Location, Location, Location: Did Humans Start Out in Southern Africa?

by Mike Macpherson, Shirley Wu, and Joanna Mountain

A young Hadza hunter

From just flecks of bone and specks of DNA, scientists have been able to piece together a story of the origin of our species. That story, by most accounts, begins in eastern Africa 100-200,000 years ago. After all, multiple lines of evidence point to eastern Africa — it’s where the oldest recognizably human bones have been found, where the linguistic diversity is richest, and it fits the available genetic data. But in this week’s issue of PNAS, researchers, including those from Stanford, UCSF and 23andMe, present much more extensive genetic evidence suggesting that humans may have originated not in eastern, but in southern Africa.

How can genetics tell you where a species originated? A general principle is that you tend to find the highest levels of genetic variation in the portion of the population that’s been around the longest. That’s because sub-populations that split off from an original population start out with just a sample of the original population’s gene pool, and it takes a very long time for new genetic variation to build up in the new sub-population.

Using this principle, one strategy for identifying the location a species originates is to measure genetic variation in several places the species lives, and look for the place the genetic variation is highest. For this study, the authors gathered new genome-wide data from three click-speaking peoples from southern Africa that have been living for millennia in relative isolation, and seven northern African peoples. They also assembled existing genome-wide data from 14 further African populations, covering eastern, western, and central Africa, resulting in a continent-wide representation of genetic variation.

With this much coverage, the researchers would have been in a position to find evidence for human origins in any part of Africa; eastern Africa would be the front-runner, but researchers have argued that northern, central and southern Africa are also plausible candidates. But they found that among all the populations they looked at, the highest levels of genetic variation were found in the southern Africa. This suggests, the authors conclude, that each of us may trace our ancestry (ignoring any contributions from Neandertals for now!) back to southern Africa, sometime less than 100,000 years ago.

Although this new genetic evidence is intriguing, it’s not the end of the story. There’s some archaeological evidence to support a southern African origin, but for now it’s fairly limited. And these new data are also consistent with a scenario where humankind arose in eastern Africa, but later migrated to southern Africa. Studies sampling genetic diversity in further African populations may help clarify the early history of our species.

Dr. Mountain in Africa during her time in the Peace Corps

The insights of this study were enabled by genome-wide genetic data of the sort that 23andMe generates. In fact, they used exactly the kind of data that 23andMe generates; the southern African Sandawe, Hadza, and Khomani individuals were all genotyped on our 580,000-SNP v2 platform, just like many of our customers. 23andMe was proud to participate in this study, which was actually launched almost 15 years ago by 23andMe’s Senior Director of Research, Joanna Mountain. Dr. Mountain collected samples for the Hadza in Tanzania and initiated the recent sample collection in South Africa. We are also proud to note that the study’s lead and second author, Brenna Henn and Christopher Gignoux, are former members of Team 23andMe. Brenna and Chris made many contributions to 23andMe’s product, most visibly to the Maternal and Paternal Line features.