DNA Reveals That Chimps and Bonobos Had Sex in the Past

Their prehistoric liaisons mirror those between our own ancestors, Neanderthals, and other groups of early humans.

Two bonobos (Finbarr O'Reilly / Reuters)

Every year, thousands of chimpanzees are illegally yanked from their homes in Central and West Africa, and shipped to Asia and the Middle East to serve as pets or entertainment. Most of them are babies. Most of them die on the way.

Occasionally, the endangered animals are found by airport officials and confiscated—but then what? “A chimp doesn’t come with a ticket or a sign,” says Christina Hvilsom, from Copenhagen Zoo. “So they don’t know where to send it back to.”

Chimps do, however, come with DNA. There are four subspecies of chimps—western, central, Nigeria-Cameroon, and eastern—each of which lives in a different part of Africa. They are genetically distinct, and Hvilsom, a geneticist by training, wondered “if their genomic landscape mimicked their geographical landscape.” In other words, by analyzing a chimp’s genome, could she work out where it came from?

The answer was yes. By analyzing the complete genomes of 65 chimps from across their entire range, Hvilsom’s team, co-led by Tomas Marques-Bonet, from Pompeu Fabra University in Barcelona, showed that genes do indeed predict geography. For the central and eastern chimps, you can work out where an individual came from to within 50 kilometers—not just to a particular country, but to a particular forest. This genetic geotagging is fuzzier for the other two subspecies, but that’s only because the team had fewer samples. With more genomes, they’ll get more precise.

The team is now working to put their research into practice, to help customs officials relocate trafficked chimps to their point of origin. But in the meantime, their results led them down an unexpected path.

As they explored the genomes of the central chimps, they kept on finding sequences that seemed to come from bonobos—a closely related ape, which tends to be smaller and gentler. “At first, we thought: Pffft, this is just a mistake,” says Hvilsom. “But we continued with a variety of techniques and kept on seeing this trend.”

The team eventually confirmed that central chimps (and to a lesser extent, the eastern and Nigeria-Cameroon ones) owe some of their DNA to their bonobo relatives. It’s a tiny proportion—less than 1 percent—but it’s there nonetheless. And this implies that the two apes must have successfully mated at some point in the past.

Bonobos and chimpanzees began to split into two species between 1.6 and 2.1 million years ago. But they didn’t stay entirely separate. Hvilsom and Marques-Bonet calculated that the two species must have been mating and exchanging genes between 200,000 and 550,000 years ago, before the central and eastern chimps had diverged into separate subspecies. The central ones still carry the legacy of those liaisons, bolstered by another wave of bonobo genes that came in around 100,000 years ago.

Chimps and bonobos have been known to mate in captivity, so it’s not surprising that they would have done so in the wild. But interbreeding isn’t just about compatibility; it’s about opportunity. The bonobos live in the Democratic Republic of the Congo, where the mighty Congo River separates them from the central chimps to the west, and the eastern chimps to the north and east. The formation of the river was probably what split chimps and bonobos into separate species in the first place, cordoning them off into separate forests and preventing them from meeting. “It’s a huge barrier,” says Hvilsom, especially since “chimps and bonobos don’t swim; they drown.”

But perhaps the river was shallower at various points in its history, allowing the once-separated apes to meet, mingle, and mate. The team are now looking into this, trying to tie the periods of gene flow that they observed to the ancient climate of Central Africa. They’re also planning to sequence the genomes of more bonobos—they only have 10 so far, which might be why they only saw bonobo DNA in chimp genomes and not the other way around. “I can’t figure out why it would go in only one direction,” says Hvilsom.

The team’s results mirror what we know about human evolution. In 2010, scientists showed that in every person outside of Africa, a small percent of DNA came from Neanderthals. Likewise, Aboriginal Australians and Pacific Islanders inherited part of their genomes from the Denisovans—another group of early humans, known only from a finger bone and two teeth.

It seems that as our ancestors left Africa and spread around the world, we met and mated with other groups of early humans that had already colonized Asia and Europe, picking up their genes as a result. We now carry traces of those cousins within us—Neanderthals, Denisovans, and likely other as-yet-unidentified hominids, too.

This flow of genes from one species to another is called introgression, and it complicates our understanding of our history. The origin of species feels like a process of division, where one population splits into two distinct ones, creating neatly branching family trees. That’s a fiction. “Gone are the days of neat branching trees,” writes Adam Rutherford in his book A Brief History of Everyone Who Ever Lived. “If we are to look at the evolution that led to where we are now, instead of the nice neat tree, I think it could be reasonably described as one big, million-year clusterfuck.”

This seems to be a common leitmotif in hominid evolution. For example, it seems that after humans initially diverged from chimps, we spent a long time exchanging genes—read: having sex—before separating permanently. Chimps and bonobos clearly did the same. And the various chimp subspecies are still exchanging genes between each other.

To Mary Gonder, from Drexel University, this implies that they aren’t just passively drifting apart due to geographical barriers. Instead, it’s likely that “natural selection is pulling them apart from each other,” perhaps by adapting them to local diseases or environmental challenges. And that’s another reason why the original goal of Hvilsom’s work—tracking the origin of trafficked chimpanzees—is so vital. You need to send them back to the right home.