Orangutan DNA reveals deep family ties

WASHINGTON U.-ST. LOUIS (US) — The genome of the orangutan has remained remarkably stable through the ages, allowing it to stay healthy and adapt to changes in the environment.

The DNA of a Sumatran orangutan has been sequenced by an international team of scientists. With this genome as a reference, the scientists then sequenced the genomes of five additional Sumatran and five Bornean orangutans.

Some 13 million DNA variations were cataloged—a valuable resource that is expected to 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.

‘Details of their research are reported in the journal Nature.

The orangutan genome adds detail to the evolutionary tree and gives scientists insights into the unique aspects of human DNA that set man apart from the great apes, their closest relatives.

Human and orangutan genomes are 97 percent identical.

However, in a surprising discovery, the researchers found that at least in some ways, the orangutan genome evolved more slowly than the genomes of humans and chimpanzees, which are about 99 percent similar.

“The average orangutan is more diverse—genetically speaking—than the average human,” says Devin Locke, an evolutionary geneticist at Washington University in St. Louis and the study’s lead author.

“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.”

“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,” says senior author Richard Wilson, director of Washington University’s Genome Center, which led the project.

“This compares with chimpanzees and humans, both of which have experienced large-scale structural rearrangements of their genome that may have accelerated their evolution.”

A genome reads much like an instruction book for creating and sustaining a particular species. The chromosomes are the chapters and within every chapter are paragraphs, sentences, words, and single letters, which are like the individual bases of the DNA sequence.

“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.”

One possible clue to the lack of structural rearrangement in orangutan DNA is a profound lack of repetitive “Alu” elements. These short stretches of DNA make up about 10 percent of the human genome and can pop up in unexpected places to create new mutations or genetic rearrangements.

The human genome possesses about 5,000 human-specific Alus, while the chimp has about 2,000 chimp-specific Alus.

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

The new research shows that the Sumatran and Bornean orangutans diverged some 400,000 years ago. Earlier estimates had put the split at about 1 million years ago. Today, only about 50,000 Bornean and 7,000 Sumatran orangutans still live in the wild.

But in a finding that seems counterintuitive, the researchers found 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.”

Studies of orangutans are important because these great apes, in particular, are under intense ecological pressure. Their numbers continue to erode 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.”

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

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