditions. This might be due to differences in stability of methylated and non-methylated DNA. Our study indicates that storage conditions and time may be a critical factor for epigenetic methylation studies and require rigorous validation. For reliable analyses we, therefore, recommend to perform epigenetic analysis directly after sample collection.
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Affiliation(s)
- Charlotte Schröder
- Institut für Klinische Chemie und Pathobiochemie, Klinikum rechts der Isar, Technische Universität München, München, Germany
| | - Werner Steimer
- Institut für Klinische Chemie und Pathobiochemie, Klinikum rechts der Isar, Technische Universität München, München, Germany
- * E-mail:
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158
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Inferring genetic origins and phenotypic traits of George Bähr, the architect of the Dresden Frauenkirche. Sci Rep 2018; 8:2115. [PMID: 29391530 PMCID: PMC5794802 DOI: 10.1038/s41598-018-20180-z] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2017] [Accepted: 01/11/2018] [Indexed: 12/25/2022] Open
Abstract
For historic individuals, the outward appearance and other phenotypic characteristics remain often non-resolved. Unfortunately, images or detailed written sources are only scarcely available in many cases. Attempts to study historic individuals with genetic data so far focused on hypervariable regions of mitochondrial DNA and to some extent on complete mitochondrial genomes. To elucidate the potential of in-solution based genome-wide SNP capture methods - as now widely applied in population genetics - we extracted DNA from the 17th century remains of George Bähr, the architect of the Dresdner Frauenkirche. We were able to identify the remains to be of male origin, showing sufficient DNA damage, deriving from a single person and being thus likely authentic. Furthermore, we were able to show that George Bähr had light skin pigmentation and most likely brown eyes. His genomic DNA furthermore points to a Central European origin. We see this analysis as an example to demonstrate the prospects that new in-solution SNP capture methods can provide for historic cases of forensic interest, using methods well established in ancient DNA (aDNA) research and population genetics.
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159
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Exposito-Alonso M, Becker C, Schuenemann VJ, Reiter E, Setzer C, Slovak R, Brachi B, Hagmann J, Grimm DG, Chen J, Busch W, Bergelson J, Ness RW, Krause J, Burbano HA, Weigel D. The rate and potential relevance of new mutations in a colonizing plant lineage. PLoS Genet 2018; 14:e1007155. [PMID: 29432421 PMCID: PMC5825158 DOI: 10.1371/journal.pgen.1007155] [Citation(s) in RCA: 73] [Impact Index Per Article: 12.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2017] [Revised: 02/23/2018] [Accepted: 12/13/2017] [Indexed: 01/08/2023] Open
Abstract
By following the evolution of populations that are initially genetically homogeneous, much can be learned about core biological principles. For example, it allows for detailed studies of the rate of emergence of de novo mutations and their change in frequency due to drift and selection. Unfortunately, in multicellular organisms with generation times of months or years, it is difficult to set up and carry out such experiments over many generations. An alternative is provided by "natural evolution experiments" that started from colonizations or invasions of new habitats by selfing lineages. With limited or missing gene flow from other lineages, new mutations and their effects can be easily detected. North America has been colonized in historic times by the plant Arabidopsis thaliana, and although multiple intercrossing lineages are found today, many of the individuals belong to a single lineage, HPG1. To determine in this lineage the rate of substitutions-the subset of mutations that survived natural selection and drift-, we have sequenced genomes from plants collected between 1863 and 2006. We identified 73 modern and 27 herbarium specimens that belonged to HPG1. Using the estimated substitution rate, we infer that the last common HPG1 ancestor lived in the early 17th century, when it was most likely introduced by chance from Europe. Mutations in coding regions are depleted in frequency compared to those in other portions of the genome, consistent with purifying selection. Nevertheless, a handful of mutations is found at high frequency in present-day populations. We link these to detectable phenotypic variance in traits of known ecological importance, life history and growth, which could reflect their adaptive value. Our work showcases how, by applying genomics methods to a combination of modern and historic samples from colonizing lineages, we can directly study new mutations and their potential evolutionary relevance.
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Affiliation(s)
- Moises Exposito-Alonso
- Department of Molecular Biology, Max Planck Institute for Developmental Biology, Tübingen, Germany
- Research Group for Ancient Genomics and Evolution, Max Planck Institute for Developmental Biology, Tübingen, Germany
| | - Claude Becker
- Department of Molecular Biology, Max Planck Institute for Developmental Biology, Tübingen, Germany
| | - Verena J. Schuenemann
- Institute of Archaeological Sciences, University of Tübingen, Tübingen, Germany
- Senckenberg Center for Human Evolution and Paleoenvironment, University of Tübingen, Tübingen, Germany
| | - Ella Reiter
- Institute of Archaeological Sciences, University of Tübingen, Tübingen, Germany
| | - Claudia Setzer
- Gregor Mendel Institute, Austrian Academy of Sciences, Vienna, Austria
| | - Radka Slovak
- Gregor Mendel Institute, Austrian Academy of Sciences, Vienna, Austria
| | - Benjamin Brachi
- Department of Ecology and Evolution, University of Chicago, Chicago, Illinois, United States of America
| | - Jörg Hagmann
- Department of Molecular Biology, Max Planck Institute for Developmental Biology, Tübingen, Germany
| | - Dominik G. Grimm
- Department of Molecular Biology, Max Planck Institute for Developmental Biology, Tübingen, Germany
| | - Jiahui Chen
- Department of Ecology and Evolution, University of Chicago, Chicago, Illinois, United States of America
- Institute of Tibet Plateau Research, Chinese Academy of Sciences, Beijing, China
| | - Wolfgang Busch
- Gregor Mendel Institute, Austrian Academy of Sciences, Vienna, Austria
| | - Joy Bergelson
- Department of Ecology and Evolution, University of Chicago, Chicago, Illinois, United States of America
| | - Rob W. Ness
- Department of Biology, University of Toronto Mississauga, Mississauga, Ontario, Canada
| | - Johannes Krause
- Institute of Archaeological Sciences, University of Tübingen, Tübingen, Germany
- Senckenberg Center for Human Evolution and Paleoenvironment, University of Tübingen, Tübingen, Germany
- Department of Archeogenetics, Max Planck Institute for the Science of Human History, Jena, Germany
| | - Hernán A. Burbano
- Research Group for Ancient Genomics and Evolution, Max Planck Institute for Developmental Biology, Tübingen, Germany
| | - Detlef Weigel
- Department of Molecular Biology, Max Planck Institute for Developmental Biology, Tübingen, Germany
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160
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Salmonella enterica genomes from victims of a major sixteenth-century epidemic in Mexico. Nat Ecol Evol 2018; 2:520-528. [PMID: 29335577 DOI: 10.1038/s41559-017-0446-6] [Citation(s) in RCA: 115] [Impact Index Per Article: 19.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2017] [Accepted: 12/07/2017] [Indexed: 11/08/2022]
Abstract
Indigenous populations of the Americas experienced high mortality rates during the early contact period as a result of infectious diseases, many of which were introduced by Europeans. Most of the pathogenic agents that caused these outbreaks remain unknown. Through the introduction of a new metagenomic analysis tool called MALT, applied here to search for traces of ancient pathogen DNA, we were able to identify Salmonella enterica in individuals buried in an early contact era epidemic cemetery at Teposcolula-Yucundaa, Oaxaca in southern Mexico. This cemetery is linked, based on historical and archaeological evidence, to the 1545-1550 CE epidemic that affected large parts of Mexico. Locally, this epidemic was known as 'cocoliztli', the pathogenic cause of which has been debated for more than a century. Here, we present genome-wide data from ten individuals for Salmonella enterica subsp. enterica serovar Paratyphi C, a bacterial cause of enteric fever. We propose that S. Paratyphi C be considered a strong candidate for the epidemic population decline during the 1545 cocoliztli outbreak at Teposcolula-Yucundaa.
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161
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Günther T, Malmström H, Svensson EM, Omrak A, Sánchez-Quinto F, Kılınç GM, Krzewińska M, Eriksson G, Fraser M, Edlund H, Munters AR, Coutinho A, Simões LG, Vicente M, Sjölander A, Jansen Sellevold B, Jørgensen R, Claes P, Shriver MD, Valdiosera C, Netea MG, Apel J, Lidén K, Skar B, Storå J, Götherström A, Jakobsson M. Population genomics of Mesolithic Scandinavia: Investigating early postglacial migration routes and high-latitude adaptation. PLoS Biol 2018; 16:e2003703. [PMID: 29315301 PMCID: PMC5760011 DOI: 10.1371/journal.pbio.2003703] [Citation(s) in RCA: 107] [Impact Index Per Article: 17.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2017] [Accepted: 12/04/2017] [Indexed: 02/07/2023] Open
Abstract
Scandinavia was one of the last geographic areas in Europe to become habitable for humans after the Last Glacial Maximum (LGM). However, the routes and genetic composition of these postglacial migrants remain unclear. We sequenced the genomes, up to 57× coverage, of seven hunter-gatherers excavated across Scandinavia and dated from 9,500–6,000 years before present (BP). Surprisingly, among the Scandinavian Mesolithic individuals, the genetic data display an east–west genetic gradient that opposes the pattern seen in other parts of Mesolithic Europe. Our results suggest two different early postglacial migrations into Scandinavia: initially from the south, and later, from the northeast. The latter followed the ice-free Norwegian north Atlantic coast, along which novel and advanced pressure-blade stone-tool techniques may have spread. These two groups met and mixed in Scandinavia, creating a genetically diverse population, which shows patterns of genetic adaptation to high latitude environments. These potential adaptations include high frequencies of low pigmentation variants and a gene region associated with physical performance, which shows strong continuity into modern-day northern Europeans. The Scandinavian peninsula was the last part of Europe to be colonized after the Last Glacial Maximum. The migration routes, cultural networks, and the genetic makeup of the first Scandinavians remain elusive and several hypotheses exist based on archaeology, climate modeling, and genetics. By analyzing the genomes of early Scandinavian hunter-gatherers, we show that their migrations followed two routes: one from the south and another from the northeast along the ice-free Norwegian Atlantic coast. These groups met and mixed in Scandinavia, creating a population more diverse than contemporaneous central and western European hunter-gatherers. As northern Europe is associated with cold and low light conditions, we investigated genomic patterns of adaptation to these conditions and genes known to be involved in skin pigmentation. We demonstrate that Mesolithic Scandinavians had higher levels of light pigmentation variants compared to the respective source populations of the migrations, suggesting adaptation to low light levels and a surprising signal of genetic continuity in TMEM131, a gene that may be involved in long-term adaptation to the cold.
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Affiliation(s)
- Torsten Günther
- Department of Organismal Biology, Uppsala University, Uppsala, Sweden
- * E-mail: (TG); (JS); (AG); (MJ)
| | - Helena Malmström
- Department of Organismal Biology, Uppsala University, Uppsala, Sweden
| | - Emma M. Svensson
- Department of Organismal Biology, Uppsala University, Uppsala, Sweden
| | - Ayça Omrak
- Department of Archaeology and Classical Studies, Stockholm University, Stockholm, Sweden
| | | | - Gülşah M. Kılınç
- Department of Organismal Biology, Uppsala University, Uppsala, Sweden
- Department of Archaeology and Classical Studies, Stockholm University, Stockholm, Sweden
- Middle East Technical University, Department of Biological Sciences, Ankara, Turkey
| | - Maja Krzewińska
- Department of Archaeology and Classical Studies, Stockholm University, Stockholm, Sweden
| | - Gunilla Eriksson
- Department of Archaeology and Classical Studies, Stockholm University, Stockholm, Sweden
| | - Magdalena Fraser
- Department of Organismal Biology, Uppsala University, Uppsala, Sweden
- Department of Archaeology and Ancient History, Uppsala University-Campus Gotland, Visby, Sweden
| | - Hanna Edlund
- Department of Organismal Biology, Uppsala University, Uppsala, Sweden
| | | | | | - Luciana G. Simões
- Department of Organismal Biology, Uppsala University, Uppsala, Sweden
| | - Mário Vicente
- Department of Organismal Biology, Uppsala University, Uppsala, Sweden
| | - Anders Sjölander
- Department of Organismal Biology, Uppsala University, Uppsala, Sweden
| | | | - Roger Jørgensen
- Tromsø University Museum, University of Tromsø-The Arctic University of Norway, Tromsø, Norway
| | - Peter Claes
- Department of Electrical Engineering, Center for Processing Speech and Images, Katholieke Universiteit Leuven, Leuven, Belgium
| | - Mark D. Shriver
- Department of Anthropology, Penn State University, State College, Pennsylvania, United States of America
| | - Cristina Valdiosera
- Department of Archaeology and History, La Trobe University, Melbourne, Australia
| | - Mihai G. Netea
- Department of Internal Medicine and Radboud Center for Infectious Diseases, Radboud University Medical Center, Nijmegen, the Netherlands
| | - Jan Apel
- Department of Archaeology and Ancient History, Lund University, Lund, Sweden
| | - Kerstin Lidén
- Department of Archaeology and Classical Studies, Stockholm University, Stockholm, Sweden
- Tromsø University Museum, University of Tromsø-The Arctic University of Norway, Tromsø, Norway
| | - Birgitte Skar
- Department of Archaeology and Cultural History, Norwegian University of Science and Technology University Museum, Trondheim, Norway
| | - Jan Storå
- Department of Archaeology and Classical Studies, Stockholm University, Stockholm, Sweden
- * E-mail: (TG); (JS); (AG); (MJ)
| | - Anders Götherström
- Department of Archaeology and Classical Studies, Stockholm University, Stockholm, Sweden
- SciLifeLab, Uppsala and Stockholm, Sweden
- * E-mail: (TG); (JS); (AG); (MJ)
| | - Mattias Jakobsson
- Department of Organismal Biology, Uppsala University, Uppsala, Sweden
- SciLifeLab, Uppsala and Stockholm, Sweden
- * E-mail: (TG); (JS); (AG); (MJ)
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162
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Patterson Ross Z, Klunk J, Fornaciari G, Giuffra V, Duchêne S, Duggan AT, Poinar D, Douglas MW, Eden JS, Holmes EC, Poinar HN. The paradox of HBV evolution as revealed from a 16th century mummy. PLoS Pathog 2018; 14:e1006750. [PMID: 29300782 PMCID: PMC5754119 DOI: 10.1371/journal.ppat.1006750] [Citation(s) in RCA: 60] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2017] [Accepted: 11/13/2017] [Indexed: 12/11/2022] Open
Abstract
Hepatitis B virus (HBV) is a ubiquitous viral pathogen associated with large-scale morbidity and mortality in humans. However, there is considerable uncertainty over the time-scale of its origin and evolution. Initial shotgun data from a mid-16th century Italian child mummy, that was previously paleopathologically identified as having been infected with Variola virus (VARV, the agent of smallpox), showed no DNA reads for VARV yet did for hepatitis B virus (HBV). Previously, electron microscopy provided evidence for the presence of VARV in this sample, although similar analyses conducted here did not reveal any VARV particles. We attempted to enrich and sequence for both VARV and HBV DNA. Although we did not recover any reads identified as VARV, we were successful in reconstructing an HBV genome at 163.8X coverage. Strikingly, both the HBV sequence and that of the associated host mitochondrial DNA displayed a nearly identical cytosine deamination pattern near the termini of DNA fragments, characteristic of an ancient origin. In contrast, phylogenetic analyses revealed a close relationship between the putative ancient virus and contemporary HBV strains (of genotype D), at first suggesting contamination. In addressing this paradox we demonstrate that HBV evolution is characterized by a marked lack of temporal structure. This confounds attempts to use molecular clock-based methods to date the origin of this virus over the time-frame sampled so far, and means that phylogenetic measures alone cannot yet be used to determine HBV sequence authenticity. If genuine, this phylogenetic pattern indicates that the genotypes of HBV diversified long before the 16th century, and enables comparison of potential pathogenic similarities between modern and ancient HBV. These results have important implications for our understanding of the emergence and evolution of this common viral pathogen.
