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Insights into hominid evolution from the gorilla genome sequence

Author

Listed:
  • Aylwyn Scally

    (Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus)

  • Julien Y. Dutheil

    (Bioinformatics Research Center, Aarhus University, C.F. Møllers Allé 8, 8000 Aarhus C, Denmark
    Present addresses: Institut des Sciences de l'Évolution – Montpellier (I.S.E.-M.), Université de Montpellier II – CC 064, 34095 Montpellier Cedex 05, France (J.Y.D); Centre for Genomic Research, Institute of Integrative Biology, University of Liverpool, Crown Street, Liverpool L69 7ZB, UK (I.G.); Division of Biological Anthropology, University of Cambridge, Fitzwilliam Street, Cambridge CB2 1QH, UK (B.Y.); EASIH, University of Cambridge, Addenbrooke’s Hospital, Cambridge CB2 0QQ, UK (A.S.R.); Oxford Nanopore Technologies, Edmund Cartwright House, 4 Robert Robinson Avenue, Oxford OX4 4GA, UK (D.J.T.); Institute of Microbiology, Chinese Academy of Sciences, Datun Road, Chaoyang District, Beijing 100101, China (B.Z.); The Genome Analysis Centre, Norwich Research Park, Norwich NR4 7UH, UK (J.R.).)

  • LaDeana W. Hillier

    (University of Washington School of Medicine)

  • Gregory E. Jordan

    (European Bioinformatics Institute, Wellcome Trust Genome Campus)

  • Ian Goodhead

    (Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus
    Present addresses: Institut des Sciences de l'Évolution – Montpellier (I.S.E.-M.), Université de Montpellier II – CC 064, 34095 Montpellier Cedex 05, France (J.Y.D); Centre for Genomic Research, Institute of Integrative Biology, University of Liverpool, Crown Street, Liverpool L69 7ZB, UK (I.G.); Division of Biological Anthropology, University of Cambridge, Fitzwilliam Street, Cambridge CB2 1QH, UK (B.Y.); EASIH, University of Cambridge, Addenbrooke’s Hospital, Cambridge CB2 0QQ, UK (A.S.R.); Oxford Nanopore Technologies, Edmund Cartwright House, 4 Robert Robinson Avenue, Oxford OX4 4GA, UK (D.J.T.); Institute of Microbiology, Chinese Academy of Sciences, Datun Road, Chaoyang District, Beijing 100101, China (B.Z.); The Genome Analysis Centre, Norwich Research Park, Norwich NR4 7UH, UK (J.R.).)

  • Javier Herrero

    (European Bioinformatics Institute, Wellcome Trust Genome Campus)

  • Asger Hobolth

    (Bioinformatics Research Center, Aarhus University, C.F. Møllers Allé 8, 8000 Aarhus C, Denmark)

  • Tuuli Lappalainen

    (University of Geneva Medical School, Rue Michel-Servet 1, 1211 Geneva 4, Switzerland)

  • Thomas Mailund

    (Bioinformatics Research Center, Aarhus University, C.F. Møllers Allé 8, 8000 Aarhus C, Denmark)

  • Tomas Marques-Bonet

    (University of Washington School of Medicine
    Institut de Biologia Evolutiva (UPF-CSIC)
    Institucio Catalana de Recerca i Estudis Avançats)

  • Shane McCarthy

    (Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus)

  • Stephen H. Montgomery

    (University of Cambridge, Downing Street, Cambridge CB2 3EJ, UK)

  • Petra C. Schwalie

    (European Bioinformatics Institute, Wellcome Trust Genome Campus)

  • Y. Amy Tang

    (Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus)

  • Michelle C. Ward

    (University of Cambridge, Hutchison/MRC Research Centre, Hills Road, Cambridge CB2 0XZ, UK
    Cancer Research UK, Cambridge Research Institute, Li Ka Shing Centre, Robinson Way, Cambridge CB2 0RE, UK)

  • Yali Xue

    (Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus)

