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.

September 23, 2017

No, Afrikaners do not have British or English ancestry

Filed under: Afrikaner,Afrikaner genotype,Ancestry,Boer — Razib Khan @ 9:58 pm


In my post below on the non-European ancestry of Afrikaners, several readers mentioned that friends of Afrikaner background were rather chagrined to have reported British ancestry from genetic tests. The cultural reason for this is well known: many Afrikaners exhibit hostility toward British imperialism due to the deprivation and death which was the consequence of their resistance to the expansion of the Empire during the Second Boer War. This is above and beyond the antipathy which was manifestly made obvious by the fact that with the transfer of the Cape Colony to the British in the early 19th century thousands of white farmers migrated into the hinterlands to escape the new power (in part to preserve their customs, such as slavery).

By the 20th century, this anti-British aspect of Boer identity manifested itself in pro-German sentiments, as can be seen in the film The Power of One.

But the reality is that it is strange for Afrikaners to have British ancestry. Yes, they are not exclusively Dutch, with substantial German and French (Huguenot) components in their background. And there has been some recent intermarriage with English speaking whites. But presumably that’s recent enough that people would know.

Rather, I think what is happening is that genetic tests do not have the power to distinguish well between English and Dutch ancestry. In fact, the minority ancestry from Anglo-Saxons in southeast Britain would have stronger affinities with the Dutch than most of the island.

To figure out what was going on I asked people on Twitter for 23andMe profiles. I got a response from someone whose results I posted above. This individual has Boer ancestry, mostly Dutch, going back to the late 17th century on his mother’s side and late 18th century on his father’s side. And you see 17% “British” ancestry. He also provided his wife’s 23andMe output. Her ancestry dates back to the late 17th century on both paternal and maternal sides, so it is not a surprise she has more non-European ancestry:

She is 18% British. In fact, the European ancestry fractions of both these individuals are rather similar when it comes to “French-German”, British, and Scandinavian. I suspect what we’re seeing here is what the algorithm pops out quanta wise for Dutch.

I took the South African individuals who had some non-European ancestry, and ran them on Admixture and projected a PCA with British and Dutch individuals. You can make your own judgment, but I think these are definitely people who are of mostly Dutch ancestry.

January 21, 2012

The quest for an Afrikaner genotype

Update: If interested, please email me at contactgnxp -at- gmail -dot- com. Also, I am getting some feedback via 23andMe that people with white South African matches noticed Africa segments in many of the ancestry paintings. This has definitely increased by probability that the admixture proportion is ~5 percent. There will probably be a few genotypes coming in shortly, but I am going to see if I can get more people typed (fundraising appeal pending!).

It’s been a while since I’ve gone looking for genotypes of particular ethnic groups. The results were rather good for the Tutsi and Malagasy. So I thought I’d venture out again, despite being a bit busy. Here’s what I want: the genotype of an Afrikaner (or several). A few years ago South African geneticist J. M. Greeff did an analysis of his own pedigree, and estimated that he had ~6 percent non-European ancestry (he did validate this with some genetic markers; e.g., his father’s mtDNA is of the M haplogroup, which is almost always Indian). This is in line with other genealogists who have estimated, about 5 percent non-European heritage. How much should we trust these non-biological studies? The genomic estimates of African American ancestry being ~20 percent European were anticipated by analyses of family histories from text records, so we certainly shouldn’t dismiss them (in fact, it seems possible that these analyses will underestimate non-European ancestry because of cryptic individuals in the pedigrees).

And we have plenty of records of people of non-European ancestry contributing to the Afrikaner population in any case. Greeff found the records for his own pedigree, but the first Governor of the Dutch Cape Colony was himself of mixed-race (his mother was Eurasian). The question is is a matter of degree. Are Afrikaners like American whites, with hardly any non-European ancestry (~1 percent or less), or like Latin American whites, with significant non-European ancestry (~5 to 20 percent)? My own bet is that they’ll be in the middle. The proportion of non-European ancestry is low enough that individuals such as Sandra Laing are very rare indeed. But if the 5 percent estimate is valid, and almost of all these ancestors were women, then a larger proportion of the mtDNA is going to be non-European.


So how do we do this? Well, I need an autosomal genotype. I’ll take it anyway I can get it. But, if you don’t have one, but are willing to let me analyze your own genotype, and, are of 100 percent known Afrikaner descent, then we can probably figure out a way to purchase you a kit.

Why does this matter? I guess you could ask why any science matters. I’m a little confused as to why no one has done this before. There’s plenty of work on the cultural cousins of the Afrikaners, the Cape Coloureds. My working assumption is that except for the initial decades of the Cape Colony, when women were in severe shortage and the color line was not as strict, most of the non-European gene flow into the Afrikaners is going to be from the Cape Coloureds. This means that like the Cape Coloureds the Afrikaners carry within them the genetic variation of a huge swath of the world’s population. The non-European ancestry of the Afrikaners is naturally part African. Bantu and Khoisan. But there is also considerable Asian, from South and East Asia. Though this leaves out the Middle East and the New World, you have here most of extant genetic variation in human populations.

There are approximately 3 million Afrikaners in South Africa. What if these were the only human beings left on earth? At 5 percent that’s 150,000 non-Europeans, with a mix of Southeast Asians, Chinese, Indians, Khoisan, and Bantu. Because of diminishing returns you’ll actually have enough variation in just a few thousand individuals of any given ethnic group to capture most of its genetic character. In other words you could in theory reconstitute the Chinese and Khoisan from these Afrikaners.

Addendum: The paper, Complete Khoisan and Bantu genomes from southern Africa, has one “South African European.” But I suspect that this individual is author Vanessa M Hayes, and she is not an Afrikaner to my knowledge.

Image credit: Wikipedia

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