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Affiliation(s)
- Zoe Patterson Ross
- Marie Bashir Institute for Infectious Diseases and Biosecurity, Charles Perkins Centre, School of Life and Environmental Sciences and Sydney Medical School, The University of Sydney, Sydney, New South Wales, Australia
| | - Jennifer Klunk
- McMaster Ancient DNA Centre, Department of Anthropology, McMaster University, Hamilton, ON, Canada
| | - Gino Fornaciari
- Division of Paleopathology, Department of Translational Research on New Technologies in Medicine and Surgery, University of Pisa, Pisa, Italy
| | - Valentina Giuffra
- Division of Paleopathology, Department of Translational Research on New Technologies in Medicine and Surgery, University of Pisa, Pisa, Italy
| | - Sebastian Duchêne
- Department of Biochemistry and Molecular Biology, Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, Parkville, Victoria, Australia
| | - Ana T. Duggan
- McMaster Ancient DNA Centre, Department of Anthropology, McMaster University, Hamilton, ON, Canada
| | - Debi Poinar
- McMaster Ancient DNA Centre, Department of Anthropology, McMaster University, Hamilton, ON, Canada
| | - Mark W. Douglas
- Storr Liver Centre, The Westmead Institute for Medical Research, The University of Sydney and Westmead Hospital, Westmead, New South Wales, Australia
| | - John-Sebastian Eden
- Marie Bashir Institute for Infectious Diseases and Biosecurity, Charles Perkins Centre, School of Life and Environmental Sciences and Sydney Medical School, The University of Sydney, Sydney, New South Wales, Australia
| | - Edward C. Holmes
- Marie Bashir Institute for Infectious Diseases and Biosecurity, Charles Perkins Centre, School of Life and Environmental Sciences and Sydney Medical School, The University of Sydney, Sydney, New South Wales, Australia
| | - Hendrik N. Poinar
- McMaster Ancient DNA Centre, Department of Anthropology, McMaster University, Hamilton, ON, Canada
- Michael G. DeGroote Institute for Infectious Disease Research and the Department of Biochemistry, McMaster University, Hamilton, ON, Canada
- Humans and the Microbiome Program, Canadian Institute for Advanced Research, Toronto, ON, Canada
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163
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164
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Llamas B, Willerslev E, Orlando L. Human evolution: a tale from ancient genomes. Philos Trans R Soc Lond B Biol Sci 2017; 372:rstb.2015.0484. [PMID: 27994125 DOI: 10.1098/rstb.2015.0484] [Citation(s) in RCA: 37] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/05/2016] [Indexed: 12/21/2022] Open
Abstract
The field of human ancient DNA (aDNA) has moved from mitochondrial sequencing that suffered from contamination and provided limited biological insights, to become a fully genomic discipline that is changing our conception of human history. Recent successes include the sequencing of extinct hominins, and true population genomic studies of Bronze Age populations. Among the emerging areas of aDNA research, the analysis of past epigenomes is set to provide more new insights into human adaptation and disease susceptibility through time. Starting as a mere curiosity, ancient human genetics has become a major player in the understanding of our evolutionary history.This article is part of the themed issue 'Evo-devo in the genomics era, and the origins of morphological diversity'.
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Affiliation(s)
- Bastien Llamas
- Australian Centre for ADNA, School of Biological Sciences, University of Adelaide, Adelaide, South Australia 5005, Australia
| | - Eske Willerslev
- Centre for GeoGenetics, Natural History Museum of Denmark, Øster Voldgade 5-7, 1350 K Copenhagen, Denmark.,Department of Zoology, University of Cambridge, Downing Street, Cambridge CB2 3EJ, UK.,Wellcome Genome Campus Hinxton, Wellcome Trust Sanger Institute, Cambridge CB10 1SA, UK
| | - Ludovic Orlando
- Centre for GeoGenetics, Natural History Museum of Denmark, Øster Voldgade 5-7, 1350 K Copenhagen, Denmark .,Laboratoire d'Anthropobiologie Moléculaire et d'Imagerie de Synthèse, Université de Toulouse, University Paul Sabatier, CNRS UMR 5288, 31000 Toulouse, France
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165
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Pečnerová P, Palkopoulou E, Wheat CW, Skoglund P, Vartanyan S, Tikhonov A, Nikolskiy P, van der Plicht J, Díez-Del-Molino D, Dalén L. Mitogenome evolution in the last surviving woolly mammoth population reveals neutral and functional consequences of small population size. Evol Lett 2017; 1:292-303. [PMID: 30283657 PMCID: PMC6121868 DOI: 10.1002/evl3.33] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2017] [Accepted: 11/06/2017] [Indexed: 01/25/2023] Open
Abstract
The onset of the Holocene was associated with a global temperature increase, which led to a rise in sea levels and isolation of the last surviving population of woolly mammoths on Wrangel Island. Understanding what happened with the population's genetic diversity at the time of the isolation and during the ensuing 6000 years can help clarify the effects of bottlenecks and subsequent limited population sizes in species approaching extinction. Previous genetic studies have highlighted questions about how the Holocene Wrangel population was established and how the isolation event affected genetic diversity. Here, we generated high‐quality mitogenomes from 21 radiocarbon‐dated woolly mammoths to compare the ancestral large and genetically diverse Late Pleistocene Siberian population and the small Holocene Wrangel population. Our results indicate that mitogenome diversity was reduced to one single haplotype at the time of the isolation, and thus that the Holocene Wrangel Island population was established by a single maternal lineage. Moreover, we show that the ensuing small effective population size coincided with fixation of a nonsynonymous mutation, and a comparative analysis of mutation rates suggests that the evolutionary rate was accelerated in the Holocene population. These results suggest that isolation on Wrangel Island led to an increase in the frequency of deleterious genetic variation, and thus are consistent with the hypothesis that strong genetic drift in small populations leads to purifying selection being less effective in removing deleterious mutations.
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Affiliation(s)
- Patrícia Pečnerová
- Department of Bioinformatics and Genetics Swedish Museum of Natural History Stockholm Sweden.,Department of Zoology Stockholm University Stockholm Sweden
| | - Eleftheria Palkopoulou
- Department of Bioinformatics and Genetics Swedish Museum of Natural History Stockholm Sweden.,Department of Zoology Stockholm University Stockholm Sweden.,Department of Genetics Harvard Medical School Boston Massachusetts 02115
| | | | - Pontus Skoglund
- Department of Genetics Harvard Medical School Boston Massachusetts 02115.,Broad Institute of Harvard and MIT Cambridge Massachusetts 02142
| | - Sergey Vartanyan
- North-East Interdisciplinary Scientific Research Institute N.A.N.A. Shilo Far East Branch, Russian Academy of Sciences (NEISRI FEB RAS) Magadan Russia
| | - Alexei Tikhonov
- Zoological Institute of Russian Academy of Sciences Saint-Petersburg Russia.,Institute of Applied Ecology of the North North-Eastern Federal University Yakutsk Russia
| | - Pavel Nikolskiy
- Geological Institute of the Russian Academy of Sciences Moscow Russia
| | - Johannes van der Plicht
- Centre for Isotope Research Groningen University Groningen The Netherlands.,Faculty of Archaeology Leiden University Leiden The Netherlands
| | - David Díez-Del-Molino
- Department of Bioinformatics and Genetics Swedish Museum of Natural History Stockholm Sweden
| | - Love Dalén
- Department of Bioinformatics and Genetics Swedish Museum of Natural History Stockholm Sweden
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166
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Prüfer K, de Filippo C, Grote S, Mafessoni F, Korlević P, Hajdinjak M, Vernot B, Skov L, Hsieh P, Peyrégne S, Reher D, Hopfe C, Nagel S, Maricic T, Fu Q, Theunert C, Rogers R, Skoglund P, Chintalapati M, Dannemann M, Nelson BJ, Key FM, Rudan P, Kućan Ž, Gušić I, Golovanova LV, Doronichev VB, Patterson N, Reich D, Eichler EE, Slatkin M, Schierup MH, Andrés AM, Kelso J, Meyer M, Pääbo S. A high-coverage Neandertal genome from Vindija Cave in Croatia. Science 2017; 358:655-658. [PMID: 28982794 PMCID: PMC6185897 DOI: 10.1126/science.aao1887] [Citation(s) in RCA: 328] [Impact Index Per Article: 46.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2017] [Accepted: 09/27/2017] [Indexed: 12/30/2022]
Abstract
To date, the only Neandertal genome that has been sequenced to high quality is from an individual found in Southern Siberia. We sequenced the genome of a female Neandertal from ~50,000 years ago from Vindija Cave, Croatia, to ~30-fold genomic coverage. She carried 1.6 differences per 10,000 base pairs between the two copies of her genome, fewer than present-day humans, suggesting that Neandertal populations were of small size. Our analyses indicate that she was more closely related to the Neandertals that mixed with the ancestors of present-day humans living outside of sub-Saharan Africa than the previously sequenced Neandertal from Siberia, allowing 10 to 20% more Neandertal DNA to be identified in present-day humans, including variants involved in low-density lipoprotein cholesterol concentrations, schizophrenia, and other diseases.
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Affiliation(s)
- Kay Prüfer
- Max Planck Institute for Evolutionary Anthropology, 04103 Leipzig, Germany.
| | - Cesare de Filippo
- Max Planck Institute for Evolutionary Anthropology, 04103 Leipzig, Germany
| | - Steffi Grote
- Max Planck Institute for Evolutionary Anthropology, 04103 Leipzig, Germany
| | - Fabrizio Mafessoni
- Max Planck Institute for Evolutionary Anthropology, 04103 Leipzig, Germany
| | - Petra Korlević
- Max Planck Institute for Evolutionary Anthropology, 04103 Leipzig, Germany
| | - Mateja Hajdinjak
- Max Planck Institute for Evolutionary Anthropology, 04103 Leipzig, Germany
| | - Benjamin Vernot
- Max Planck Institute for Evolutionary Anthropology, 04103 Leipzig, Germany
| | - Laurits Skov
- Bioinformatics Research Centre, Aarhus University, DK-8000 Aarhus C, Denmark
| | - Pinghsun Hsieh
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA 98195, USA
| | - Stéphane Peyrégne
- Max Planck Institute for Evolutionary Anthropology, 04103 Leipzig, Germany
| | - David Reher
- Max Planck Institute for Evolutionary Anthropology, 04103 Leipzig, Germany
| | - Charlotte Hopfe
- Max Planck Institute for Evolutionary Anthropology, 04103 Leipzig, Germany
| | - Sarah Nagel
- Max Planck Institute for Evolutionary Anthropology, 04103 Leipzig, Germany
| | - Tomislav Maricic
- Max Planck Institute for Evolutionary Anthropology, 04103 Leipzig, Germany
| | - Qiaomei Fu
- Key Laboratory of Vertebrate Evolution and Human Origins of Chinese Academy of Sciences, Institute of Vertebrate Paleontology and Paleoanthropology, Chinese Academy of Sciences, Beijing 100044, China
| | - Christoph Theunert
- Max Planck Institute for Evolutionary Anthropology, 04103 Leipzig, Germany
- Department of Integrative Biology, University of California, Berkeley, CA 94720-3140, USA
| | - Rebekah Rogers
- Department of Integrative Biology, University of California, Berkeley, CA 94720-3140, USA
| | - Pontus Skoglund
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | | | - Michael Dannemann
- Max Planck Institute for Evolutionary Anthropology, 04103 Leipzig, Germany
| | - Bradley J Nelson
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA 98195, USA
| | - Felix M Key
- Max Planck Institute for Evolutionary Anthropology, 04103 Leipzig, Germany
| | - Pavao Rudan
- Anthropology Center of the Croatian Academy of Sciences and Arts, 10000 Zagreb, Croatia
| | - Željko Kućan
- Anthropology Center of the Croatian Academy of Sciences and Arts, 10000 Zagreb, Croatia
| | - Ivan Gušić
- Anthropology Center of the Croatian Academy of Sciences and Arts, 10000 Zagreb, Croatia
| | | | | | - Nick Patterson
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - David Reich
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
- Howard Hughes Medical Institute, Harvard Medical School, Boston, MA 02115, USA
| | - Evan E Eichler
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA 98195, USA
- Howard Hughes Medical Institute, University of Washington, Seattle, WA 98195, USA
| | - Montgomery Slatkin
- Department of Integrative Biology, University of California, Berkeley, CA 94720-3140, USA
| | - Mikkel H Schierup
- Bioinformatics Research Centre, Aarhus University, DK-8000 Aarhus C, Denmark
| | - Aida M Andrés
- Max Planck Institute for Evolutionary Anthropology, 04103 Leipzig, Germany
| | - Janet Kelso
- Max Planck Institute for Evolutionary Anthropology, 04103 Leipzig, Germany
| | - Matthias Meyer
- Max Planck Institute for Evolutionary Anthropology, 04103 Leipzig, Germany
| | - Svante Pääbo
- Max Planck Institute for Evolutionary Anthropology, 04103 Leipzig, Germany.