  • Bryndis Yngvadottir

    (Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus
    Present addresses: Institut des Sciences de l'Évolution – Montpellier (I.S.E.-M.), Université de Montpellier II – CC 064, 34095 Montpellier Cedex 05, France (J.Y.D); Centre for Genomic Research, Institute of Integrative Biology, University of Liverpool, Crown Street, Liverpool L69 7ZB, UK (I.G.); Division of Biological Anthropology, University of Cambridge, Fitzwilliam Street, Cambridge CB2 1QH, UK (B.Y.); EASIH, University of Cambridge, Addenbrooke’s Hospital, Cambridge CB2 0QQ, UK (A.S.R.); Oxford Nanopore Technologies, Edmund Cartwright House, 4 Robert Robinson Avenue, Oxford OX4 4GA, UK (D.J.T.); Institute of Microbiology, Chinese Academy of Sciences, Datun Road, Chaoyang District, Beijing 100101, China (B.Z.); The Genome Analysis Centre, Norwich Research Park, Norwich NR4 7UH, UK (J.R.).)

  • Can Alkan

    (University of Washington School of Medicine
    Howard Hughes Medical Institute, University of Washington)

  • Lars N. Andersen

    (Bioinformatics Research Center, Aarhus University, C.F. Møllers Allé 8, 8000 Aarhus C, Denmark)

  • Qasim Ayub

    (Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus)

  • Edward V. Ball

    (Institute of Medical Genetics, Cardiff University)

  • Kathryn Beal

    (European Bioinformatics Institute, Wellcome Trust Genome Campus)

  • Brenda J. Bradley

    (University of Cambridge, Downing Street, Cambridge CB2 3EJ, UK
    Yale University, 10 Sachem Street, New Haven, Connecticut 06511, USA)

  • Yuan Chen

    (Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus)

  • Chris M. Clee

    (Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus)

  • Stephen Fitzgerald

    (European Bioinformatics Institute, Wellcome Trust Genome Campus)

  • Tina A. Graves

    (The Genome Institute at Washington University, Washington University School of Medicine)

  • Yong Gu

    (Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus)

  • Paul Heath

    (Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus)

  • Andreas Heger

    (MRC Functional Genomics Unit, University of Oxford, Anatomy and Genetics, South Parks Road, Oxford OX1 3QX, UK)

  • Emre Karakoc

    (University of Washington School of Medicine)

  • Anja Kolb-Kokocinski

    (Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus)

  • Gavin K. Laird

    (Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus)

  • Gerton Lunter

    (Wellcome Trust Centre for Human Genetics)

  • Stephen Meader

    (MRC Functional Genomics Unit, University of Oxford, Anatomy and Genetics, South Parks Road, Oxford OX1 3QX, UK)

  • Matthew Mort

    (Institute of Medical Genetics, Cardiff University)

  • James C. Mullikin

    (Comparative Genomics Unit, Genome Technology Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland, 20892-2152, USA)

  • Kasper Munch

    (Bioinformatics Research Center, Aarhus University, C.F. Møllers Allé 8, 8000 Aarhus C, Denmark)

  • Timothy D. O’Connor

    (University of Cambridge, Downing Street, Cambridge CB2 3EJ, UK)

  • Andrew D. Phillips

    (Institute of Medical Genetics, Cardiff University)

  • Javier Prado-Martinez

    (Institut de Biologia Evolutiva (UPF-CSIC))

  • Anthony S. Rogers

    (Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus
    Present addresses: Institut des Sciences de l'Évolution – Montpellier (I.S.E.-M.), Université de Montpellier II – CC 064, 34095 Montpellier Cedex 05, France (J.Y.D); Centre for Genomic Research, Institute of Integrative Biology, University of Liverpool, Crown Street, Liverpool L69 7ZB, UK (I.G.); Division of Biological Anthropology, University of Cambridge, Fitzwilliam Street, Cambridge CB2 1QH, UK (B.Y.); EASIH, University of Cambridge, Addenbrooke’s Hospital, Cambridge CB2 0QQ, UK (A.S.R.); Oxford Nanopore Technologies, Edmund Cartwright House, 4 Robert Robinson Avenue, Oxford OX4 4GA, UK (D.J.T.); Institute of Microbiology, Chinese Academy of Sciences, Datun Road, Chaoyang District, Beijing 100101, China (B.Z.); The Genome Analysis Centre, Norwich Research Park, Norwich NR4 7UH, UK (J.R.).)

