The orangutan, the most sedentary of the great apes, has unusually stable DNA, too. Researchers have just completed the sequencing of the entire genome of our orange-haired relative, and they have found to their surprise that its DNA has changed much less dramatically over time than has that of humans or chimpanzees. "The orangutan is the odd man out," says Devin Locke, a structural geneticist at Washington University School of Medicine in St. Louis, Missouri, who headed the orangutan sequencing project.
The orangutan genome had one other big surprise. Locke and colleagues sequenced six Sumatran and five Bornean orangutans, which are classified as different species. The apes have been physically separated for at least 21,000 years—the last time land bridges between the two islands existed—and earlier studies estimated that they became distinct species more than 1 million years ago. But the new analysis, reported online today in Nature, rewrites history: it appears they parted ways just 400,000 years ago. "Most previous studies used small sets of markers and a limited amount of DNA sequence," says Locke. "The statistical power is so much greater when you have the whole genome at your disposal."
The orangutan now joins chimpanzees and humans as the third great ape to have its genome sequenced. "The orangutan genome is a wonderful resource," says evolutionary geneticist Svante Pääbo of the Max Planck Institute for Evolutionary Anthropology in Leipzig, Germany. "It will help clarify how each part of human and African ape genomes are related to each other and evolved."
Such insights are already coming in. Orangutans originated some 12 million to 16 million years ago, giving their genomes much more time to evolve than those of humans and chimpanzees, which split into their own lineages 5 million to 6 million years ago. But a comparison of the three genomes shows that humans and chimpanzees lose or gain new genes at twice the rate of orangutans.
The reason may have to do with stretches of DNA called retrotransposons. These key drivers of evolution jump around the genome, creating new genes, crippling existing ones, or altering gene regulation. The new data reveal that common retrotransposons known as Alu elements have moved around the orangutan genome much less than they have in the human and chimpanzee genomes. "I don't want to say that [Alu retrotransposition events] are shut off in orangutans, but they've been suppressed," says Locke.
The researchers also discovered that, over time, the structure of orangutan chromosomes has changed little, which may be linked to the Alu element finding. Other researchers have suggested that the robust structural variation in humans and chimps may have spurred increased intelligence. But Locke notes that orangutans are also highly intelligent. "If orangutans have had very little structural variation, maybe this decouples structural variation from intelligence," he says.
A separate but related study published today in Genome Research reports yet another unexpected finding from a comparison of the three great ape genomes. A team led by Mikkel H. Schierup and Thomas Mailund of Aarhus University in Denmark (both co-authors of the Nature report) discovered that some regions of the human genome more closely resemble the orangutan than the chimpanzee. This reflects the fact that at the time humans split off from a common ancestor with chimps, both species had the same ancestral orangutan DNA. But humans and chimpanzees have evolved separately for millions of years. In the process, chimps for mysterious reasons lost some orangutan DNA that humans retained.
More surprises are sure to come as researchers compare the genomes of even more apes. Projects to sequence the other two great apes, gorillas and bonobos, are under way.