Insights into hominid evolution from the gorilla genome sequence

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, Stephen H. Montgomery, Petra C. Schwalie, Y. Amy Tang, Michelle C. Ward, Yali Xue, Bryndis Yngvadottir, Can Alkan, Lars N. Andersen, Qasim Ayub, Edward V. Ball, Kathryn Beal, Brenda J. Bradley, Yuan Chen, Chris M. Clee, Stephen Fitzgerald, Tina A. Graves, Yong Gu, Paul Heath, Andreas Heger, Emre Karakoc, Anja Kolb-Kokocinski, Gavin K. Laird, Gerton Lunter, Stephen Meader, Matthew Mort, James C. Mullikin, Kasper Munch, Timothy D. O’Connor, Andrew D. Phillips, Javier Prado-Martinez, Anthony S. Rogers, Saba Sajjadian, Dominic Schmidt, Katy Shaw, Jared T. Simpson, Peter D. Stenson, Daniel J. Turner, Linda Vigilant, Albert J. Vilella, Weldon Whitener, Baoli Zhu, David N. Cooper, Pieter de Jong, Emmanouil T. Dermitzakis, Evan E. Eichler, Paul Flicek, Nick Goldman, Nicholas I. Mundy, Zemin Ning, Duncan T. Odom, Chris P. Ponting, Michael A. Quail, Oliver A. Ryder, Stephen M. Searle, Wesley C. Warren, Richard K. Wilson, Mikkel H. Schierup, Jane Rogers, Chris Tyler-Smith and Richard Durbin ()
Additional contact information
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
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
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
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
Yali Xue: Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus
Bryndis Yngvadottir: Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus
Can Alkan: University of Washington School of Medicine
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
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
Saba Sajjadian: University of Washington School of Medicine
Dominic Schmidt: University of Cambridge, Hutchison/MRC Research Centre, Hills Road, Cambridge CB2 0XZ, 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
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
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
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
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
Chris Tyler-Smith: Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus
Richard Durbin: Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus

Nature, 2012, vol. 483, issue 7388, 169-175

Abstract: 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.

Date: 2012
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DOI: 10.1038/nature10842

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