1. Broad Institute of MIT and Harvard, 320 Charles Street, Cambridge, Massachusetts 02141, USA
2. Division of Health Sciences and Technology, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, Massachusetts 02139, USA
3. Genome Sequencing Center, Washington University School of Medicine, Campus Box 8501, 4444 Forest Park Avenue, St Louis, Missouri 63108, USA
4. Genome Sciences, University of Washington School of Medicine, 1705 NE Pacific Street, Seattle, Washington 98195, USA
5. Max Planck Institute of Evolutionary Anthropology, Deutscher Platz 6, D-04103 Leipzig, Germany
6. University of California, San Diego, 9500 Gilman Drive, La Jolla, California 92093, USA
7. Department of Genetics and Microbiology, University of Bari, 70126 Bari, Italy
8. EMBL, Meyerhofstrasse 1, Heidelberg D-69117, Germany
9. Max Delbrück Center for Molecular Medicine (MDC), Bobert-Rössle-Strasse 10, D-13125 Berlin, Germany
10. Children's Hospital Oakland Research Institute, 747 52nd Street, Oakland, California 94609, USA
11. Department of Genetics, Yale University School of Medicine, 333 Cedar Street, New Haven, Connecticut 06520, USA
12. Institute for Systems Biology, 1441 North 34th Street, Seattle, Washington 98103, USA
13. Department of Genetics, Case Western Reserve University, 10900 Euclid Avenue, Cleveland, Ohio 44106, USA
14. Department of Computer Science, Iowa State University, 226 Atanasoff Hall, Ames, Iowa 50011, USA
15. Department of Statistics, Harvard University, 1 Oxford Street, Cambridge, Massachusetts 02138, USA
16. University of California, Santa Cruz, Center for Biomolecular Science and Engineering, 1156 High Street, Santa Cruz, California 95064, USA
17. Departamento de Bioquimica y Biologia Molecular, Instituto Universitario de Oncologia del Principado de Asturias, Universidad de Oviedo, C/Fernando Bongera s/n, 33006 Oviedo, Spain
18. The Pennsylvania State University, Center for Comparative Genomics and Bioinformatics and Department of Biology, University Park, Pennsylvania 16802, USA
19. Department of Structural Biology, Weizmann Institute of Science, Rehovot 76100, Israel
20. Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA
21. Departments of Anthropology and of Organismic and Evolutionary Biology, Harvard University, 11 Divinity Avenue, Cambridge, Massachusetts 02138, USA
22. Department of Systems Biology, Harvard Medical School, Boston, Massachusetts 02115, USA
23. Whitehead Institute for Biomedical Research, Cambridge, Massachusetts 02142, USA
24. Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
25. *Lists of participants and affiliations appear at the end of the paper

Correspondence to: Correspondence and requests for materials should be addressed to R.H.W. (Email: waterston@gs.washington.edu) E.S.L. (Email: lander@broad.mit.edu) or R.K.W. (Email: rwilson@watson.wustl.edu).

Abstract

Here we present a draft genome sequence of the common chimpanzee (Pan troglodytes). Through comparison with the human genome, we have generated a largely complete catalogue of the genetic differences that have accumulated since the human and chimpanzee species diverged from our common ancestor, constituting approximately thirty-five million single-nucleotide changes, five million insertion/deletion events, and various chromosomal rearrangements. We use this catalogue to explore the magnitude and regional variation of mutational forces shaping these two genomes, and the strength of positive and negative selection acting on their genes. In particular, we find that the patterns of evolution in human and chimpanzee protein-coding genes are highly correlated and dominated by the fixation of neutral and slightly deleterious alleles. We also use the chimpanzee genome as an outgroup to investigate human population genetics and identify signatures of selective sweeps in recent human evolution.

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