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Duplication Shaped Primate Genomes, Study Finds

NEW YORK (GenomeWeb News) – A flurry of segmental duplication events — including those in the genome of the common ancestor to humans and great apes — may have created a combination of genomic instability and flexibility that contributed to primate evolution, according to a new study appearing online today in Nature.

Researchers from the US, Spain, and Italy used whole-genome sequence detection to create segmental duplication maps of four different primate genomes: human, chimpanzee, orangutans, and macaques. Their results suggest that there were duplications in the orangutan, chimp, and human ancestor followed by a bout of duplications before the divergence of humans and chimps about 10 million years ago.

Such events may have produced regions in the human genome that are prone to reorganization. "Because of the architecture of the human genome, genetic material is constantly being added and deleted in certain regions," senior author Evan Eichler, a geneticist at the University of Washington, said in a statement. "These are really like volcanoes in the genome, blowing out pieces of DNA."

Humans, chimpanzees, orangutans, and macaques share a common ancestor going back roughly 25 million years ago. Macaques diverged from this tree first, followed by orangutans. The lineages leading to humans and chimpanzees share a much more recent common ancestor and diverged from one another about six million years ago.

Humans and great apes still share many genetic sequences and cytogenetic features, though the phenotypic differences between the groups are more pronounced. The hominid group also seems to be prone to gene loss and gain, although the rate of other genetic changes — such as single base pair changes and retrotransposon activity — appears to be slower than that observed in monkeys and some other animal groups.

Eichler and his team used whole-genome shotgun sequence detection to compare the duplication content in the macaque, orangutan, chimpanzee, and human genomes. By mapping sequence from all four species against the human reference assembly and pinpointing sites with more coverage depth and divergence, the researchers detected 73 million bases representing duplications in at least one of the species tested.

Their subsequent analysis suggests that a duplication event occurred after macaques, an Old World monkey, branched off from the primate tree about 25 million years ago. "We find that the ancestral branch leading to human and African great apes shows the most significant increase in duplication activity both in terms of base pairs and in terms of events," the authors noted.

The researchers also detected a burst of duplication events before the divergence of lineages leading to humans and chimpanzees — as single base substitutions and retrotransposon activity were waning. Consequently, the human and chimpanzee genomes share segmental duplications absent from the genomes of macaques or orangutans.

The duplication rate seems to have slowed down again after the chimp and human lineages diverged from one another, though, and just 10 million bases or so of duplicated sequence was human specific.

And the results suggest that ancient duplications in the genome increased the odds of having new duplications spring up nearby. "These observations emphasize that unique sequences flanking more ancient duplications have a much higher probability of segmental duplication and the duplication proves itself is not random," the authors wrote.

When the researchers looked at the duplications found only in the human genome, they found that these duplications included 39 partial human genes and 17 complete genes. Overall, the team reported that full-length hominid genes in duplicated regions appear to be under positive selection, suggesting they are advantageous in some way.

By delving into these regions, the researchers noted, it may be possible to uncover new insights into the development of uniquely human traits, including human cognition, communication, and disease.

"Geneticists have to figure out the genes in these regions and how variation leads to different aspects of the human condition such as disease. Then, they can pass that information on to neuroscientists and biochemists who can work out what these proteins are and what they do," Eichler said. "There is the possibility that these genes might be important for language or for aspects of cognition, though much more work has to be done before we'll be able to say that for sure."

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