Copy number variation and evolution in humans and chimpanzees

  1. George H. Perry1,2,6,
  2. Fengtang Yang3,
  3. Tomas Marques-Bonet4,
  4. Carly Murphy2,
  5. Tomas Fitzgerald3,
  6. Arthur S. Lee2,
  7. Courtney Hyland2,
  8. Anne C. Stone1,
  9. Matthew E. Hurles3,
  10. Chris Tyler-Smith3,
  11. Evan E. Eichler4,
  12. Nigel P. Carter3,
  13. Charles Lee2,5, and
  14. Richard Redon3,6,7
  1. 1 School of Human Evolution & Social Change, Arizona State University, Tempe, Arizona 85287, USA;
  2. 2 Department of Pathology, Brigham & Women’s Hospital, Boston, Massachusetts 02115, USA;
  3. 3 Wellcome Trust Sanger Institute, Hinxton, Cambridge CB10 1SA, United Kingdom;
  4. 4 Department of Genome Sciences, University of Washington School of Medicine and the Howard Hughes Medical Institute, Seattle, Washington 98195, USA;
  5. 5 Harvard Medical School, Boston, Massachusetts 02115, USA

  1. ↵6 These authors contributed equally to this work.

Abstract

Copy number variants (CNVs) underlie many aspects of human phenotypic diversity and provide the raw material for gene duplication and gene family expansion. However, our understanding of their evolutionary significance remains limited. We performed comparative genomic hybridization on a single human microarray platform to identify CNVs among the genomes of 30 humans and 30 chimpanzees as well as fixed copy number differences between species. We found that human and chimpanzee CNVs occur in orthologous genomic regions far more often than expected by chance and are strongly associated with the presence of highly homologous intrachromosomal segmental duplications. By adapting population genetic analyses for use with copy number data, we identified functional categories of genes that have likely evolved under purifying or positive selection for copy number changes. In particular, duplications and deletions of genes with inflammatory response and cell proliferation functions may have been fixed by positive selection and involved in the adaptive phenotypic differentiation of humans and chimpanzees.

Footnotes

| Table of Contents

This Article

  1. Published in Advance September 4, 2008, doi: 10.1101/gr.082016.108 Genome Res. 18: 1698-1710 Copyright © 2008, Cold Spring Harbor Laboratory Press

Article Category

Share

Preprint Server



Current Issue

  1. February 2024, 34 (2)
  1. Current Issue
  1. Alert me to new issues of Genome Research