Published online 5 September 2011 | Nature | doi:10.1038/news.2011.518

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Analysis suggests genetic mixing occurred in Africa around 35,000 years ago.

Native African genomes still contain signs of ancient mixing with other species. Giacomo Pirozzi/PANOS

Our ancestors bred with other species in the Homo genus, according to a study published today in the Proceedings of the National Academy of Sciences1. The authors say that up to 2% of the genomes of some modern African populations may originally come from a closely related species.

Palaeontologists have long wondered whether modern humans came from a single, genetically isolated population of hominins or whether we are a genetic mix of various hominin species.

Last year, an analysis comparing the Neanderthal genome sequence to that of modern H. sapiens showed that some interbreeding did take place between the two species in Europe some time between 80 and 30,000 years ago and that, to a certain extent, Neanderthals 'live on' in the genes of modern humans2.

It has been a mystery whether similar genetic mixing took place among Homo species even earlier, before the populations that became modern humans left Africa.

To find out, evolutionary biologist Michael Hammer at the University of Arizona in Tucson and his colleagues studied DNA from two African hunter-gatherer groups, the Biaka Pygmies and the San, as well as from a West African agricultural population known as the Mandenka.

Each of these groups is descended from populations that are thought to have remained in Africa, meaning they would have avoided the genetic bottleneck effect that usually occurs with migration. This means the groups show particularly high genetic diversity, which makes their genomes more likely to have retained evidence of ancient genetic mixing.

“We need to modify the standard model of human origins.” Michael Hammer

University of Arizona, Tucson

To find signs of infiltration from other Homo species, the researchers looked at 61 non-coding DNA regions in all three groups. Because direct comparison to archaic specimens wasn't possible, the authors used computer models to simulate how infiltration from different populations might have affected patterns of variation within modern genomes.

Then they looked for such patterns of variation in the DNA of the three African populations. On chromosomes 4, 13 and 18, the researchers found genetic regions that were more divergent on average than known modern sequences at the same locations, hinting at a different origin.

Mixing things up

Hammer and his colleagues argue that roughly 2% of the genetic material found in these modern African populations was inserted into the human genome some 35,000 years ago. They say these sequences must have come from a now-extinct member of the Homo genus that broke away from the modern human lineage around 700,000 years ago.

Hammer says this disproves the conventional view that we are descended from a single population that arose in Africa and replaced all other Homo species without interbreeding. "We need to modify the standard model of human origins," he says.

Geneticist Sarah Tishkoff, who studies population genetics and human evolution at the University of Pennsylvania in Philadelphia, is more cautious. "This raises the possibility that there may have been ancient admixture with archaic populations," she says.

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But some researchers will require yet more convincing. "The authors model differences in very small parameters, such as the difference between no admixture and 1-2% admixture with an archaic population," says anthropologist Brenna Henn, a graduate student at Stanford University in Palo Alto, California. "The ability to discern complex models of demographic history with such a small data set, when many of the basic features of African genomes and history remain unknown, concerns me."

Tishkoff would also like to see further work. "Analyses of whole genome sequences of these populations will be necessary to more definitively test this hypothesis," she says.