Copy number variation analysis in the great apes reveals species-specific patterns of structural variation
- Elodie Gazave1,10,11,
- Fleur Darré1,10,12,
- Carlos Morcillo-Suarez1,2,
- Natalia Petit-Marty1,
- Angel Carreño1,
- Urko M. Marigorta1,
- Oliver A. Ryder3,
- Antoine Blancher4,
- Mariano Rocchi5,
- Elena Bosch1,6,
- Carl Baker7,
- Tomàs Marquès-Bonet1,7,
- Evan E. Eichler7,8 and
- Arcadi Navarro1,2,9,13
- 1Institute of Evolutionary Biology (UPF-CSIC), PRBB, 08003 Barcelona, Spain;
- 2National Institute for Bioinformatics, Universitat Pompeu Fabra, 08003 Barcelona, Spain;
- 3San Diego Zoo, Institute for Conservation and Research, Escondido, California 92027-7000, USA;
- 4Laboratoire d'immunogénétique moléculaire, EA3034, Faculté de Médecine Purpan, Toulouse cedex 4, 31062 France;
- 5Department of Genetics and Microbiology, University of Bari, Bari 70125, Italy;
- 6CIBER en Epidemiologia y Salud Pública (CIBERESP), 08003 Barcelona, Spain;
- 7Department of Genome Sciences, University of Washington School of Medicine, Seattle, Washington 98195, USA;
- 8Howard Hughes Medical Institute, Seattle, Washington 98195, USA;
- 9Institució Catalana de Recerca i Estudis Avançats (ICREA), 08010 Barcelona, Catalonia, Spain
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↵10 These authors contributed equally to this work.
Abstract
Copy number variants (CNVs) are increasingly acknowledged as an important source of evolutionary novelties in the human lineage. However, our understanding of their significance is still hindered by the lack of primate CNV data. We performed intraspecific comparative genomic hybridizations to identify loci harboring copy number variants in each of the four great apes: bonobos, chimpanzees, gorillas, and orangutans. For the first time, we could analyze differences in CNV location and frequency in these four species, and compare them with human CNVs and primate segmental duplication (SD) maps. In addition, for bonobo and gorilla, patterns of CNV and nucleotide diversity were studied in the same individuals. We show that CNVs have been subject to different selective pressures in different lineages. Evidence for purifying selection is stronger in gorilla CNVs overlapping genes, while positive selection appears to have driven the fixation of structural variants in the orangutan lineage. In contrast, chimpanzees and bonobos present high levels of common structural polymorphism, which is indicative of relaxed purifying selection together with the higher mutation rates induced by the known burst of segmental duplication in the ancestor of the African apes. Indeed, the impact of the duplication burst is noticeable by the fact that bonobo and chimpanzee share more CNVs with gorilla than expected. Finally, we identified a number of interesting genomic regions that present high-frequency CNVs in all great apes, while containing only very rare or even pathogenic structural variants in humans.
Footnotes
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↵13 Corresponding author.
E-mail arcadi.navarro{at}upf.edu.
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[Supplemental material is available for this article.]
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Article published online before print. Article, supplemental material, and publication date are at http://www.genome.org/cgi/doi/10.1101/gr.117242.110.
- Received October 29, 2010.
- Accepted July 28, 2011.
- Copyright © 2011 by Cold Spring Harbor Laboratory Press
