A few years ago I got some South African genotypes. Some of the individuals were clearly African. A few mapped perfectly upon Northern Europeans. But many of the samples consistently were European but shifted toward non-European populations.
Based on history of the assimilation of slaves into the European population of Cape Colony in the 18th century, my assumption is that these individuals are Afrikaners.
Recently I realized that Brenna Henn had released some more Khoisan samples, so I decided to look at this question of admixture again. The two Khoisan populations are the Nama and the Khomani. I removed those with lots of Bantu and European admixture and combined them together into one population.
Running unsupervised Admixture shows how distinct the South African whites are.
The average Utah white in this sample (this population is a mix of British, German, and Scandinavian in ancestry) is 99% European modal cluster, and 1% South Asian. The average for the white South Africans in this data set is 94% European modal cluster. The residual is 1% East Asian (Dai modal), 1% Khosian, 1% non-Khoisan African, and 2% South Asian.
I ran Treemix a bunch of times, and every single plot came out like this when I ran it for three migrations:
The gene flow from the Utah whites to the Gujuratis is simply an artifact of the fact that the Gujurati sample is mixed caste, and some of the Brahmin or Lohannas have more “Ancestral North Indian.” The gene flow from the Europeans to the Khoisan is probably real, or, might be due to pastoralist admixture via East Africans. The last migration arrow goes from the African populations to the South African whites, with a shift toward the Khoisan.
I also ran a three population test where A is the outgroup, and B and C are a clade. A significantly negative f3-statistic indicates admixture in population A. The negative values are listed below:
| A | B | C | f3 | f3-error | Z-score |
| Gujrati | Dai | UtahWhite | -0.00121718 | 0.000140141 | -8.68539 |
| South_Africa | EsanNigeria | UtahWhite | -0.00127718 | 0.000147982 | -8.63059 |
| South_Africa | Khoisan_SA | UtahWhite | -0.0012928 | 0.000151416 | -8.53802 |
| Gujrati | South_Africa | Dai | -0.000778791 | 0.000155656 | -5.00329 |
| South_Africa | Dai | UtahWhite | -0.000541974 | 0.000133262 | -4.06699 |
| South_Africa | UtahWhite | Gujrati | -0.000103581 | 8.46193e-05 | -1.22408 |
This aligns well with the Admixture results. Afrikaners have both African ancestries, and, Asian ancestry.
In James Michener’s The Covenant one of the plot lines alludes to mixed ancestry in one of the Afrikaner families. The results above suggest that mixed ancestry is very common, and perhaps ubiquitous, in this population. True, there are some Afrikaners such as Hendrik Verwoerd who migrated to South Africa from the Netherlands in the past century or so, but these are uncommon to my knowledge.
Interesting. Is there a way to find out to what degree the non-european ancestry has been mediated by the cape coloured population?
My neighbor is a South African Mormon who discovered mixed ancestry in a genetic test. His grandma turned out to be a family secret, a reclassified Cape Coloured. Married to a White man with kids before their church helped them fix it. Apparently it isn’t rare at all. Her ancestry comes across as South Asian, African, and English, and at first he was most upset about the English part!
Razib, would you recommend the Giliomee book?
yeah but read with thompson’s book A History of South Africa.
Interesting. Is there a way to find out to what degree the non-european ancestry has been mediated by the cape coloured population?
what we term ‘cape coloreds’ really only emerged in last few centuries. so it’s kind of a ‘not even wrong’ issue. otoh we could check to see if local ancestry analysis indicated admixture a few centuries ago.
My neighbor is a South African Mormon who discovered mixed ancestry in a genetic test. His grandma turned out to be a family secret, a reclassified Cape Coloured. Married to a White man with kids before their church helped them fix it. Apparently it isn’t rare at all. Her ancestry comes across as South Asian, African, and English, and at first he was most upset about the English part!
well, these results indicate that it’s not typical though. admixture is even at low levels. indicates mixed well into pop.
at first he was most upset about the English part!
Yup. It’s not unusual for some Afrikaners to resent and dislike “the English” even to this day. One of my friends does. He rails against the English. He’s quite vitriolic about the “whole English were the root of all evil in what became RSA” thing. He’s very proud about his Dutch and German ancestry, and looks askance at people with English heritage.
He was a bit aghast when he and his wife had their 23andme test done recently. His beloved Afrikaner wife turned out to have significant British/Irish ancestry as well as a small amount of African and Southeast Asian ancestry. He himself is >1% African. I got a kick out of telling him he was blacker than I.
Not exactly on point, because your PCA is fine, but how does anyone who lacks a painter’s ability to distinguish colors and a watch-makers eye for fine detail, read the PCA charts with 30+ different populations represented by various colors and shapes and hundreds of data points? Yet, they seem to be increasingly common in the literature.
re: english. i need to look in detail, but i’m suspecting that that might be an artifact of lack of resolution btwn dutch and english ancestry.
