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

February 15, 2012

Update on the Afrikaner genotype

Filed under: Afrikaner,Personal genomics — Razib Khan @ 8:50 pm

Since my original post on the Afrikaner genotype, I’ve gotten many responses. No genotypes yet though. At some point I need to organize how to pay for typing many individuals. Currently my intent is to pay for those who will allow their identities to be public so that people can confirm their genealogies. Other people have emailed me to say that Afrikaners with whom they have shared genotypes on 23andMe often have African or Asian ancestral segments. But all hearsay so far.

In other news, I’ve got a Dinka gentoype I’ll be analyzing soon (some minor technical issues with merging datasets has delayed this some).

April 27, 2010

The ancestry of one Afrikaner

Filed under: Afrikaner,Anthroplogy,Genetics,Pedigree,science,South Africa — Razib Khan @ 5:41 am

A few weeks ago I reviewed a paper on the the genetics of the Cape Coloured population. Within it there was a refrence to another paper, Deconstructing Jaco: genetic heritage of an Afrikaner. The title refers to the author himself. It was an analysis of his own pedigree going back to the 17th century, along with his mtDNA, his father’s mtDNA, and his Y lineage. The genetics is a bit thin, but the pedigree information is of Scandinavian quality from what I can tell. Praised the records of the Reformed Church!

The author’s utilizes an inversion of the typical method whereby a survey of a population may give some insight into individuals within that population. Rather, he leverages the thorough church records of his Afrikaner community, and his local roots, to paint a picture of his own ancestry. Then he compares the results to those of the community as a whole. Though an N of 1 certainly has limits it seems that the author concludes that he is relatively representative because some of the statistics that emerge out of pedigree analysis seem to fall in line with what genealogists working with the whole community have found. Additionally, it is clearly that he has deep roots within the historic Afrikaner nation, so assuming random mating and little population substructure, inferences from his pedigree may have some general utility.

Afrikaners apparently have some peculiarities genetically which has made them of some interest to scientists. It turns out that they seem to exhibit high frequencies of classical Mendelian diseases, a hallmark of inbreeding or population bottlenecks. This aligns well with the thesis that Afrikaners are the descendants of a small group of founders who arrived in the 17th century and entered into a long phase of demographic expansion, which culminated with their long Trek into the veld to escape English domination as well as perpetuate their practice of slavery (James Michner’s The Covenant is a fictionalization of this). As I have observed before the primacy of the “first settler” seems to loom large in the minds of demographers.

J. M. Greef, the author of the above paper, seems to refute this simple story in his own genealogy, though not the core aspect of the importance of the first founders. First the abstract:

It is often assumed that Afrikaners stem from a small number of Dutch immigrants. As a result they should be genetically homogeneous, show founder effects and be rather inbred. By disentangling my own South African pedigree, that is on average 12 generations deep, I try to quantify the genetic heritage of an Afrikaner. As much as 6% of my genes have been contributed by slaves from Africa, Madagascar and India, and a woman from China. This figure compares well to other genetic and genealogical estimates. Seventy three percent of my lineages coalesce into common founders, and I am related in excess of 10 times to 20 founder ancestors (30 times to Willem Schalk van der Merwe). Significant founder effects are thus possible. The overrepresentation of certain founder ancestors is in part explained by the fact that they had more children. This is remarkable given that they lived more than 300 years (or 12 generations) ago. DECONSTRUCT, a new program for pedigree analysis, identified 125 common ancestors in my pedigree. However, these common ancestors are so distant from myself, paths of between 16 and 25 steps in length, that my inbreeding coefficient is not unusually high (f approximately 0.0019).

Inbreeding coefficient is the probability that one’s two alleles are identical by descent. That is, they come from the same individual. For example, in the case of Elisabeth Fritzl her children have many genes where the alleles are identical by descent because half of her own genes are from her father, some many of his alleles will come back to reside within the same individual as part of a diploid pair. J. M. Greef notes that his inbreeding coefficient is about twice as high as is the norm for the typical European. Europe is a region of relatively low consanguinity, so this is a stringent reference. In some populations the inbreeding coefficient can be as high as 0.01. In short, he’s not too inbred.

That being said, the data within his pedigree do seem to show disproportionate contribution by some ancestors. This makes sense for two primary reasons. First, some component of reproductive variance is random (often modeled as a poisson distribution). Second, some component of reproductive variance is due to innate fitness (e.g., the Genghis Khan Y haplotype may be a case of this). Equality of contribution just isn’t in the cards.

