Humans in southern Africa were an isolated population until recently

"Collectively, the genetic variants in this population are outside the range of previously described human diversity. What's distinct? Estimates of the timing of when this ancient south African population branched off from any modern-day populations place the split at over 200,000 years ago, or roughly around the origin of modern humans themselves. But this wasn't some odd, isolated group; estimates of population size based on the frequency of genetic variation suggest it was substantial."

"Instead, the researchers suggest that climate and geography kept the group separate from other African populations and that southern Africa may have served as a climate refuge, providing a safe area from which modern humans could expand out to the rest of the continent when conditions were favorable. That's consistent with the finding that some of the ancient populations in eastern and western Africa contain some southern African variants by around 5,000 years ago."

"As far as genetic traits are concerned, the population looked like pretty much everyone else present at the time: brown eyes, high skin pigmentation, and no lactose tolerance. None of the older individuals had genetic resistance to malaria or sleeping sickness that are found in modern populations. In terms of changes that affect proteins, the most common are found in genes involved in immune function. More unusually, genes that affect kidney function also show a lot of variation."

Genetic analysis shows a southern African population whose variants fall outside previously described human diversity. This population split from other modern populations over 200,000 years ago and maintained a substantial population size. Climate and geography produced isolation, with southern Africa acting as a climate refuge that allowed later expansion when conditions improved. By about 5,000 years ago, some eastern and western African populations carried southern African variants. Phenotypically, individuals had brown eyes, high skin pigmentation, and lacked lactose tolerance. There was no genetic resistance to malaria or sleeping sickness. Protein-affecting changes concentrate in immune-related genes and unusually in genes linked to kidney function.

Read at Ars Technica