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.
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Accession codes
Accessions
European Nucleotide Archive
Data deposits
All sequence data have been submitted to the European Nucleotide Archive (ENA) and are available under the following accessions: Altai Neanderthal: ERP002097, Mezmaiskaya Neanderthal: ERP002447. The data from the 25 present-day human genomes and 13 experimentally phased present-day genomes are available as a public dataset from http://aws.amazon.com/datasets/ and from http://cdna.eva.mpg.de/neandertal/altai/.
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Acknowledgements
We thank M. Hammer, C. Winkler and W. Klitz for sharing DNA samples; W. Huttner and his group, B. Peter, J. G. Schraiber and M. A. Yang for helpful discussions; and A. Lewis and R. Qiu for technical assistance. N.P. and D.R. are grateful for the chance to discuss these results with Peter Waddell who independently found evidence of a deeply diverged hominin admixing into the Denisova genome. D.R. and E.E.E. are Howard Hughes Medical Institute Investigators. D.R. and N.P. were supported by NSF grant number 1032255 and NIH grant GM100233; E.E.E. by NIH grant HG002385; J.S. by grant HG006283 from the National Genome Research Institute (NHGRI); S.S. by a post-doctoral fellowship from the Harvard University Science of the Human Past Program; F.J. and M.S. in part by a grant from the NIH (R01-GM40282); P.H.S. by an HHMI International Student Fellowship. We thank the team at the NIH Intramural Sequencing Center and Alice Young in particular, for generating some of the sequence reported here. This research was supported in part by the Paul G. Allen Family Foundation. Major funding support came from the Presidential Innovation Fund of the Max Planck Society.
Author information
Affiliations
Contributions
S.Saw., A.H. and Q.F. performed the experiments; K.P., F.R., N.P., F.J., S.San., S.Saw., A.H., G.R., P.H.S., C.d.F., M.D., Q.F., M.Ki., M.Ku., M.L., M.M., M.O., M.Si., C.T., H.L., S.M., A.T., P.M., J.P., J.C.M., S.H.V., R.E.G., I.H., P.L.F.J., J.O.K., J.S., E.E.E., E.S.L., T.E.B., M.Sl., D.R., J.K., and S.P. analysed genetic data; L.V.G., V.B.D., M.V.S., A.P.D. and B.V. analysed archaeological and anthropological data; H.B. and H.C. provided samples and reagents; K.P., J.K. and S.P. wrote and edited the manuscript with input from all authors.
Corresponding authors
Correspondence to Montgomery Slatkin or 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 Heterozygosity estimates for the Altai Neanderthal individual, the Denisovan individual, non-Africans and Africans.
The bars for the latter two give the range of heterozygosity observed among 15 non-African and 10 African individuals, respectively (Supplementary Information section 9).
Extended Data Figure 2 Neanderthal-introgressed loci in Denisova.
Divergence of the Altai Neanderthal to the most closely related Denisovan haplotype in windows of at least 200 kb on chromosome 6. Divergence is given as percentage of human–chimpanzee divergence and bars represent ± 1 standard error.
Supplementary information
Supplementary Information
This file contains Supplementary Text, Tables and Figures – see contents page for details. (PDF 16537 kb)
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Prüfer, K., Racimo, F., Patterson, N. et al. The complete genome sequence of a Neanderthal from the Altai Mountains. Nature 505, 43–49 (2014). https://doi.org/10.1038/nature12886
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