Figure 2 shows the distribution of relationships within the pedigree:

Panel a illustrates that one individual is an ancestor of the author 30 times over! Many individuals are ancestors only once. Panel b shows relatedness, and again, some individuals are much closer to the author than others, with a skewed distribution. Panel c shows the number of generations between the ancestor and the author. The median number is well above ten generations, so the author has deep roots in South Africa. Finally, panel d shows the number of steps between his parents for any given ancestor. Because the author’s parents are both Afrikaners they share many common ancestors, but the steps between seem relatively large, and confirms that the author is not particularly inbred (if the parents were first cousins naturally there would be much shorter steps to common ancestors). It is clear disproportionate amount of J. M. Greef’s genes come from early settlers. This makes sense insofar as demographic expansion was likely front loaded, with later settlers having less of a chance to make an impact on an already large population.

The following table shows the contribution by various European and non-European groups to the author’s ancestry, as well as estimates for the total Afrikaner population in earlier studies on the right.


Note one point: only a minority of the ancestry of the author and Afrikaners are ethnically Dutch. This is important, because it shows how culture can spread and overwhelm ancestry. The Dutch imposed their language upon the French Huguenots, and their religion upon the Germans (who I presume were mostly Lutheran if they were from northern Germany, though a minority were Reformed or Catholic surely). Obviously the Reformed Calvinist religion and Afrikaans language both have a unique stamp in South Africa, but the connection of the Afrikaners to the Netherlands remained profound rather late in history. The Prime Minister of South Africa from 1958-1966 was born in the Netherlands. And yet another fact hard to deny is that the Huguenot French component seems to have persevered to a greater extent culturally than the German. The last Afrikaner President was named F. W. de Klerk, his surname being a form of Le Clerc. Another prominent South African head of state was Daniel Francois Malan. The author observes:

It is not clear if my higher estimate of French contribution is because of a systematic mistake in Heese’s (1970) estimate, or if it is because of a quirkiness in my own ancestry. It seemed to be the case that when a lineage hit the French Huguenots it stayed in this group. It will be interesting to compare the degree of inbreeding of the early generations of Huguenots to the other early immigrants. In the light of the calculations of Heyer et al. (2005) there is an interesting possibility that the cultural inheritance of fitness may have led to a systematic bias in Afrikaners, since Huguenots tended to be more educated and trained than German emigrants who tended to be soldiers. We are currently investigating this hypothesis.

There is a joke that the Baltic possessions of the Swedish monarchy were conquered with Finnish soldiers. Similarly, the Dutch overseas colonial possessions were staffed, especially at a lower level, by the rural male population surplus of northern Germany. A great many of these, likely the vast majority, never returned home and died abroad. These men contributed greatly to the census size of the Afrikaner population during much of its history, but it seems plausible that their fitness was far lower than the established Dutch and Huguenot groups because they lacked the resources and capital to flourish in a world which was much closer to the Malthusian edge than today. Many people don’t leave descendants, and it seems plausible that these Germans were fated not to do so to a far greater extent than the Dutch and Huguenots whom they were employed to protect and serve. Because of the genetic closeness of the north German and Dutch populations (in reality, Dutch are really simply another group of north Germans who transformed their regional identity into a national one for various reasons) I doubt that more thorough genetic testing will resolve this, rather, more pedigree analysis needs to be done on other individuals. But it’s an insight into the fact that social parameters have often been crucial to fitness in the human past.

As for the non-white component, the author’s results match those of previous researchers. He confirmed the likely probability of these results by the fact that his father carries mtDNA group M, which is most diverse in India. And in fact his father’s maternal lineage does trace back to a woman who was likely an Indian slave (slave women had particular surnames indicating their origin). My previous posts on the Coloureds highlighted the large Asiatic component to their ancestry, and it looks like previous researchers ignored this and focused on the Khoisan and Bantu. They also attempted to calculate ancestry based on classical markers which were found in African populations, and are present in low frequencies in Afrikaners, but that might ignore Asian signature markers (additionally, I assume that there was some natural selection for G6PD alleles). A survey of the total genomes of Afrikaners should be able to resolve the details of their ancestry, but it seems that the Afrikaners are far more colored than white Americans, by a factor of 5, but far less than white Latin Americans like Argentineans, probably by a factor of 5.

Finally, the author was also able to assess whether his ancestors exhibited a trade between quantity and quality in terms of their optimal number of offspring. In other words, did those who favored an extreme r or K selected strategy suffer vis-a-vis those who produced a more moderate number of offspring, not too low, and not too high? The author did not find any evidence of a tradeoff, and an optimal fitness. He was careful not to generalize too much, especially in light of the fact that Dutch colonial South Africa was an atypical society in many ways. I assume that living on the frontier means not having to say you’re sorry if you breed too much or too little.

Citation: Greeff, J. (2007). Deconstructing Jaco: Genetic Heritage of an Afrikaner Annals of Human Genetics, 71 (5), 674-688 DOI: 10.1111/j.1469-1809.2007.00363.x

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