Refinement of primate copy number variation hotspots identifies candidate genomic regions evolving under positive selection

Background: Copy number variants (CNVs), defined as losses and gains of segments of genomic DNA, are a major source of genomic variation. Results: In this study, we identified over 2,000 human CNVs that overlap with orthologous chimpanzee or orthologous macaque CNVs. Of these, 170 CNVs overlap with both chimpanzee and macaque CNVs, and these were collapsed into 34 hotspot regions of CNV formation. Many of these hotspot regions of CNV formation are functionally relevant, with a bias toward genes involved in immune function, some of which were previously shown to evolve under balancing selection in humans. The genes in these primate CNV formation hotspots have significant differential expression levels between species and show evidence for positive selection, indicating that they have evolved under species-specific, directional selection. Conclusions: These hotspots of primate CNV formation provide a novel perspective on divergence and selective pressures acting on these genomic regions.