A High-Coverage Genome Sequence from an Archaic Denisovan Individual

Matthias Meyer; Martin Kircher; Marie-Theres Gansauge; Heng Li; Fernando Racimo; Swapan Mallick; Joshua G. Schraiber; Flora Jay; Kay Prüfer; Cesare de Filippo; Peter H. Sudmant; Can Alkan; Qiaomei Fu; Ron Do; Nadin Rohland; Arti Tandon; Michael Siebauer; Richard E. Green; Katarzyna Bryc; Adrian W. Briggs; Udo Stenzel; Jesse Dabney; Jay Shendure; Jacob Kitzman; Michael F. Hammer; Michael V. Shunkov; Anatoli P. Derevianko; Nick Patterson; Aida M. Andrés; Evan E. Eichler; Montgomery Slatkin; David Reich; Janet Kelso; Svante Pääbo

doi:10.1126/science.1224344

Research Article

A High-Coverage Genome Sequence from an Archaic Denisovan Individual

Matthias Meyer¹,*,^‡,
Martin Kircher¹,*,^†,
Marie-Theres Gansauge¹,
Heng Li²,
Fernando Racimo¹,
Swapan Mallick²,³,
Joshua G. Schraiber⁴,
Flora Jay⁴,
Kay Prüfer¹,
Cesare de Filippo¹,
Peter H. Sudmant⁶,
Can Alkan⁴,⁵,
Qiaomei Fu¹,⁷,
Ron Do²,
Nadin Rohland²,³,
Arti Tandon²,³,
Michael Siebauer¹,
Richard E. Green⁸,
Katarzyna Bryc³,
Adrian W. Briggs³,
Udo Stenzel¹,
Jesse Dabney¹,
Jay Shendure⁶,
Jacob Kitzman⁶,
Michael F. Hammer⁹,
Michael V. Shunkov¹⁰,
Anatoli P. Derevianko¹⁰,
Nick Patterson²,
Aida M. Andrés¹,
Evan E. Eichler⁶,¹¹,
Montgomery Slatkin⁴,
David Reich²,³,*,^‡,
Janet Kelso¹,
Svante Pääbo¹,^‡

¹Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, D-04103 Leipzig, Germany.
²Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA 02142, USA.
³Department of Genetics, Harvard Medical School, Boston, MA 02115, USA.
⁴Department of Integrative Biology, University of California, Berkeley, CA 94720, USA.
⁵Department of Computer Engineering, Bilkent University, 06800 Ankara, Turkey.
⁶Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA 98195, USA.
⁷CAS-MPS Joint Laboratory for Human Evolution, Institute of Vertebrate Paleontology and Paleoanthropology, Chinese Academy of Sciences, 100044 Beijing, China.
⁸Jack Baskin School of Engineering, University of California, Santa Cruz, CA 95064, USA.
⁹Arizona Research Laboratories, Division of Biotechnology, University of Arizona, Tucson, AZ 85721, USA.
¹⁰Palaeolithic Department, Institute of Archaeology and Ethnography, Russian Academy of Sciences, Siberian Branch, 630090 Novosibirsk, Russia.
¹¹Howard Hughes Medical Institute, Seattle, WA 98195, USA.

↵‡To whom correspondence should be addressed. E-mail: mmeyer{at}eva.mpg.de (M.M.); reich{at}genetics.med.harvard.edu (D.R.); paabo{at}eva.mpg.de (S.P.)

↵* These authors contributed equally to this work.

↵† Present address: Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA.

See allHide authors and affiliations

Science 30 Aug 2012:
1224344
DOI: 10.1126/science.1224344

Matthias Meyer

1Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, D-04103 Leipzig, Germany.

Find this author on Google Scholar
Find this author on PubMed
Search for this author on this site

Martin Kircher

1Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, D-04103 Leipzig, Germany.

Find this author on Google Scholar
Find this author on PubMed
Search for this author on this site

Marie-Theres Gansauge

1Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, D-04103 Leipzig, Germany.

Find this author on Google Scholar
Find this author on PubMed
Search for this author on this site

Heng Li

2Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA 02142, USA.

Find this author on Google Scholar
Find this author on PubMed
Search for this author on this site

Fernando Racimo

1Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, D-04103 Leipzig, Germany.

Find this author on Google Scholar
Find this author on PubMed
Search for this author on this site

Swapan Mallick

2Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA 02142, USA.3Department of Genetics, Harvard Medical School, Boston, MA 02115, USA.

Find this author on Google Scholar
Find this author on PubMed
Search for this author on this site

Joshua G. Schraiber

4Department of Integrative Biology, University of California, Berkeley, CA 94720, USA.

Find this author on Google Scholar
Find this author on PubMed
Search for this author on this site

Flora Jay

4Department of Integrative Biology, University of California, Berkeley, CA 94720, USA.

Find this author on Google Scholar
Find this author on PubMed
Search for this author on this site

Kay Prüfer

1Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, D-04103 Leipzig, Germany.

Find this author on Google Scholar
Find this author on PubMed
Search for this author on this site

Cesare de Filippo

1Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, D-04103 Leipzig, Germany.

Find this author on Google Scholar
Find this author on PubMed
Search for this author on this site

Peter H. Sudmant

6Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA 98195, USA.

