1
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Essel E, Zavala EI, Schulz-Kornas E, Kozlikin MB, Fewlass H, Vernot B, Shunkov MV, Derevianko AP, Douka K, Barnes I, Soulier MC, Schmidt A, Szymanski M, Tsanova T, Sirakov N, Endarova E, McPherron SP, Hublin JJ, Kelso J, Pääbo S, Hajdinjak M, Soressi M, Meyer M. Ancient human DNA recovered from a Palaeolithic pendant. Nature 2023:10.1038/s41586-023-06035-2. [PMID: 37138083 DOI: 10.1038/s41586-023-06035-2] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2022] [Accepted: 03/30/2023] [Indexed: 05/05/2023]
Abstract
Artefacts made from stones, bones and teeth are fundamental to our understanding of human subsistence strategies, behaviour and culture in the Pleistocene. Although these resources are plentiful, it is impossible to associate artefacts to specific human individuals1 who can be morphologically or genetically characterized, unless they are found within burials, which are rare in this time period. Thus, our ability to discern the societal roles of Pleistocene individuals based on their biological sex or genetic ancestry is limited2-5. Here we report the development of a non-destructive method for the gradual release of DNA trapped in ancient bone and tooth artefacts. Application of the method to an Upper Palaeolithic deer tooth pendant from Denisova Cave, Russia, resulted in the recovery of ancient human and deer mitochondrial genomes, which allowed us to estimate the age of the pendant at approximately 19,000-25,000 years. Nuclear DNA analysis identifies the presumed maker or wearer of the pendant as a female individual with strong genetic affinities to a group of Ancient North Eurasian individuals who lived around the same time but were previously found only further east in Siberia. Our work redefines how cultural and genetic records can be linked in prehistoric archaeology.
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Affiliation(s)
- Elena Essel
- Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany.
| | - Elena I Zavala
- Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
- Department of Biology, San Francisco State University, San Francisco, CA, USA
- Department of Molecular and Cell Biology, University of California, Berkeley, CA, USA
| | - Ellen Schulz-Kornas
- Department of Cariology, Endodontology and Periodontology, University of Leipzig, Leipzig, Germany
| | - Maxim B Kozlikin
- Institute of Archaeology and Ethnography, Siberian Branch, Russian Academy of Sciences, Novosibirsk, Russia
| | - Helen Fewlass
- Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Benjamin Vernot
- Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Michael V Shunkov
- Institute of Archaeology and Ethnography, Siberian Branch, Russian Academy of Sciences, Novosibirsk, Russia
| | - Anatoly P Derevianko
- Institute of Archaeology and Ethnography, Siberian Branch, Russian Academy of Sciences, Novosibirsk, Russia
| | - Katerina Douka
- Department of Evolutionary Anthropology, Faculty of Life Sciences, University of Vienna, Vienna, Austria
- Human Evolution and Archaeological Sciences (HEAS) Research Network, University of Vienna, Vienna, Austria
| | - Ian Barnes
- Earth Sciences Department, Natural History Museum, London, UK
| | - Marie-Cécile Soulier
- Maison de la Recherche, Université de Toulouse-Jean Jaurès, CNRS UMR 5608 TRACES, Toulouse, France
| | - Anna Schmidt
- Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Merlin Szymanski
- Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Tsenka Tsanova
- Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
- Department of Chemistry "Giacomo Ciamician", Alma Mater Studiorum, University of Bologna, Bologna, Italy
| | - Nikolay Sirakov
- National Institute of Archaeology with Museum, Bulgarian Academy of Sciences, Sofia, Bulgaria
| | | | | | - Jean-Jacques Hublin
- Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
- Chaire de Paléoanthropologie, Collège de France, Paris, France
| | - Janet Kelso
- Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Svante Pääbo
- Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Mateja Hajdinjak
- Ancient Genomics Laboratory, The Francis Crick Institute, London, UK
- Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Marie Soressi
- Faculty of Archaeology, Leiden University, Leiden, The Netherlands.
| | - Matthias Meyer
- Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany.
