title: Chimpanzee genomic diversity reveals ancient admixture with bonobos.
abstract: Our closest living relatives, chimpanzees and bonobos, have a complex demographic history. We analyzed the high-coverage whole genomes of 75 wild-born chimpanzees and bonobos from 10 countries in Africa. We found that chimpanzee population substructure makes genetic information a good predictor of geographic origin at country and regional scales. Multiple lines of evidence suggest that gene flow occurred from bonobos into the ancestors of central and eastern chimpanzees between 200,000 and 550,000 years ago, probably with subsequent spread into Nigeria-Cameroon chimpanzees. Together with another, possibly more recent contact (after 200,000 years ago), bonobos contributed less than 1% to the central chimpanzee genomes. Admixture thus appears to have been widespread during hominid evolution.
authors: Institut de Biologia Evolutiva (Consejo Superior de Investigaciones Científicas-Universitat Pompeu Fabra), Barcelona Biomedical Research Park, Doctor Aiguader 88, Barcelona, Catalonia 08003, Spain.
authors: Marc
authors: M
authors: de Manuel
authors: Institut de Biologia Evolutiva (Consejo Superior de Investigaciones Científicas-Universitat Pompeu Fabra), Barcelona Biomedical Research Park, Doctor Aiguader 88, Barcelona, Catalonia 08003, Spain.
authors: Martin
authors: M
authors: Kuhlwilm
authors: Section for Computational and RNA Biology, Department of Biology, University of Copenhagen, 2200 Copenhagen, Denmark. Center for Zoo and Wild Animal Health, Copenhagen Zoo, 2000 Frederiksberg, Denmark.
authors: Peter
authors: P
authors: Frandsen
authors: Computational and Molecular Population Genetics, Institute of Ecology and Evolution, University of Berne, 3012 Berne, Switzerland. Swiss Institute of Bioinformatics, 1015 Lausanne, Switzerland.
authors: Vitor C
authors: VC
authors: Sousa
authors: Department of Genetics, University of Cambridge, Cambridge CB2 3EH, UK.
authors: Tariq
authors: T
authors: Desai
authors: Institut de Biologia Evolutiva (Consejo Superior de Investigaciones Científicas-Universitat Pompeu Fabra), Barcelona Biomedical Research Park, Doctor Aiguader 88, Barcelona, Catalonia 08003, Spain. Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton CB10 1SA, UK.
authors: Javier
authors: J
authors: Prado-Martinez
authors: Institut de Biologia Evolutiva (Consejo Superior de Investigaciones Científicas-Universitat Pompeu Fabra), Barcelona Biomedical Research Park, Doctor Aiguader 88, Barcelona, Catalonia 08003, Spain.
authors: Jessica
authors: J
authors: Hernandez-Rodriguez
authors: Computational and Molecular Population Genetics, Institute of Ecology and Evolution, University of Berne, 3012 Berne, Switzerland. Swiss Institute of Bioinformatics, 1015 Lausanne, Switzerland.
authors: Isabelle
authors: I
authors: Dupanloup
authors: National Centre for Genomic Analysis-Centre for Genomic Regulation, Barcelona Institute of Science and Technology, 08028 Barcelona, Spain. Universitat Pompeu Fabra, 08003 Barcelona, Spain.
authors: Oscar
authors: O
authors: Lao
authors: Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton CB10 1SA, UK. Institute of Molecular and Cell Biology, University of Tartu, Tartu 51010, Estonia.
authors: Pille
authors: P
authors: Hallast
authors: Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, 04103, Leipzig, Germany.
authors: Joshua M
authors: JM
authors: Schmidt
authors: Institut de Biologia Evolutiva (Consejo Superior de Investigaciones Científicas-Universitat Pompeu Fabra), Barcelona Biomedical Research Park, Doctor Aiguader 88, Barcelona, Catalonia 08003, Spain.
authors: José María
authors: JM
authors: Heredia-Genestar
authors: Department of Life Sciences and Biotechnology, University of Ferrara, 44121 Ferrara, Italy.
authors: Andrea
authors: A
authors: Benazzo
authors: Department of Life Sciences and Biotechnology, University of Ferrara, 44121 Ferrara, Italy.
authors: Guido
authors: G
authors: Barbujani
authors: Department of Human Genetics, University of Chicago, Chicago, IL 60637, USA.
authors: Benjamin M
authors: BM
authors: Peter
authors: Institut de Biologia Evolutiva (Consejo Superior de Investigaciones Científicas-Universitat Pompeu Fabra), Barcelona Biomedical Research Park, Doctor Aiguader 88, Barcelona, Catalonia 08003, Spain.
authors: Lukas F K
authors: LF
authors: Kuderna
authors: Institut de Biologia Evolutiva (Consejo Superior de Investigaciones Científicas-Universitat Pompeu Fabra), Barcelona Biomedical Research Park, Doctor Aiguader 88, Barcelona, Catalonia 08003, Spain.
