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Great ape genetic diversity and population history

Author

Listed:
  • Javier Prado-Martinez

    (Institut de Biologia Evolutiva, (CSIC-Universitat Pompeu Fabra), PRBB, Doctor Aiguader 88, Barcelona, Catalonia 08003, Spain)

  • Peter H. Sudmant

    (University of Washington, 3720 15th Avenue NE, Seattle, Washington 98195, USA)

  • Jeffrey M. Kidd

    (University of Michigan, 1241 E. Catherine Street, Ann Arbor, Michigan 48109, USA
    Stanford University, 300 Pasteur Drive, Lane L301, Stanford, California 94305, USA)

  • Heng Li

    (Harvard Medical School, Boston, 77 Avenue Louis Pasteur, Massachusetts 02115, USA)

  • Joanna L. Kelley

    (Stanford University, 300 Pasteur Drive, Lane L301, Stanford, California 94305, USA)

  • Belen Lorente-Galdos

    (Institut de Biologia Evolutiva, (CSIC-Universitat Pompeu Fabra), PRBB, Doctor Aiguader 88, Barcelona, Catalonia 08003, Spain)

  • Krishna R. Veeramah

    (Arizona Research Laboratories, University of Arizona, 1041 E. Lowell Street, Tucson, Arizona 85721, USA)

  • August E. Woerner

    (Arizona Research Laboratories, University of Arizona, 1041 E. Lowell Street, Tucson, Arizona 85721, USA)

  • Timothy D. O’Connor

    (University of Washington, 3720 15th Avenue NE, Seattle, Washington 98195, USA)

  • Gabriel Santpere

    (Institut de Biologia Evolutiva, (CSIC-Universitat Pompeu Fabra), PRBB, Doctor Aiguader 88, Barcelona, Catalonia 08003, Spain)

  • Alexander Cagan

    (Max Planck Institute for Evolutionary Anthropology, Deutscher Platz 6, Leipzig, 04103, Germany)

  • Christoph Theunert

    (Max Planck Institute for Evolutionary Anthropology, Deutscher Platz 6, Leipzig, 04103, Germany)

  • Ferran Casals

    (Institut de Biologia Evolutiva, (CSIC-Universitat Pompeu Fabra), PRBB, Doctor Aiguader 88, Barcelona, Catalonia 08003, Spain)

  • Hafid Laayouni

    (Institut de Biologia Evolutiva, (CSIC-Universitat Pompeu Fabra), PRBB, Doctor Aiguader 88, Barcelona, Catalonia 08003, Spain)

  • Kasper Munch

    (Bioinformatics Research Centre, Aarhus University, DK-8000 Aarhus C, Denmark)

  • Asger Hobolth

    (Bioinformatics Research Centre, Aarhus University, DK-8000 Aarhus C, Denmark)

  • Anders E. Halager

    (Bioinformatics Research Centre, Aarhus University, DK-8000 Aarhus C, Denmark)

  • Maika Malig

    (University of Washington, 3720 15th Avenue NE, Seattle, Washington 98195, USA)

  • Jessica Hernandez-Rodriguez

    (Institut de Biologia Evolutiva, (CSIC-Universitat Pompeu Fabra), PRBB, Doctor Aiguader 88, Barcelona, Catalonia 08003, Spain)

  • Irene Hernando-Herraez

    (Institut de Biologia Evolutiva, (CSIC-Universitat Pompeu Fabra), PRBB, Doctor Aiguader 88, Barcelona, Catalonia 08003, Spain)

  • Kay Prüfer

    (Max Planck Institute for Evolutionary Anthropology, Deutscher Platz 6, Leipzig, 04103, Germany)

  • Marc Pybus

    (Institut de Biologia Evolutiva, (CSIC-Universitat Pompeu Fabra), PRBB, Doctor Aiguader 88, Barcelona, Catalonia 08003, Spain)

  • Laurel Johnstone

    (Arizona Research Laboratories, University of Arizona, 1041 E. Lowell Street, Tucson, Arizona 85721, USA)

  • Michael Lachmann

    (Max Planck Institute for Evolutionary Anthropology, Deutscher Platz 6, Leipzig, 04103, Germany)

  • Can Alkan

    (Bilkent University, Faculty of Engineering, Ankara, 06800, Turkey)

  • Dorina Twigg

    (University of Michigan, 1241 E. Catherine Street, Ann Arbor, Michigan 48109, USA)

  • Natalia Petit

    (Institut de Biologia Evolutiva, (CSIC-Universitat Pompeu Fabra), PRBB, Doctor Aiguader 88, Barcelona, Catalonia 08003, Spain)

  • Carl Baker

    (University of Washington, 3720 15th Avenue NE, Seattle, Washington 98195, USA)

  • Fereydoun Hormozdiari

    (University of Washington, 3720 15th Avenue NE, Seattle, Washington 98195, USA)