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2
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Morley MW, Goldberg P, Uliyanov VA, Kozlikin MB, Shunkov MV, Derevianko AP, Jacobs Z, Roberts RG. Author Correction: Hominin and animal activities in the microstratigraphic record from Denisova Cave (Altai Mountains, Russia). Sci Rep 2022; 12:1545. [PMID: 35075148 PMCID: PMC8786877 DOI: 10.1038/s41598-021-03251-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/04/2022] Open
Affiliation(s)
- Mike W Morley
- Centre for Archaeological Science, School of Earth, Atmospheric and Life Sciences, University of Wollongong, Wollongong, New South Wales, 2522, Australia. .,Archaeology, College of Humanities and Social Sciences, Flinders University, Adelaide, South Australia, 5042, Australia.
| | - Paul Goldberg
- Centre for Archaeological Science, School of Earth, Atmospheric and Life Sciences, University of Wollongong, Wollongong, New South Wales, 2522, Australia.,Institut für Naturwissenschaftliche Archäologie, Eberhard-Karls-Universität Tübingen, Rümelinstrasse 23, 72070, Tübingen, Germany
| | - Vladimir A Uliyanov
- Institute of Archaeology and Ethnography, Russian Academy of Sciences, Siberian Branch, Novosibirsk, 630090, Russia.,Lomonosov Moscow State University, Moscow, 119991, Russia
| | - Maxim B Kozlikin
- Institute of Archaeology and Ethnography, Russian Academy of Sciences, Siberian Branch, Novosibirsk, 630090, Russia
| | - Michael V Shunkov
- Institute of Archaeology and Ethnography, Russian Academy of Sciences, Siberian Branch, Novosibirsk, 630090, Russia.,Novosibirsk State University, Novosibirsk, 630090, Russia
| | - Anatoly P Derevianko
- Institute of Archaeology and Ethnography, Russian Academy of Sciences, Siberian Branch, Novosibirsk, 630090, Russia
| | - Zenobia Jacobs
- Centre for Archaeological Science, School of Earth, Atmospheric and Life Sciences, University of Wollongong, Wollongong, New South Wales, 2522, Australia.,Australian Research Council (ARC) Centre of Excellence for Australian Biodiversity and Heritage, University of Wollongong, Wollongong, New South Wales, 2522, Australia
| | - Richard G Roberts
- Centre for Archaeological Science, School of Earth, Atmospheric and Life Sciences, University of Wollongong, Wollongong, New South Wales, 2522, Australia.,Australian Research Council (ARC) Centre of Excellence for Australian Biodiversity and Heritage, University of Wollongong, Wollongong, New South Wales, 2522, Australia
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3
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Brown S, Massilani D, Kozlikin MB, Shunkov MV, Derevianko AP, Stoessel A, Jope-Street B, Meyer M, Kelso J, Pääbo S, Higham T, Douka K. The earliest Denisovans and their cultural adaptation. Nat Ecol Evol 2022; 6:28-35. [PMID: 34824388 PMCID: PMC7612221 DOI: 10.1038/s41559-021-01581-2] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2020] [Accepted: 09/23/2021] [Indexed: 11/15/2022]
Abstract
Since the initial identification of the Denisovans a decade ago, only a handful of their physical remains have been discovered. Here we analysed ~3,800 non-diagnostic bone fragments using collagen peptide mass fingerprinting to locate new hominin remains from Denisova Cave (Siberia, Russia). We identified five new hominin bones, four of which contained sufficient DNA for mitochondrial analysis. Three carry mitochondrial DNA of the Denisovan type and one was found to carry mtDNA of the Neanderthal type. The former come from the same archaeological layer near the base of the cave's sequence and are the oldest securely dated evidence of Denisovans at 200 ka (thousand years ago) (205-192 ka at 68.2% or 217-187 ka at 95% probability). The stratigraphic context in which they were located contains a wealth of archaeological material in the form of lithics and faunal remains, allowing us to determine the material culture associated with these early hominins and explore their behavioural and environmental adaptations. The combination of bone collagen fingerprinting and genetic analyses has so far more-than-doubled the number of hominin bones at Denisova Cave and has expanded our understanding of Denisovan and Neanderthal interactions, as well as their archaeological signatures.
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Affiliation(s)
- Samantha Brown
- Max Planck Institute for the Science of Human History, Jena, Germany. .,Institute for Scientific Archaeology, University of Tübingen, Tübingen, Germany.
| | - Diyendo Massilani
- Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany.
