The Khoisan – A Rich Genetic History

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By Michelle Mukonyora

The Khoisan people are descendants of two tribes, the hunter-gatherer San and the pastoral KhoiKhoi. Unfortunately, arrivals of the Bantu and White settlers put the Khoisan at the risk of extinction. The Khoisan were dispossessed of their land, which is an integral part of their livelihood, and today they remain a marginalized society. This is unfortunate because of the rich contribution they have made to South African culture. The unique clicks of their language are an integral part of the Xhosa and Zulu languages, and parts of their culture have been incorporated into those of the people in Namaqualand. From a genetic perspective, the KhoiSan are an important population to study, because them and their ancestors were at some point the largest population on earth. Today, the Khoisan are the most genetically diverse group, and they possess the most ancient Y-chromosomes, and mitochondrial DNA.

A Khoisan family in the Kalahari Desert. Image credit: Alive2Green
Genomics as a source of information about where we came from
Genomics studies involve determining the complete DNA sequences of organisms, and these complete sequences are known as genomes. Large-scale genomics studies may be used to investigate human evolution. They continuously reveal new information about how modern humans came about, and the migration patterns of our ancestors. The diversity of modern-day humans’ genomes is a reflection of the geographical diversity to which we have adapted.
Combined genomics and ancient climatic data help explain observed patterns in human evolution
After the Khoisan and non-Khoisan (ancestors of the Bantu and non-Africans) populations diverged, the non-Khoisan experienced a decline in what is known as effective population size, simultaneously losing half of their diversity. The decline in effective population size of the non-Khoisan took place 30-120 thousand years ago (kya). This coincides with what has been deduced about ancient climatic changes around the same time. Between 84 and 94kya, increased rainfall in southern Africa, and drier conditions in central and western Africa were observed. The increased rainfall would have been advantageous to the KhoiSan, but the drier conditions would have added negative selective pressures on the non-Khoisan.
Vegetation Map of Africa During the Last Glacial Maximum. Image credit: University of California Berkley
Today, the Khoisan are divided into the northern and southern Khoisan. These two groups separated as recently as 21-26kya. It is interesting that the respective Khoisan languages diverged and coevolved separately despite their relatively close geographical proximity. In contrast, Bantu languages are more similar in structure, despite the large geographical areas they occupy. Coevolution of the northern and southern Khoisan languages is the result of having been settled in their respective regions for a long time. Researchers believe that the forced separation was the result of the Last Glacial Maximum approximately 24,5kya. The Last Glacial Maximum resulted in much of southwest Africa being desert and semi-desert.
In most of the evolutionary genomics studies, Africa has been under-represented, which is unfortunate because of the high genetic diversity within its populations. Combining the results of genomics studies with research from other disciplines, such as climatic studies, is key to painting a clearer picture of why we came to be who we are.