  • Saba Sajjadian

    (University of Washington School of Medicine)

  • Dominic Schmidt

    (University of Cambridge, Hutchison/MRC Research Centre, Hills Road, Cambridge CB2 0XZ, UK
    Cancer Research UK, Cambridge Research Institute, Li Ka Shing Centre, Robinson Way, Cambridge CB2 0RE, UK)

  • Katy Shaw

    (Institute of Medical Genetics, Cardiff University)

  • Jared T. Simpson

    (Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus)

  • Peter D. Stenson

    (Institute of Medical Genetics, Cardiff University)

  • Daniel J. Turner

    (Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus
    Present addresses: Institut des Sciences de l'Évolution – Montpellier (I.S.E.-M.), Université de Montpellier II – CC 064, 34095 Montpellier Cedex 05, France (J.Y.D); Centre for Genomic Research, Institute of Integrative Biology, University of Liverpool, Crown Street, Liverpool L69 7ZB, UK (I.G.); Division of Biological Anthropology, University of Cambridge, Fitzwilliam Street, Cambridge CB2 1QH, UK (B.Y.); EASIH, University of Cambridge, Addenbrooke’s Hospital, Cambridge CB2 0QQ, UK (A.S.R.); Oxford Nanopore Technologies, Edmund Cartwright House, 4 Robert Robinson Avenue, Oxford OX4 4GA, UK (D.J.T.); Institute of Microbiology, Chinese Academy of Sciences, Datun Road, Chaoyang District, Beijing 100101, China (B.Z.); The Genome Analysis Centre, Norwich Research Park, Norwich NR4 7UH, UK (J.R.).)

  • Linda Vigilant

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

  • Albert J. Vilella

    (European Bioinformatics Institute, Wellcome Trust Genome Campus)

  • Weldon Whitener

    (Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus)

  • Baoli Zhu

    (Children’s Hospital Oakland Research Institute
    Present addresses: Institut des Sciences de l'Évolution – Montpellier (I.S.E.-M.), Université de Montpellier II – CC 064, 34095 Montpellier Cedex 05, France (J.Y.D); Centre for Genomic Research, Institute of Integrative Biology, University of Liverpool, Crown Street, Liverpool L69 7ZB, UK (I.G.); Division of Biological Anthropology, University of Cambridge, Fitzwilliam Street, Cambridge CB2 1QH, UK (B.Y.); EASIH, University of Cambridge, Addenbrooke’s Hospital, Cambridge CB2 0QQ, UK (A.S.R.); Oxford Nanopore Technologies, Edmund Cartwright House, 4 Robert Robinson Avenue, Oxford OX4 4GA, UK (D.J.T.); Institute of Microbiology, Chinese Academy of Sciences, Datun Road, Chaoyang District, Beijing 100101, China (B.Z.); The Genome Analysis Centre, Norwich Research Park, Norwich NR4 7UH, UK (J.R.).)

  • David N. Cooper

    (Institute of Medical Genetics, Cardiff University)

  • Pieter de Jong

    (Children’s Hospital Oakland Research Institute)

  • Emmanouil T. Dermitzakis

    (University of Geneva Medical School, Rue Michel-Servet 1, 1211 Geneva 4, Switzerland)

  • Evan E. Eichler

    (University of Washington School of Medicine
    Howard Hughes Medical Institute, University of Washington)

  • Paul Flicek

    (European Bioinformatics Institute, Wellcome Trust Genome Campus)

  • Nick Goldman

    (European Bioinformatics Institute, Wellcome Trust Genome Campus)

  • Nicholas I. Mundy

    (University of Cambridge, Downing Street, Cambridge CB2 3EJ, UK)

  • Zemin Ning

    (Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus)

  • Duncan T. Odom

    (Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus
    University of Cambridge, Hutchison/MRC Research Centre, Hills Road, Cambridge CB2 0XZ, UK
    Cancer Research UK, Cambridge Research Institute, Li Ka Shing Centre, Robinson Way, Cambridge CB2 0RE, UK)