| | - Maxim B. Kozlikin
- Institute of Archeology and Ethnography of the Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia
| | - Michael V. Shunkov
- Institute of Archeology and Ethnography of the Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia
| | - Anatoly P. Derevianko
- Institute of Archeology and Ethnography of the Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia
| | - Alexander Stoessel
- Max Planck Institute for the Science of Human History, Jena, Germany,Institute for Archaeological Sciences, University of Tübingen, Tübingen, Germany,Institute of Zoology and Evolutionary Research, Friedrich Schiller University Jena, Jena, Germany
| | - Blair Jope-Street
- Max Planck Institute for the Science of Human History, Jena, Germany
| | - Matthias Meyer
- Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Janet Kelso
- Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Svante Pääbo
- Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Thomas Higham
- Oxford Radiocarbon Accelerator Unit, RLAHA, University of Oxford, Oxford, UK,Department of Evolutionary Anthropology, Faculty of Life Sciences, University of Vienna, Austria
| | - Katerina Douka
- Max Planck Institute for the Science of Human History, Jena, Germany. .,Department of Evolutionary Anthropology, Faculty of Life Sciences, University of Vienna, Vienna, Austria.
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4
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Brown S, Wang N, Oertle A, Kozlikin MB, Shunkov MV, Derevianko AP, Comeskey D, Jope-Street B, Harvey VL, Chowdhury MP, Buckley M, Higham T, Douka K. Zooarchaeology through the lens of collagen fingerprinting at Denisova Cave. Sci Rep 2021; 11:15457. [PMID: 34326389 PMCID: PMC8322063 DOI: 10.1038/s41598-021-94731-2] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2021] [Accepted: 07/15/2021] [Indexed: 11/09/2022] Open
Abstract
Denisova Cave, a Pleistocene site in the Altai Mountains of Russian Siberia, has yielded significant fossil and lithic evidence for the Pleistocene in Northern Asia. Abundant animal and human bones have been discovered at the site, however, these tend to be highly fragmented, necessitating new approaches to identifying important hominin and faunal fossils. Here we report the results for 8253 bone fragments using ZooMS. Through the integration of this new ZooMS-based data with the previously published macroscopically-identified fauna we aim to create a holistic picture of the zooarchaeological record of the site. We identify trends associated with climate variability throughout the Middle and Upper Pleistocene as well as patterns explaining the process of bone fragmentation. Where morphological analysis of bones from the site have identified a high proportion of carnivore bones (30.2%), we find that these account for only 7.6% of the ZooMS assemblage, with large mammals between 3 and 5 more abundant overall. Our analysis suggests a cyclical pattern in fragmentation of bones which sees initial fragmentation by hominins using percussive tools and secondary carnivore action, such as gnawing and digestion, likely furthering the initial human-induced fragmentation.
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Affiliation(s)
- Samantha Brown
- Institute for Scientific Archaeology, Eberhard Karls University of Tübingen, Tübingen, Germany. .,Max Planck Institute for the Science of Human History, Jena, Germany.
| | - Naihui Wang
- Max Planck Institute for the Science of Human History, Jena, Germany
| | - Annette Oertle
- Max Planck Institute for the Science of Human History, Jena, Germany
| | - Maxim B Kozlikin
- Institute of Archeology and Ethnography, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia
| | - Michael V Shunkov
- Institute of Archeology and Ethnography, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia
| | - Anatoly P Derevianko
- Institute of Archeology and Ethnography, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, Russia
| | - Daniel Comeskey
- Oxford Radiocarbon Accelerator Unit, RLAHA, University of Oxford, Oxford, OX1 3QY, UK
| | - Blair Jope-Street
- Max Planck Institute for the Science of Human History, Jena, Germany
| | - Virginia L Harvey
- Department of Earth and Environmental Sciences, School of Natural Sciences, The University of Manchester, Manchester, M13 9PL, UK.,Manchester Institute of Biotechnology, The University of Manchester, Manchester, M1 7DN, UK
| | - Manasij Pal Chowdhury
- Department of Earth and Environmental Sciences, School of Natural Sciences, The University of Manchester, Manchester, M13 9PL, UK.,Manchester Institute of Biotechnology, The University of Manchester, Manchester, M1 7DN, UK
| | - Michael Buckley
- Department of Earth and Environmental Sciences, School of Natural Sciences, The University of Manchester, Manchester, M13 9PL, UK.,Manchester Institute of Biotechnology, The University of Manchester, Manchester, M1 7DN, UK
| | - Thomas Higham
- Oxford Radiocarbon Accelerator Unit, RLAHA, University of Oxford, Oxford, OX1 3QY, UK.,Department of Evolutionary Anthropology, Faculty of Life Sciences, University of Vienna, Vienna, Austria
| | - Katerina Douka
- Max Planck Institute for the Science of Human History, Jena, Germany. .,Department of Evolutionary Anthropology, Faculty of Life Sciences, University of Vienna, Vienna, Austria.
