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The complete genome sequence of a Neanderthal from the Altai Mountains

Author

Listed:
  • 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
    Harvard Medical School)

  • 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
    Harvard Medical School)

  • Michael Dannemann

    (Max Planck Institute for Evolutionary Anthropology, 04103 Leipzig, Germany)

  • Qiaomei Fu

    (Max Planck Institute for Evolutionary Anthropology, 04103 Leipzig, Germany
    Key Laboratory of Vertebrate Evolution and Human Origins of Chinese Academy of Sciences, Institute of Vertebrate Paleontology and Paleoanthropology, Chinese Academy of Sciences)

  • Martin Kircher

    (Max Planck Institute for Evolutionary Anthropology, 04103 Leipzig, Germany
    University of Washington)

  • 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
    Harvard Medical School)

  • 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
    Present address: Ludwig-Maximilians-Universität München, Martinsried, 82152 Munich, Germany.)

  • 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
    Howard Hughes Medical Institute)

  • 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
    Harvard Medical School
    Howard Hughes Medical Institute, Harvard Medical School)

  • Janet Kelso

    (Max Planck Institute for Evolutionary Anthropology, 04103 Leipzig, Germany)

  • Svante Pääbo

    (Max Planck Institute for Evolutionary Anthropology, 04103 Leipzig, Germany)

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.

Suggested Citation

  • 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 & Mich, 2014. "The complete genome sequence of a Neanderthal from the Altai Mountains," Nature, Nature, vol. 505(7481), pages 43-49, January.
    • Handle: RePEc:nat:nature:v:505:y:2014:i:7481:d:10.1038_nature12886
    DOI: 10.1038/nature12886
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    Cited by:

    1. Sook Wah Yee & Luis Ferrández-Peral & Pol Alentorn-Moron & Claudia Fontsere & Merve Ceylan & Megan L. Koleske & Niklas Handin & Virginia M. Artegoitia & Giovanni Lara & Huan-Chieh Chien & Xujia Zhou &, 2024. "Illuminating the function of the orphan transporter, SLC22A10, in humans and other primates," Nature Communications, Nature, vol. 15(1), pages 1-17, December.
    2. Angus C. Chu, 2023. "Natural selection and Neanderthal extinction in a Malthusian economy," Journal of Population Economics, Springer;European Society for Population Economics, vol. 36(3), pages 1641-1656, July.
    3. Rogers, Alan R. & Bohlender, Ryan J., 2015. "Bias in estimators of archaic admixture," Theoretical Population Biology, Elsevier, vol. 100(C), pages 63-78.
    4. Kai Yuan & Xumin Ni & Chang Liu & Yuwen Pan & Lian Deng & Rui Zhang & Yang Gao & Xueling Ge & Jiaojiao Liu & Xixian Ma & Haiyi Lou & Taoyang Wu & Shuhua Xu, 2021. "Refining models of archaic admixture in Eurasia with ArchaicSeeker 2.0," Nature Communications, Nature, vol. 12(1), pages 1-15, December.
    5. Julian Petersen & Lukas Englmaier & Artem V. Artemov & Irina Poverennaya & Ruba Mahmoud & Thibault Bouderlique & Marketa Tesarova & Ruslan Deviatiiarov & Anett Szilvásy-Szabó & Evgeny E. Akkuratov & D, 2023. "A previously uncharacterized Factor Associated with Metabolism and Energy (FAME/C14orf105/CCDC198/1700011H14Rik) is related to evolutionary adaptation, energy balance, and kidney physiology," Nature Communications, Nature, vol. 14(1), pages 1-22, December.
    6. Delis, Manthos D. & Dioikitopoulos, Evangelos V. & Ongena, Steven, 2023. "Population diversity and financial risk-taking," Journal of Banking & Finance, Elsevier, vol. 151(C).

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