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167
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Marshall C, Sturk-Andreaggi K, Daniels-Higginbotham J, Oliver RS, Barritt-Ross S, McMahon TP. Performance evaluation of a mitogenome capture and Illumina sequencing protocol using non-probative, case-type skeletal samples: Implications for the use of a positive control in a next-generation sequencing procedure. Forensic Sci Int Genet 2017; 31:198-206. [DOI: 10.1016/j.fsigen.2017.09.001] [Citation(s) in RCA: 49] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2017] [Revised: 08/08/2017] [Accepted: 09/05/2017] [Indexed: 11/24/2022]
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168
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Environmental DNA as a tool for ecological monitoring of fungal communities. UKRAINIAN BOTANICAL JOURNAL 2017. [DOI: 10.15407/ukrbotj74.05.442] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
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169
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Carøe C, Gopalakrishnan S, Vinner L, Mak SST, Sinding MHS, Samaniego JA, Wales N, Sicheritz‐Pontén T, Gilbert MTP. Single‐tube library preparation for degraded
DNA. Methods Ecol Evol 2017. [DOI: 10.1111/2041-210x.12871] [Citation(s) in RCA: 153] [Impact Index Per Article: 21.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Christian Carøe
- Natural History Museum of DenmarkUniversity of Copenhagen Copenhagen Denmark
- Department of Bio and Health InformaticsCenter for Biological Sequence AnalysisTechnical University of Denmark Lyngby Denmark
| | | | - Lasse Vinner
- Natural History Museum of DenmarkUniversity of Copenhagen Copenhagen Denmark
| | - Sarah S. T. Mak
- Natural History Museum of DenmarkUniversity of Copenhagen Copenhagen Denmark
| | - Mikkel Holger S. Sinding
- Natural History Museum of DenmarkUniversity of Copenhagen Copenhagen Denmark
- Natural History MuseumUniversity of Oslo Blindern Oslo Norway
| | - José A. Samaniego
- Natural History Museum of DenmarkUniversity of Copenhagen Copenhagen Denmark
| | - Nathan Wales
- Natural History Museum of DenmarkUniversity of Copenhagen Copenhagen Denmark
| | - Thomas Sicheritz‐Pontén
- Department of Bio and Health InformaticsCenter for Biological Sequence AnalysisTechnical University of Denmark Lyngby Denmark
| | - M. Thomas P. Gilbert
- Natural History Museum of DenmarkUniversity of Copenhagen Copenhagen Denmark
- Trace and Environmental DNA LaboratoryDepartment of Environment and AgricultureCurtin University Perth WA Australia
- NTNU University Museum Trondheim Norway
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170
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Sikora M, Seguin-Orlando A, Sousa VC, Albrechtsen A, Korneliussen T, Ko A, Rasmussen S, Dupanloup I, Nigst PR, Bosch MD, Renaud G, Allentoft ME, Margaryan A, Vasilyev SV, Veselovskaya EV, Borutskaya SB, Deviese T, Comeskey D, Higham T, Manica A, Foley R, Meltzer DJ, Nielsen R, Excoffier L, Mirazon Lahr M, Orlando L, Willerslev E. Ancient genomes show social and reproductive behavior of early Upper Paleolithic foragers. Science 2017; 358:659-662. [DOI: 10.1126/science.aao1807] [Citation(s) in RCA: 203] [Impact Index Per Article: 29.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2017] [Accepted: 09/25/2017] [Indexed: 01/01/2023]
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171
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Abstract
Analyzing the conditions in which past individuals lived is key to understanding the environments and cultural transitions to which humans had to adapt. Here, we suggest a methodology to probe into past environments, using reconstructed premortem DNA methylation maps of ancient individuals. We review a large body of research showing that differential DNA methylation is associated with changes in various external and internal factors, and propose that loci whose DNA methylation level is environmentally responsive could serve as markers to infer about ancient daily life, diseases, nutrition, exposure to toxins, and more. We demonstrate this approach by showing that hunger-related DNA methylation changes are found in ancient hunter-gatherers. The strategy we present here opens a window to reconstruct previously inaccessible aspects of the lives of past individuals.
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Affiliation(s)
- David Gokhman
- Department of Genetics, The Alexander Silberman Institute of Life Sciences, Faculty of Science, The Hebrew University of Jerusalem Edmond J. Safra Campus, Givat Ram, Jerusalem, Israel
| | - Anat Malul
- Department of Genetics, The Alexander Silberman Institute of Life Sciences, Faculty of Science, The Hebrew University of Jerusalem Edmond J. Safra Campus, Givat Ram, Jerusalem, Israel
| | - Liran Carmel
- Department of Genetics, The Alexander Silberman Institute of Life Sciences, Faculty of Science, The Hebrew University of Jerusalem Edmond J. Safra Campus, Givat Ram, Jerusalem, Israel
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172
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Skoglund P, Thompson JC, Prendergast ME, Mittnik A, Sirak K, Hajdinjak M, Salie T, Rohland N, Mallick S, Peltzer A, Heinze A, Olalde I, Ferry M, Harney E, Michel M, Stewardson K, Cerezo-Román JI, Chiumia C, Crowther A, Gomani-Chindebvu E, Gidna AO, Grillo KM, Helenius IT, Hellenthal G, Helm R, Horton M, López S, Mabulla AZP, Parkington J, Shipton C, Thomas MG, Tibesasa R, Welling M, Hayes VM, Kennett DJ, Ramesar R, Meyer M, Pääbo S, Patterson N, Morris AG, Boivin N, Pinhasi R, Krause J, Reich D. Reconstructing Prehistoric African Population Structure. Cell 2017; 171:59-71.e21. [PMID: 28938123 PMCID: PMC5679310 DOI: 10.1016/j.cell.2017.08.049] [Citation(s) in RCA: 185] [Impact Index Per Article: 26.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2016] [Revised: 07/01/2017] [Accepted: 08/29/2017] [Indexed: 02/06/2023]
Abstract
We assembled genome-wide data from 16 prehistoric Africans. We show that the anciently divergent lineage that comprises the primary ancestry of the southern African San had a wider distribution in the past, contributing approximately two-thirds of the ancestry of Malawi hunter-gatherers ∼8,100-2,500 years ago and approximately one-third of the ancestry of Tanzanian hunter-gatherers ∼1,400 years ago. We document how the spread of farmers from western Africa involved complete replacement of local hunter-gatherers in some regions, and we track the spread of herders by showing that the population of a ∼3,100-year-old pastoralist from Tanzania contributed ancestry to people from northeastern to southern Africa, including a ∼1,200-year-old southern African pastoralist. The deepest diversifications of African lineages were complex, involving either repeated gene flow among geographically disparate groups or a lineage more deeply diverging than that of the San contributing more to some western African populations than to others. We finally leverage ancient genomes to document episodes of natural selection in southern African populations. PAPERCLIP.
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Affiliation(s)
- Pontus Skoglund
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA.
| | | | - Mary E Prendergast
- Radcliffe Institute for Advanced Study, Harvard University, Cambridge, MA 02138, USA
| | - Alissa Mittnik
- Max Planck Institute for the Science of Human History, Jena 07745, Germany; Institute for Archeological Sciences, Eberhard-Karls-University, Tuebingen 72070, Germany
| | - Kendra Sirak
- Department of Anthropology, Emory University, Atlanta, GA 30322, USA; School of Archaeology and Earth Institute, University College Dublin, Dublin 4, Ireland
| | - Mateja Hajdinjak
- Max Planck Institute for Evolutionary Anthropology, Leipzig 04103, Germany
| | - Tasneem Salie
- Division of Human Genetics, Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Cape Town 7925, South Africa
| | - Nadin Rohland
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
| | - Swapan Mallick
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA; Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA
| | - Alexander Peltzer
- Max Planck Institute for the Science of Human History, Jena 07745, Germany; Integrative Transcriptomics, Centre for Bioinformatics, University of Tuebingen, Tuebingen 72076, Germany
| | - Anja Heinze
- Max Planck Institute for Evolutionary Anthropology, Leipzig 04103, Germany
| | - Iñigo Olalde
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA
| | - Matthew Ferry
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA; Howard Hughes Medical Institute, Harvard Medical School, Boston, MA 02115, USA
| | - Eadaoin Harney
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA; Howard Hughes Medical Institute, Harvard Medical School, Boston, MA 02115, USA; Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA 02138, USA
| | - Megan Michel
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA; Howard Hughes Medical Institute, Harvard Medical School, Boston, MA 02115, USA
| | - Kristin Stewardson
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA; Howard Hughes Medical Institute, Harvard Medical School, Boston, MA 02115, USA
| | - Jessica I Cerezo-Román
- Department of Geography and Anthropology, California State Polytechnic University, Pomona, Pomona, CA 91768, USA
| | - Chrissy Chiumia
- Malawi Department of Museums and Monuments, Lilongwe 3, Malawi
| | - Alison Crowther
- Max Planck Institute for the Science of Human History, Jena 07745, Germany; School of Social Science, The University of Queensland, Brisbane, Queensland 4072, Australia
| | | | | | - Katherine M Grillo
- Department of Archaeology and Anthropology, University of Wisconsin - La Crosse, La Crosse, WI 54601, USA
| | - I Taneli Helenius
- Department of Genetics, Evolution and Environment, University College London, London WC1E 6BT, UK
| | - Garrett Hellenthal
- Department of Genetics, Evolution and Environment, University College London, London WC1E 6BT, UK
| | - Richard Helm
- Canterbury Archaeological Trust, Canterbury CT1 2LU, UK
| | - Mark Horton
- Department Archaeology and Anthropology, University of Bristol, Bristol BS8 1UU, UK
| | - Saioa López
- Department of Genetics, Evolution and Environment, University College London, London WC1E 6BT, UK
| | | | - John Parkington
- Department of Archaeology, University of Cape Town, Cape Town 7700, South Africa
| | - Ceri Shipton
- McDonald Institute for Archaeological Research, Cambridge CB2 3ER, UK; British Institute in Eastern Africa, Nairobi 30710, Kenya
| | - Mark G Thomas
- Department of Genetics, Evolution and Environment, University College London, London WC1E 6BT, UK
| | - Ruth Tibesasa
- Department of Anthropology and Archaeology, University of Pretoria, Pretoria 0083, South Africa
| | - Menno Welling
- African Studies Centre Leiden, Leiden University, Leiden 2300 RB, Netherlands; African Heritage Ltd, Zomba, Malawi
| | - Vanessa M Hayes
- Genomics and Epigenetics Division, Garvan Institute of Medical Research, Darlinghurst, NSW 2010, Australia; Central Clinical School, University of Sydney, Camperdown, NSW 2050, Australia; School of Health Systems and Public Health, University of Pretoria, Gezina 0031, South Africa
| | - Douglas J Kennett
- Department of Anthropology and Institutes for Energy and the Environment, Pennsylvania State University, University Park, PA 16802, USA
| | - Raj Ramesar
- Division of Human Genetics, Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Cape Town 7925, South Africa
| | - Matthias Meyer
- Max Planck Institute for Evolutionary Anthropology, Leipzig 04103, Germany
| | - Svante Pääbo
- Max Planck Institute for Evolutionary Anthropology, Leipzig 04103, Germany
| | - Nick Patterson
- Radcliffe Institute for Advanced Study, Harvard University, Cambridge, MA 02138, USA; Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA
| | - Alan G Morris
- Department of Archaeology, University of Cape Town, Cape Town 7700, South Africa
| | - Nicole Boivin
- Max Planck Institute for the Science of Human History, Jena 07745, Germany
| | - Ron Pinhasi
- School of Archaeology and Earth Institute, University College Dublin, Dublin 4, Ireland; Department of Anthropology, University of Vienna, Althanstrasse 14, 1090 Vienna, Austria
| | - Johannes Krause
- Max Planck Institute for the Science of Human History, Jena 07745, Germany; Institute for Archeological Sciences, Eberhard-Karls-University, Tuebingen 72070, Germany
| | - David Reich
- Department of Genetics, Harvard Medical School, Boston, MA 02115, USA; Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA; Howard Hughes Medical Institute, Harvard Medical School, Boston, MA 02115, USA.
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173
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Chen L, Liu P, Evans TC, Ettwiller LM. DNA damage is a pervasive cause of sequencing errors, directly confounding variant identification. Science 2017; 355:752-756. [PMID: 28209900 DOI: 10.1126/science.aai8690] [Citation(s) in RCA: 154] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2016] [Accepted: 01/23/2017] [Indexed: 12/20/2022]
Abstract
Mutations in somatic cells generate a heterogeneous genomic population and may result in serious medical conditions. Although cancer is typically associated with somatic variations, advances in DNA sequencing indicate that cell-specific variants affect a number of phenotypes and pathologies. Here, we show that mutagenic damage accounts for the majority of the erroneous identification of variants with low to moderate (1 to 5%) frequency. More important, we found signatures of damage in most sequencing data sets in widely used resources, including the 1000 Genomes Project and The Cancer Genome Atlas, establishing damage as a pervasive cause of sequencing errors. The extent of this damage directly confounds the determination of somatic variants in these data sets.
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Affiliation(s)
- Lixin Chen
- New England Biolabs Inc., 240 County Road, Ipswich, MA 01938-2723, USA
| | - Pingfang Liu
- New England Biolabs Inc., 240 County Road, Ipswich, MA 01938-2723, USA
| | - Thomas C Evans
- New England Biolabs Inc., 240 County Road, Ipswich, MA 01938-2723, USA.
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174
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Do H, Molania R, Mitchell PL, Vaiskunaite R, Murdoch JD, Dobrovic A. Reducing Artifactual EGFR T790M Mutations in DNA from Formalin-Fixed Paraffin-Embedded Tissue by Use of Thymine-DNA Glycosylase. Clin Chem 2017; 63:1506-1514. [DOI: 10.1373/clinchem.2017.271932] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2017] [Accepted: 06/19/2017] [Indexed: 11/06/2022]
Abstract
Abstract
BACKGROUND
False-positive EGFR T790M mutations have been reported in formalin-fixed lung tumors, but the cause of the false positives has not been identified. The T790M mutation results from a C>T change at the cytosine of a CpG dinucleotide. The presence or absence of methylation at this cytosine has different consequences following deamination, resulting in a thymine or uracil, respectively, both of which however result in an artifactual change. Uracil-DNA glycosylase (UDG) can be used to eliminate DNA templates with uracil residues but is not active against artifactual thymines. We therefore investigated the use of thymine-DNA glycosylase (TDG) to reduce artifactual T790M mutations.
METHODS
Formalin-fixed normal lung tissues and lung squamous cell carcinomas were tested to measure the frequency of false-positive EGFR mutations by use of droplet digital PCR before and after treatment with either UDG or TDG. Methylation at the cytosine at EGFR T790 was assessed by pyrosequencing and by analysis of public databases.
