Researchers found that Khoe and San tribes of the sub-Sahara are descendants of the earliest diversification event in the history of all humans, some 1,00,000 years ago.
The findings, involving 220 participants representing 11 populations across southern Africa, showed around 2.3 million DNA variants per individual, the 'Daily Mail' reported.
This was thought to be due to interbreeding and genetic stratification - non-random mating between groups.
A team of international scientists from Sweden and South Africa conducted the largest genomic study ever among the click-speaking Khoe and San groups.
Researchers estimate that the San populations from northern Namibia and Angola separated from the Khoe and San populations living in South Africa as early as 25,000 -- 40,000 years ago.
"There is astonishing ethnic diversity among the Khoe-San group," Dr Carina Schlebusch, of Witwatersrand University in Johannesburg, said.
Also Read
"We were able to see many aspects of the colorful history that gave rise to this diversity in their DNA," Schlebusch said.
Many scientists believe modern humans originated from one region in Africa before spreading into Europe and Asia about 60,000 years ago.
Others theorise there were several 'movements' out of Africa.
"It is possible that modern humans emerged from a non-homogeneous group," said author Mattias Jakobsson from Sweden's Uppsala University.
The genetic data also showed how generations of Khoe-San adapted to their environment which involved muscle function, immune response, and UV-light protection.
The findings are published in the journal 'Science'.