Is it not also the case that Afrikaners (as a group) have a lot of French ancestry? (Not that this would necessarily be “genetically visible” but would perhaps be upsetting to an Afrikaner who is proud of his Dutch / German heritage)
Is it not also the case that Afrikaners (as a group) have a lot of French ancestry? (Not that this would necessarily be “genetically visible” but would perhaps be upsetting to an Afrikaner who is proud of his Dutch / German heritage)
not a lot, but this is well known to south africans. they still keep the french names. fw de klerk being a clear example.
15 Afrikaners found on Gedmatch. Their results in Eurogenes K36 which help differentiate many specific non-Euro admixtures
https://s26.postimg.org/dxdlapz55/boers.jpg
Is it not also the case that Afrikaners (as a group) have a lot of French ancestry? (Not that this would necessarily be “genetically visible” but would perhaps be upsetting to an Afrikaner who is proud of his Dutch / German heritage)
No, because the Huguenot French assimilated into the originally Dutch colonial Afrikaner culture, as did the Germans. I am by no means an expert on South African history, but the sense I get is that the major cultural, linguistic, and political division among South African whites has been that between the Afrikaner and the English.
South African genealogists have long been aware of the significant indigenous and slave ancestry of the Afrikaner population. The researcher C.C. de Villiers in the 19th Century compiled genealogies of most of the common family names of the Dutch period in his book “Genealogies of Old South African Families” (revised by C. Pama and republished in the 1960’s and again in the 1980’s) – following these genealogies to their root will often reveal an ancestor “van Bengal” or coyly “K.” for “van de Kaap” signifying a freed slave.
The subject was brought into focus by the publication in 1984 by Dr. H.F. Heese of the book “Groep sonder grense” (Group without boundaries). This book caused quite a stir with the then apartheid government. It has been translated into English as “Cape Melting Pot” by Delia Robertson. From the introduction to the English translation:
“Dr. Heese exposed, more comprehensively and scientifically than anyone before him, the racially mixed origins of South Africa’s so-called white population”
Today there are many researchers who have published on the topic. There is much on the subject on the excellent genealogical website “The First Fifty Years” (http://www.e-family.co.za/ffy/)
Anyone with Afrikaner ancestry who researches their genealogy will quickly run into this, personally I have identified several freed slaves of East Indian or West African origin – on the other hand many ancestors were also slave owners of course.
I’m a supposedly white South African… Via a couple of marriages i now have Angolan, Indian and Indonesian blood running through my veins. On the European side i have a huge assortment, so many so i won’t bother with a list… I am truly a soul without a home. Most recently i have grandparents from the Netherlands and a great grand father which was a British soldier on the other side… I am truly a melting pot of nations without a true home
When one look at ship records (also church records) so much as one third of the Afrikaner gene pool is from French Huguenot lineage. A known fact they all grew up with, taking into account history taught in their schools.
French Huguenots who fled to South Africa (an incomplete list):
AURET, BLIGNAUT / BLIGNAULT, BOSHOFF, BRUWER, BUYS, CILLIERS / CILLIE, CORDIER, CRONJE, DE CLERCQ / DE KLERK, DELPORT, DE VILLIERS, DU PLESSIS, DU PREEZ, DURAND, DU TOIT, FAURE, FOUCHE, FOURIE, GILLIOMEE, GOUWS / GOUS, HUGO, JACOBS, JORDAAN, JOUBERT, LABUSCHAGNE, LE GRANGE, LE RICHE, LE ROUX, LE SEUR, LOMBARD, MALAN, MALHERBE, MARAIS, MINNAAR, MOUTON, NAUDE, NEL, NORTJE, PIENAAR, RETIEF, ROUSSEAU / ROUSSOUW /ROSSOUW, ROUX, SENEKAL, TAILLEFERT / TAILLEFER, TERBLANCHE / TERREBLANCHE, THERON, VILJOEN, VIVIER(S)
https://www.geni.com/projects/French-Huguenots-who-emigrated-to-South-Africa/8652
Huguenot Ships to the Cape – Project Index
https://www.geni.com/projects/Huguenot-Ships-to-the-Cape-Project-Index/38315
Deconstructing Jaco: genetic heritage of an Afrikaner. Ann Hum Genet 71: 674-688
https://www.researchgate.net/publication/6312111_Greeff_JM_Deconstructing_Jaco_genetic_heritage_of_an_Afrikaner_Ann_Hum_Genet_71_674-688
Afrikaner women ‘more faithful’ over 300 years – study
New research into 23 common Afrikaans surnames has found that the incidence of “false fatherhoods” was lower than 1% over the last 300 years, according to a report by Radio Sonder Grendse.
http://m.news24.com/news24/SouthAfrica/News/Afrikaners-can-trust-their-genealogical-heritage-study-20151028