There was even genetic variance among the Khoe-San populations of South Africa, which split from the rest of humanity at least 100,000 years ago (Image: ImageBroker/Rex Features)

The melting pot of early human history has just been given a good stir. The largest study of genetic variance across present-day populations in southern Africa suggests that there is no single place in Africa from which all modern humans emerged. Instead, our species is the result of mixing between numerous early human populations across a vast area.

Mattias Jakobsson at Uppsala University, Sweden, and his colleagues analysed around 2.3 million single nucleotide polymorphisms (SNPs) – variations in DNA that are useful for comparing regions of the genome between populations – in 220 individuals from 11 southern African populations.

“When we start digging into this data, the most striking result is the deep population structure that we find,” says Jakobsson. This structure suggests that modern humans emerged from a geographically diverse group, in contrast to the “bottleneck” theory in which all humans alive today are descended from a single, relatively homogenous group of people.


“This is important,” says Robert Foley at the University of Cambridge, who was not involved in the study. “One of the big questions has always been where in Africa humans evolved. Given the size of the continent – three times the size of Europe – saying we evolved in Africa does not really answer the question.”

Genomic studies let us investigate the question more fully, says Foley. “Just as today, the earliest modern humans and their descendants lived in populations that did not have clear-cut boundaries, but existed in a world of other African populations,” he says.

The study suggests that population structure continued to be complicated even after modern humans had evolved. It showed that one group that survives to this day – the click-speaking Khoe-San of the Kalahari – was one of the earliest to separate from the rest of humanity, at least 100,000 years ago.

However, the study also found divergence within the Khoe-San themselves, with the Namibean and Angolan groups in the north having separated from those in South Africa as early as 25,000 to 40,000 years ago.

“Most astonishing to me is the deep divergence among the Khoe-San populations,” says Brenna Henn at Stanford University, California. “This really suggests we need to understand the structure of southern African populations in much finer detail.”

The team also identified some of the genes that make us look the way we do – such as those affecting eyebrow ridges and the shape of the rib cage. Since these date back to a time before the Khoe-San split from the rest of humanity, the researchers say that our modern anatomy is at least that old.

“This study is likely to have considerable impact in the field, although perhaps in unexpected ways,” says Murray Cox at Massey University in Palmerston North, New Zealand. “It certainly tells us new things about our history, but more importantly, it highlights the complexity of that history. In many respects, the study raises a lot of questions about our very earliest ancestors that we haven’t thought to ask before.”

Journal reference: Science, DOI: 10.1126/science.1227721