A new study of copy number variation in chimpanzee genome

Both Razib and John Lynch, of Science Blogs, have pulled a fast one on us about an interesting new study published recently in PNAS. The paper is titled, “Hotspots for copy number variation in chimpanzees and humans ” and it comes from some people at ASU’s School of Human Evolution and Social Change. The abstract reads,

“Copy number variation is surprisingly common among humans and can be involved in phenotypic diversity and variable susceptibility to complex diseases, but little is known of the extent of copy number variation in nonhuman primates. We have used two array-based comparative genomic hybridization platforms to identify a total of 355 copy number variants (CNVs) in the genomes of 20 wild-born chimpanzees (Pan troglodytes) and have compared the identified chimpanzee CNVs to known human CNVs from previous studies. Many CNVs were observed in the corresponding regions in both chimpanzees and humans; especially those CNVs of higher frequency. Strikingly, these loci are enriched 20-fold for ancestral segmental duplications, which may facilitate CNV formation through nonallelic homologous recombination mechanisms. Therefore, some of these regions may be unstable “hotspots ” for the genesis of copy number variation, with recurrent duplications and deletions occurring across and within species. “

Which basically means that “hotspots ” are most likely a key feature in the evolution of genetically determined morphology and behavioral characteristics of chimps. Hotspots are places in the genome of an organism that show signs of lots of work, like duplications and deletions. In studying the chimpanzee genome, Perry et. al., has found these hotspots but they call them a super scientific term also known as copy number variants. Here’s what George Perry has to say about his findings,

“We found that chimpanzees have many copy number variants, [actually… ] 355 copy number variants among the genomes of these 20 unrelated chimpanzees… and found that the overall chimpanzee genetic diversity may be more extensive than was previously thought — duplications or deletions of large segments of DNA — in the same regions of the genome as do humans. What this suggests is that some regions of the genomes are inherently unstable in both humans and chimpanzees… This is a relatively new area of research and this is the first time this has been investigated on a genome-wide scale in a population sample of nonhuman primates. These copy number variants may be very significant from an evolutionary perspective, and they’re important to study and understand.

We talk about genetic diseases and cures, but first you have to find out that genetic differences such as copy number variants are there. And then you can study what they’re involved in and what they mean from a morphological variation and disease standpoint.

Ultimately, we can use information about within-a-species variation to identify unusual patterns between species. This may highlight copy number differences between humans and chimpanzees that were somehow involved in the evolution of human-specific traits. This study is an important first step, not the ultimate answer, but an exciting first step in studying the evolution of copy number variant regions and their downstream implications for disease and phenotypic variation. “

I will try to get my grubby hands on the article tomorrow, where I have access potentially to PNAS.

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