  • Marcos Fernandez-Callejo

    (Institut de Biologia Evolutiva, (CSIC-Universitat Pompeu Fabra), PRBB, Doctor Aiguader 88, Barcelona, Catalonia 08003, Spain)

  • Marc Dabad

    (Institut de Biologia Evolutiva, (CSIC-Universitat Pompeu Fabra), PRBB, Doctor Aiguader 88, Barcelona, Catalonia 08003, Spain)

  • Michael L. Wilson

    (University of Minnesota)

  • Laurie Stevison

    (Institute for Human Genetics, University of California San Francisco)

  • Cristina Camprubí

    (Departament de Biologia Cel.lular, Fisiologia i Immunologia, Universitat Autònoma de Barcelona, Cerdanyola del Vallès, Catalonia 08193, Spain)

  • Tiago Carvalho

    (Institut de Biologia Evolutiva, (CSIC-Universitat Pompeu Fabra), PRBB, Doctor Aiguader 88, Barcelona, Catalonia 08003, Spain)

  • Aurora Ruiz-Herrera

    (Departament de Biologia Cel.lular, Fisiologia i Immunologia, Universitat Autònoma de Barcelona, Cerdanyola del Vallès, Catalonia 08193, Spain
    Institut de Biotecnologia i de Biomedicina. Universitat Autònoma de Barcelona, Cerdanyola del Vallès, Catalonia 08193, Spain)

  • Laura Vives

    (University of Washington, 3720 15th Avenue NE, Seattle, Washington 98195, USA)

  • Marta Mele

    (Institut de Biologia Evolutiva, (CSIC-Universitat Pompeu Fabra), PRBB, Doctor Aiguader 88, Barcelona, Catalonia 08003, Spain
    Present address: Centre for Genomic Regulation (CRG), C/Dr Aiguader, 88, 08003 Barcelona, Spain.)

  • Teresa Abello

    (Parc Zoològic de Barcelona, Barcelona, Catalonia 08003, Spain)

  • Ivanela Kondova

    (Biomedical Primate Research Centre, P.O. Box 3306, 2280 GH, Rijswijk, The Netherlands)

  • Ronald E. Bontrop

    (Biomedical Primate Research Centre, P.O. Box 3306, 2280 GH, Rijswijk, The Netherlands)

  • Anne Pusey

    (Duke University)

  • Felix Lankester

    (Limbe Wildlife Centre, BP 878, Limbe, Cameroon
    Paul G. Allen School for Global Animal Health, Washington State University)

  • John A. Kiyang

    (Limbe Wildlife Centre, BP 878, Limbe, Cameroon)

  • Richard A. Bergl

    (North Carolina Zoological Park)

  • Elizabeth Lonsdorf

    (Franklin and Marshall College)

  • Simon Myers

    (Oxford University, 1 South Parks Road, Oxford OX1 3TG, UK)

  • Mario Ventura

    (University of Bari, Bari 70126, Italy)

  • Pascal Gagneux

    (University of California San Diego)

  • David Comas

    (Institut de Biologia Evolutiva, (CSIC-Universitat Pompeu Fabra), PRBB, Doctor Aiguader 88, Barcelona, Catalonia 08003, Spain)

  • Hans Siegismund

    (Bioinformatics, University of Copenhagen, Copenhagen 2200, Denmark)

  • Julie Blanc

    (Centro Nacional de Análisis Genómico (CNAG), PCB, Barcelona, Catalonia 08028, Spain)

  • Lidia Agueda-Calpena

    (Centro Nacional de Análisis Genómico (CNAG), PCB, Barcelona, Catalonia 08028, Spain)

  • Marta Gut

    (Centro Nacional de Análisis Genómico (CNAG), PCB, Barcelona, Catalonia 08028, Spain)

  • Lucinda Fulton

    (Genome Sequencing Center, Washington University School of Medicine)

  • Sarah A. Tishkoff

    (Department of Biology and Genetics. University of Pennsylvania)

  • James C. Mullikin

    (National Institutes of Health Intramural Sequencing Center (NISC))

  • Richard K. Wilson

    (Genome Sequencing Center, Washington University School of Medicine)

  • Ivo G. Gut

    (Centro Nacional de Análisis Genómico (CNAG), PCB, Barcelona, Catalonia 08028, Spain)

  • Mary Katherine Gonder

    (Biological Sciences, University at Albany, State University of New York)

  • Oliver A. Ryder

    (San Diego Zoo’s Institute for Conservation Research, 15600 San Pasqual Valley Road, Escondido, California 92027, USA)

  • Beatrice H. Hahn

    (Perelman School of Medicine, University of Pennsylvania)

