An early modern human from Romania with a recent Neanderthal ancestor

Journal name:
Nature
Volume:
524,
Pages:
216–219
Date published:
DOI:
doi:10.1038/nature14558
Received
Accepted
Published online

Neanderthals are thought to have disappeared in Europe approximately 39,000–41,000 years ago but they have contributed 1–3% of the DNA of present-day people in Eurasia1. Here we analyse DNA from a 37,000–42,000-year-old2 modern human from Peştera cu Oase, Romania. Although the specimen contains small amounts of human DNA, we use an enrichment strategy to isolate sites that are informative about its relationship to Neanderthals and present-day humans. We find that on the order of 6–9% of the genome of the Oase individual is derived from Neanderthals, more than any other modern human sequenced to date. Three chromosomal segments of Neanderthal ancestry are over 50 centimorgans in size, indicating that this individual had a Neanderthal ancestor as recently as four to six generations back. However, the Oase individual does not share more alleles with later Europeans than with East Asians, suggesting that the Oase population did not contribute substantially to later humans in Europe.

At a glance

Figures

  1. Allele sharing between the Oase 1 individual and other genomes.
    Figure 1: Allele sharing between the Oase 1 individual and other genomes.

    Each point indicates the extent to which the Oase 1 genome shares alleles with one or other of a pair of genomes from different populations indicated above and below (see Extended Data Table 1 for numbers). Z-scores with an absolute value greater than 2 indicate an excess of allele sharing (grey).

  2. Spatial distribution of alleles matching Neanderthals in modern humans.
    Figure 2: Spatial distribution of alleles matching Neanderthals in modern humans.

    Coloured vertical lines indicate alleles shared with Neanderthals and no colour indicates alleles shared with the great majority of West Africans. D, Dinka; F, French; H, Han; K, Kostenki 14; O, Oase 1; U, Ust’-Ishim. The seven grey bars indicate segments of putative recent Neanderthal ancestry. This analysis is based on 78,055 sites. Numbers refer to chromosomes.

  3. Mitochondrial DNA tree for Oase 1 and other modern humans.
    Extended Data Fig. 1: Mitochondrial DNA tree for Oase 1 and other modern humans.

    The consensus sequences for all Oase 1 fragments and for deaminated fragments are shown. The tree is rooted with a Neanderthal mtDNA (Vindija33.25).

Tables

  1. Allele sharing between early modern humans and other humans
    Extended Data Table 1: Allele sharing between early modern humans and other humans
  2. Allele sharing between early modern humans and other humans (transversions only)
    Extended Data Table 2: Allele sharing between early modern humans and other humans (transversions only)
  3. Testing whether archaic genomes share more alleles with Oase 1 than with other modern humans
    Extended Data Table 3: Testing whether archaic genomes share more alleles with Oase 1 than with other modern humans
  4. Estimated fraction of the Oase 1 genome that derives from Neanderthals
    Extended Data Table 4: Estimated fraction of the Oase 1 genome that derives from Neanderthals
  5. Counts of putative Neanderthal alleles in six modern humans
    Extended Data Table 5: Counts of putative Neanderthal alleles in six modern humans
  6. Ancient DNA libraries made from the Oase 1 mandible
    Extended Data Table 6: Ancient DNA libraries made from the Oase 1 mandible
  7. Sequencing metrics on the five libraries for the four capture probe panels
    Extended Data Table 7: Sequencing metrics on the five libraries for the four capture probe panels
  8. Effect of filtering on amount of nuclear data available
    Extended Data Table 8: Effect of filtering on amount of nuclear data available
  9. Genomes merged with the Oase 1 data
    Extended Data Table 9: Genomes merged with the Oase 1 data

Accession codes

Primary accessions

European Nucleotide Archive

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Author information

  1. These authors contributed equally to this work.

    • Qiaomei Fu &
    • Mateja Hajdinjak

Affiliations

  1. Key Laboratory of Vertebrate Evolution and Human Origins of Chinese Academy of Sciences, IVPP, CAS, Beijing 100044, China

    • Qiaomei Fu
  2. Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA

    • Qiaomei Fu,
    • Swapan Mallick,
    • Pontus Skoglund,
    • Nadin Rohland,
    • Iosif Lazaridis &
    • David Reich
  3. Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, Leipzig 04103, Germany

    • Qiaomei Fu,
    • Mateja Hajdinjak,
    • Birgit Nickel,
    • Bence Viola,
    • Kay Prüfer,
    • Matthias Meyer,
    • Janet Kelso &
    • Svante Pääbo
  4. “Emil Racoviţă” Institute of Speleology, Cluj Branch, 400006 Cluj, Romania

    • Oana Teodora Moldovan
  5. “Emil Racoviţă” Institute of Speleology, Department of Geospeleology and Paleontology, 010986 Bucharest 12, Romania

    • Silviu Constantin
  6. Broad Institute of MIT and Harvard, Cambridge, Massachusetts 02142, USA

    • Swapan Mallick,
    • Nick Patterson &
    • David Reich
  7. Department of Human Evolution, Max Planck Institute for Evolutionary Anthropology, Leipzig 04103, Germany

    • Swapan Mallick &
    • Bence Viola
  8. Department of Anthropology, University of Toronto, Toronto, Ontario, M5S 2S2, Canada

    • Bence Viola
  9. Howard Hughes Medical Institute, Harvard Medical School, Boston, Massachusetts, 02115, USA

    • David Reich

Contributions

N.P., K.P., M.M., J.K., D.R. and S.P. supervised the study. S.C. and O.T.M. collected and analysed archaeological material. Q.F., M.H. and B.N. performed laboratory work. Q.F., M.H., S.M., P.S., N.P., N.R., I.L., B.V., K.P., J.K. and D.R. analysed data. Q.F., S.M., M.M. and D.R. designed capture probes. D.R. and S.P. wrote the manuscript with the help of all co-authors.

Competing financial interests

The authors declare no competing financial interests.

Corresponding authors

Correspondence to:

The aligned sequences have been deposited in the European Nucleotide Archive under accession number PRJEB8987.

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Supplementary information

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