A High-Coverage Genome Sequence from an Archaic Denisovan Individual
Ancient Genomics
The Denisovans were archaic humans closely related to Neandertals, whose populations overlapped with the ancestors of modern-day humans. Using a single-stranded library preparation method, Meyer et al. (p. 222, published online 30 August) provide a detailed analysis of a high-quality Denisovan genome. The genomic sequence provides evidence for very low rates of heterozygosity in the Denisova, probably not because of recent inbreeding, but instead because of a small population size. The genome sequence also illuminates the relationships between humans and archaics, including Neandertals, and establishes a catalog of genetic changes within the human lineage.
Abstract
We present a DNA library preparation method that has allowed us to reconstruct a high-coverage (30×) genome sequence of a Denisovan, an extinct relative of Neandertals. The quality of this genome allows a direct estimation of Denisovan heterozygosity indicating that genetic diversity in these archaic hominins was extremely low. It also allows tentative dating of the specimen on the basis of “missing evolution” in its genome, detailed measurements of Denisovan and Neandertal admixture into present-day human populations, and the generation of a near-complete catalog of genetic changes that swept to high frequency in modern humans since their divergence from Denisovans.
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Supplementary Material
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References and Notes
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Science
Volume 338 | Issue 6104
12 October 2012
12 October 2012
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Copyright © 2012, American Association for the Advancement of Science.
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Received: 7 May 2012
Accepted: 14 August 2012
Published in print: 12 October 2012
Acknowledgments
The Denisovan sequence reads are available from the European Nucleotide Archive (ENA) under study accession ERP001519. The present-day human sequence reads are available from the Short Read Archive (SRA) under accession SRA047577. Alignments and genotype calls for each of the sequenced individuals are available at www.eva.mpg.de/denisova/. In addition, the Denisovan sequence reads and alignments are available as a public data set via Amazon Web Services (AWS) at http://aws.amazon.com/datasets/2357/ and as a track in the University of California, Santa Cruz genome browser. We thank D. Falush, P. Johnson, J. Krause, M. Lachmann, S. Sawyer, L. Vigilant and B. Viola for comments, help, and suggestions; A. Aximu, B. Höber, B. Höffner, A. Weihmann, T. Kratzer, and R. Roesch for expert technical assistance; R. Schultz for help with data management; and M. Schreiber for improvement of graphics. The Presidential Innovation Fund of the Max Planck Society made this project possible. D.R. and N.P. are grateful for support from NSF HOMINID grant no. 1032255 and NIH grant GM100233. J.G.S., F.J., and M.S. were supported by NIH grant R01-GM40282 to M.S. P.H.S. is supported by an HHMI International Student Fellowship. F.R. is supported by a German Academic Exchange Service (DAAD) study scholarship. E.E.E. is on the scientific advisory boards for Pacific Biosciences, Inc., SynapDx Corp, and DNAnexus, Inc.
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