  • Chris P. Ponting

    (MRC Functional Genomics Unit, University of Oxford, Anatomy and Genetics, South Parks Road, Oxford OX1 3QX, UK)

  • Michael A. Quail

    (Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus)

  • Oliver A. Ryder

    (San Diego Zoo’s Institute for Conservation Research)

  • Stephen M. Searle

    (Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus)

  • Wesley C. Warren

    (The Genome Institute at Washington University, Washington University School of Medicine)

  • Richard K. Wilson

    (The Genome Institute at Washington University, Washington University School of Medicine)

  • Mikkel H. Schierup

    (Bioinformatics Research Center, Aarhus University, C.F. Møllers Allé 8, 8000 Aarhus C, Denmark)

  • Jane Rogers

    (Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus
    Present addresses: Institut des Sciences de l'Évolution – Montpellier (I.S.E.-M.), Université de Montpellier II – CC 064, 34095 Montpellier Cedex 05, France (J.Y.D); Centre for Genomic Research, Institute of Integrative Biology, University of Liverpool, Crown Street, Liverpool L69 7ZB, UK (I.G.); Division of Biological Anthropology, University of Cambridge, Fitzwilliam Street, Cambridge CB2 1QH, UK (B.Y.); EASIH, University of Cambridge, Addenbrooke’s Hospital, Cambridge CB2 0QQ, UK (A.S.R.); Oxford Nanopore Technologies, Edmund Cartwright House, 4 Robert Robinson Avenue, Oxford OX4 4GA, UK (D.J.T.); Institute of Microbiology, Chinese Academy of Sciences, Datun Road, Chaoyang District, Beijing 100101, China (B.Z.); The Genome Analysis Centre, Norwich Research Park, Norwich NR4 7UH, UK (J.R.).)

  • Chris Tyler-Smith

    (Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus)

  • Richard Durbin

    (Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus)

Abstract

Gorillas are humans’ closest living relatives after chimpanzees, and are of comparable importance for the study of human origins and evolution. Here we present the assembly and analysis of a genome sequence for the western lowland gorilla, and compare the whole genomes of all extant great ape genera. We propose a synthesis of genetic and fossil evidence consistent with placing the human–chimpanzee and human–chimpanzee–gorilla speciation events at approximately 6 and 10 million years ago. In 30% of the genome, gorilla is closer to human or chimpanzee than the latter are to each other; this is rarer around coding genes, indicating pervasive selection throughout great ape evolution, and has functional consequences in gene expression. A comparison of protein coding genes reveals approximately 500 genes showing accelerated evolution on each of the gorilla, human and chimpanzee lineages, and evidence for parallel acceleration, particularly of genes involved in hearing. We also compare the western and eastern gorilla species, estimating an average sequence divergence time 1.75 million years ago, but with evidence for more recent genetic exchange and a population bottleneck in the eastern species. The use of the genome sequence in these and future analyses will promote a deeper understanding of great ape biology and evolution.

Suggested Citation

  • Aylwyn Scally & Julien Y. Dutheil & LaDeana W. Hillier & Gregory E. Jordan & Ian Goodhead & Javier Herrero & Asger Hobolth & Tuuli Lappalainen & Thomas Mailund & Tomas Marques-Bonet & Shane McCarthy &, 2012. "Insights into hominid evolution from the gorilla genome sequence," Nature, Nature, vol. 483(7388), pages 169-175, March.
    • Handle: RePEc:nat:nature:v:483:y:2012:i:7388:d:10.1038_nature10842
    DOI: 10.1038/nature10842
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    Cited by:

    1. M. C. Rühlemann & C. Bang & J. F. Gogarten & B. M. Hermes & M. Groussin & S. Waschina & M. Poyet & M. Ulrich & C. Akoua-Koffi & T. Deschner & J. J. Muyembe-Tamfum & M. M. Robbins & M. Surbeck & R. M. , 2024. "Functional host-specific adaptation of the intestinal microbiome in hominids," Nature Communications, Nature, vol. 15(1), pages 1-17, December.

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