Razib Khan One-stop-shopping for all of my content

September 27, 2017

Yes I think about 1% of Afrikaner ancestry is probably Khoikhoi

Filed under: Afrikaner,Afrikaner genotype,Afrikaners,Khoisan — Razib Khan @ 7:48 pm

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.

November 6, 2011

The hunter-gatherers within us


Lesley-Ann Brandt

One of the reasons that the HGDP populations are weighted toward indigenous groups is that there was the understanding that these populations may not be long for the world in their current form. But the Taino genome reconstruction illustrates that even if populations are no longer with us…they are still within us. With that in mind I decided to do some quick “back-of-the-envelope” calculations in relation to the Khoisan people of southern Africa. These are the descendants of the populations which were presumably there before the Bantu, and the basal relationship of the Bushmen to other human lineages is probably a partial testament to their long term residence in this region of Africa.

There are about 300,000 speakers of Khoisan languages left (mostly in South Africa and Namibia). These individuals are not all unmixed in their ancestry. If you look at some of the public genotypes available you can find Bantu African and European ancestry in Bushmen (the European may have come from Griqua). There are about 4 million Cape Coloureds and 8 million Xhosa. Both of these groups have some Khoisan ancestry. Let’s assume that the Cape Coloured are 20% Khoisan, and the Xhosa are 10% Khoisan. This is probably a moderately conservative, but I think it’s close from what I’ve seen. Multiplying that out you get 1.6 million Khoisan represented by the Cape Coloured and the Xhosa. That’s a ratio of over 5:1 in terms of the ancestral components attributed to Khoisan in modern populations being in those groups which don’t identify as Khoisan. This is probably a major underestimate, as other Bantu populations besides the Xhosa likely have some Khoisan ancestry, though less.


This came to mind because I recently watched Spartacus: Blood and Sand with some friends (or at least the first season). We were curious about the background of one of the characters, Lesley-Ann Brandt. From her blog you can find out this about her ethnic background:

You’re probably still asking what makes a “Coloured”, “Coloured”. Well like the name suggests, it is someone of many colours. My heritage consists of German, ( my last name), Indian, British and Spanish. My mother has the Indian, but is very fair and could be mistaken for white if you’ve never met her or you’re not from South Africa.

Her father however was a very dark man with Indian heritage. Her mother had an olive complexion. My father on the other hand has mostly European heritage, (a white German grandfather on his fathers side and a white British Grandfather and Spanish grandmother on his mothers side), but looks much darker than me. On my dad’s side, my grandfather had really dark olive colouring with green eyes and my grandmother was often mistaken as white during Apartheid. She would often sneak into white only grocery stores to buy food because no one really questioned her.

With all due respect to Ms. Brandt, just looking at her face and knowing that she’s Cape Coloured, her Khoisan ancestry seems rather clear to me in her features. From what I have read there’s some stigma associated with this int the Coloured community, or was, so perhaps that is why she seems to be ignorant of it, and attributes her visible non-white features to her Indian ancestry. Her father’s ancestry in particular doesn’t make sense in light of the phenotype she’s attributing to him.

But none of this really matters now. Genotyping would, and will, clear all of these issues up. Well, at least the scientific ones.

Image credits: Ian Beatty and Lesley-Ann Brandt.

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