Find this author on Google Scholar
Find this author on PubMed
Search for this author on this site

Can Alkan

4Department of Integrative Biology, University of California, Berkeley, CA 94720, USA.5Department of Computer Engineering, Bilkent University, 06800 Ankara, Turkey.

Find this author on Google Scholar
Find this author on PubMed
Search for this author on this site

Qiaomei Fu

1Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, D-04103 Leipzig, Germany.7CAS-MPS Joint Laboratory for Human Evolution, Institute of Vertebrate Paleontology and Paleoanthropology, Chinese Academy of Sciences, 100044 Beijing, China.

Find this author on Google Scholar
Find this author on PubMed
Search for this author on this site

Ron Do

2Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA 02142, USA.

Find this author on Google Scholar
Find this author on PubMed
Search for this author on this site

Nadin Rohland

2Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA 02142, USA.3Department of Genetics, Harvard Medical School, Boston, MA 02115, USA.

Find this author on Google Scholar
Find this author on PubMed
Search for this author on this site

Arti Tandon

2Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA 02142, USA.3Department of Genetics, Harvard Medical School, Boston, MA 02115, USA.

Find this author on Google Scholar
Find this author on PubMed
Search for this author on this site

Michael Siebauer

1Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, D-04103 Leipzig, Germany.

Find this author on Google Scholar
Find this author on PubMed
Search for this author on this site

Richard E. Green

8Jack Baskin School of Engineering, University of California, Santa Cruz, CA 95064, USA.

Find this author on Google Scholar
Find this author on PubMed
Search for this author on this site

Katarzyna Bryc

3Department of Genetics, Harvard Medical School, Boston, MA 02115, USA.

Find this author on Google Scholar
Find this author on PubMed
Search for this author on this site

Adrian W. Briggs

3Department of Genetics, Harvard Medical School, Boston, MA 02115, USA.

Find this author on Google Scholar
Find this author on PubMed
Search for this author on this site

Udo Stenzel

1Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, D-04103 Leipzig, Germany.

Find this author on Google Scholar
Find this author on PubMed
Search for this author on this site

Jesse Dabney

1Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, D-04103 Leipzig, Germany.

Find this author on Google Scholar
Find this author on PubMed
Search for this author on this site

Jay Shendure

6Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA 98195, USA.

Find this author on Google Scholar
Find this author on PubMed
Search for this author on this site

Jacob Kitzman

6Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA 98195, USA.

Find this author on Google Scholar
Find this author on PubMed
Search for this author on this site

Michael F. Hammer

9Arizona Research Laboratories, Division of Biotechnology, University of Arizona, Tucson, AZ 85721, USA.

Find this author on Google Scholar
Find this author on PubMed
Search for this author on this site

Michael V. Shunkov

10Palaeolithic Department, Institute of Archaeology and Ethnography, Russian Academy of Sciences, Siberian Branch, 630090 Novosibirsk, Russia.

Find this author on Google Scholar
Find this author on PubMed
Search for this author on this site

Anatoli P. Derevianko

10Palaeolithic Department, Institute of Archaeology and Ethnography, Russian Academy of Sciences, Siberian Branch, 630090 Novosibirsk, Russia.

Find this author on Google Scholar
Find this author on PubMed
Search for this author on this site

Nick Patterson

2Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA 02142, USA.

Find this author on Google Scholar
Find this author on PubMed
Search for this author on this site

Aida M. Andrés

1Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, D-04103 Leipzig, Germany.

Find this author on Google Scholar
Find this author on PubMed
Search for this author on this site

Evan E. Eichler

6Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA 98195, USA.11Howard Hughes Medical Institute, Seattle, WA 98195, USA.

Find this author on Google Scholar
Find this author on PubMed
Search for this author on this site

Montgomery Slatkin

4Department of Integrative Biology, University of California, Berkeley, CA 94720, USA.

Find this author on Google Scholar
Find this author on PubMed
Search for this author on this site

David Reich

2Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA 02142, USA.3Department of Genetics, Harvard Medical School, Boston, MA 02115, USA.

Find this author on Google Scholar
Find this author on PubMed
Search for this author on this site

Janet Kelso

1Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, D-04103 Leipzig, Germany.

Find this author on Google Scholar
Find this author on PubMed
Search for this author on this site

Svante Pääbo

1Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, D-04103 Leipzig, Germany.

Find this author on Google Scholar
Find this author on PubMed
Search for this author on this site

Article
Figures & Data
Info & Metrics
eLetters
PDF

You are currently viewing the abstract.

View Full Text

Log in to view the full text

via AAAS login

AAAS login provides access to Science for AAAS members, and access to other journals in the Science family to users who have purchased individual subscriptions.

Become a AAAS member
Activate account
Add journals
Account help

As a service to the community, this article is available for free. Existing users log in.

Become a AAAS member
Account help

Log in through your institution

More options

Purchase digital access to this article

Download and print this article for your personal scholarly, research, and educational use.

Purchase this issue in print

Buy a single issue of Science for just $15 USD.

Abstract

We present a DNA library preparation method that has allowed us to reconstruct a high-coverage (30X) 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.

View Full Text

A High-Coverage Genome Sequence from an Archaic Denisovan Individual

Abstract

Article Tools