Ancient DNA from South Africa rock shelter reveals the same human population stayed there for 9,000 years

Oakhurst rock shelter is an archaeological site near the town of George on the southern coast of South Africa. It is set into a sandstone cliff above a stream in a valley forested by towering old yellowwood trees.

Archaeologists first started excavating Oakhurst in the 1930s. What makes the site special is the record of human occupation there, which spans 12,000 years. Not only have rock art, stone tools and ceramic fragments been found there, but also the remains of 46 people. That's rare: most very old burials found in South Africa (from the last 40,000 years) have been of single individuals.

New technology is making it possible to keep learning more from previously discovered archaeological material. For our own research team, Oakhurst offered an opportunity to reconstruct the genomes of the site's inhabitants through time, and to assess their genetic relationships to people living in the region today.

A genome is the genetic information about a living organism. This information gets passed down from one generation to the next, forming a record of the past. Studying ancient genomes — a field known as archaeogenetics — helps us understand the history of living people and the movements of populations.

We were able to generate 13 ancient genomes from skeletal human remains at Oakhurst. They included the oldest ancient DNA from the region to date, from two individuals who lived around 10,000 years ago.

The findings show that the population history of southernmost Africa is different from other regions of the world. People didn't arrive here in waves, replacing other populations and mixing with them. Instead there was long-lasting genetic continuity throughout the entire span for these 13 individuals, from 10,000 until as recently as 1,300 years ago.

Human genetic diversity and history

Archaeogenetics has revealed much about human history in Asia and Europe. There has been less success in Africa, because of the environmental conditions. Ancient DNA isn't well preserved when average temperatures are high. So far, fewer than two dozen genomes from South Africa, Botswana and Zambia have been published.