The complete genome sequence of a Neanderthal from the Altai Mountains

Kay Prüfer, Fernando Racimo, Nick Patterson, Flora Jay, Sriram Sankararaman, Susanna Sawyer, Anja Heinze, Gabriel Renaud, Peter H. Sudmant, Cesare de Filippo, Heng Li, Swapan Mallick, Michael Dannemann, Qiaomei Fu, Martin Kircher, Martin Kuhlwilm, Michael Lachmann, Matthias Meyer, Matthias Ongyerth, Michael Siebauer, Christoph Theunert, Arti Tandon, Priya Moorjani, Joseph Pickrell, James C. Mullikin, Samuel H. Vohr, Richard E. Green, Ines Hellmann, Philip L. F. Johnson, Hélène Blanche, Howard Cann, Jacob O. Kitzman, Jay Shendure, Evan E. Eichler, Ed S. Lein, Trygve E. Bakken, Liubov V. Golovanova, Vladimir B. Doronichev, Michael V. Shunkov, Anatoli P. Derevianko, Bence Viola, Montgomery Slatkin (), David Reich (), Janet Kelso and Svante Pääbo ()
Additional contact information
Kay Prüfer: Max Planck Institute for Evolutionary Anthropology, 04103 Leipzig, Germany
Fernando Racimo: University of California
Nick Patterson: Broad Institute of MIT and Harvard
Flora Jay: University of California
Sriram Sankararaman: Broad Institute of MIT and Harvard
Susanna Sawyer: Max Planck Institute for Evolutionary Anthropology, 04103 Leipzig, Germany
Anja Heinze: Max Planck Institute for Evolutionary Anthropology, 04103 Leipzig, Germany
Gabriel Renaud: Max Planck Institute for Evolutionary Anthropology, 04103 Leipzig, Germany
Peter H. Sudmant: University of Washington
Cesare de Filippo: Max Planck Institute for Evolutionary Anthropology, 04103 Leipzig, Germany
Heng Li: Broad Institute of MIT and Harvard
Swapan Mallick: Broad Institute of MIT and Harvard
Michael Dannemann: Max Planck Institute for Evolutionary Anthropology, 04103 Leipzig, Germany
Qiaomei Fu: Max Planck Institute for Evolutionary Anthropology, 04103 Leipzig, Germany
Martin Kircher: Max Planck Institute for Evolutionary Anthropology, 04103 Leipzig, Germany
Martin Kuhlwilm: Max Planck Institute for Evolutionary Anthropology, 04103 Leipzig, Germany
Michael Lachmann: Max Planck Institute for Evolutionary Anthropology, 04103 Leipzig, Germany
Matthias Meyer: Max Planck Institute for Evolutionary Anthropology, 04103 Leipzig, Germany
Matthias Ongyerth: Max Planck Institute for Evolutionary Anthropology, 04103 Leipzig, Germany
Michael Siebauer: Max Planck Institute for Evolutionary Anthropology, 04103 Leipzig, Germany
Christoph Theunert: Max Planck Institute for Evolutionary Anthropology, 04103 Leipzig, Germany
Arti Tandon: Broad Institute of MIT and Harvard
Priya Moorjani: Harvard Medical School
Joseph Pickrell: Harvard Medical School
James C. Mullikin: Genome Technology Branch and NIH Intramural Sequencing Center, National Human Genome Research Institute, National Institutes of Health
Samuel H. Vohr: University of California
Richard E. Green: University of California
Ines Hellmann: Max F. Perutz Laboratories, Mathematics and Bioscience Group, Campus Vienna Biocenter 5, Vienna 1030, Austria
Philip L. F. Johnson: Emory University
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: University of Washington
Jay Shendure: University of Washington
Evan E. Eichler: University of Washington
Ed S. Lein: Allen Institute for Brain Science
Trygve E. Bakken: Allen Institute for Brain Science
Liubov V. Golovanova: ANO Laboratory of Prehistory 14 Linia 3-11, St. Petersburg 1990 34, Russia
Vladimir B. Doronichev: ANO Laboratory of Prehistory 14 Linia 3-11, St. Petersburg 1990 34, Russia
Michael V. Shunkov: Institute of Archaeology and Ethnography, Russian Academy of Sciences, Siberian Branch, 630090 Novosibirsk, Russia
Anatoli P. Derevianko: Institute of Archaeology and Ethnography, Russian Academy of Sciences, Siberian Branch, 630090 Novosibirsk, Russia
Bence Viola: Max Planck Institute for Evolutionary Anthropology, 04103 Leipzig, Germany
Montgomery Slatkin: University of California
David Reich: Broad Institute of MIT and Harvard
Janet Kelso: Max Planck Institute for Evolutionary Anthropology, 04103 Leipzig, Germany
Svante Pääbo: Max Planck Institute for Evolutionary Anthropology, 04103 Leipzig, Germany

Nature, 2014, vol. 505, issue 7481, 43-49

Abstract: 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.

Date: 2014
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DOI: 10.1038/nature12886

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