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5
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Zavala EI, Jacobs Z, Vernot B, Shunkov MV, Kozlikin MB, Derevianko AP, Essel E, de Fillipo C, Nagel S, Richter J, Romagné F, Schmidt A, Li B, O'Gorman K, Slon V, Kelso J, Pääbo S, Roberts RG, Meyer M. Pleistocene sediment DNA reveals hominin and faunal turnovers at Denisova Cave. Nature 2021; 595:399-403. [PMID: 34163072 PMCID: PMC8277575 DOI: 10.1038/s41586-021-03675-0] [Citation(s) in RCA: 32] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2021] [Accepted: 05/27/2021] [Indexed: 12/31/2022]
Abstract
Denisova Cave in southern Siberia is the type locality of the Denisovans, an archaic hominin group who were related to Neanderthals1–4. The dozen hominin remains recovered from the deposits also include Neanderthals5,6 and the child of a Neanderthal and a Denisovan7, which suggests that Denisova Cave was a contact zone between these archaic hominins. However, uncertainties persist about the order in which these groups appeared at the site, the timing and environmental context of hominin occupation, and the association of particular hominin groups with archaeological assemblages5,8–11. Here we report the analysis of DNA from 728 sediment samples that were collected in a grid-like manner from layers dating to the Pleistocene epoch. We retrieved ancient faunal and hominin mitochondrial (mt)DNA from 685 and 175 samples, respectively. The earliest evidence for hominin mtDNA is of Denisovans, and is associated with early Middle Palaeolithic stone tools that were deposited approximately 250,000 to 170,000 years ago; Neanderthal mtDNA first appears towards the end of this period. We detect a turnover in the mtDNA of Denisovans that coincides with changes in the composition of faunal mtDNA, and evidence that Denisovans and Neanderthals occupied the site repeatedly—possibly until, or after, the onset of the Initial Upper Palaeolithic at least 45,000 years ago, when modern human mtDNA is first recorded in the sediments. Ancient mitochondrial DNA from sediments reveals the sequence of Denisovan, Neanderthal and faunal occupation of Denisova Cave, and evidence for the appearance of modern humans at least 45,000 years ago.
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Affiliation(s)
- Elena I Zavala
- Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany.
| | - Zenobia Jacobs
- Centre for Archaeological Science, School of Earth, Atmospheric and Life Sciences, University of Wollongong, Wollongong, New South Wales, Australia. .,Australian Research Council Centre of Excellence for Australian Biodiversity and Heritage, University of Wollongong, Wollongong, New South Wales, Australia.
| | - Benjamin Vernot
- Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Michael V Shunkov
- Institute of Archaeology and Ethnography, Russian Academy of Sciences, Siberian Branch, Novosibirsk, Russia
| | - Maxim B Kozlikin
- Institute of Archaeology and Ethnography, Russian Academy of Sciences, Siberian Branch, Novosibirsk, Russia
| | - Anatoly P Derevianko
- Institute of Archaeology and Ethnography, Russian Academy of Sciences, Siberian Branch, Novosibirsk, Russia
| | - Elena Essel
- Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Cesare de Fillipo
- Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Sarah Nagel
- Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Julia Richter
- Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Frédéric Romagné
- Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Anna Schmidt
- Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Bo Li
- Centre for Archaeological Science, School of Earth, Atmospheric and Life Sciences, University of Wollongong, Wollongong, New South Wales, Australia.,Australian Research Council Centre of Excellence for Australian Biodiversity and Heritage, University of Wollongong, Wollongong, New South Wales, Australia
| | - Kieran O'Gorman
- Centre for Archaeological Science, School of Earth, Atmospheric and Life Sciences, University of Wollongong, Wollongong, New South Wales, Australia
| | - Viviane Slon
- Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany.,Department of Anatomy and Anthropology, Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel.,Department of Human Molecular Genetics and Biochemistry, Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel.,The Shmunis Family Anthropology Institute, The Dan David Center for Human Evolution and Biohistory Research, Tel Aviv University, Tel Aviv, Israel
| | - Janet Kelso
- Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Svante Pääbo
- Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Richard G Roberts
- Centre for Archaeological Science, School of Earth, Atmospheric and Life Sciences, University of Wollongong, Wollongong, New South Wales, Australia. .,Australian Research Council Centre of Excellence for Australian Biodiversity and Heritage, University of Wollongong, Wollongong, New South Wales, Australia.
| | - Matthias Meyer
- Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany.
