Genetics studies of 10,000 year old human remains reveals the genetic makeup of ancient South Africans, with surprising links to the present.
In the South African summer of 1932, the site of the Oakhurst Rockshelter was excavated for the first time. Within it was found a set of graves, and within them, the skeletal remains of ancient humans. The archaeologists that excavated those remains would have never imagined the sort of information that could be learnt from them almost 100 years later – by a combined team of researchers from the University of Cape Town and the Max Planck Institute for Evolutionary Anthropology in Leipzig.
In archaeology, there are two main ways to look at how populations change over time. The first, and for a long time the only, way is by looking at artefacts – the things people left behind, and how the way they make them changes as new ideas are introduced. A more recent method is through DNA studies that compare the genetics of samples from across time and space in order to see where and when populations changed and moved. This, along with the older artefact-based method, provides a much more comprehensive view of changes over time.
The Oakhurst Rockshelter was especially well-suited for a study like this, having multiple burials, spanning across the Holocene (the period since the end of the last Ice Age), from approximately 10,000 to 1,300?years Before Present (BP), alongside many artefacts. The researchers expected to see many demographic shifts over time, from the spread of herders from Northern Africa, to western African ancestry linked to the Bantu languages.
How was the study carried out? As with any case involving human remains, ethical considerations needed to be taken into account. Permission to use the remains (stored in the University of Cape Town human skeletal repository) was granted after consultation with representatives from the San community. Only individuals with loose, broken or previously glued bones were chosen to be sampled, along with a single tooth per individual. These samples were then sent to the Max Planck Institute for Evolutionary Anthropology for analysis, where bone and tooth powder was collected. Carbon-14 dating was also conducted. The ancient DNA could then be extracted from the powder and compared, using an analysis of 24 contemporary San, Khoekhoe and Bantu-speaking populations from Namibia, Botswana and South Africa
What did they find? Surprisingly, the remains were genetically quite similar to San and Khoekhoe groups living in that same region today. Not only that, their results also indicate that between 10,000 and 1,300?years BP, no ancestry from outside present-day South Africa arrived at the Oakhurst rockshelter. Significant change was only seen in the genomes of a 1,200-year-old pastoralist and four Iron Age farmers. Researchers were able to use this to estimate the introduction of non-Southern African ancestry at around 1,068?years BP, which is aligned with previous research and the introduction of herding and farming to the region, and changes in subsistence and settlement patterns among coastal and near-coastal communities.
Why does this matter? Archaeological research of genetics has previously shown that across the Holocene, the demographics of Stone Age Europe, Asia, and North Africa experienced several episodes of large-scale migrations, either in the form of admixture with newcomers, or by total replacement of the established inhabitants. In Ireland, we see this in the form of our own ancestry largely deriving from Bronze Age migrations, rather than the earlier Mesolithic and Neolithic arrivals. This was generally assumed to be the case in South Africa as well, but as this study shows, it was not. This has a significant impact on our understanding of technology use in South Africa prior to 1300 years BP, as it suggests new innovations were being made locally instead of new ideas being brought in by new people.
Much of our human past is lost to us. Writing was only invented approximately 5,300 years ago, and took many years to spread across the world from there, only becoming widespread here in Ireland during the 5th century. Aside from occasional pieces of preserved oral histories or art, anything from before then went unrecorded. ‘History’ as we know it is quite a recent development – out of the 300,000 year existence of our species, less than 2% of it is the domain of historians. That’s where archaeologists come in – and as studies like this show, there’s a lot we can learn about the past from what was left behind. As of this April, it has only been 21 years since the human genome was fully sequenced. This, along with techniques for extracting DNA from ancient remains, created an entirely new field of archeology – the study of ancient DNA. From identifying entirely new human species such as Denisovans, to overturning long-held beliefs about ancient migrations, ancient DNA has, and will continue to tell us more about our past than those archaeologists from 1932 could have ever imagined.