RESULTS
Artifactual EGFR T790M mutations were detected in all of the archival formalin-fixed normal lung and lung squamous cell carcinomas at mutant allele frequencies of 1% or lower. The cytosine at EGFR T790 showed high levels of methylation in all lung cancer samples and normal tissues. Pretreatment of the formalin-fixed DNA with either UDG or TDG reduced the false EGFR T790M mutations, but a greater reduction was seen with the TDG treatment.
CONCLUSIONS
Both U:G and T:G lesions in formalin-fixed tissue are sources of false-positive EGFR T790M mutations. This is the first report of the use of TDG to reduce sequence artifacts in formalin-fixed DNA and is applicable to the accurate detection of mutations arising at methylated cytosines.
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Affiliation(s)
- Hongdo Do
- Translational Genomics and Epigenomics Laboratory, Olivia Newton-John Cancer Research Institute, Melbourne, Australia
- School of Cancer Medicine, La Trobe University, Melbourne, Australia
- Department of Pathology, University of Melbourne, Melbourne, Australia
| | - Ramyar Molania
- Translational Genomics and Epigenomics Laboratory, Olivia Newton-John Cancer Research Institute, Melbourne, Australia
- Department of Medicine, University of Melbourne, Melbourne, Australia
| | - Paul L Mitchell
- Department of Medical Oncology, Austin Health, Melbourne, Australia
| | | | | | - Alexander Dobrovic
- Translational Genomics and Epigenomics Laboratory, Olivia Newton-John Cancer Research Institute, Melbourne, Australia
- School of Cancer Medicine, La Trobe University, Melbourne, Australia
- Department of Pathology, University of Melbourne, Melbourne, Australia
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175
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Mackie M, Hendy J, Lowe AD, Sperduti A, Holst M, Collins MJ, Speller CF. Preservation of the metaproteome: variability of protein preservation in ancient dental calculus. SCIENCE AND TECHNOLOGY OF ARCHAEOLOGICAL RESEARCH 2017; 3:74-86. [PMID: 29098079 PMCID: PMC5633013 DOI: 10.1080/20548923.2017.1361629] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/10/2017] [Accepted: 07/16/2017] [Indexed: 05/25/2023]
Abstract
Proteomic analysis of dental calculus is emerging as a powerful tool for disease and dietary characterisation of archaeological populations. To better understand the variability in protein results from dental calculus, we analysed 21 samples from three Roman-period populations to compare: 1) the quantity of extracted protein; 2) the number of mass spectral queries; and 3) the number of peptide spectral matches and protein identifications. We found little correlation between the quantity of calculus analysed and total protein identifications, as well as no systematic trends between site location and protein preservation. We identified a wide range of individual variability, which may be associated with the mechanisms of calculus formation and/or post-depositional contamination, in addition to taphonomic factors. Our results suggest dental calculus is indeed a stable, long-term reservoir of proteins as previously reported, but further systematic studies are needed to identify mechanisms associated with protein entrapment and survival in dental calculus.
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Affiliation(s)
- Meaghan Mackie
- BioArCh, Department of Archaeology, University of York, York, UK
| | - Jessica Hendy
- BioArCh, Department of Archaeology, University of York, York, UK
- Max Planck Institute for the Science of Human History, Jena, Germany
| | - Abigail D. Lowe
- BioArCh, Department of Archaeology, University of York, York, UK
- Department of Earth Sciences, Natural History Museum, London, UK
| | | | - Malin Holst
- BioArCh, Department of Archaeology, University of York, York, UK
- York Osteoarchaeology Ltd
| | - Matthew J. Collins
- BioArCh, Department of Archaeology, University of York, York, UK
- EvoGenomics Section, Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark
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176
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Swarts K, Gutaker RM, Benz B, Blake M, Bukowski R, Holland J, Kruse-Peeples M, Lepak N, Prim L, Romay MC, Ross-Ibarra J, Sanchez-Gonzalez JDJ, Schmidt C, Schuenemann VJ, Krause J, Matson RG, Weigel D, Buckler ES, Burbano HA. Genomic estimation of complex traits reveals ancient maize adaptation to temperate North America. Science 2017; 357:512-515. [DOI: 10.1126/science.aam9425] [Citation(s) in RCA: 127] [Impact Index Per Article: 18.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2017] [Accepted: 06/29/2017] [Indexed: 01/24/2023]
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177
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Key FM, Posth C, Krause J, Herbig A, Bos KI. Mining Metagenomic Data Sets for Ancient DNA: Recommended Protocols for Authentication. Trends Genet 2017; 33:508-520. [PMID: 28688671 DOI: 10.1016/j.tig.2017.05.005] [Citation(s) in RCA: 52] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2017] [Revised: 05/19/2017] [Accepted: 05/24/2017] [Indexed: 12/21/2022]
Abstract
While a comparatively young area of research, investigations relying on ancient DNA data have been highly valuable in revealing snapshots of genetic variation in both the recent and the not-so-recent past. Born out of a tradition of single-locus PCR-based approaches that often target individual species, stringent criteria for both data acquisition and analysis were introduced early to establish high standards of data quality. Today, the immense volume of data made available through next-generation sequencing has significantly increased the analytical resolution offered by processing ancient tissues and permits parallel analyses of host and microbial communities. The adoption of this new approach to data acquisition, however, requires an accompanying update on methods of DNA authentication, especially given that ancient molecules are expected to exist in low proportions in archaeological material, where an environmental signal is likely to dominate. In this review, we provide a summary of recent data authentication approaches that have been successfully used to distinguish between endogenous and nonendogenous DNA sequences in metagenomic data sets. While our discussion mostly centers on the detection of ancient human and ancient bacterial pathogen DNA, their applicability is far wider.
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Affiliation(s)
- Felix M Key
- Max Planck Institute for the Science of Human History, Jena, Germany.
| | - Cosimo Posth
- Max Planck Institute for the Science of Human History, Jena, Germany
| | - Johannes Krause
- Max Planck Institute for the Science of Human History, Jena, Germany
| | - Alexander Herbig
- Max Planck Institute for the Science of Human History, Jena, Germany
| | - Kirsten I Bos
- Max Planck Institute for the Science of Human History, Jena, Germany.
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178
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Schuenemann VJ, Peltzer A, Welte B, van Pelt WP, Molak M, Wang CC, Furtwängler A, Urban C, Reiter E, Nieselt K, Teßmann B, Francken M, Harvati K, Haak W, Schiffels S, Krause J. Ancient Egyptian mummy genomes suggest an increase of Sub-Saharan African ancestry in post-Roman periods. Nat Commun 2017; 8:15694. [PMID: 28556824 PMCID: PMC5459999 DOI: 10.1038/ncomms15694] [Citation(s) in RCA: 86] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2016] [Accepted: 04/20/2017] [Indexed: 12/19/2022] Open
Abstract
Egypt, located on the isthmus of Africa, is an ideal region to study historical population dynamics due to its geographic location and documented interactions with ancient civilizations in Africa, Asia and Europe. Particularly, in the first millennium BCE Egypt endured foreign domination leading to growing numbers of foreigners living within its borders possibly contributing genetically to the local population. Here we present 90 mitochondrial genomes as well as genome-wide data sets from three individuals obtained from Egyptian mummies. The samples recovered from Middle Egypt span around 1,300 years of ancient Egyptian history from the New Kingdom to the Roman Period. Our analyses reveal that ancient Egyptians shared more ancestry with Near Easterners than present-day Egyptians, who received additional sub-Saharan admixture in more recent times. This analysis establishes ancient Egyptian mummies as a genetic source to study ancient human history and offers the perspective of deciphering Egypt's past at a genome-wide level. Archaeological and historical records had shown ancient Egypt before and after Ptolemaic and Roman periods to be a hub of human migration and exchange. Here, Schuenemann and colleagues analyse ancient mitochondrial and nuclear DNA to investigate the genetic history of Egypt.
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Affiliation(s)
- Verena J Schuenemann
- Institute for Archaeological Sciences, University of Tübingen, 72070 Tübingen, Germany.,Senckenberg Centre for Human Evolution and Palaeoenvironment, University of Tübingen, 72070 Tübingen, Germany
| | - Alexander Peltzer
- Integrative Transcriptomics, Center for Bioinformatics, University of Tübingen, 72076 Tübingen, Germany.,Department for Archaeogenetics, Max Planck Institute for the Science of Human History, 07745 Jena, Germany
| | - Beatrix Welte
- Institute for Archaeological Sciences, University of Tübingen, 72070 Tübingen, Germany
| | - W Paul van Pelt
- Division of Archaeology, University of Cambridge, Cambridge CB2 3DZ, UK
| | - Martyna Molak
- Museum and Institute of Zoology, Polish Academy of Sciences, 00-679 Warsaw, Poland
| | - Chuan-Chao Wang
- Department for Archaeogenetics, Max Planck Institute for the Science of Human History, 07745 Jena, Germany
| | - Anja Furtwängler
- Institute for Archaeological Sciences, University of Tübingen, 72070 Tübingen, Germany
| | - Christian Urban
- Institute for Archaeological Sciences, University of Tübingen, 72070 Tübingen, Germany
| | - Ella Reiter
- Institute for Archaeological Sciences, University of Tübingen, 72070 Tübingen, Germany
| | - Kay Nieselt
- Integrative Transcriptomics, Center for Bioinformatics, University of Tübingen, 72076 Tübingen, Germany
| | - Barbara Teßmann
- Berlin Society of Anthropology, Ethnology and Prehistory, 10997 Berlin, Germany
| | - Michael Francken
- Institute for Archaeological Sciences, University of Tübingen, 72070 Tübingen, Germany
| | - Katerina Harvati
- Institute for Archaeological Sciences, University of Tübingen, 72070 Tübingen, Germany.,Senckenberg Centre for Human Evolution and Palaeoenvironment, University of Tübingen, 72070 Tübingen, Germany.,DFG Centre for Advanced Studies 'Words, Bones, Genes, Tools: Tracking Linguistic, Cultural and Biological Trajectories of the Human Past', University of Tübingen, 72070 Tübingen, Germany
| | - Wolfgang Haak
- Department for Archaeogenetics, Max Planck Institute for the Science of Human History, 07745 Jena, Germany.,School of Biological Sciences, The University of Adelaide, Adelaide, South Australia 5005, Australia
| | - Stephan Schiffels
- Department for Archaeogenetics, Max Planck Institute for the Science of Human History, 07745 Jena, Germany
| | - Johannes Krause
- Institute for Archaeological Sciences, University of Tübingen, 72070 Tübingen, Germany.,Senckenberg Centre for Human Evolution and Palaeoenvironment, University of Tübingen, 72070 Tübingen, Germany.,Department for Archaeogenetics, Max Planck Institute for the Science of Human History, 07745 Jena, Germany
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179
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Librado P, Gamba C, Gaunitz C, Der Sarkissian C, Pruvost M, Albrechtsen A, Fages A, Khan N, Schubert M, Jagannathan V, Serres-Armero A, Kuderna LFK, Povolotskaya IS, Seguin-Orlando A, Lepetz S, Neuditschko M, Thèves C, Alquraishi S, Alfarhan AH, Al-Rasheid K, Rieder S, Samashev Z, Francfort HP, Benecke N, Hofreiter M, Ludwig A, Keyser C, Marques-Bonet T, Ludes B, Crubézy E, Leeb T, Willerslev E, Orlando L. Ancient genomic changes associated with domestication of the horse. Science 2017; 356:442-445. [DOI: 10.1126/science.aam5298] [Citation(s) in RCA: 111] [Impact Index Per Article: 15.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/30/2023]
Abstract
Ancient genomics of horse domesticationThe domestication of the horse was a seminal event in human cultural evolution. Libradoet al.obtained genome sequences from 14 horses from the Bronze and Iron Ages, about 2000 to 4000 years ago, soon after domestication. They identified variants determining coat color and genes selected during the domestication process. They could also see evidence of admixture with archaic horses and the demography of the domestication process, which included the accumulation of deleterious variants. The horse appears to have undergone a different type of domestication process than animals that were domesticated simply for food.Science, this issue p.442
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Affiliation(s)
- Pablo Librado
- Centre for GeoGenetics, Natural History Museum of Denmark, Øster Voldgade 5-7, 1350K Copenhagen, Denmark
| | - Cristina Gamba
- Centre for GeoGenetics, Natural History Museum of Denmark, Øster Voldgade 5-7, 1350K Copenhagen, Denmark
| | - Charleen Gaunitz
- Centre for GeoGenetics, Natural History Museum of Denmark, Øster Voldgade 5-7, 1350K Copenhagen, Denmark
| | - Clio Der Sarkissian
- Centre for GeoGenetics, Natural History Museum of Denmark, Øster Voldgade 5-7, 1350K Copenhagen, Denmark
| | - Mélanie Pruvost
- Institut Jacques Monod, UMR 7592 CNRS, Université Paris Diderot, 75205 Paris cedex 13, France
| | - Anders Albrechtsen
- Bioinformatics Center, Department of Biology, University of Copenhagen, 2200N Copenhagen, Denmark
| | - Antoine Fages
- Centre for GeoGenetics, Natural History Museum of Denmark, Øster Voldgade 5-7, 1350K Copenhagen, Denmark
- Laboratoire d’Anthropobiologie Moléculaire et d’Imagerie de Synthèse, CNRS UMR 5288, Université de Toulouse, Université Paul Sabatier, 31000 Toulouse, France
| | - Naveed Khan
- Centre for GeoGenetics, Natural History Museum of Denmark, Øster Voldgade 5-7, 1350K Copenhagen, Denmark
- Department of Biotechnology, Abdul Wali Khan University, Mardan, Pakistan
| | - Mikkel Schubert
- Centre for GeoGenetics, Natural History Museum of Denmark, Øster Voldgade 5-7, 1350K Copenhagen, Denmark
| | | | - Aitor Serres-Armero
- Institute of Evolutionary Biology (CSIC-UPF), Departament de Ciències Experimentals i de la Salut, Universitat Pompeu Fabra, 08003 Barcelona, Spain
