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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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Prüfer K, Racimo F, Patterson N, Jay F, Sankararaman S, Sawyer S, Heinze A, Renaud G, Sudmant PH, de Filippo C, Li H, Mallick S, Dannemann M, Fu Q, Kircher M, Kuhlwilm M, Lachmann M, Meyer M, Ongyerth M, Siebauer M, Theunert C, Tandon A, Moorjani P, Pickrell J, Mullikin JC, Vohr SH, Green RE, Hellmann I, Johnson PLF, Blanche H, Cann H, Kitzman JO, Shendure J, Eichler EE, Lein ES, Bakken TE, Golovanova LV, Doronichev VB, Shunkov MV, Derevianko AP, Viola B, Slatkin M, Reich D, Kelso J, Pääbo S. The complete genome sequence of a Neanderthal from the Altai Mountains. Nature 2013; 505:43-9. [PMID: 24352235 PMCID: PMC4031459 DOI: 10.1038/nature12886] [Citation(s) in RCA: 1130] [Impact Index Per Article: 102.7] [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: 09/05/2013] [Accepted: 11/15/2013] [Indexed: 12/13/2022]
Abstract
We present a high-quality genome sequence of a Neanderthal woman from Siberia. We show that her parents were related at the level of half-siblings and that mating among close relatives was common among her recent ancestors. We also sequenced the genome of a Neanderthal from the Caucasus to low coverage. An analysis of the relationships and population history of available archaic genomes and 25 present-day human genomes shows that several gene flow events occurred among Neanderthals, Denisovans and early modern humans, possibly including gene flow into Denisovans from an unknown archaic group. Thus, interbreeding, albeit of low magnitude, occurred among many hominin groups in the Late Pleistocene. In addition, the high-quality Neanderthal genome allows us to establish a definitive list of substitutions that became fixed in modern humans after their separation from the ancestors of Neanderthals and Denisovans.
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Affiliation(s)
- Kay Prüfer
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, 04103 Leipzig, Germany
| | - Fernando Racimo
- Department of Integrative Biology, University of California, Berkeley, California 94720-3140, USA
| | - Nick Patterson
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, USA
| | - Flora Jay
- Department of Integrative Biology, University of California, Berkeley, California 94720-3140, USA
| | - Sriram Sankararaman
- 1] Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, USA [2] Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Susanna Sawyer
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, 04103 Leipzig, Germany
| | - Anja Heinze
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, 04103 Leipzig, Germany
| | - Gabriel Renaud
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, 04103 Leipzig, Germany
| | - Peter H Sudmant
- Department of Genome Sciences, University of Washington, Seattle, Washington 98195, USA
| | - Cesare de Filippo
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, 04103 Leipzig, Germany
| | - Heng Li
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, USA
| | - Swapan Mallick
- 1] Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, USA [2] Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Michael Dannemann
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, 04103 Leipzig, Germany
| | - Qiaomei Fu
- 1] Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, 04103 Leipzig, Germany [2] 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
| | - Martin Kircher
- 1] Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, 04103 Leipzig, Germany [2] Department of Genome Sciences, University of Washington, Seattle, Washington 98195, USA
| | - Martin Kuhlwilm
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, 04103 Leipzig, Germany
| | - Michael Lachmann
- 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
| | - Matthias Ongyerth
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, 04103 Leipzig, Germany
| | - Michael Siebauer
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, 04103 Leipzig, Germany
| | - Christoph Theunert
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, 04103 Leipzig, Germany
| | - Arti Tandon
- 1] Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, USA [2] Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Priya Moorjani
- Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Joseph Pickrell
- Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA
| | - James C Mullikin
- Genome Technology Branch and NIH Intramural Sequencing Center, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland 20892, USA
| | - Samuel H Vohr
- Department of Biomolecular Engineering, University of California, Santa Cruz, California 95064, USA
| | - Richard E Green
- Department of Biomolecular Engineering, University of California, Santa Cruz, California 95064, USA
| | - Ines Hellmann
- 1] Max F. Perutz Laboratories, Mathematics and Bioscience Group, Campus Vienna Biocenter 5, Vienna 1030, Austria [2] Ludwig-Maximilians-Universität München, Martinsried, 82152 Munich, Germany
| | | | - Hélène Blanche
- Fondation Jean Dausset, Centre d'Étude du Polymorphisme Humain (CEPH), 75010 Paris, France
| | - Howard Cann
- Fondation Jean Dausset, Centre d'Étude du Polymorphisme Humain (CEPH), 75010 Paris, France
| | - Jacob O Kitzman
- Department of Genome Sciences, University of Washington, Seattle, Washington 98195, USA
| | - Jay Shendure
- Department of Genome Sciences, University of Washington, Seattle, Washington 98195, USA
| | - Evan E Eichler
- 1] Department of Genome Sciences, University of Washington, Seattle, Washington 98195, USA [2] Howard Hughes Medical Institute, Seattle, Washington 98195, USA
| | - Ed S Lein
- Allen Institute for Brain Science, Seattle, Washington 98103, USA
| | - Trygve E Bakken
- Allen Institute for Brain Science, Seattle, Washington 98103, USA
| | | | | | - Michael V Shunkov
- Palaeolithic Department, Institute of Archaeology and Ethnography, Russian Academy of Sciences, Siberian Branch, 630090 Novosibirsk, Russia
| | - Anatoli P Derevianko
- Palaeolithic Department, Institute of Archaeology and Ethnography, Russian Academy of Sciences, Siberian Branch, 630090 Novosibirsk, Russia
| | - Bence Viola
- Department of Human Evolution, Max Planck Institute for Evolutionary Anthropology, 04103 Leipzig, Germany
| | - Montgomery Slatkin
- Department of Integrative Biology, University of California, Berkeley, California 94720-3140, USA
| | - David Reich
- 1] Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, USA [2] Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA [3] Howard Hughes Medical Institute, Harvard Medical School, Boston, Massachusetts 02115, USA
| | - Janet Kelso
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, 04103 Leipzig, Germany
| | - Svante Pääbo
- Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, 04103 Leipzig, Germany
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