Genetic history of an archaic hominin group from Denisova Cave in Siberia

Journal name:
Nature
Volume:
468,
Pages:
1053–1060
Date published:
DOI:
doi:10.1038/nature09710
Received
Accepted
Published online

Abstract

Using DNA extracted from a finger bone found in Denisova Cave in southern Siberia, we have sequenced the genome of an archaic hominin to about 1.9-fold coverage. This individual is from a group that shares a common origin with Neanderthals. This population was not involved in the putative gene flow from Neanderthals into Eurasians; however, the data suggest that it contributed 4–6% of its genetic material to the genomes of present-day Melanesians. We designate this hominin population ‘Denisovans’ and suggest that it may have been widespread in Asia during the Late Pleistocene epoch. A tooth found in Denisova Cave carries a mitochondrial genome highly similar to that of the finger bone. This tooth shares no derived morphological features with Neanderthals or modern humans, further indicating that Denisovans have an evolutionary history distinct from Neanderthals and modern humans.

At a glance

Figures

  1. A neighbour-joining tree based on pairwise autosomal DNA sequence divergences for five ancient and five present-day hominins.
    Figure 1: A neighbour-joining tree based on pairwise autosomal DNA sequence divergences for five ancient and five present-day hominins.

    Vindija 33.16, Vindija 33.25 and Vindija 33.26 refer to the catalogue numbers of the Neanderthal bones.

  2. Relationship of present-day populations to the Denisova individual and Neanderthals based on 255,077 SNPs.
    Figure 2: Relationship of present-day populations to the Denisova individual and Neanderthals based on 255,077 SNPs.

    Principal component analysis of the means of 53 present-day human populations projected onto the top two principal components defined by Denisova, Neanderthal and chimpanzee. The seven ‘African’ populations are San, Mbuti, Biaka, Bantu Kenya, Bantu South Africa, Yoruba and Mandenka; the ‘Non-African’ populations are 44 diverse groups from outside Africa except for Papuan and Bougainville islanders.

  3. A model of population history compatible with the data.
    Figure 3: A model of population history compatible with the data.

    N denotes effective population size, t denotes time of population separation, f denotes amount of gene flow and tGF denotes time of gene flow.

  4. Morphology of the Denisova molar.
    Figure 4: Morphology of the Denisova molar.

    a, b, Occlusal (a) and mesial (b) views. c, Comparison of the Denisova molar to diverse third molars, in a biplot of the mesiodistal and buccolingual lengths (in mm). AMH, anatomically modern humans; SH, Sima de los Huesos. Supplementary Fig. 12.1 presents a similar comparison to second molars.

Accession codes

Primary accessions

EMBL/GenBank/DDBJ

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Author information

  1. These authors contributed equally to this work.

    • David Reich,
    • Richard E. Green,
    • Martin Kircher,
    • Johannes Krause,
    • Nick Patterson,
    • Eric Y. Durand &
    • Bence Viola

Affiliations

  1. Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA

    • David Reich,
    • Adrian W. Briggs &
    • Swapan Mallick
  2. Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, USA

    • David Reich,
    • Nick Patterson,
    • Swapan Mallick &
    • Heng Li
  3. Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Leipzig 04103, Germany

    • Richard E. Green,
    • Martin Kircher,
    • Johannes Krause,
    • Bence Viola,
    • Adrian W. Briggs,
    • Udo Stenzel,
    • Tomislav Maricic,
    • Qiaomei Fu,
    • Matthias Meyer,
    • Mark Stoneking,
    • Janet Kelso &
    • Svante Pääbo
  4. Department of Biomolecular Engineering, University of California, Santa Cruz 95064, USA

    • Richard E. Green
  5. Institut für Naturwissenschaftliche Archäologie, University of Tübingen, Tübingen 72070, Germany

    • Johannes Krause
  6. Department of Integrative Biology, University of California, Berkeley, California 94720, USA

    • Eric Y. Durand &
    • Montgomery Slatkin
  7. Department of Human Evolution, Max Planck Institute for Evolutionary Anthropology, Leipzig 04103, Germany

    • Bence Viola,
    • Michael Richards,
    • Sahra Talamo &
    • Jean-Jacques Hublin
  8. Department of Biology, Emory University, Atlanta, Georgia 30322, USA

    • Philip L. F. Johnson
  9. Division of Biological Sciences, University of Montana, Missoula, Montana 59812, USA

    • Jeffrey M. Good
  10. Howard Hughes Medical Institute, Department of Genome Sciences, University of Washington, Seattle, Washington 98195, USA

    • Tomas Marques-Bonet,
    • Can Alkan &
    • Evan E. Eichler
  11. Institute of Evolutionary Biology (UPF-CSIC), 08003 Barcelona, Spain

    • Tomas Marques-Bonet
  12. CAS-MPS Joint Laboratory for Human Evolution and Archeometry, Institute of Vertebrate Paleontology and Paleoanthropology of Chinese Academy of Sciences, Beijing 100044, China

    • Qiaomei Fu
  13. Department of Anthropology, University of British Columbia, Vancouver, British Columbia V6T 1Z1, Canada

    • Michael Richards
  14. Palaeolithic Department, Institute of Archaeology & Ethnography, Russian Academy of Sciences, Siberian Branch, Novosibirsk 630090, Russia

    • Michael V. Shunkov &
    • Anatoli P. Derevianko

Contributions

J.Kr., T.M., Q.F. and M.M. performed the experiments; D.R., R.E.G., M.K., J.Kr., N.P., E.Y.D., A.W.B., U.S., P.L.F.J., T.M., J.M.G., T.B.-M., C.A., S.M., H.L., E.E.E., M.St., J.Ke., M.Sl. and S.P. analysed genetic data; B.V., M.R., S.T., M.V.S., A.P.D. and J.-J.H. analysed archaeological and anthropological data; D.R. and S.P. wrote and edited the manuscript.

Competing financial interests

The authors declare no competing financial interests.

Corresponding authors

Correspondence to:

The raw sequence data from the two Denisova fossils, the seven present-day humans, and the tooth mtDNA have been deposited in the European Nucleotide Archive at EMBL-EBI under accession numbers ERP000318, ERP000121 and FR695060, respectively. The alignments of Denisova sequence reads to the human and chimpanzee genomes are accessible for browsing and download from http://genome.ucsc.edu/Denisova.

Author details

Supplementary information

PDF files

  1. Supplementary Information (4.5M)

    This file contains 13 Supplementary Information sections (see Table of Contents), which include Supplementary Data, Supplementary Figures, Supplementary Tables and additional references. For Supplementary Data 1 Please go to the following link to access this file: http://bioinf.eva.mpg.de/download/DenisovaGenome/Denisova_Neandertal_catalog.tgz

Excel files

  1. Supplementary Data 2 (60K)

    This spreadsheet describes the 13 regions of potential admixture from Neandertals into modern humans as described in Green et al., Science 328:710 (2010).

Additional data