  • Arcadi Navarro

    (Institut de Biologia Evolutiva, (CSIC-Universitat Pompeu Fabra), PRBB, Doctor Aiguader 88, Barcelona, Catalonia 08003, Spain
    Instituto Nacional de Bioinformatica, UPF, Barcelona, Catalonia 08003, Spain
    Institució Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, Catalonia 08010, Spain)

  • Joshua M. Akey

    (University of Washington, 3720 15th Avenue NE, Seattle, Washington 98195, USA)

  • Jaume Bertranpetit

    (Institut de Biologia Evolutiva, (CSIC-Universitat Pompeu Fabra), PRBB, Doctor Aiguader 88, Barcelona, Catalonia 08003, Spain)

  • David Reich

    (Harvard Medical School, Boston, 77 Avenue Louis Pasteur, Massachusetts 02115, USA)

  • Thomas Mailund

    (Bioinformatics Research Centre, Aarhus University, DK-8000 Aarhus C, Denmark)

  • Mikkel H. Schierup

    (Bioinformatics Research Centre, Aarhus University, DK-8000 Aarhus C, Denmark
    Aarhus University)

  • Christina Hvilsom

    (Bioinformatics, University of Copenhagen, Copenhagen 2200, Denmark
    Copenhagen Zoo, DK 2000 Frederiksberg, Denmark)

  • Aida M. Andrés

    (Max Planck Institute for Evolutionary Anthropology, Deutscher Platz 6, Leipzig, 04103, Germany)

  • Jeffrey D. Wall

    (Institute for Human Genetics, University of California San Francisco)

  • Carlos D. Bustamante

    (Stanford University, 300 Pasteur Drive, Lane L301, Stanford, California 94305, USA)

  • Michael F. Hammer

    (Arizona Research Laboratories, University of Arizona, 1041 E. Lowell Street, Tucson, Arizona 85721, USA)

  • Evan E. Eichler

    (University of Washington, 3720 15th Avenue NE, Seattle, Washington 98195, USA
    Howard Hughes Medical Institute, 3720 15th Avenue NE)

  • Tomas Marques-Bonet

    (Institut de Biologia Evolutiva, (CSIC-Universitat Pompeu Fabra), PRBB, Doctor Aiguader 88, Barcelona, Catalonia 08003, Spain
    Institució Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, Catalonia 08010, Spain)

Abstract

High-coverage sequencing of 79 (wild and captive) individuals representing all six non-human great ape species has identified over 88 million single nucleotide polymorphisms providing insight into ape genetic variation and evolutionary history and enabling comparison with human genetic diversity.

Suggested Citation

  • Javier Prado-Martinez & Peter H. Sudmant & Jeffrey M. Kidd & Heng Li & Joanna L. Kelley & Belen Lorente-Galdos & Krishna R. Veeramah & August E. Woerner & Timothy D. O’Connor & Gabriel Santpere & Alex, 2013. "Great ape genetic diversity and population history," Nature, Nature, vol. 499(7459), pages 471-475, July.
    • Handle: RePEc:nat:nature:v:499:y:2013:i:7459:d:10.1038_nature12228
    DOI: 10.1038/nature12228
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    Cited by:

    1. Sook Wah Yee & Luis Ferrández-Peral & Pol Alentorn-Moron & Claudia Fontsere & Merve Ceylan & Megan L. Koleske & Niklas Handin & Virginia M. Artegoitia & Giovanni Lara & Huan-Chieh Chien & Xujia Zhou &, 2024. "Illuminating the function of the orphan transporter, SLC22A10, in humans and other primates," Nature Communications, Nature, vol. 15(1), pages 1-17, December.
    2. Liye Zhang & Neahga Leonard & Rick Passaro & Mai Sy Luan & Pham Tuyen & Le Thi Ngoc Han & Nguyen Huy Cam & Larry Vogelnest & Michael Lynch & Amanda E. Fine & Nguyen Thi Thanh Nga & Nguyen Long & Benja, 2024. "Genomic adaptation to small population size and saltwater consumption in the critically endangered Cat Ba langur," Nature Communications, Nature, vol. 15(1), pages 1-14, December.
    3. Emily E. Wroblewski & Lisbeth A. Guethlein & Aaron G. Anderson & Weimin Liu & Yingying Li & Sara E. Heisel & Andrew Jesse Connell & Jean-Bosco N. Ndjango & Paco Bertolani & John A. Hart & Terese B. Ha, 2023. "Malaria-driven adaptation of MHC class I in wild bonobo populations," Nature Communications, Nature, vol. 14(1), pages 1-11, December.
    4. Yirong Shi & Yiwei Niu & Peng Zhang & Huaxia Luo & Shuai Liu & Sijia Zhang & Jiajia Wang & Yanyan Li & Xinyue Liu & Tingrui Song & Tao Xu & Shunmin He, 2023. "Characterization of genome-wide STR variation in 6487 human genomes," Nature Communications, Nature, vol. 14(1), pages 1-18, December.

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