By Elizabeth Pennisi, Science Now, March 7, 2012
Ever since the human genome was sequenced a decade ago, researchers have dreamed about deciphering DNA from our three great ape cousins as well. Now the final remaining genome, that of the gorilla, is in hand, and it reveals interesting connections between us and them. Surprisingly, parts of our genome are more similar to the gorilla's than they are to the chimp's, and a few of the same genes previously thought key to our unique evolution are key to theirs, too.
Today there are four groups of great apes: chimps and bonobos, humans, gorillas, and orangutans. The genome of the chimp—our closest relative—was published in 2005; the orangutan sequence came out in early 2011. Now researchers have analyzed the DNA of a western lowland gorilla named Kamilah, who lives at the San Diego Zoo. In addition, they sequenced DNA from three other gorillas, including one eastern lowland gorilla, a rare species estimated at only 20,000 individuals. "It's essential to have all of the great ape genomes in order to understand the features of our own genome that make humans unique," says Gregory Wray, an evolutionary biologist at Duke University in Durham, North Carolina, who was not involved in the study. Adds paleoanthropologist David Begun of the University of Toronto in Canada: "It will allow us to begin to identify genetic changes specific to humans since our divergence from chimps."
Humans and apes are nearly identical in the vast majority of base pairs, or letters of the genetic code: The human genome is 1.37% different from the chimp's; 1.75% different from the gorilla's; and 3.4% different from the orangutan's, researchers from the Wellcome Trust Sanger Institute in Hinxton, U.K., and their colleagues report today in Nature. Although chimps and humans are indeed closest kin, 15% of the human genome more closely matches the gorilla's. Those genes' activity patterns are similar too, says Sanger evolutionary genomicist and lead author of the study Aylwyn Scally: "Some of our functional biology is more gorillalike than chimplike."
Moreover, with all the great ape genomes to compare, researchers are better able to assess when gorillas, chimps, and humans evolved—a matter of current debate. The molecular data indicate that humans and chimps went their separate ways only about 4.5 million years ago. But fossils that old and older look either ape or protohuman, so some paleontologists argue for a split as far back as 7 million years ago. Scally's group comes up with a date of about 6 million years ago, adjusting what would have been a more recent estimate by assuming that the mutation rate slowed over time in ape evolution. Another possible complication is that interbreeding may have occurred in the incipient species, slowing the actual separation of the DNA into distinct genomes, Scally points out. The authors suggest that ancestors of the gorilla separated from the human-chimp line about 10 million years ago, consistent with previous estimates.
"I am very happy to see the authors conclude [with] divergence dates that are consistent with both the fossil and genetic records," Begun says. "Usually one line of evidence is used to discredit the other."
The comparison with other sequenced genomes revealed that over the course of great ape evolution, about 90% of the genome has been influenced by natural selection. In each of the chimp, human, and gorilla, more than 500 genes have been evolving faster than expected, suggesting that they have changed in a way that confers some advantage. In the gorilla, one of the faster-evolving genes is involved in the hardening of skin, as happens in the knuckle pads for knuckle walking. Hearing genes that have evolved rapidly in humans also show accelerated evolution in gorillas. Some researchers had thought that those human genes might partly underlie language evolution, but that idea will need some rethinking now, Scally says. The researchers also saw parallel acceleration in the evolution of genes for brain development in gorillas and humans.
As part of the study, Scally and colleagues compared the genomes of eastern and western lowland gorillas and concluded that the species split up 0.5 million years ago but continued to interbreed a little after that. Moreover, many millennia ago, for some unknown reason, the eastern lowland gorilla population severely shrank, causing low genetic diversity and low numbers. Some researchers have suggested that the small population is due to recent human activity, but the new analysis suggests "it's a long-term thing," Scally says. "That's not to say that current human activity hasn't been a big threat."
Much more work remains to be done comparing the gorilla genome with other great apes. But already "it has provided a lot of important information regarding mechanisms and timing of speciation, gene evolution, [and] gene flow between [species and] subspecies," says gylcobiologist and great ape expert Ajit Varki of the University of California, San Diego, who was not involved in the study. "This information is, of course, of great interest to many investigators."