- Center for Genomic Regulation (CNAG-CRG), Barcelona Institute of Science and Technology (BIST), Baldiri i Reixac 4, 08028 Barcelona, Spain
| | - Lukas F. K. Kuderna
- Institute of Evolutionary Biology (CSIC-UPF), Departament de Ciències Experimentals i de la Salut, Universitat Pompeu Fabra, 08003 Barcelona, Spain
- Center for Genomic Regulation (CNAG-CRG), Barcelona Institute of Science and Technology (BIST), Baldiri i Reixac 4, 08028 Barcelona, Spain
| | - Inna S. Povolotskaya
- Institute of Evolutionary Biology (CSIC-UPF), Departament de Ciències Experimentals i de la Salut, Universitat Pompeu Fabra, 08003 Barcelona, Spain
- Center for Genomic Regulation (CNAG-CRG), Barcelona Institute of Science and Technology (BIST), Baldiri i Reixac 4, 08028 Barcelona, Spain
| | - Andaine Seguin-Orlando
- Centre for GeoGenetics, Natural History Museum of Denmark, Øster Voldgade 5-7, 1350K Copenhagen, Denmark
- National High-Throughput DNA Sequencing Center, Copenhagen, Denmark
| | - Sébastien Lepetz
- Centre National de la Recherche Scientifique, Muséum national d’histoire naturelle, Sorbonne Universités, Archéozoologie, Archéobotanique, Sociétés, Pratiques et Environnements (UMR 7209), 55 rue Buffon, 75005 Paris, France
| | | | - Catherine Thèves
- Laboratoire d’Anthropobiologie Moléculaire et d’Imagerie de Synthèse, CNRS UMR 5288, Université de Toulouse, Université Paul Sabatier, 31000 Toulouse, France
| | - Saleh Alquraishi
- Zoology Department, College of Science, King Saud University, Riyadh 11451, Saudi Arabia
| | - Ahmed H. Alfarhan
- Zoology Department, College of Science, King Saud University, Riyadh 11451, Saudi Arabia
| | - Khaled Al-Rasheid
- Zoology Department, College of Science, King Saud University, Riyadh 11451, Saudi Arabia
| | - Stefan Rieder
- Agroscope, Swiss National Stud Farm, 1580 Avenches, Switzerland
| | - Zainolla Samashev
- Branch of Institute of Archaeology Margulan, Republic Avenue 24-405, 010000 Astana, Republic of Kazakhstan
| | - Henri-Paul Francfort
- CNRS, UMR 7041 Archéologie et Sciences de l’Antiquité, Archéologie de l'Asie Centrale, Maison René Ginouvès, 21 allée de l’Université, 92023 Nanterre, France
| | - Norbert Benecke
- German Archaeological Institute, Department of Natural Sciences, Berlin, 14195 Berlin, Germany
| | - Michael Hofreiter
- University of Potsdam, Faculty of Mathematics and Natural Sciences, Institute for Biochemistry and Biology, Karl-Liebknecht-Strasse 24-25, 14476 Potsdam, Germany
| | - Arne Ludwig
- Department of Evolutionary Genetics, Leibniz Institute for Zoo and Wildlife Research, Berlin 10315, Germany
| | - Christine Keyser
- Laboratoire d’Anthropobiologie Moléculaire et d’Imagerie de Synthèse, CNRS UMR 5288, Université de Toulouse, Université Paul Sabatier, 31000 Toulouse, France
- Institut de Médecine Légale, Université de Strasbourg, Strasbourg, France
| | - Tomas Marques-Bonet
- Institute of Evolutionary Biology (CSIC-UPF), Departament de Ciències Experimentals i de la Salut, Universitat Pompeu Fabra, 08003 Barcelona, Spain
- Center for Genomic Regulation (CNAG-CRG), Barcelona Institute of Science and Technology (BIST), Baldiri i Reixac 4, 08028 Barcelona, Spain
- Catalan Institution of Research and Advanced Studies (ICREA), Passeig de Lluís Companys, 23, 08010, Barcelona, Spain
| | - Bertrand Ludes
- Laboratoire d’Anthropobiologie Moléculaire et d’Imagerie de Synthèse, CNRS UMR 5288, Université de Toulouse, Université Paul Sabatier, 31000 Toulouse, France
- Institut Médico-Légal, Université Paris Descartes, Paris, France
| | - Eric Crubézy
- Laboratoire d’Anthropobiologie Moléculaire et d’Imagerie de Synthèse, CNRS UMR 5288, Université de Toulouse, Université Paul Sabatier, 31000 Toulouse, France
| | - Tosso Leeb
- Institute of Genetics, University of Bern, 3001 Bern, Switzerland
| | - Eske Willerslev
- Centre for GeoGenetics, Natural History Museum of Denmark, Øster Voldgade 5-7, 1350K Copenhagen, Denmark
| | - Ludovic Orlando
- Centre for GeoGenetics, Natural History Museum of Denmark, Øster Voldgade 5-7, 1350K Copenhagen, Denmark
- Laboratoire d’Anthropobiologie Moléculaire et d’Imagerie de Synthèse, CNRS UMR 5288, Université de Toulouse, Université Paul Sabatier, 31000 Toulouse, France
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180
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Abstract
Most reconstruction methods for genomes of ancient origin that are used today require a closely related reference. In order to identify genomic rearrangements or the deletion of whole genes, de novo assembly has to be used. However, because of inherent problems with ancient DNA, its de novo assembly is highly complicated. In order to tackle the diversity in the length of the input reads, we propose a two-layer approach, where multiple assemblies are generated in the first layer, which are then combined in the second layer. We used this two-layer assembly to generate assemblies for two different ancient samples and compared the results to current de novo assembly approaches. We are able to improve the assembly with respect to the length of the contigs and can resolve more repetitive regions.
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Affiliation(s)
- Alexander Seitz
- Center for Bioinformatics (ZBIT), Integrative Transcriptomics, Eberhard-Karls-Universität Tübingen , Tübingen , Germany
| | - Kay Nieselt
- Center for Bioinformatics (ZBIT), Integrative Transcriptomics, Eberhard-Karls-Universität Tübingen , Tübingen , Germany
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181
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Gutaker RM, Burbano HA. Reinforcing plant evolutionary genomics using ancient DNA. CURRENT OPINION IN PLANT BIOLOGY 2017; 36:38-45. [PMID: 28160617 DOI: 10.1016/j.pbi.2017.01.002] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/05/2016] [Revised: 12/07/2016] [Accepted: 01/13/2017] [Indexed: 05/11/2023]
Abstract
Improved understanding of ancient DNA (aDNA) biochemical properties coupled with application of next generation sequencing (NGS) methods enabled sequencing and authenticating genomes of historical samples. This advancement ignited a revolution in plant evolutionary genomics by allowing direct observations of past molecular diversity. Analyses of genomes sequenced from temporally distributed samples of Gossypium sp., Phytophthora infestans and Arabidopsis thaliana improved our understanding of the evolutionary rates and time scales at which genome remodeling takes place. Comparison of historical samples of barley (Hordeum vulgare) and maize (Zea mays ssp. mays) with their present-day counterparts enabled assessment of selection during different stages of domestication. These examples show how aDNA already improved our evolutionary inferences. Increasing quality and amount of sequencing data retrieved from historical plants will further advance our understanding of plant evolution.
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Affiliation(s)
- Rafal M Gutaker
- Research Group for Ancient Genomics and Evolution, Department of Molecular Biology, Max Planck Institute for Developmental Biology, Spemannstr. 37-39, Tuebingen 72076, Germany
| | - Hernán A Burbano
- Research Group for Ancient Genomics and Evolution, Department of Molecular Biology, Max Planck Institute for Developmental Biology, Spemannstr. 37-39, Tuebingen 72076, Germany.
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182
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Comparing Ancient DNA Preservation in Petrous Bone and Tooth Cementum. PLoS One 2017; 12:e0170940. [PMID: 28129388 PMCID: PMC5271384 DOI: 10.1371/journal.pone.0170940] [Citation(s) in RCA: 93] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2016] [Accepted: 01/12/2017] [Indexed: 01/08/2023] Open
Abstract
Large-scale genomic analyses of ancient human populations have become feasible partly due to refined sampling methods. The inner part of petrous bones and the cementum layer in teeth roots are currently recognized as the best substrates for such research. We present a comparative analysis of DNA preservation in these two substrates obtained from the same human skulls, across a range of different ages and preservation environments. Both substrates display significantly higher endogenous DNA content (average of 16.4% and 40.0% for teeth and petrous bones, respectively) than parietal skull bone (average of 2.2%). Despite sample-to-sample variation, petrous bone overall performs better than tooth cementum (p = 0.001). This difference, however, is driven largely by a cluster of viking skeletons from one particular locality, showing relatively poor molecular tooth preservation (<10% endogenous DNA). In the remaining skeletons there is no systematic difference between the two substrates. A crude preservation (good/bad) applied to each sample prior to DNA-extraction predicted the above/below 10% endogenous DNA threshold in 80% of the cases. Interestingly, we observe signficantly higher levels of cytosine to thymine deamination damage and lower proportions of mitochondrial/nuclear DNA in petrous bone compared to tooth cementum. Lastly, we show that petrous bones from ancient cremated individuals contain no measurable levels of authentic human DNA. Based on these findings we discuss the pros and cons of sampling the different elements.
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183
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Feldman M, Harbeck M, Keller M, Spyrou MA, Rott A, Trautmann B, Scholz HC, Päffgen B, Peters J, McCormick M, Bos K, Herbig A, Krause J. A High-Coverage Yersinia pestis Genome from a Sixth-Century Justinianic Plague Victim. Mol Biol Evol 2016; 33:2911-2923. [PMID: 27578768 PMCID: PMC5062324 DOI: 10.1093/molbev/msw170] [Citation(s) in RCA: 86] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
The Justinianic Plague, which started in the sixth century and lasted to the mid eighth century, is thought to be the first of three historically documented plague pandemics causing massive casualties. Historical accounts and molecular data suggest the bacterium Yersinia pestis as its etiological agent. Here we present a new high-coverage (17.9-fold) Y. pestis genome obtained from a sixth-century skeleton recovered from a southern German burial site close to Munich. The reconstructed genome enabled the detection of 30 unique substitutions as well as structural differences that have not been previously described. We report indels affecting a lacl family transcription regulator gene as well as nonsynonymous substitutions in the nrdE, fadJ, and pcp genes, that have been suggested as plague virulence determinants or have been shown to be upregulated in different models of plague infection. In addition, we identify 19 false positive substitutions in a previously published lower-coverage Y. pestis genome from another archaeological site of the same time period and geographical region that is otherwise genetically identical to the high-coverage genome sequence reported here, suggesting low-genetic diversity of the plague during the sixth century in rural southern Germany.
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Affiliation(s)
- Michal Feldman
- Max Planck Institute for the Science of Human History, Jena, Germany
- Institute for Archaeological Sciences, Archaeo- and Palaeogenetics, University of Tübingen, Tübingen, Germany
| | - Michaela Harbeck
- SNSB, State Collection of Anthropology and Palaeoanatomy, Munich, Germany
| | - Marcel Keller
- Max Planck Institute for the Science of Human History, Jena, Germany
- SNSB, State Collection of Anthropology and Palaeoanatomy, Munich, Germany
| | - Maria A. Spyrou
- Max Planck Institute for the Science of Human History, Jena, Germany
- Institute for Archaeological Sciences, Archaeo- and Palaeogenetics, University of Tübingen, Tübingen, Germany
| | - Andreas Rott
- SNSB, State Collection of Anthropology and Palaeoanatomy, Munich, Germany
| | - Bernd Trautmann
- SNSB, State Collection of Anthropology and Palaeoanatomy, Munich, Germany
| | - Holger C. Scholz
- Bundeswehr Institute of Microbiology, Munich, Germany
- German Center for Infection Research (DZIF), Munich, Germany
| | - Bernd Päffgen
- Institute for Pre- and Protohistoric Archaeology and Archaeology of the Roman Provinces, Ludwig-Maximilian University Munich, Germany
| | - Joris Peters
- SNSB, State Collection of Anthropology and Palaeoanatomy, Munich, Germany
- Institute of Palaeoanatomy, Domestication Research and the History of Veterinary Medicine, Ludwig-Maximilian University of Munich, Germany
| | - Michael McCormick
- Department of History, Harvard University, Initiative for the Science of the Human Past
| | - Kirsten Bos
- Max Planck Institute for the Science of Human History, Jena, Germany
- Institute for Archaeological Sciences, Archaeo- and Palaeogenetics, University of Tübingen, Tübingen, Germany
| | - Alexander Herbig
- Max Planck Institute for the Science of Human History, Jena, Germany
- Institute for Archaeological Sciences, Archaeo- and Palaeogenetics, University of Tübingen, Tübingen, Germany
| | - Johannes Krause
- Max Planck Institute for the Science of Human History, Jena, Germany
- Institute for Archaeological Sciences, Archaeo- and Palaeogenetics, University of Tübingen, Tübingen, Germany
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184
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Bolnick DA, Raff JA, Springs LC, Reynolds AW, Miró-Herrans AT. Native American Genomics and Population Histories. ANNUAL REVIEW OF ANTHROPOLOGY 2016. [DOI: 10.1146/annurev-anthro-102215-100036] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Studies of Native American genetic diversity and population history have been transformed over the last decade by important developments in anthropological genetics. During this time, researchers have adopted new DNA technologies and computational approaches for analyzing genomic data, and they have become increasingly sensitive to the views of research participants and communities. As new methods are applied to long-standing questions, and as more research is conducted in collaboration with indigenous communities, we are gaining new insights into the history and diversity of indigenous populations. This review discusses the recent methodological advances and genetic studies that have improved our understanding of Native American genomics and population histories. We synthesize current knowledge about Native American genomic variation and build a model of population history in the Americas. We also discuss the broader implications of this research for anthropology and related disciplines, and we highlight challenges and other considerations for future research.