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6
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Vernot B, Zavala EI, Gómez-Olivencia A, Jacobs Z, Slon V, Mafessoni F, Romagné F, Pearson A, Petr M, Sala N, Pablos A, Aranburu A, de Castro JMB, Carbonell E, Li B, Krajcarz MT, Krivoshapkin AI, Kolobova KA, Kozlikin MB, Shunkov MV, Derevianko AP, Viola B, Grote S, Essel E, Herráez DL, Nagel S, Nickel B, Richter J, Schmidt A, Peter B, Kelso J, Roberts RG, Arsuaga JL, Meyer M. Unearthing Neanderthal population history using nuclear and mitochondrial DNA from cave sediments. Science 2021; 372:science.abf1667. [PMID: 33858989 DOI: 10.1126/science.abf1667] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2020] [Accepted: 03/31/2021] [Indexed: 12/15/2022]
Abstract
Bones and teeth are important sources of Pleistocene hominin DNA, but are rarely recovered at archaeological sites. Mitochondrial DNA (mtDNA) has been retrieved from cave sediments but provides limited value for studying population relationships. We therefore developed methods for the enrichment and analysis of nuclear DNA from sediments and applied them to cave deposits in western Europe and southern Siberia dated to between 200,000 and 50,000 years ago. We detected a population replacement in northern Spain about 100,000 years ago, which was accompanied by a turnover of mtDNA. We also identified two radiation events in Neanderthal history during the early part of the Late Pleistocene. Our work lays the ground for studying the population history of ancient hominins from trace amounts of nuclear DNA in sediments.
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Affiliation(s)
- Benjamin Vernot
- Department of Evolutionary Genetics, Max-Planck-Institute for Evolutionary Anthropology, Leipzig, Germany.
| | - Elena I Zavala
- Department of Evolutionary Genetics, Max-Planck-Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Asier Gómez-Olivencia
- Departamento de Geología, Facultad de Ciencia y Tecnología, Universidad del País Vasco-Euskal Herriko Unibertsitatea (UPV/EHU), Leioa, Spain.,Sociedad de Ciencias Aranzadi, Donostia-San Sebastián, Spain.,Centro Mixto UCM-ISCIII de Evolución y Comportamiento Humanos, Madrid, Spain
| | - Zenobia Jacobs
- Centre for Archaeological Science, School of Earth, Atmospheric and Life Sciences, University of Wollongong, Wollongong, New South Wales, Australia.,Australian Research Council (ARC) Centre of Excellence for Australian Biodiversity and Heritage, University of Wollongong, Wollongong, New South Wales, Australia
| | - Viviane Slon
- Department of Evolutionary Genetics, Max-Planck-Institute for Evolutionary Anthropology, Leipzig, Germany.,Department of Anatomy and Anthropology and Department of Human Molecular Genetics and Biochemistry, Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel.,The Dan David Center for Human Evolution and Biohistory Research, Tel Aviv University, 6997801 Tel Aviv, Israel
| | - Fabrizio Mafessoni
- Department of Evolutionary Genetics, Max-Planck-Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Frédéric Romagné
- Department of Evolutionary Genetics, Max-Planck-Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Alice Pearson
- Department of Evolutionary Genetics, Max-Planck-Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Martin Petr
- Department of Evolutionary Genetics, Max-Planck-Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Nohemi Sala
- Centro Mixto UCM-ISCIII de Evolución y Comportamiento Humanos, Madrid, Spain.,Centro Nacional de Investigación Sobre la Evolución Humana (CENIEH), Burgos, Spain
| | - Adrián Pablos
- Centro Mixto UCM-ISCIII de Evolución y Comportamiento Humanos, Madrid, Spain.,Centro Nacional de Investigación Sobre la Evolución Humana (CENIEH), Burgos, Spain
| | - Arantza Aranburu
- Departamento de Geología, Facultad de Ciencia y Tecnología, Universidad del País Vasco-Euskal Herriko Unibertsitatea (UPV/EHU), Leioa, Spain.,Sociedad de Ciencias Aranzadi, Donostia-San Sebastián, Spain
| | | | - Eudald Carbonell
- Institut Català de Paleoecologia Humana i Evolució Social (IPHES), Universitat Rovira i Virgili, Tarragona, Spain.,Àrea de Prehistòria, Universitat Rovira i Virgili, Tarragona, Spain
| | - Bo Li