authors: Ferran
authors: F
authors: Casals
authors: Department of Primatology, Max Planck Institute for Evolutionary Anthropology, 04103 Leipzig, Germany.
authors: Samuel
authors: S
authors: Angedakin
authors: Department of Primatology, Max Planck Institute for Evolutionary Anthropology, 04103 Leipzig, Germany.
authors: Mimi
authors: M
authors: Arandjelovic
authors: Department of Primatology, Max Planck Institute for Evolutionary Anthropology, 04103 Leipzig, Germany.
authors: Christophe
authors: C
authors: Boesch
authors: Department of Primatology, Max Planck Institute for Evolutionary Anthropology, 04103 Leipzig, Germany.
authors: Hjalmar
authors: H
authors: Kühl
authors: Department of Primatology, Max Planck Institute for Evolutionary Anthropology, 04103 Leipzig, Germany.
authors: Linda
authors: L
authors: Vigilant
authors: School of Human Evolution and Social Change and Institute of Human Origins, Arizona State University, Tempe, AZ 85287, USA.
authors: Kevin
authors: K
authors: Langergraber
authors: Department of Human Genetics, University of Chicago, Chicago, IL 60637, USA.
authors: John
authors: J
authors: Novembre
authors: National Centre for Genomic Analysis-Centre for Genomic Regulation, Barcelona Institute of Science and Technology, 08028 Barcelona, Spain.
authors: Marta
authors: M
authors: Gut
authors: National Centre for Genomic Analysis-Centre for Genomic Regulation, Barcelona Institute of Science and Technology, 08028 Barcelona, Spain.
authors: Ivo
authors: I
authors: Gut
authors: Institut de Biologia Evolutiva (Consejo Superior de Investigaciones Científicas-Universitat Pompeu Fabra), Barcelona Biomedical Research Park, Doctor Aiguader 88, Barcelona, Catalonia 08003, Spain. National Centre for Genomic Analysis-Centre for Genomic Regulation, Barcelona Institute of Science and Technology, 08028 Barcelona, Spain. Institucio Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, Catalonia 08010, Spain.
authors: Arcadi
authors: A
authors: Navarro
authors: Center for Zoo and Wild Animal Health, Copenhagen Zoo, 2000 Frederiksberg, Denmark.
authors: Frands
authors: F
authors: Carlsen
authors: Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, 04103, Leipzig, Germany.
authors: Aida M
authors: AM
authors: Andrés
authors: Section for Computational and RNA Biology, Department of Biology, University of Copenhagen, 2200 Copenhagen, Denmark.
authors: Hans R
authors: HR
authors: Siegismund
authors: Department of Genetics, University of Cambridge, Cambridge CB2 3EH, UK.
authors: Aylwyn
authors: A
authors: Scally
authors: Computational and Molecular Population Genetics, Institute of Ecology and Evolution, University of Berne, 3012 Berne, Switzerland. Swiss Institute of Bioinformatics, 1015 Lausanne, Switzerland.
authors: Laurent
authors: L
authors: Excoffier
authors: Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton CB10 1SA, UK.
authors: Chris
authors: C
authors: Tyler-Smith
authors: Department of Evolutionary Genetics, Max Planck Institute for Evolutionary Anthropology, 04103, Leipzig, Germany.
authors: Sergi
authors: S
authors: Castellano
authors: Wellcome Trust Sanger Institute, Wellcome Genome Campus, Hinxton CB10 1SA, UK.
authors: Yali
authors: Y
authors: Xue
authors: Center for Zoo and Wild Animal Health, Copenhagen Zoo, 2000 Frederiksberg, Denmark. ch@zoo.dk tomas.marques@upf.edu.
authors: Christina
authors: C
authors: Hvilsom
authors: Institut de Biologia Evolutiva (Consejo Superior de Investigaciones Científicas-Universitat Pompeu Fabra), Barcelona Biomedical Research Park, Doctor Aiguader 88, Barcelona, Catalonia 08003, Spain. National Centre for Genomic Analysis-Centre for Genomic Regulation, Barcelona Institute of Science and Technology, 08028 Barcelona, Spain. Institucio Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, Catalonia 08010, Spain. ch@zoo.dk tomas.marques@upf.edu.
authors: Tomas
authors: T
authors: Marques-Bonet
mesh_terms: D000818:Animals; D002163:Cameroon; D019143:Evolution, Molecular; D051456:Gene Flow; D014644:Genetic Variation; D016678:Genome; D023281:Genomics; D006239:Haplotypes; D009549:Nigeria; D019974:Pan paniscus / Q000235:genetics*; D002679:Pan troglodytes / Q000235:genetics*; D011153:Population