Nuclear and mitochondrial DNA sequences from two Denisovan individuals
Susanna Sawyer a,1, Gabriel Renaud a,1, Bence Viola b,c,d, Jean-Jacques Hublin c, Marie-Theres Gansauge a, Michael V. Shunkov d,e, Anatoly P. Derevianko d,f, Kay Prüfer a, Janet Kelso a, and Svante Pääbo a,2
aDepartment of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, D-04103 Leipzig, Germany;
bDepartment of Anthropology, University of Toronto, Toronto, ON M5S 2S2, Canada;
cDepartment of Human Evolution, Max Planck Institute for Evolutionary Anthropology, D-04103 Leipzig, Germany;
dInstitute of Archaeology and Ethnography, Russian Academy of Sciences, Novosibirsk, RU-630090, Russia;
eNovosibirsk National Research State University, Novosibirsk, RU-630090, Russia;
fAltai State University, Barnaul, RU-656049, Russia
Contributed by Svante Pääbo, October 13, 2015 (sent for review April 16, 2015; reviewed by Hendrik N. Poinar, Fred H. Smith, and Chris B. Stringer)
Significance
Denisovans are a sister group of Neandertals that were identified on the basis of a nuclear genome sequence from a bone from Denisova Cave (Siberia). The only other Denisovan specimen described to date is a molar from the same site. We present here nuclear DNA sequences from this molar and a morphological description, as well as mitochondrial and nuclear DNA sequences from another molar from Denisova Cave, thus extending the number of Denisovan individuals known to three. The nuclear DNA sequence diversity among the Denisovans is higher than among Neandertals, but lower than among present-day humans. The mtDNA of one molar has accumulated fewer substitutions than the mtDNAs of the other two specimens, suggesting Denisovans were present in the region over several millennia.
Abstract
Denisovans, a sister group of Neandertals, have been described on the basis of a nuclear genome sequence from a finger phalanx (Denisova 3) found in Denisova Cave in the Altai Mountains. The only other Denisovan specimen described to date is a molar (Denisova 4) found at the same site. This tooth carries a mtDNA sequence similar to that of Denisova 3. Here we present nuclear DNA sequences from Denisova 4 and a morphological description, as well as mitochondrial and nuclear DNA sequence data, from another molar (Denisova 8) found in Denisova Cave in 2010. This new molar is similar to Denisova 4 in being very large and lacking traits typical of Neandertals and modern humans. Nuclear DNA sequences from the two molars form a clade with Denisova 3. The mtDNA of Denisova 8 is more diverged and has accumulated fewer substitutions than the mtDNAs of the other two specimens, suggesting Denisovans were present in the region over an extended period. The nuclear DNA sequence diversity among the three Denisovans is comparable to that among six Neandertals, but lower than that among present-day humans.
Denisovans ancient DNA Neandertals
Footnotes
1S.S. and G.R. contributed equally to this work.
2To whom correspondence should be addressed. Email: paabo{at}eva.mpg.de.
Author contributions: S.S. and S.P. designed research; S.S., G.R., B.V., and M.-T.G. performed research; M.V.S. and A.P.D. contributed new reagents/analytic tools; S.S., G.R., B.V., J.-J.H., K.P., and J.K. analyzed data; and S.S., G.R., B.V., J.K., and S.P. wrote the paper.
Reviewers: H.N.P., McMaster University; F.H.S., Illinois State University; and C.B.S., The Natural History Museum, London.
The authors declare no conflict of interest.
Data deposition: The sequence reported in this paper has been deposited in the European Nucleotide Archive database (accession no. PRJEB10828). The mitochondrial assembly of Denisovq 8 has been deposited in the GenBank database (accession no. KT780370).
This article contains supporting information online at www.pnas.org/lookup/suppl/doi:10.1073/pnas.1519905112/-/DCSupplemental.
Freely available online through the PNAS open access option.
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