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Affiliation(s)
- Deborah A. Bolnick
- Department of Anthropology, University of Texas at Austin, Austin, Texas 78712;, , ,
- Population Research Center, University of Texas at Austin, Austin, Texas 78712
| | - Jennifer A. Raff
- Department of Anthropology, University of Kansas, Lawrence, Kansas 66045-7556
| | - Lauren C. Springs
- Department of Anthropology, University of Texas at Austin, Austin, Texas 78712;, , ,
| | - Austin W. Reynolds
- Department of Anthropology, University of Texas at Austin, Austin, Texas 78712;, , ,
- Department of Integrative Biology, University of Texas at Austin, Austin, Texas 78712
| | - Aida T. Miró-Herrans
- Department of Anthropology, University of Texas at Austin, Austin, Texas 78712;, , ,
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185
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Hanghøj K, Seguin-Orlando A, Schubert M, Madsen T, Pedersen JS, Willerslev E, Orlando L. Fast, Accurate and Automatic Ancient Nucleosome and Methylation Maps with epiPALEOMIX. Mol Biol Evol 2016; 33:3284-3298. [PMID: 27624717 PMCID: PMC5100044 DOI: 10.1093/molbev/msw184] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
The first epigenomes from archaic hominins (AH) and ancient anatomically modern humans (AMH) have recently been characterized, based, however, on a limited number of samples. The extent to which ancient genome-wide epigenetic landscapes can be reconstructed thus remains contentious. Here, we present epiPALEOMIX, an open-source and user-friendly pipeline that exploits post-mortem DNA degradation patterns to reconstruct ancient methylomes and nucleosome maps from shotgun and/or capture-enrichment data. Applying epiPALEOMIX to the sequence data underlying 35 ancient genomes including AMH, AH, equids and aurochs, we investigate the temporal, geographical and preservation range of ancient epigenetic signatures. We first assess the quality of inferred ancient epigenetic signatures within well-characterized genomic regions. We find that tissue-specific methylation signatures can be obtained across a wider range of DNA preparation types than previously thought, including when no particular experimental procedures have been used to remove deaminated cytosines prior to sequencing. We identify a large subset of samples for which DNA associated with nucleosomes is protected from post-mortem degradation, and nucleosome positioning patterns can be reconstructed. Finally, we describe parameters and conditions such as DNA damage levels and sequencing depth that limit the preservation of epigenetic signatures in ancient samples. When such conditions are met, we propose that epigenetic profiles of CTCF binding regions can be used to help data authentication. Our work, including epiPALEOMIX, opens for further investigations of ancient epigenomes through time especially aimed at tracking possible epigenetic changes during major evolutionary, environmental, socioeconomic, and cultural shifts.
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Affiliation(s)
- Kristian Hanghøj
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark.,Laboratoire d'Anthropobiologie Moléculaire et d'Imagerie de Synthèse, Université de Toulouse, University Paul Sabatier, Toulouse, France
| | - Andaine Seguin-Orlando
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark.,Danish National High-Throughput DNA Sequencing Center, Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark
| | - Mikkel Schubert
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark
| | - Tobias Madsen
- Department of Molecular Medicine (MOMA), Aarhus University Hospital, Aarhus, Denmark.,Bioinformatics Research Centre (BiRC), Aarhus University, Aarhus, Denmark
| | - Jakob Skou Pedersen
- Department of Molecular Medicine (MOMA), Aarhus University Hospital, Aarhus, Denmark.,Bioinformatics Research Centre (BiRC), Aarhus University, Aarhus, Denmark
| | - Eske Willerslev
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark.,Department of Zoology, University of Cambridge, Cambridge, United Kingdom.,Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, United Kingdom
| | - Ludovic Orlando
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark .,Laboratoire d'Anthropobiologie Moléculaire et d'Imagerie de Synthèse, Université de Toulouse, University Paul Sabatier, Toulouse, France
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186
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Vai S, Lari M, Caramelli D. DNA Sequencing in Cultural Heritage. Top Curr Chem (Cham) 2016; 374:8. [PMID: 27572991 DOI: 10.1007/s41061-015-0009-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2015] [Accepted: 12/31/2015] [Indexed: 12/17/2022]
Abstract
During the last three decades, DNA analysis on degraded samples revealed itself as an important research tool in anthropology, archaeozoology, molecular evolution, and population genetics. Application on topics such as determination of species origin of prehistoric and historic objects, individual identification of famous personalities, characterization of particular samples important for historical, archeological, or evolutionary reconstructions, confers to the paleogenetics an important role also for the enhancement of cultural heritage. A really fast improvement in methodologies in recent years led to a revolution that permitted recovering even complete genomes from highly degraded samples with the possibility to go back in time 400,000 years for samples from temperate regions and 700,000 years for permafrozen remains and to analyze even more recent material that has been subjected to hard biochemical treatments. Here we propose a review on the different methodological approaches used so far for the molecular analysis of degraded samples and their application on some case studies.
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Affiliation(s)
- Stefania Vai
- Department of Biology, University of Florence, Via del Proconsolo 12, 50122, Florence, Italy.
| | - Martina Lari
- Department of Biology, University of Florence, Via del Proconsolo 12, 50122, Florence, Italy
| | - David Caramelli
- Department of Biology, University of Florence, Via del Proconsolo 12, 50122, Florence, Italy
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187
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Heckeberg NS, Erpenbeck D, Wörheide G, Rössner GE. Systematic relationships of five newly sequenced cervid species. PeerJ 2016; 4:e2307. [PMID: 27602278 PMCID: PMC4991894 DOI: 10.7717/peerj.2307] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2015] [Accepted: 07/09/2016] [Indexed: 11/20/2022] Open
Abstract
Cervid phylogenetics has been puzzling researchers for over 150 years. In recent decades, molecular systematics has provided new input for both the support and revision of the previous results from comparative anatomy but has led to only partial consensus. Despite all of the efforts to reach taxon-wide species sampling over the last two decades, a number of cervid species still lack molecular data because they are difficult to access in the wild. By extracting ancient DNA from museum specimens, in this study, we obtained partial mitochondrial cytochrome b gene sequences for Mazama bricenii, Mazama chunyi, Muntiacus atherodes, Pudu mephistophiles, and Rusa marianna, including three holotypes. These new sequences were used to enrich the existing mitochondrial DNA alignments and yielded the most taxonomically complete data set for cervids to date. Phylogenetic analyses provide new insights into the evolutionary history of these five species. However, systematic uncertainties within Muntiacus persist and resolving phylogenetic relationships within Pudu and Mazama remain challenging.
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Affiliation(s)
- Nicola S Heckeberg
- Department for Earth and Environmental Sciences, Palaeontology & Geobiology, Ludwig-Maximilians-Universität München, Munich, Germany; SNSB-Bayerische Staatssammlung für Paläontologie und Geologie, Munich, Germany; Department of Zoology, University of Cambridge, Cambridge, United Kingdom
| | - Dirk Erpenbeck
- Department for Earth and Environmental Sciences, Palaeontology & Geobiology, Ludwig-Maximilians-Universität München, Munich, Germany; GeoBio-Center, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Gert Wörheide
- Department for Earth and Environmental Sciences, Palaeontology & Geobiology, Ludwig-Maximilians-Universität München, Munich, Germany; SNSB-Bayerische Staatssammlung für Paläontologie und Geologie, Munich, Germany; GeoBio-Center, Ludwig-Maximilians-Universität München, Munich, Germany
| | - Gertrud E Rössner
- Department for Earth and Environmental Sciences, Palaeontology & Geobiology, Ludwig-Maximilians-Universität München, Munich, Germany; SNSB-Bayerische Staatssammlung für Paläontologie und Geologie, Munich, Germany; GeoBio-Center, Ludwig-Maximilians-Universität München, Munich, Germany
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188
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Mohandesan E, Speller CF, Peters J, Uerpmann HP, Uerpmann M, De Cupere B, Hofreiter M, Burger PA. Combined hybridization capture and shotgun sequencing for ancient DNA analysis of extinct wild and domestic dromedary camel. Mol Ecol Resour 2016; 17:300-313. [PMID: 27289015 PMCID: PMC5324683 DOI: 10.1111/1755-0998.12551] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2016] [Revised: 04/28/2016] [Accepted: 05/06/2016] [Indexed: 12/29/2022]
Abstract
The performance of hybridization capture combined with next‐generation sequencing (NGS) has seen limited investigation with samples from hot and arid regions until now. We applied hybridization capture and shotgun sequencing to recover DNA sequences from bone specimens of ancient‐domestic dromedary (Camelus dromedarius) and its extinct ancestor, the wild dromedary from Jordan, Syria, Turkey and the Arabian Peninsula, respectively. Our results show that hybridization capture increased the percentage of mitochondrial DNA (mtDNA) recovery by an average 187‐fold and in some cases yielded virtually complete mitochondrial (mt) genomes at multifold coverage in a single capture experiment. Furthermore, we tested the effect of hybridization temperature and time by using a touchdown approach on a limited number of samples. We observed no significant difference in the number of unique dromedary mtDNA reads retrieved with the standard capture compared to the touchdown method. In total, we obtained 14 partial mitochondrial genomes from ancient‐domestic dromedaries with 17–95% length coverage and 1.27–47.1‐fold read depths for the covered regions. Using whole‐genome shotgun sequencing, we successfully recovered endogenous dromedary nuclear DNA (nuDNA) from domestic and wild dromedary specimens with 1–1.06‐fold read depths for covered regions. Our results highlight that despite recent methodological advances, obtaining ancient DNA (aDNA) from specimens recovered from hot, arid environments is still problematic. Hybridization protocols require specific optimization, and samples at the limit of DNA preservation need multiple replications of DNA extraction and hybridization capture as has been shown previously for Middle Pleistocene specimens.
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Affiliation(s)
- Elmira Mohandesan
- Research Institute of Wildlife Ecology, Vetmeduni Vienna, Savoyenstraße 1, 1160, Vienna, Austria.,Institute of Population Genetics, Vetmeduni Vienna, Veterinärplatz 1, 1210, Vienna, Austria
| | - Camilla F Speller
- BioArCh, Department of Archaeology, University of York, Wentworth Way, York, YO10 5DD, UK
| | - Joris Peters
- Department of Veterinary Sciences, Institute of Palaeoanatomy, Domestication Research and the History of Veterinary Medicine, Ludwig-Maximilians-Universität München (LMU Munich), 80539, Munich, Germany.,Staatliche Naturwissenschaftliche Sammlungen Bayerns, Bavarian State Collection of Anthropology and Palaeoanatomy, 80333, Munich, Germany
| | - Hans-Peter Uerpmann
- Abteilung Archäozoologie, Institut für Naturwissenschaftliche Archäologie, Eberhard-Karls-Universität Tübingen, Rümelinstrasse 23, 7207, Tübingen, Germany
| | - Margarethe Uerpmann
- Staatliche Naturwissenschaftliche Sammlungen Bayerns, Bavarian State Collection of Anthropology and Palaeoanatomy, 80333, Munich, Germany
| | - Bea De Cupere
- Royal Belgian Institute of Natural Sciences, Vautierstraat 29, B-1000, Brussels, Belgium
| | - Michael Hofreiter
- BioArCh, Department of Archaeology, University of York, Wentworth Way, York, YO10 5DD, UK.,Evolutionary and Adaptive Genomics, Department of Mathematics and Natural Sciences, Institute for Biochemistry and Biology, University of Potsdam, Karl-Liebknecht-Street 24-25, Potsdam, 14476, Germany
| | - Pamela A Burger
- Research Institute of Wildlife Ecology, Vetmeduni Vienna, Savoyenstraße 1, 1160, Vienna, Austria
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189
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Arbeithuber B, Makova KD, Tiemann-Boege I. Artifactual mutations resulting from DNA lesions limit detection levels in ultrasensitive sequencing applications. DNA Res 2016; 23:547-559. [PMID: 27477585 PMCID: PMC5144678 DOI: 10.1093/dnares/dsw038] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2016] [Accepted: 06/25/2016] [Indexed: 11/13/2022] Open
Abstract
The need in cancer research or evolutionary biology to detect rare mutations or variants present at very low frequencies (<10−5) poses an increasing demand on lowering the detection limits of available methods. Here we demonstrated that amplifiable DNA lesions introduce important error sources in ultrasensitive technologies such as single molecule PCR (smPCR) applications (e.g. droplet-digital PCR), or next-generation sequencing (NGS) based methods. Using templates with known amplifiable lesions (8-oxoguanine, deaminated 5-methylcytosine, uracil, and DNA heteroduplexes), we assessed with smPCR and duplex sequencing that templates with these lesions were amplified very efficiently by proofreading polymerases (except uracil), leading to G->T, and to a lesser extent, to unreported G->C substitutions at 8-oxoguanine lesions, and C->T transitions in amplified uracil containing templates. Long heat incubations common in many DNA extraction protocols significantly increased the number of G->T substitutions. Moreover, in ∼50-80% smPCR reactions we observed the random amplification preference of only one of both DNA strands explaining the known ‘PCR jackpot effect’, with the result that a lesion became indistinguishable from a true mutation or variant. Finally, we showed that artifactual mutations derived from uracil and 8-oxoguanine could be significantly reduced by DNA repair enzymes.
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Affiliation(s)
- Barbara Arbeithuber
- Institute of Biophysics, Johannes Kepler University, Linz 4020, Austria.,Department of Biology, Pennsylvania State University, University Park, PA 16802, USA
| | - Kateryna D Makova
- Department of Biology, Pennsylvania State University, University Park, PA 16802, USA
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190
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Abstract
The Neanderthals' northern distribution, hunting techniques, and orbit breadths suggest that they were more active in dim light than modern humans. We surveyed visual opsin genes from four Neanderthals and two other archaic hominids to see if they provided additional support for this hypothesis. This analysis was motivated by the observation that alleles responsible for anomalous trichromacy in humans are more common in northern latitudes, by data suggesting that these variants might enhance vision in mesopic conditions, and by the observation that dim light active species often have fewer opsin genes than diurnal relatives. We also looked for evidence of convergent amino acid substitutions in Neanderthal opsins and orthologs from crepuscular or nocturnal species. The Altai Neanderthal, the Denisovan, and the Ust'-Ishim early modern human had opsin genes that encoded proteins identical to orthologs in the human reference genome. Opsins from the Vindija Cave Neanderthals (three females) had many nonsynonymous substitutions, including several predicted to influence colour vision (e.g., stop codons). However, the functional implications of these observations were difficult to assess, given that "control" loci, where no substitutions were expected, differed from humans to the same extent. This left unresolved the test for colour vision deficiencies in Vindija Cave Neanderthals.