- Centre for Archaeological Science, School of Earth, Atmospheric and Life Sciences, University of Wollongong, Wollongong, New South Wales, Australia.,Australian Research Council (ARC) Centre of Excellence for Australian Biodiversity and Heritage, University of Wollongong, Wollongong, New South Wales, Australia
| | - Maciej T Krajcarz
- Institute of Geological Sciences, Polish Academy of Sciences, Warszawa, Poland
| | - Andrey I Krivoshapkin
- Institute of Archaeology and Ethnography, Russian Academy of Sciences, Novosibirsk, Russia.,Novosibirsk State University, Novosibirsk, Russia
| | - Kseniya A Kolobova
- Institute of Archaeology and Ethnography, Russian Academy of Sciences, Novosibirsk, Russia
| | - Maxim B Kozlikin
- Institute of Archaeology and Ethnography, Russian Academy of Sciences, Novosibirsk, Russia
| | - Michael V Shunkov
- Institute of Archaeology and Ethnography, Russian Academy of Sciences, Novosibirsk, Russia
| | - Anatoly P Derevianko
- Institute of Archaeology and Ethnography, Russian Academy of Sciences, Novosibirsk, Russia
| | - Bence Viola
- Department of Anthropology, University of Toronto, Toronto, Ontario, Canada
| | - Steffi Grote
- Department of Evolutionary Genetics, Max-Planck-Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Elena Essel
- Department of Evolutionary Genetics, Max-Planck-Institute for Evolutionary Anthropology, Leipzig, Germany
| | - David López Herráez
- Department of Evolutionary Genetics, Max-Planck-Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Sarah Nagel
- Department of Evolutionary Genetics, Max-Planck-Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Birgit Nickel
- Department of Evolutionary Genetics, Max-Planck-Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Julia Richter
- Department of Evolutionary Genetics, Max-Planck-Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Anna Schmidt
- Department of Evolutionary Genetics, Max-Planck-Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Benjamin Peter
- Department of Evolutionary Genetics, Max-Planck-Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Janet Kelso
- Department of Evolutionary Genetics, Max-Planck-Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Richard G Roberts
- Centre for Archaeological Science, School of Earth, Atmospheric and Life Sciences, University of Wollongong, Wollongong, New South Wales, Australia.,Australian Research Council (ARC) Centre of Excellence for Australian Biodiversity and Heritage, University of Wollongong, Wollongong, New South Wales, Australia
| | - Juan-Luis Arsuaga
- Centro Mixto UCM-ISCIII de Evolución y Comportamiento Humanos, Madrid, Spain.,Departamento de Paleontología, Facultad Ciencias Geológicas, Universidad Complutense de Madrid, Madrid, Spain
| | - Matthias Meyer
- Department of Evolutionary Genetics, Max-Planck-Institute for Evolutionary Anthropology, Leipzig, Germany.
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7
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Petr M, Hajdinjak M, Fu Q, Essel E, Rougier H, Crevecoeur I, Semal P, Golovanova LV, Doronichev VB, Lalueza-Fox C, de la Rasilla M, Rosas A, Shunkov MV, Kozlikin MB, Derevianko AP, Vernot B, Meyer M, Kelso J. The evolutionary history of Neanderthal and Denisovan Y chromosomes. Science 2020; 369:1653-1656. [PMID: 32973032 DOI: 10.1126/science.abb6460] [Citation(s) in RCA: 40] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2020] [Accepted: 08/06/2020] [Indexed: 12/31/2022]
Abstract
Ancient DNA has provided new insights into many aspects of human history. However, we lack comprehensive studies of the Y chromosomes of Denisovans and Neanderthals because the majority of specimens that have been sequenced to sufficient coverage are female. Sequencing Y chromosomes from two Denisovans and three Neanderthals shows that the Y chromosomes of Denisovans split around 700 thousand years ago from a lineage shared by Neanderthals and modern human Y chromosomes, which diverged from each other around 370 thousand years ago. The phylogenetic relationships of archaic and modern human Y chromosomes differ from the population relationships inferred from the autosomal genomes and mirror mitochondrial DNA phylogenies, indicating replacement of both the mitochondrial and Y chromosomal gene pools in late Neanderthals. This replacement is plausible if the low effective population size of Neanderthals resulted in an increased genetic load in Neanderthals relative to modern humans.
