The settlement of Southern Africa was for a long time a mystery. With today’s science of DNA analysis, it looks like the mystery has been solved. Through the analysis of the DNA message a more complete picture of the settlement of Southern Africa could be built which was previously not possible.
According to the original theory the exodus of Homo Sapiens out of Africa happened about 65,000 years back. It was assumed that the exodus only happened in one direction - until now with DNA testing which revealed a different story.
The discovery that changed the original theory was the European DNA contained by the Khoikhoi people of the Cape in spite of the years of isolation. The unexpected snippets of DNA most resembled sequences from southern Europeans, including Sardinians, Italians and people from the Basque region. Dating methods suggested they made their way into the Khoikhoi DNA sometime between 900 and 1800 years ago.
To explain the findings archaeological and linguistic studies of the region suggest that a subset of the Khoikhoi, known as the Khoe-Kwadi speakers, arrived in southern Africa from east Africa around 2,200 years ago. The Khoikhoi were pastoralists who make their living from herding cows and sheep. The suggestion is that they introduced herding to a region that was otherwise dominated by hunter-gatherers - the San tribes.
It was determined by David Reich and his team that the proportion of Eurasian DNA in the Khoikhoi can be as much as 14 percent of western Eurasian ancestry. When they looked at the east African tribes from which the Khoikhoi descended, they found a much stronger proportion of Eurasian DNA – up to 50 percent. In a 2012 study by Luca Pagani found non-African genes in people living in Ethiopia. The study also confirm that the Eurasian genes made their way into east African genomes around 3,000 years ago. About a millennium later, the ancestors of the Khoikhoi headed south, carrying a weaker signal of the Eurasian DNA into southern Africa.
Today the colonisation of Southern Africa can be summarised in four different waves. The first wave happened about 140,000 years ago when human populations from East or Central Africa moved southwards and colonised western southern Africa which gave rise to the present-day San hunter-gatherers. This happened before the exodus out of Africa.
The second wave was more recently about 2,000 years ago when the colonist from north and eastern Africa gave rise to the pastoral Khoikhoi people. The origin is speculated to be Ethiopia where the European DNA became part of the Khoikhoi ancestors about 1,000 years before the trek south.
The Third wave happened a few hundreds years later - about 1700 year ago - when mainly the Nguni Bantu-speaking black Africans moved from Central Africa to settle in the south-eastern regions of Southern Africa. Some tribes of the Nguni mix with the Khoikhoi to form the Xhosa tribes of today (Nelson Mandela was a Xhosa).
The fourth wave happened in the modern age when Europeans settled Southern Africa in 1652 - nearly 400 years ago.
Sources:
https://www.newscientist.com/article/dn24988-humanitys-forgotten-return-to-africa-revealed-in-dna/
https://theconversation.com/how-the-origin-of-the-khoisan-tells-us-that-race-has-no-place-in-human-ancestry-53594