January 26, 2011

Researchers Perform Genomic Analysis Of Orangutans

According to a recently published genome analysis of orangutans, the two populations of the creatures in the forests of Borneo and Sumatra have similarities and differences between the Great Ape family and their human cousins.

"As more information about primates becomes known, we find additional genes for which there is positive selection," said Dr. Kim Worley, associate professor in the Baylor College of Medicine Human Genome Sequencing Center and an author of the report that appears in the recent issue of the journal Nature. 

The study includes a "deep" or intricately defined genome sequence of a Sumatran orangutan and less detailed genomic studies of five Sumatran and five Bornean orangutan genomes.

The scientists reveal intriguing clues about the evolution of great apes, including humans, and showcase the immense genetic diversity across and within Sumatran and Bornea orangutans. 

"The average orangutan is more diverse "“ genetically speaking "“ than the average human," lead author Devin Locke, an evolutionary geneticist at Washington University's Genome Center, said in a statement. "We found deep diversity in both Bornean and Sumatran orangutans, but it's unclear whether this level of diversity can be maintained in light of continued widespread deforestation."

The scientists catalogued about 13 million DNA variations in the orangutans.  This resource could help conservationists assess the genetic diversity of orangutan populations both in the wild and in captivity and help set priorities for aiding subpopulations based on their genetic health.

The researchers found that human and orangutan genomes are 97 percent identical.

However, the team also found that at least in some ways, the orangutan genome evolved slower than the genomes of humans and chimpanzees, which are about 99 percent similar.

"In terms of evolution, the orangutan genome is quite special among great apes in that it has been extraordinarily stable over the past 15 million years," senior author Richard K. Wilson, PhD, director of Washington University's Genome Center, which led the project, said in a press release "This compares with chimpanzees and humans, both of which have experienced large-scale structural rearrangements of their genome that may have accelerated their evolution."

The genome reads like an instruction book for creating and sustaining a particular species.

"If you are editing a book on your computer, you can highlight a paragraph and copy and paste it, delete it or invert it," Wilson explains. "Duplications, deletions and inversions of DNA are types of structural variations. When we look at the genomes of humans and chimps, we see an acceleration of structural changes over the course of evolutionary history. But for whatever reason, orangutans did not participate in that acceleration, and that was a surprise."

According to the researchers, one clue to the lack of structural rearrangement in orangutan DNA is a profound lack of repetitive "Alu" elements.

These DNA segments make up about 10 percent of the human genome and can pop up in unexpected places to create new mutations or genetic rearrangements.

"In the orangutan genome, we found only 250 new Alu copies over a 15 million-year time span," Locke says. "This is the closest thing we have to a smoking gun that may explain the structural stability in the orangutan genome."

The initial Sumatran orangutan genome was sequenced by using legacy technology. 

The National Human Genome Research Institute, the National Science Foundation and other organizations funded the project.

According to the new research, Sumatran and Bornean orangutans diverged about 400,000 years ago.  Only bout 50,000 Bornean and 7,000 Sumatran orangutans still live in the wild today.

The team found that the smaller population of Sumatran orangutans is genetically more diverse than their Bornean cousins.

"It's quite a mystery how Sumatran orangutans obtained this genetic diversity or whether there has been cleansing of diversity in the Borneans," Locke explains. "We can begin to search for answers using the catalog of genetic variation we developed."

The population of orangutans continues to drop as humans encroach further on their habitat.

"Orangutans spend more than 95 percent of their time in the trees," Locke says. "They travel through the trees, nest in trees and forage for food in trees. But all the genetic diversity in the world can't save them in the wild if their habitat is destroyed."


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