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Affiliation(s)
- John S Taylor
- Department of Biology, University of Victoria, Station CSC, P.O. Box 3020, Victoria, BC V8W 3N5, Canada.,Department of Biology, University of Victoria, Station CSC, P.O. Box 3020, Victoria, BC V8W 3N5, Canada
| | - Thomas E Reimchen
- Department of Biology, University of Victoria, Station CSC, P.O. Box 3020, Victoria, BC V8W 3N5, Canada.,Department of Biology, University of Victoria, Station CSC, P.O. Box 3020, Victoria, BC V8W 3N5, Canada
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191
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Lazaridis I, Nadel D, Rollefson G, Merrett DC, Rohland N, Mallick S, Fernandes D, Novak M, Gamarra B, Sirak K, Connell S, Stewardson K, Harney E, Fu Q, Gonzalez-Fortes G, Jones ER, Roodenberg SA, Lengyel G, Bocquentin F, Gasparian B, Monge JM, Gregg M, Eshed V, Mizrahi AS, Meiklejohn C, Gerritsen F, Bejenaru L, Blüher M, Campbell A, Cavalleri G, Comas D, Froguel P, Gilbert E, Kerr SM, Kovacs P, Krause J, McGettigan D, Merrigan M, Merriwether DA, O'Reilly S, Richards MB, Semino O, Shamoon-Pour M, Stefanescu G, Stumvoll M, Tönjes A, Torroni A, Wilson JF, Yengo L, Hovhannisyan NA, Patterson N, Pinhasi R, Reich D. Genomic insights into the origin of farming in the ancient Near East. Nature 2016; 536:419-24. [PMID: 27459054 PMCID: PMC5003663 DOI: 10.1038/nature19310] [Citation(s) in RCA: 478] [Impact Index Per Article: 59.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2016] [Accepted: 07/18/2016] [Indexed: 12/19/2022]
Abstract
We report genome-wide ancient DNA from 44 ancient Near Easterners ranging in time between ~12,000 and 1,400 bc, from Natufian hunter-gatherers to Bronze Age farmers. We show that the earliest populations of the Near East derived around half their ancestry from a 'Basal Eurasian' lineage that had little if any Neanderthal admixture and that separated from other non-African lineages before their separation from each other. The first farmers of the southern Levant (Israel and Jordan) and Zagros Mountains (Iran) were strongly genetically differentiated, and each descended from local hunter-gatherers. By the time of the Bronze Age, these two populations and Anatolian-related farmers had mixed with each other and with the hunter-gatherers of Europe to greatly reduce genetic differentiation. The impact of the Near Eastern farmers extended beyond the Near East: farmers related to those of Anatolia spread westward into Europe; farmers related to those of the Levant spread southward into East Africa; farmers related to those of Iran spread northward into the Eurasian steppe; and people related to both the early farmers of Iran and to the pastoralists of the Eurasian steppe spread eastward into South Asia.
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192
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Morozova I, Flegontov P, Mikheyev AS, Bruskin S, Asgharian H, Ponomarenko P, Klyuchnikov V, ArunKumar G, Prokhortchouk E, Gankin Y, Rogaev E, Nikolsky Y, Baranova A, Elhaik E, Tatarinova TV. Toward high-resolution population genomics using archaeological samples. DNA Res 2016; 23:295-310. [PMID: 27436340 PMCID: PMC4991838 DOI: 10.1093/dnares/dsw029] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2015] [Accepted: 05/22/2016] [Indexed: 12/30/2022] Open
Abstract
The term ‘ancient DNA’ (aDNA) is coming of age, with over 1,200 hits in the PubMed database, beginning in the early 1980s with the studies of ‘molecular paleontology’. Rooted in cloning and limited sequencing of DNA from ancient remains during the pre-PCR era, the field has made incredible progress since the introduction of PCR and next-generation sequencing. Over the last decade, aDNA analysis ushered in a new era in genomics and became the method of choice for reconstructing the history of organisms, their biogeography, and migration routes, with applications in evolutionary biology, population genetics, archaeogenetics, paleo-epidemiology, and many other areas. This change was brought by development of new strategies for coping with the challenges in studying aDNA due to damage and fragmentation, scarce samples, significant historical gaps, and limited applicability of population genetics methods. In this review, we describe the state-of-the-art achievements in aDNA studies, with particular focus on human evolution and demographic history. We present the current experimental and theoretical procedures for handling and analysing highly degraded aDNA. We also review the challenges in the rapidly growing field of ancient epigenomics. Advancement of aDNA tools and methods signifies a new era in population genetics and evolutionary medicine research.
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Affiliation(s)
- Irina Morozova
- Institute of Evolutionary Medicine, University of Zurich, Zurich, Switzerland
| | - Pavel Flegontov
- Department of Biology and Ecology, Faculty of Science, University of Ostrava, Ostrava, Czech Republic Bioinformatics Center, A.A. Kharkevich Institute for Information Transmission Problems, Russian Academy of Sciences, Moscow, Russian Federation
| | - Alexander S Mikheyev
- Ecology and Evolution Unit, Okinawa Institute of Science and Technology Graduate University, Okinawa, Japan
| | - Sergey Bruskin
- Vavilov Institute of General Genetics RAS, Moscow, Russia
| | - Hosseinali Asgharian
- Department of Computational and Molecular Biology, University of Southern California, Los Angeles, CA, USA
| | - Petr Ponomarenko
- Center for Personalized Medicine, Children's Hospital Los Angeles, Los Angeles, CA, USA Spatial Sciences Institute, University of Southern California, Los Angeles, CA, USA
| | | | | | - Egor Prokhortchouk
- Research Center of Biotechnology RAS, Moscow, Russia Department of Biology, Lomonosov Moscow State University, Russia
| | | | - Evgeny Rogaev
- Vavilov Institute of General Genetics RAS, Moscow, Russia University of Massachusetts Medical School, Worcester, MA, USA
| | - Yuri Nikolsky
- Vavilov Institute of General Genetics RAS, Moscow, Russia F1 Genomics, San Diego, CA, USA School of Systems Biology, George Mason University, VA, USA
| | - Ancha Baranova
- School of Systems Biology, George Mason University, VA, USA Research Centre for Medical Genetics, Moscow, Russia Atlas Biomed Group, Moscow, Russia
| | - Eran Elhaik
- Department of Animal & Plant Sciences, University of Sheffield, Sheffield, South Yorkshire, UK
| | - Tatiana V Tatarinova
- Bioinformatics Center, A.A. Kharkevich Institute for Information Transmission Problems, Russian Academy of Sciences, Moscow, Russian Federation Center for Personalized Medicine, Children's Hospital Los Angeles, Los Angeles, CA, USA Spatial Sciences Institute, University of Southern California, Los Angeles, CA, USA
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193
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Mascher M, Schuenemann VJ, Davidovich U, Marom N, Himmelbach A, Hübner S, Korol A, David M, Reiter E, Riehl S, Schreiber M, Vohr SH, Green RE, Dawson IK, Russell J, Kilian B, Muehlbauer GJ, Waugh R, Fahima T, Krause J, Weiss E, Stein N. Genomic analysis of 6,000-year-old cultivated grain illuminates the domestication history of barley. Nat Genet 2016; 48:1089-93. [PMID: 27428749 DOI: 10.1038/ng.3611] [Citation(s) in RCA: 73] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2016] [Accepted: 06/13/2016] [Indexed: 12/17/2022]
Abstract
The cereal grass barley was domesticated about 10,000 years before the present in the Fertile Crescent and became a founder crop of Neolithic agriculture. Here we report the genome sequences of five 6,000-year-old barley grains excavated at a cave in the Judean Desert close to the Dead Sea. Comparison to whole-exome sequence data from a diversity panel of present-day barley accessions showed the close affinity of ancient samples to extant landraces from the Southern Levant and Egypt, consistent with a proposed origin of domesticated barley in the Upper Jordan Valley. Our findings suggest that barley landraces grown in present-day Israel have not experienced major lineage turnover over the past six millennia, although there is evidence for gene flow between cultivated and sympatric wild populations. We demonstrate the usefulness of ancient genomes from desiccated archaeobotanical remains in informing research into the origin, early domestication and subsequent migration of crop species.
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Affiliation(s)
- Martin Mascher
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, Seeland, Germany.,German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Leipzig, Germany
| | - Verena J Schuenemann
- Institute for Archaeological Sciences, University of Tübingen, Tübingen, Germany.,Senckenberg Center for Human Evolution and Paleoenvironment, University of Tübingen, Tübingen, Germany
| | - Uri Davidovich
- Institute of Archaeology, Hebrew University, Jerusalem, Israel
| | - Nimrod Marom
- Laboratory of Archaeozoology, Zinman Institute of Archaeology, University of Haifa, Haifa, Israel
| | - Axel Himmelbach
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, Seeland, Germany
| | - Sariel Hübner
- Department of Botany, University of British Columbia, Vancouver, British Columbia, Canada.,Department of Biotechnology, Tel Hai College, Upper Galilee, Israel
| | - Abraham Korol
- Institute of Evolution, University of Haifa, Haifa, Israel.,Department of Evolutionary and Environmental Biology, University of Haifa, Haifa, Israel
| | - Michal David
- Martin (Szusz) Department of Land of Israel Studies and Archaeology, Bar-Ilan University, Ramat-Gan, Israel
| | - Ella Reiter
- Institute for Archaeological Sciences, University of Tübingen, Tübingen, Germany
| | - Simone Riehl
- Institute for Archaeological Sciences, University of Tübingen, Tübingen, Germany.,Senckenberg Center for Human Evolution and Paleoenvironment, University of Tübingen, Tübingen, Germany
| | - Mona Schreiber
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, Seeland, Germany
| | - Samuel H Vohr
- Department of Biomolecular Engineering, University of California, Santa Cruz, Santa Cruz, California, USA
| | - Richard E Green
- Department of Biomolecular Engineering, University of California, Santa Cruz, Santa Cruz, California, USA
| | - Ian K Dawson
- Cell and Molecular Sciences, James Hutton Institute, Invergowrie, Dundee, UK
| | - Joanne Russell
- Cell and Molecular Sciences, James Hutton Institute, Invergowrie, Dundee, UK
| | - Benjamin Kilian
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, Seeland, Germany
| | - Gary J Muehlbauer
- Department of Plant Biology, University of Minnesota, St. Paul, Minnesota, USA.,Department of Agronomy and Plant Genetics, University of Minnesota, St. Paul, Minnesota, USA
| | - Robbie Waugh
- Cell and Molecular Sciences, James Hutton Institute, Invergowrie, Dundee, UK.,Division of Plant Sciences, University of Dundee, Dundee, UK
| | - Tzion Fahima
- Institute of Evolution, University of Haifa, Haifa, Israel.,Department of Evolutionary and Environmental Biology, University of Haifa, Haifa, Israel
| | - Johannes Krause
- Institute for Archaeological Sciences, University of Tübingen, Tübingen, Germany.,Senckenberg Center for Human Evolution and Paleoenvironment, University of Tübingen, Tübingen, Germany.,Max Planck Institute for the Science of Human History, Jena, Germany
| | - Ehud Weiss
- Martin (Szusz) Department of Land of Israel Studies and Archaeology, Bar-Ilan University, Ramat-Gan, Israel
| | - Nils Stein
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, Seeland, Germany
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194
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Zhenilo SV, Sokolov A, Prokhortchouk EB. Epigenetics of Ancient DNA. Acta Naturae 2016; 8:72-76. [PMID: 27795845 PMCID: PMC5081710] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2016] [Indexed: 10/27/2022] Open
Abstract
Initially, the study of DNA isolated from ancient specimens had been based on the analysis of the primary nucleotide sequence. This approach has allowed researchers to study the evolutionary changes that occur in different populations and determine the influence of the environment on genetic selection. However, the improvement of methodological approaches to genome-wide analysis has opened up new possibilities in the search for the epigenetic mechanisms involved in the regulation of gene expression. It was discovered recently that the methylation status of the regulatory elements of the HOXD cluster and MEIS1 gene changed during human evolution. Epigenetic changes in these genes played a key role in the evolution of the limbs of modern humans. Recent works have demonstrated that it is possible to determine the transcriptional activity of genes in ancient DNA samples by combining information on DNA methylation and the DNAaseI hypersensitive sequences located at the transcription start sites of genes. In the nearest future, if a preserved fossils brain is found, it will be possible to identify the evolutionary changes in the higher nervous system associated with epigenetic differences.
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Affiliation(s)
- S. V. Zhenilo
- Institute of Bioengineering, Federal Research Center “Fundamentals of Biotechnology”, Russian Academy of Sciences, prospect 60-letiya Oktyabrya, Str. 7/1, Moscow, 117312, Russia
| | - A.S. Sokolov
- Institute of Bioengineering, Federal Research Center “Fundamentals of Biotechnology”, Russian Academy of Sciences, prospect 60-letiya Oktyabrya, Str. 7/1, Moscow, 117312, Russia
| | - E. B. Prokhortchouk
- Institute of Bioengineering, Federal Research Center “Fundamentals of Biotechnology”, Russian Academy of Sciences, prospect 60-letiya Oktyabrya, Str. 7/1, Moscow, 117312, Russia
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195
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Weiß CL, Schuenemann VJ, Devos J, Shirsekar G, Reiter E, Gould BA, Stinchcombe JR, Krause J, Burbano HA. Temporal patterns of damage and decay kinetics of DNA retrieved from plant herbarium specimens. ROYAL SOCIETY OPEN SCIENCE 2016; 3:160239. [PMID: 27429780 PMCID: PMC4929915 DOI: 10.1098/rsos.160239] [Citation(s) in RCA: 67] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/05/2016] [Accepted: 05/24/2016] [Indexed: 05/04/2023]
Abstract
Herbaria archive a record of changes of worldwide plant biodiversity harbouring millions of specimens that contain DNA suitable for genome sequencing. To profit from this resource, it is fundamental to understand in detail the process of DNA degradation in herbarium specimens. We investigated patterns of DNA fragmentation and nucleotide misincorporation by analysing 86 herbarium samples spanning the last 300 years using Illumina shotgun sequencing. We found an exponential decay relationship between DNA fragmentation and time, and estimated a per nucleotide fragmentation rate of 1.66 × 10(-4) per year, which is six times faster than the rate estimated for ancient bones. Additionally, we found that strand breaks occur specially before purines, and that depurination-driven DNA breakage occurs constantly through time and can to a great extent explain decreasing fragment length over time. Similar to what has been found analysing ancient DNA from bones, we found a strong correlation between the deamination-driven accumulation of cytosine to thymine substitutions and time, which reinforces the importance of substitution patterns to authenticate the ancient/historical nature of DNA fragments. Accurate estimations of DNA degradation through time will allow informed decisions about laboratory and computational procedures to take advantage of the vast collection of worldwide herbarium specimens.
