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An early modern human from Romania with a recent Neanderthal ancestor

Nature 524, 216–219 (13 August 2015) | Download Citation

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Abstract

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.

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Accessions

Primary accessions

European Nucleotide Archive

Data deposits

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

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Acknowledgements

We thank E. Trinkaus for facilitating the sampling of Oase 1, J. Krause for help with sampling and initial DNA analyses, A. Aximu for help with DNA hybridization captures and library preparation, and E. Trinkaus and L. Vigilant for critical reading of the manuscript. Q.F. is funded in part by the Chinese Academy of Sciences (XDA05130202) and the Special Foundation of the President of the Chinese Academy of Sciences (2015-2016). O.T.M. and S.C. are supported by the Romanian National Research Council through project PCCE 31/2010 (Karst Climate Archives). D.R. is supported by US National Science Foundation HOMINID grant BCS-1032255, US National Institutes of Health grant GM100233, and the Howard Hughes Medical Institute. The laboratory work was funded by the Presidential Innovation Fund of the Max Planck Society.

Author information

    • Qiaomei Fu
    •  & Mateja Hajdinjak

    These authors contributed equally to this work.

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

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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 interests

The authors declare no competing financial interests.

Corresponding authors

Correspondence to David Reich or Svante Pääbo.

Extended data

Extended data figures

  1. 1.

    Mitochondrial DNA tree for Oase 1 and other modern humans.

Extended data tables

  1. 1.

    Allele sharing between early modern humans and other humans

  2. 2.

    Allele sharing between early modern humans and other humans (transversions only)

  3. 3.

    Testing whether archaic genomes share more alleles with Oase 1 than with other modern humans

  4. 4.

    Estimated fraction of the Oase 1 genome that derives from Neanderthals

  5. 5.

    Counts of putative Neanderthal alleles in six modern humans

  6. 6.

    Ancient DNA libraries made from the Oase 1 mandible

  7. 7.

    Sequencing metrics on the five libraries for the four capture probe panels

  8. 8.

    Effect of filtering on amount of nuclear data available

  9. 9.

    Genomes merged with the Oase 1 data

Supplementary information

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    Supplementary Information

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    Supplementary Data

    This file contains Supplementary Data 1a.

  2. 2.

    Supplementary Data

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    Supplementary Data

    This file contains Supplementary Data 1c.

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    Supplementary Data

    This file contains Supplementary Data 2a.

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    Supplementary Data

    This file contains Supplementary Data 2b.

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    Supplementary Data

    This file contains Supplementary Data 2c.

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    Supplementary Data

    This file contains Supplementary Data 2d.

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    Supplementary Data

    This file contains Supplementary Data 3a.

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    Supplementary Data

    This file contains Supplementary Data 3b.

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    Supplementary Data

    This file contains Supplementary Data 3c.

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    Supplementary Data

    This file contains Supplementary Data 3d.

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    Supplementary Data

    This file contains Supplementary Data 3e.

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    Supplementary Data

    This file contains Supplementary Data 3f.

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DOI

https://doi.org/10.1038/nature14558

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