title: Copy number variation analysis in the great apes reveals species-specific patterns of structural variation.
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.
authors.affiliation: Institute of Evolutionary Biology (UPF-CSIC), PRBB, 08003 Barcelona, Spain.
authors.forename: Elodie
authors.initials: E
authors.lastname: Gazave
authors.forename: Fleur
authors.initials: F
authors.lastname: Darré
authors.forename: Carlos
authors.initials: C
authors.lastname: Morcillo-Suarez
authors.forename: Natalia
authors.initials: N
authors.lastname: Petit-Marty
authors.forename: Angel
authors.initials: A
authors.lastname: Carreño
authors.forename: Urko M
authors.initials: UM
authors.lastname: Marigorta
authors.forename: Oliver A
authors.initials: OA
authors.lastname: Ryder
authors.forename: Antoine
authors.initials: A
authors.lastname: Blancher
authors.forename: Mariano
authors.initials: M
authors.lastname: Rocchi
authors.forename: Elena
authors.initials: E
authors.lastname: Bosch
authors.forename: Carl
authors.initials: C
authors.lastname: Baker
authors.forename: Tomàs
authors.initials: T
authors.lastname: Marquès-Bonet
authors.forename: Evan E
authors.initials: EE
authors.lastname: Eichler
authors.forename: Arcadi
authors.initials: A
authors.lastname: Navarro
mesh_terms: D000818:Animals; D022004:Chromosome Structures; D055028:Comparative Genomic Hybridization; D056915:DNA Copy Number Variations; D006071:Gorilla gorilla / Q000235:genetics*; D006801:Humans; D019974:Pan paniscus / Q000235:genetics*; D002679:Pan troglodytes / Q000235:genetics*; D010802:Phylogeny; D011110:Polymorphism, Genetic; D057079:Pongo / Q000235:genetics*; D056916:Segmental Duplications, Genomic