The team, which included geneticists and archaeologists from the universities of Cape Town and Pretoria, said their findings gave the first glimpses of population distribution before farmers and animal herders swept across the continent about 3,000 years ago.
They also identified a population that spanned an area from the southern tip of Africa to the equator about 1,400 years ago, and said the group shared ancestry with today's Khoi-San.
Delving into the deep ancestry of African groups has been impossible until recently because genetic material degrades too rapidly in warm, humid climates. But the team found DNA lasts longer in small, dense ear bones, and used those in their tests.