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A chimp

This chimp has bonobo DNA in its genome.

Kevin Langergraber

Chimps and bonobos had flings—and swapped genes—in the past

Tens of thousands of years ago, modern humans slept around with Neandertals and swapped some genes. Now, it turns out one of our closest living relatives, chimpanzees, also dallied with another species. New research reveals that chimps mixed it up with bonobos at least twice during the 2 million years since these great apes started evolving their own identities. Although it’s not yet clear whether the acquired genes were ultimately beneficial or harmful, the finding strengthens the idea that such cross-species mating played an important role in the evolution of the great apes.

"What they found was really cool," says Michael Arnold, an evolutionary biologist at the University of Georgia in Athens who was not involved in the work. "It adds to a growing body of work showing that species exchange genes," says Peter Grant, an evolutionary biologist from Princeton University who was also not involved with the study.

Bonobos (Pan paniscus) live in Democratic Republic of the Congo, just across the Congo River from their closest living relatives, the chimpanzees (P. troglodytes), who are spread out between western and central Africa. (Chimps are bigger and have a male-dominated society instead of a female-dominated one.) Populations of both apes are shrinking because of deforestation and hunting. Chimps now live in fragmented populations that have become different enough to qualify as four subspecies; the western, eastern, and Nigeria-Cameroon chimpanzees are much less common than the central chimpanzees. Before the 1930s, bonobos were considered a subspecies of chimp as well and were called pygmy chimps, but researchers decided based on physical differences that these smaller apes are distinctive enough to warrant separate species status.

Although in the classical view species are not supposed to be able to interbreed successfully, that was and still is not always true of bonobos and chimpanzees, says Christina Hvilsom, a conservation geneticist at the Copenhagen Zoo. She and her colleagues uncovered this liaison when they examined the complete genomes of 75 chimps and bonobos from 10 African countries. They had been comparing as many great ape genomes as possible in order to help conserve the animals: They sought genetic differences that could help pinpoint the geographic origin of a confiscated ape and so identify where illegal hunting occurred. But Hvilsom was also intrigued by the discovery in 2010 of Neandertal DNA in the human genome. She wanted to see whether humans' closest relatives also dallied beyond species boundaries.

Using the same tests that uncovered hybridization among humans, she and her colleagues determined that 1% of the central chimpanzee’s genome is bonobo DNA. The genetic analysis indicates that this inbreeding happened during two time periods: 1.5 million years ago bonobo ancestors mixed with the ancestor of the eastern and central chimps. Then, just 200,000 years ago, central chimps got another boost of bonobo genes, the team reports today in Science. In contrast, the western chimp subspecies has no bonobo DNA, the researchers note, suggesting that only those chimps living close to the Congo River entertained bonobo consorts.

That chimps have a trace of bonobo DNA suggests getting together was a challenge for the two species. "Neither of them like swimming, so the Congo River is a major barrier," Mallet says. (Up to 4% of human DNA today came from extinct relatives.)

These findings come on the heels of other genome analyses—such as between coyotes, dogs, and wolves—showing such gene flow between species. "The more we look at genomes, the more it seems to be found," Mallet says. "It's going to be pretty common," he predicts.

The chimp-bonobo results help "us to understand the nature of speciation," says A. Rus Hoelzel, an evolutionary biologist at Durham University in the United Kingdom. How two species form depends on whether the environment encourages their separation, whether the dividing populations are big enough to survive on their own, and other factors. “When those things change, the path to speciation may also change, or potentially even reverse."

Because there’s so little bonobo DNA in the chimps, Hvilsom and her colleagues suggest that for chimps, the bonobo genes were disadvantageous. But Arnold thinks that once more analyses are done, the researchers will find that at least some of the acquired DNA was beneficial, just as certain genes for immunity and high-altitude survival, obtained from other human species, were for us. And Mallet wonders whether there was a ménage à trois of sorts between the ancestors of chimps, bonobos, and humans in the distant past. There are some suggestive similarities: Both chimps and bonobos have some very humanlike behaviors, the former engaging in warfare and the latter being known for their playfulness, he says, and there may be other shared traits as well. There could be other explanations for these shared traits, but, he adds, early in human evolution, "It's possible there was gene flow between all three species.”