An early modern human from Romania with a recent Neanderthal ancestor

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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Figure 1: Allele sharing between the Oase 1 individual and other genomes.
Figure 2: Spatial distribution of alleles matching Neanderthals in modern humans.

Accession codes

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.

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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.

Corresponding authors

Correspondence to David Reich or Svante Pääbo.

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The authors declare no competing financial interests.

Extended data figures and tables

Extended Data Figure 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).

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

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Fu, Q., Hajdinjak, M., Moldovan, O. et al. An early modern human from Romania with a recent Neanderthal ancestor. Nature 524, 216–219 (2015). https://doi.org/10.1038/nature14558

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