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Affiliation(s)
- Martin Petr
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, D-04103 Leipzig, Germany.
| | - Mateja Hajdinjak
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, D-04103 Leipzig, Germany.,The Francis Crick Institute, NW1 1AT London, UK
| | - Qiaomei Fu
- Key Laboratory of Vertebrate Evolution and Human Origins of Chinese Academy of Sciences, IVPP, CAS, Beijing 100044, China.,CAS Center for Excellence in Life and Paleoenvironment, Beijing 100044, China.,University of Chinese Academy of Sciences, Beijing 100049, China
| | - Elena Essel
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, D-04103 Leipzig, Germany
| | - Hélène Rougier
- Department of Anthropology, California State University, Northridge, Northridge, CA 91330-8244, USA
| | | | - Patrick Semal
- Royal Belgian Institute of Natural Sciences, 1000 Brussels, Belgium
| | | | | | - Carles Lalueza-Fox
- Institute of Evolutionary Biology, Consejo Superior de Investigaciones Científicas, Universitat Pompeu Fabra, 08003 Barcelona, Spain
| | - 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, Consejo Superior de Investigaciones Científicas, 28006 Madrid, Spain
| | - Michael V Shunkov
- Institute of Archaeology and Ethnography, Siberian Branch, Russian Academy of Sciences, Novosibirsk, Russia
| | - Maxim B Kozlikin
- Institute of Archaeology and Ethnography, Siberian Branch, Russian Academy of Sciences, Novosibirsk, Russia
| | - Anatoli P Derevianko
- Institute of Archaeology and Ethnography, Siberian Branch, Russian Academy of Sciences, Novosibirsk, Russia
| | - Benjamin Vernot
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, D-04103 Leipzig, Germany
| | - Matthias Meyer
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, D-04103 Leipzig, Germany
| | - Janet Kelso
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, D-04103 Leipzig, Germany.
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8
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Morley MW, Goldberg P, Uliyanov VA, Kozlikin MB, Shunkov MV, Derevianko AP, Jacobs Z, Roberts RG. Hominin and animal activities in the microstratigraphic record from Denisova Cave (Altai Mountains, Russia). Sci Rep 2019; 9:13785. [PMID: 31558742 PMCID: PMC6763451 DOI: 10.1038/s41598-019-49930-3] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2019] [Accepted: 09/03/2019] [Indexed: 11/15/2022] Open
Abstract
Denisova Cave in southern Siberia uniquely contains evidence of occupation by a recently discovered group of archaic hominins, the Denisovans, starting from the middle of the Middle Pleistocene. Artefacts, ancient DNA and a range of animal and plant remains have been recovered from the sedimentary deposits, along with a few fragmentary fossils of Denisovans, Neanderthals and a first-generation Neanderthal–Denisovan offspring. The deposits also contain microscopic traces of hominin and animal activities that can provide insights into the use of the cave over the last 300,000 years. Here we report the results of a micromorphological study of intact sediment blocks collected from the Pleistocene deposits in the Main and East Chambers of Denisova Cave. The presence of charcoal attests to the use of fire by hominins, but other evidence of their activities preserved in the microstratigraphic record are few. The ubiquitous occurrence of coprolites, which we attribute primarily to hyenas, indicates that the site was visited for much of its depositional history by cave-dwelling carnivores. Microscopic traces of post-depositional diagenesis, bioturbation and incipient cryoturbation are observed in only a few regions of the deposit examined here. Micromorphology can help identify areas of sedimentary deposit that are most conducive to ancient DNA preservation and could be usefully integrated with DNA analyses of sediments at archaeological sites to illuminate features of their human and environmental history that are invisible to the naked eye.
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Affiliation(s)
- Mike W Morley
- Centre for Archaeological Science, School of Earth, Atmospheric and Life Sciences, University of Wollongong, Wollongong, New South Wales, 2522, Australia. .,Archaeology, College of Humanities and Social Sciences, Flinders University, Adelaide, South Australia, 5042, Australia.
