As a follow-up to my previous two posts on Afrikaners, I wanted to reiterate something that I implied/said earlier: yes, I think about 1% of the ancestry of modern day Afrikaners derives from Khoisan pastoralists of the Cape who were resident there when the Europeans first arrived. These people are often called Khoikoi. Unlike the more famous Bushman the Khoikhoi were not hunter-gatherers. Rather, they herded cattle. Both archaeological and genetic evidence points to the fact that pastoralists arrived in southern Africa through the expansion of East African nomads, who had some Eurasian ancestry (ergo, Khoisan peoples have differing degrees of non-Khoisan African ancestry, as well as Eurasian ancestry).
Today there are no major Khoikhoi groups in South Africa that have not been extensively influenced by other populations (in Namibia the related Nama maintain tribal cohesion and continue the cultural tradition of Khoisan pastoralism). Where did the Khoikhoi go? Many died due to disease, and the privations of slavery. But, some were certainly absorbed into other populations. The Xhosa people have substantial Khoisan ancestry for example.
The plot to the left has various populations, including Dutch, whites from Utah, white South Africans, Nigerians, African Americans, Barbadians, and Bantu populations (click the image for a larger version). As well as Khoisan groups which are a combination of Nama and San Bushmen samples.
If you click the larger image you can see that the South African Bantus are shifted toward the Khoisan. The Kenyan Bantus are skewed in the direction of Eurasians…though only mildly so (no doubt due to Cushitic admixture).
The plot to the right (click to enlarge) is a zoom in. It is clear that the South African samples are very subtly shifted out of the normal Northern European cluster. If you look at the cline from the Nigerians running toward the Northern Europeans, the South African whites look to be perturbed from it. Notably, some of them are clearly shifted in the direction of the Khoisan.
Next, I ran Admixture analysis. I set the reference populations as Esan from Nigeria, Khoisan, and Dutch whites. You can see that African Americans exhibit a cline as you’d expect. A minority of their ancestry is Northern European. But mostly they are African, with the dark blue representing the Esan Nigerian reference population. This is as it should be; most of the slaves who came to America seem to have come from the Congo up the Africa coast all the way to Senegal.
The fraction of African ancestry in the South African samples is low. But observe that many of them have just as high a fraction of the red component, which comes from the Khoisan reference population. These ten mostly white South Africans average 1.4% Khoisan and 2.3% non-Khoisan African.
Finally, I decided to run Treemix and do a three population test.
With two migration edges the results make a lot of sense. The African Americans are placed next to the Nigerians, but there is a migration edge of some significance from the Northern Europeans. The South Africans are in a clade with the Dutch samples, with Utah whites being the outgroup. But, they have a migration edge from between the Esan from Nigeria and the Khoisan. Recall that there was more Nigerian-like ancestry in the South African whites than Khoisan-like ancestry according to Admixture. The gene flow edge seems to be closer to the Esan by some margin.
Finally, I ran a three population test, which tests gene flow by placing an admixed population as an outgroup to source populations. Negative statistics indicate “complex population history” not accounted for by the tree.
| Outgroup | Pop 1 | Pop 2 | f3 | Z score |
| Af_American | Netherlands | EsanNigeria | -0.0103 | -89.1922 |
| Af_American | UtahWhite | EsanNigeria | -0.0102 | -88.7189 |
| Af_American | South_Africa | EsanNigeria | -0.0099 | -87.1784 |
| Af_American | Netherlands | Khoisan_SA | -0.0034 | -16.6754 |
| Af_American | Khoisan_SA | UtahWhite | -0.0033 | -16.5408 |
| Af_American | South_Africa | Khoisan_SA | -0.0029 | -14.6855 |
| South_Africa | Netherlands | EsanNigeria | -0.0015 | -10.9174 |
| South_Africa | Netherlands | Khoisan_SA | -0.0015 | -10.5677 |
| South_Africa | UtahWhite | EsanNigeria | -0.0014 | -9.0416 |
| South_Africa | Khoisan_SA | UtahWhite | -0.0014 | -8.7962 |
| South_Africa | Netherlands | Af_American | -0.0011 | -10.0158 |
| South_Africa | Af_American | UtahWhite | -0.0010 | -8.1132 |
| UtahWhite | Netherlands | EsanNigeria | -0.0001 | -1.6344 |
| UtahWhite | Netherlands | Khoisan_SA | -0.0001 | -1.6344 |
The bottom two results can be ignored. What you see is that African Americans have the most negative f3 values with the highest z-scores. There is a drop-off from the Nigerians to the Khoisan as one of the source populations because the Nigerians are a much better fit. The values for South Africans are much lower, which makes sense in light of their lower admixture proportion. But observe that the f3 statistic for using Esan vs. Khoisan is not that different. This suggests neither group is necessarily a better proxy for the other.
As for the ethnographic details of where this ancestry came from, I think it was the proto-Cape Coloured population.