Despite what some headlines may lead you to believe, it's clear modern humans originated in Africa before spreading around the globe. It's just that we've found the spread is a bit more complicated than we might have expected, given that these early humans seem to have mated with other pre-modern humans on the trip.

But modern humans seem to have been present in Africa for over 50,000 years before spreading to other continents, and we have a much less clear picture of what was going on there. A new study of African genomes suggests that it may not be possible to assign our species a specific site of origin with Africa. But the data does identify the oldest distinct population on the planet, and hints at some of the adaptations that may have helped give modern humans a big boost.

Rather than working with complete genomes, an international team of researchers looked at sites in the genome that commonly differ between individuals (these are called SNPs, or single-nucleotide polymorphisms). This doesn't provide as much information as a genome sequence, but it's much faster and cheaper to do. As a result, the team was able to look at 2.3 million SNPs in a total of 220 different Africans.

Previous work with mitochondrial DNA suggested that members of click-speaking groups (the Khoe-San) had the greatest genetic diversity, and were therefore the most likely to be the oldest offshoot of the modern human family tree. The new study makes it possible to actually provide a date for their branch: 100,000 years, approximately the same time that modern humans are thought to have first appeared in Africa.

From there, it took over 50,000 years before the next distinct group separated off (Central Africans). They were shortly followed by East Africans, before a large diversification of West African groups. The date of the Central African branch roughly corresponds to the point where modern humans started migrating out of Africa. Whether that's a coincidence or a single set of environmental conditions triggering changes in a number of human populations isn't clear.

The presence of distinct populations in the record indicates that the African population is what's termed "structured," meaning that there are distinct populations that haven't done much sharing of genetic material. But there is also evidence of what's called admixture, or the sudden introduction of material from previously isolated populations. This is probably most dramatic in the case of the Bantu, some of Africa's most successful agriculturalists—some populations that are otherwise old show signs of a recent introduction of Bantu DNA. There's also another old group that seems to have picked up East African DNA, which may be associated with their adoption of an agricultural lifestyle.

Combined, the structure and admixture make it very difficult to determine where in Africa modern humans are likely to have first appeared. "It remains unclear whether modern humans originated from a single randomly mating population," the authors conclude, "or if modern humans emerged from a geographically structured population, potentially exchanging genetic material with archaic humans." However, the authors were able to determine a few of the traits that were likely instrumental to their success. That's because many groups contain signs of what's called a selective sweep, where a trait shows signs of having swept through a population by providing it an evolutionary advantage.

The advantage wasn't just in our brains. The Khoe-San have the highest rate of a variant associated with fast muscle performance of any population surveyed (except, perhaps, professional athletes). Another variant, found at high levels in most populations tested, is associated with muscle growth and function. Another three genes with a clear signal of selective sweep are involved in bone and cartilage formation. Yet another is associated with immune function.

That's not to say that brains weren't involved, as two of the five strongest signals were genes associated with neural problems (microcephaly and Alzheimer's), which suggests their normal role is to regulate brain function. Still, the work makes it clear that it wasn't just our brains that primed us for success.

It's possible that complete genome sequencing will eventually clarify the complex history of our origin in Africa. But if the population in Africa was heavily structured both before and after this origin, and there was heavy interbreeding going on, then deciphering the exact chain of events will be nearly impossible. If our history is that complex, it may not make sense to be talking about a single origin anyway.

Science, 2012. DOI: 10.1126/science.1227721 (About DOIs).

Listing image by Danie Ware