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Affiliation(s)
- Clemens L. Weiß
- Research Group for Ancient Genomics and Evolution, Department of Molecular Biology, Max Planck Institute for Developmental Biology, Tuebingen 72076, Germany
| | - Verena J. Schuenemann
- Institute of Archaeological Sciences, University of Tübingen, Tuebingen 72076, Germany
| | - Jane Devos
- Department of Molecular Biology, Max Planck Institute for Developmental Biology, Tuebingen 72076, Germany
| | - Gautam Shirsekar
- Department of Molecular Biology, Max Planck Institute for Developmental Biology, Tuebingen 72076, Germany
| | - Ella Reiter
- Institute of Archaeological Sciences, University of Tübingen, Tuebingen 72076, Germany
| | - Billie A. Gould
- Department of Ecology and Evolutionary Biology, Toronto, Ontario, CanadaM5S
| | - John R. Stinchcombe
- Department of Ecology and Evolutionary Biology, Toronto, Ontario, CanadaM5S
- University of Toronto, Toronto, Ontario, CanadaM5S
| | - Johannes Krause
- Institute of Archaeological Sciences, University of Tübingen, Tuebingen 72076, Germany
- Departments of Paleoanthropology and Archaeogenetics, Senckenberg Center for Human Evolution and Paleoenvironment, University of Tübingen, Tuebingen 72076, Germany
- Max Planck Institute for the Science of Human History, Jena 07743, Germany
| | - Hernán A. Burbano
- Research Group for Ancient Genomics and Evolution, Department of Molecular Biology, Max Planck Institute for Developmental Biology, Tuebingen 72076, Germany
- Author for correspondence: Hernán A. Burbano e-mail:
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196
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Racimo F, Renaud G, Slatkin M. Joint Estimation of Contamination, Error and Demography for Nuclear DNA from Ancient Humans. PLoS Genet 2016; 12:e1005972. [PMID: 27049965 PMCID: PMC4822957 DOI: 10.1371/journal.pgen.1005972] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2015] [Accepted: 03/11/2016] [Indexed: 11/18/2022] Open
Abstract
When sequencing an ancient DNA sample from a hominin fossil, DNA from present-day humans involved in excavation and extraction will be sequenced along with the endogenous material. This type of contamination is problematic for downstream analyses as it will introduce a bias towards the population of the contaminating individual(s). Quantifying the extent of contamination is a crucial step as it allows researchers to account for possible biases that may arise in downstream genetic analyses. Here, we present an MCMC algorithm to co-estimate the contamination rate, sequencing error rate and demographic parameters—including drift times and admixture rates—for an ancient nuclear genome obtained from human remains, when the putative contaminating DNA comes from present-day humans. We assume we have a large panel representing the putative contaminant population (e.g. European, East Asian or African). The method is implemented in a C++ program called ‘Demographic Inference with Contamination and Error’ (DICE). We applied it to simulations and genome data from ancient Neanderthals and modern humans. With reasonable levels of genome sequence coverage (>3X), we find we can recover accurate estimates of all these parameters, even when the contamination rate is as high as 50%. When extracting and sequencing ancient DNA from human remains, a recurrent problem is the presence of DNA from the paleontologists, archaeologists or geneticists that may have handled the fossil. If a DNA library is highly contaminated, this will introduce biases in downstream analyses, so it is important to determine the amount of extraneous DNA. Different methods exist for this purpose, but few are applicable to the nuclear genome, and none of them can extract reliable genomic information from highly contaminated samples. Thus, samples with high rates of contamination are usually discarded. Here, we present a method to jointly estimate contamination and error rates, along with demographic parameters, like drift times and admixture rates. Our method can serve to uncover important details about the evolutionary history of archaic and early modern humans from ancient DNA samples, even if those samples are highly contaminated.
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Affiliation(s)
- Fernando Racimo
- Department of Integrative Biology, University of California, Berkeley, Berkeley, California, United States of America
- * E-mail:
| | - Gabriel Renaud
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Montgomery Slatkin
- Department of Integrative Biology, University of California, Berkeley, Berkeley, California, United States of America
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197
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Gokhman D, Meshorer E, Carmel L. Epigenetics: It's Getting Old. Past Meets Future in Paleoepigenetics. Trends Ecol Evol 2016; 31:290-300. [DOI: 10.1016/j.tree.2016.01.010] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2015] [Revised: 01/18/2016] [Accepted: 01/19/2016] [Indexed: 01/08/2023]
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198
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Suchan T, Pitteloud C, Gerasimova NS, Kostikova A, Schmid S, Arrigo N, Pajkovic M, Ronikier M, Alvarez N. Hybridization Capture Using RAD Probes (hyRAD), a New Tool for Performing Genomic Analyses on Collection Specimens. PLoS One 2016; 11:e0151651. [PMID: 26999359 PMCID: PMC4801390 DOI: 10.1371/journal.pone.0151651] [Citation(s) in RCA: 82] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2015] [Accepted: 03/02/2016] [Indexed: 11/19/2022] Open
Abstract
In the recent years, many protocols aimed at reproducibly sequencing reduced-genome subsets in non-model organisms have been published. Among them, RAD-sequencing is one of the most widely used. It relies on digesting DNA with specific restriction enzymes and performing size selection on the resulting fragments. Despite its acknowledged utility, this method is of limited use with degraded DNA samples, such as those isolated from museum specimens, as these samples are less likely to harbor fragments long enough to comprise two restriction sites making possible ligation of the adapter sequences (in the case of double-digest RAD) or performing size selection of the resulting fragments (in the case of single-digest RAD). Here, we address these limitations by presenting a novel method called hybridization RAD (hyRAD). In this approach, biotinylated RAD fragments, covering a random fraction of the genome, are used as baits for capturing homologous fragments from genomic shotgun sequencing libraries. This simple and cost-effective approach allows sequencing of orthologous loci even from highly degraded DNA samples, opening new avenues of research in the field of museum genomics. Not relying on the restriction site presence, it improves among-sample loci coverage. In a trial study, hyRAD allowed us to obtain a large set of orthologous loci from fresh and museum samples from a non-model butterfly species, with a high proportion of single nucleotide polymorphisms present in all eight analyzed specimens, including 58-year-old museum samples. The utility of the method was further validated using 49 museum and fresh samples of a Palearctic grasshopper species for which the spatial genetic structure was previously assessed using mtDNA amplicons. The application of the method is eventually discussed in a wider context. As it does not rely on the restriction site presence, it is therefore not sensitive to among-sample loci polymorphisms in the restriction sites that usually causes loci dropout. This should enable the application of hyRAD to analyses at broader evolutionary scales.
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Affiliation(s)
- Tomasz Suchan
- Department of Ecology and Evolution, University of Lausanne, Lausanne, Switzerland
- * E-mail: (TS); (N. Alvarez)
| | - Camille Pitteloud
- Department of Ecology and Evolution, University of Lausanne, Lausanne, Switzerland
| | - Nadezhda S. Gerasimova
- Biology Faculty, Lomonosov Moscow State University, Moscow, Russia
- InsideDNA Ltd., London, United Kingdom
| | | | - Sarah Schmid
- Department of Ecology and Evolution, University of Lausanne, Lausanne, Switzerland
| | - Nils Arrigo
- Department of Ecology and Evolution, University of Lausanne, Lausanne, Switzerland
| | - Mila Pajkovic
- Department of Ecology and Evolution, University of Lausanne, Lausanne, Switzerland
| | - Michał Ronikier
- Institute of Botany, Polish Academy of Sciences, Kraków, Poland
| | - Nadir Alvarez
- Department of Ecology and Evolution, University of Lausanne, Lausanne, Switzerland
- * E-mail: (TS); (N. Alvarez)
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199
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Plasil M, Mohandesan E, Fitak RR, Musilova P, Kubickova S, Burger PA, Horin P. The major histocompatibility complex in Old World camelids and low polymorphism of its class II genes. BMC Genomics 2016; 17:167. [PMID: 26931144 PMCID: PMC4774177 DOI: 10.1186/s12864-016-2500-1] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2015] [Accepted: 02/18/2016] [Indexed: 11/28/2022] Open
Abstract
BACKGROUND The Major Histocompatibility Complex (MHC) is a genomic region containing genes with crucial roles in immune responses. MHC class I and class II genes encode antigen-presenting molecules expressed on the cell surface. To counteract the high variability of pathogens, the MHC evolved into a region of considerable heterogeneity in its organization, number and extent of polymorphism. Studies of MHCs in different model species contribute to our understanding of mechanisms of immunity, diseases and their evolution. Camels are economically important domestic animals and interesting biomodels. Three species of Old World camels have been recognized: the dromedary (Camelus dromedarius), Bactrian camel (Camelus bactrianus) and the wild camel (Camelus ferus). Despite their importance, little is known about the MHC genomic region, its organization and diversity in camels. The objectives of this study were to identify, map and characterize the MHC region of Old World camelids, with special attention to genetic variation at selected class MHC II loci. RESULTS Physical mapping located the MHC region to the chromosome 20 in Camelus dromedarius. Cytogenetic and comparative analyses of whole genome sequences showed that the order of the three major sub-regions is "Centromere - Class II - Class III - Class I". DRA, DRB, DQA and DQB exon 2 sequences encoding the antigen binding site of the corresponding class II antigen presenting molecules showed high degree of sequence similarity and extensive allele sharing across the three species. Unexpectedly low extent of polymorphism with low numbers of alleles and haplotypes was observed in all species, despite different geographic origins of the camels analyzed. The DRA locus was found to be polymorphic, with three alleles shared by all three species. DRA and DQA sequences retrieved from ancient DNA samples of Camelus dromedarius suggested that additional polymorphism might exist. CONCLUSIONS This study provided evidence that camels possess an MHC comparable to other mammalian species in terms of its genomic localization, organization and sequence similarity. We described ancient variation at the DRA locus, monomorphic in most species. The extent of molecular diversity of MHC class II genes seems to be substantially lower in Old World camels than in other mammalian species.
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Affiliation(s)
- Martin Plasil
- Department of Animal Genetics, Veterinary and Pharmaceutical University, Brno, Czech Republic.
- Ceitec VFU, RG Animal Immunogenomics, Brno, Czech Republic.
| | - Elmira Mohandesan
- Research Institute of Wildlife Ecology, Vetmeduni Vienna, Vienna, Austria.
- Institute of Population Genetics, Vetmeduni Vienna, Vienna, Austria.
| | - Robert R Fitak
- Institute of Population Genetics, Vetmeduni Vienna, Vienna, Austria.
- Department of Biology, Duke University, Durham, NC, USA.
| | - Petra Musilova
- Department of Genetics and Reproduction, Veterinary Research Institute, Brno, Czech Republic.
| | - Svatava Kubickova
- Department of Genetics and Reproduction, Veterinary Research Institute, Brno, Czech Republic.
| | - Pamela A Burger
- Research Institute of Wildlife Ecology, Vetmeduni Vienna, Vienna, Austria.
| | - Petr Horin
- Department of Animal Genetics, Veterinary and Pharmaceutical University, Brno, Czech Republic.
- Ceitec VFU, RG Animal Immunogenomics, Brno, Czech Republic.
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200
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Kuhlwilm M, Gronau I, Hubisz MJ, de Filippo C, Prado-Martinez J, Kircher M, Fu Q, Burbano HA, Lalueza-Fox C, de la Rasilla M, Rosas A, Rudan P, Brajkovic D, Kucan Ž, Gušic I, Marques-Bonet T, Andrés AM, Viola B, Pääbo S, Meyer M, Siepel A, Castellano S. Ancient gene flow from early modern humans into Eastern Neanderthals. Nature 2016; 530:429-33. [PMID: 26886800 DOI: 10.1038/nature16544] [Citation(s) in RCA: 216] [Impact Index Per Article: 27.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2015] [Accepted: 12/17/2015] [Indexed: 12/11/2022]
Abstract
It has been shown that Neanderthals contributed genetically to modern humans outside Africa 47,000-65,000 years ago. Here we analyse the genomes of a Neanderthal and a Denisovan from the Altai Mountains in Siberia together with the sequences of chromosome 21 of two Neanderthals from Spain and Croatia. We find that a population that diverged early from other modern humans in Africa contributed genetically to the ancestors of Neanderthals from the Altai Mountains roughly 100,000 years ago. By contrast, we do not detect such a genetic contribution in the Denisovan or the two European Neanderthals. We conclude that in addition to later interbreeding events, the ancestors of Neanderthals from the Altai Mountains and early modern humans met and interbred, possibly in the Near East, many thousands of years earlier than previously thought.
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Affiliation(s)
- Martin Kuhlwilm
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, 04103 Leipzig, Germany
| | - Ilan Gronau
- Efi Arazi School of Computer Science, Herzliya Interdisciplinary Center (IDC), Herzliya 46150, Israel
| | - Melissa J Hubisz
- Department of Biological Statistics and Computational Biology, Cornell University, Ithaca, New York 14850, USA
| | - Cesare de Filippo
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, 04103 Leipzig, Germany
| | | | - Martin Kircher
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, 04103 Leipzig, Germany.,Department of Genome Sciences, University of Washington, Seattle, Washington 98195, USA
| | - Qiaomei Fu
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, 04103 Leipzig, Germany.,Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA.,Key Laboratory of Vertebrate Evolution and Human Origins of Chinese Academy of Sciences, IVPP, CAS, Beijing 100044, China
| | - Hernán A Burbano
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, 04103 Leipzig, Germany.,Department of Molecular Biology, Max Planck Institute for Developmental Biology, 72076 Tübingen, Germany
| | | | - Marco de la Rasilla
- Área de Prehistoria, Departamento de Historia, Universidad de Oviedo, 33011 Oviedo, Spain
| | - Antonio Rosas
- Departamento de Paleobiología, Museo Nacional de Ciencias Naturales, CSIC, 28006 Madrid, Spain
| | - Pavao Rudan
- Anthropology Center of the Croatian Academy of Sciences and Arts, 10000 Zagreb, Croatia
| | - Dejana Brajkovic
- Croatian Academy of Sciences and Arts, Institute for Quaternary Paleontology and Geology, 10000 Zagreb, Croatia
| | - Željko Kucan
- Anthropology Center of the Croatian Academy of Sciences and Arts, 10000 Zagreb, Croatia
| | - Ivan Gušic
- Anthropology Center of the Croatian Academy of Sciences and Arts, 10000 Zagreb, Croatia
| | - Tomas Marques-Bonet
- Institute of Evolutionary Biology (UPF-CSIC), 08003 Barcelona, Spain.,Catalan Institution of Research and Advanced Studies (ICREA), 08010 Barcelona, Spain.,Centro Nacional de Análisis Genómico (CRG-CNAG), 08028 Barcelona, Spain
| | - Aida M Andrés
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, 04103 Leipzig, Germany
| | - Bence Viola
- Department of Anthropology, University of Toronto, Toronto, Ontario M5S 2S2, Canada.,Department of Human Evolution, Max Planck Institute for Evolutionary Anthropology, 04103 Leipzig, Germany
| | - Svante Pääbo
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, 04103 Leipzig, Germany
| | - Matthias Meyer
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, 04103 Leipzig, Germany
| | - Adam Siepel
- Department of Biological Statistics and Computational Biology, Cornell University, Ithaca, New York 14850, USA.,Simons Center for Quantitative Biology, Cold Spring Harbor Laboratory, Cold Spring Harbor, New York 11724, USA
| | - Sergi Castellano
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, 04103 Leipzig, Germany
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