Chimpanzee Subspecies Are Genetically Mixed And More Diverse Than Humans

Although information about variation in the human genome seems to be accumulating at a fast and furious pace, studies of the genetic diversity of the chimpanzee lag well behind. Scientists have managed to glean some information from scattered fragments of the chimpanzee genome, mostly from analysis of mitochondrial DNA. Mitochondrial DNA is separate from the DNA in the cell's nucleus, and appears to be inherited exclusively through the maternal line. The German team, led by Svante Pääbo and including Henrik Kaessmann and Victor Wiebe from the Max-Planck-Institute for Evolutionary Anthropology in Leipzig, Germany, decided instead to tap the virtually untouched realm of nuclear DNA variation to get a better look at chimpanzee diversity.

"When we started the study of this sequence," Kaessmann said, "we sat down to think about what a nuclear sequence that would be ideal for answering evolutionary questions should look like." Their target became Xq13.3, a section of the X chromosome that does not code for any proteins, that has a low mutation and recombination rate, and is already well-studied in humans. They sequenced and thoroughly analyzed this bit of DNA from blood taken from the three geographical subspecies of chimpanzees (eastern, central, and western African) and the bonobo, a chimpanzee cousin. Their efforts yielded an interesting crop of results.

First of all, the study revealed that the Xq13.3 sequence is almost four times as variable and three times as old in chimpanzees as it is in humans. Although this conflicts with the tale told by isolated chunks of DNA analyzed in earlier research, the findings support many other studies that characterize humans as less diverse. The researchers believe that a bottleneck or crash in the human population might have dramatically reduced its genetic diversity. "The results show a strikingly lower amount of variation in humans than in chimps," said Pääbo. "The simplest explanation for this is that at some rather recent point in the past, humans have been few in numbers. From a genetic point of view, this point could be the origin of modern humans."

Most of the variation in the chimpanzee sample comes from the central African chimpanzees, with the least amount of diversity found among the western chimpanzees. The central chimpanzee sequences also appear to be the oldest of the chimpanzee lineages. According to Pääbo, the variation is similar to what geneticists see with the human African 'Eve'. "The central chimps are the most genetically diverse and other groups seem to be derived from them. Thus, if you like, the chimp 'Eve' of this sequence lived in central Africa," he said. But Pääbo and his colleagues acknowledged that mitochondrial DNA studies, which show the most diversity in the western population, clash with this version of events.

The research team encountered another curious contradiction between the mitochondrial and nuclear genomes when they drew up an evolutionary tree for their sample. Mitochondrial studies divide the western, central, and eastern chimps into discrete groups. By contrast, the Xq13.3 sequence tree showed that the geographical subspecies were in fact highly intermixed. Why would one type of DNA paint a picture of strict barriers erected between groups and another reveal a widely intermingling population? According to the scientists, the disagreement could be a matter of timing. Since changes in mitochondrial DNA only have to spread through the maternal side of the genome, it appears to "evolve" more rapidly. Like the difference between an instant Polaroid snapshot and a photograph slowly developing in a darkroom, mitochondrial and nuclear DNA may be suited to capturing evolutionary events--such as the development of discrete subspecies--on different time scales.

In the case of the chimpanzees, "it is likely that the subspecies are old enough for the mitochondrial DNA to have become different between the subspecies, but not old enough for this to have happened to the nuclear genes," said Pääbo. Since biologists often single out genetically unique populations like subspecies as a focus of conservation efforts, this distinction could have real-life implications for protecting endangered chimpanzees.

Xq13.3 had yet another surprise up its sleeve when it came to the bond between the chimpanzee and the bonobo. Their evolutionary tree revealed a closer relationship between the two separate species than was inferred from other DNA sequences. In fact, some common chimpanzees were more genetically distant from each other than they were from bonobos, a startling fact given that the two are currently separated at the species level. The results indicate that the chimpanzee and the bonobo may have split off in separate evolutionary directions quite recently.

The researchers believe that this high degree of genetic intermixing among the chimpanzee groups makes it unlikely that any cultural differences between chimpanzee populations are due to genes determining behavior. "Rather, these differences are probably truly the result of cultural evolution, the transmission of learned behaviors from generation to generation," said Pääbo. This finding presumably gives a boost to researchers who believe that chimpanzee culture operates in a similar fashion to human culture.

The study has implications for considering human genomic diversity as well. According to Kaessmann, the high degree of diversity in the chimpanzee populations "àshows that humans are unique as a species in that we are all extremely closely related to each other--much more so than even our closest living relatives." He said that the next step would be to analyze the Xq13.3 sequence in other great apes such as gorillas and orangutans to determine if their levels of genetic variation are more similar to humans or to chimps. "The question will be: are we or the chimps exceptional among the great apes?"