A recent study in Communications Biology reports results from the largest such survey of chimpanzee genetics so far. It suggests that animals from the different groups have mixed more recently than many researchers in the field previously believed. The findings cast doubt on whether the four distinct chimp populations are true subspecies; their DNA suggests that despite the physical barriers, there’s been gene flow among the populations in the last few thousand years.
“Our data indicate that they were connected as part of a main population recently, let’s say 5,000 years ago when the forest in equatorial Africa was at its maximum,” says Jack Lester, a molecular geneticist at the Max Planck Institute for Evolutionary Anthropology in Leipzig, Germany, who led the research.
The study collected droppings left by animals from the four chimpanzee populations—from Côte D’Ivoire and Ghana in the west to Rwanda and Tanzania in the east—and then analyzed the distribution of up to 14 microsatellite markers in their DNA. It found the biggest genetic differences between animals who lived the farthest distance apart. This isolation by distance is a common pattern of genetic diversity within a single population. The analysis did not find patterns in the distribution of the microsatellite markers that corresponded with the recognized subspecies populations, indicating they had interbred relatively recently.
Geographical mixing between chimpanzees across Africa would have increased and decreased over millions of years, Lester says, as forest cover expanded and decreased with several glacial and interglacial periods. During the most recent Ice Age, which lasted from about 120,000 years ago to 11,500 years ago, forest cover fragmented and chimpanzee populations became isolated from each other. But as the ice retreated and the forest grew back, the study suggests the animals started to mix again. “We see all these smaller populations after the last glacial period ended seemed to expand back into each other and that’s when the gene flow, this connectivity we observed, resumed,” Lester adds.
The study collected more than 5,000 fecal samples from 55 sites across 18 countries over eight years. That’s a major step forwards, says Noémie Bonnin, who researches the genetics of chimpanzees at Liverpool John Moores University in the UK. “Researchers are usually very specific and focus on chimpanzees in one country or even a single site,” says Bonnin, who was not involved in the study. “To get this huge geographical distribution of samples takes incredible collaboration between so many people and organizations across Africa.”
In addition to the Max Planck Institute, authors on the new paper include experts from research stations, foundations, and institutes that study chimpanzees in Senegal, Ghana, Cameroon, Côte D’Ivoire, Gabon, Uganda, Congo, and Sierra Leone.
But not everyone in the field agrees with the paper’s central conclusion that the chimpanzee groups have mingled widely in the recent past. “There are issues with the data, the analysis, and the assumptions underlying the data,” says Katy Gonder, a chimpanzee expert at Drexel University in Philadelphia, PA. “It is really just a rehash of a pet hypothesis that has been debunked by numerous other studies with more robust data and analysis
The new study looked at the “bare minimum” of microsatellites in the chimpanzee DNA, she says, just enough to distinguish individuals from one another but not offering sufficient resolution to build up a true picture of evolutionary links among so many animals. Gonder claims prior studies that used more than 300 microsatellite regions are more reliable. “When you have closely related species or subspecies you need a lot of data to recapitulate history.”
She adds that the genetic distinctiveness of the four recognized subspecies has also been confirmed by independent studies with samples of single nucleotide polymorphisms (SNPs), complete nuclear genomes, complete mitochondrial genomes, and population genetic studies of wild chimpanzees sampled at a finer geographic scale.
Previous projects are less reliable because they were smaller, Lester insists. “Nobody has done a study at this scale, which I think is really important to be kept in mind when discussing this,” he says. “There are groups out there that really value the conservation status of chimpanzee subspecies.”
His team now intends to reanalyze the sampled DNA for patterns of SNPs, he says, which should help to confirm the relationship between the different populations.