| | - Paul Goldberg
- Centre for Archaeological Science, School of Earth, Atmospheric and Life Sciences, University of Wollongong, Wollongong, New South Wales, 2522, Australia.,Institut für Naturwissenschaftliche Archäologie, Eberhard-Karls-Universität Tübingen, Rümelinstrasse 23, Tübingen, 72070, Germany
| | - Vladimir A Uliyanov
- Institute of Archaeology and Ethnography, Russian Academy of Sciences, Siberian Branch, Novosibirsk, 630090, Russia.,Lomonosov Moscow State University, Moscow, 119991, Russia
| | - Maxim B Kozlikin
- Institute of Archaeology and Ethnography, Russian Academy of Sciences, Siberian Branch, Novosibirsk, 630090, Russia
| | - Michael V Shunkov
- Institute of Archaeology and Ethnography, Russian Academy of Sciences, Siberian Branch, Novosibirsk, 630090, Russia.,Novosibirsk State University, Novosibirsk, 630090, Russia
| | - Anatoly P Derevianko
- Institute of Archaeology and Ethnography, Russian Academy of Sciences, Siberian Branch, Novosibirsk, 630090, Russia
| | - Zenobia Jacobs
- Centre for Archaeological Science, School of Earth, Atmospheric and Life Sciences, University of Wollongong, Wollongong, New South Wales, 2522, Australia.,Australian Research Council (ARC) Centre of Excellence for Australian Biodiversity and Heritage, University of Wollongong, Wollongong, New South Wales, 2522, Australia
| | - Richard G Roberts
- Centre for Archaeological Science, School of Earth, Atmospheric and Life Sciences, University of Wollongong, Wollongong, New South Wales, 2522, Australia.,Australian Research Council (ARC) Centre of Excellence for Australian Biodiversity and Heritage, University of Wollongong, Wollongong, New South Wales, 2522, Australia
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9
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Jacobs Z, Li B, Shunkov MV, Kozlikin MB, Bolikhovskaya NS, Agadjanian AK, Uliyanov VA, Vasiliev SK, O’Gorman K, Derevianko AP, Roberts RG. Timing of archaic hominin occupation of Denisova Cave in southern Siberia. Nature 2019; 565:594-599. [DOI: 10.1038/s41586-018-0843-2] [Citation(s) in RCA: 95] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2018] [Accepted: 11/30/2018] [Indexed: 11/09/2022]
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10
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Slon V, Mafessoni F, Vernot B, de Filippo C, Grote S, Viola B, Hajdinjak M, Peyrégne S, Nagel S, Brown S, Douka K, Higham T, Kozlikin MB, Shunkov MV, Derevianko AP, Kelso J, Meyer M, Prüfer K, Pääbo S. The genome of the offspring of a Neanderthal mother and a Denisovan father. Nature 2018; 561:113-116. [PMID: 30135579 PMCID: PMC6130845 DOI: 10.1038/s41586-018-0455-x] [Citation(s) in RCA: 154] [Impact Index Per Article: 25.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2018] [Accepted: 06/18/2018] [Indexed: 12/22/2022]
Abstract
Neandertals and Denisovans are extinct groups of hominins that separated from each other more than 390,000 years ago1,2. Here we present the genome of “Denisova 11”, a bone fragment from Denisova Cave (Russia)3, and show that it comes from an individual who had a Neandertal mother and a Denisovan father. The father, whose genome bears traces of Neandertal ancestry, came from a population related to a later Denisovan found in the cave4–6. The mother came from a population more closely related to Neandertals who lived later in Europe2,7 than to an older Neandertal found in Denisova Cave8, suggesting that migrations of Neandertals between eastern and western Eurasia occurred sometime after ~120,000 years ago. The finding of a first-generation Neandertal-Denisovan offspring among the small number of archaic specimens sequenced to date suggests that mixing between Late Pleistocene hominin groups was common when they met.
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Affiliation(s)
- Viviane Slon
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany.
| | - Fabrizio Mafessoni
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Benjamin Vernot
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Cesare de Filippo
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Steffi Grote
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Bence Viola
- Department of Anthropology, University of Toronto, Toronto, Ontario, Canada.,Institute of Archaeology and Ethnography, Russian Academy of Sciences, Novosibirsk, Russia
| | - Mateja Hajdinjak
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Stéphane Peyrégne
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Sarah Nagel
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Samantha Brown
- Max Planck Institute for the Science of Human History, Jena, Germany
| | - Katerina Douka
- Max Planck Institute for the Science of Human History, Jena, Germany.,Oxford Radiocarbon Accelerator Unit, RLAHA, University of Oxford, Oxford, UK
| | - Tom Higham
- Oxford Radiocarbon Accelerator Unit, RLAHA, University of Oxford, Oxford, UK
| | - Maxim B Kozlikin
- Institute of Archaeology and Ethnography, Russian Academy of Sciences, Novosibirsk, Russia
| | - Michael V Shunkov
- Institute of Archaeology and Ethnography, Russian Academy of Sciences, Novosibirsk, Russia.,Novosibirsk State University, Novosibirsk, Russia
| | - Anatoly P Derevianko
- Institute of Archaeology and Ethnography, Russian Academy of Sciences, Novosibirsk, Russia
| | - Janet Kelso
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Matthias Meyer
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Kay Prüfer
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Svante Pääbo
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany.
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