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Ancient Interbreeding Among Chimpanzees, Bonobos Revealed in Genome Analysis

NEW YORK (GenomeWeb) – By scouring the chimpanzee genome, an international team of researchers has uncovered evidence of ancient interbreeding between chimpanzees and bonobos.

The team led by Tomàs Marquès-Bonet from University Pompeu Fabra analyzed the genomes of 65 wild-born chimpanzees (Pan troglodytes) and 10 bonobos (Pan paniscus) that hailed from 10 different African countries. As they reported today in Science, they found ancient gene flow from bonobos into the ancestors of central and eastern chimpanzees.

"This is the first study to reveal that ancient gene flow events happened amongst the living species closest to humans — the bonobos and chimpanzees," Marquès-Bonet said in a statement. "It implies that successful breeding between close species might have been actually widespread in the ancestors of humans and living apes."

Previous genomic studies have uncovered admixture between Neanderthals and ancient modern humans as well as between Denisovans and ancient modern humans.

Chimpanzees and bonobos diverged from a common ancestor between 1.5 million and 2 million years ago, and while instances of interbreeding in captivity have been noted, scientists have thought that in the wild barriers like the Congo River might have prevented such shenanigans.

To examine whether any admixture did take place between chimpanzees and bonobos, Marquès-Bonet and his colleagues analyzed chimpanzee bonobos genomes to find that chimpanzees in central and eastern Africa and in Nigeria-Cameroon shared significantly more derived alleles with bonobos than did western chimps. While this difference between eastern and western chimps was previously thought to be due to genetic drift in the western subspecies, the researchers said that their analysis — which included more high-coverage data than previous studies — instead suggests that there was ancient gene flow from bonobos into chimpanzees, particularly eastern and central chimps.

Similarly, the researchers reported that central chimpanzees harbored nearly an order of magnitude more introgressed regions — regions with low divergence to bonobos and high heterozygosity — than western chimpanzees.

Marquès-Bonet and his colleagues also developed demographic models, and these further indicated that there is a complex admixture history between chimpanzees and bonobos. In particular, they noted that low-level gene flow occurred between eastern and central chimpanzees and bonobos.

The researchers also traced the timing of these admixture events to between 200,000 years and 550,000 years ago, well after when the chimpanzee and bonobo lineages diverged. They also noted that more recent contact, after 200,000 years, might have also taken place.

"We found that central and eastern chimpanzees share significantly more genetic material with bonobos than the other chimpanzee subspecies," the Sanger Institute's Yali Xue said in a statement. "These chimpanzees have at least 1 percent of their genomes derived from bonobos. This shows that there wasn't a clean separation, but that the initial divergence was followed by occasional episodes of mixing between the species."

Durham University's Rus Hoelzel added in a related commentary in Science that these findings "contribut[e] to our increasing appreciation for the complexities of the process of speciation."

At the same time, Marquès-Bonet and his colleagues also reported in their paper that principal component and population clustering analyses of the chimpanzee genomes uncovered local stratification among central and eastern chimpanzee populations. This, the researchers said, suggests that a chimp's genome sequence could be used to determine what region the animal is from, a prediction they confirmed using low-coverage sequences from six chimps whose origins were known.

"This can aid the release of illegally captured chimpanzees back into the right place in the wild and provide key evidence for action against the captors," Sanger's Chris Tyler Smith noted.