Evidence that Afrikaners surely have non-European ancestry

By Razib Khan | March 23, 2013 2:46 am

I was reviewing some literature for a blog-post-to-come and I noticed a figure in a paper I’ve long been aware of which indicates to me that Afrikaners surely have a non-trivial proportion of non-European ancestry. The paper is Population differences of two coding SNPs in pigmentation-related genes SLC24A5 and SLC45A2. It’s a forensics result. Basically SLC24A5 is useful for differentiating West Eurasians from Africans and East Asians, Amerindians, and Oceanians. But it is not too useful in distinguishing between West Eurasians. The “European” derived variant SNP within this locus is actually present at ~50% frequency as far south and east as India. In contrast, the “European” derived variant of SLC45A2 decreases much more rapidly outside of Europe, so it is a more plausible European-diagnostic-marker.

The figure below illustrates the results from the paper:

Here’s what you need to know about the samples:

Randomly selected individuals from populations sampled were Chinese from Guangzhou (South China), Uygurs from Urumqi (West China), Ghanaians from Accra, Xhosans (Africans) and European-Africans from Cape Town, and Sinhalese and Tamils from Sri Lanka. The numbers of samples analyzed were 80 for Chinese, 121 for Ghanaians, 101 for Xhosans, 101 for Europeans, 55 for Uygurs, 54 for Sinhalese, and 58 for Tamils.

The abbreviations should be self-evident now. What struck me when I thought about it is that the ancestral allele frequency for SLC24A5 is way too high for a Northern European population. If these are 101 whites from Cape Town, presumably they are a mix of Afrikaners (Cape Dutch variety) and English speakers. I am surprised to see any ancestral variants of SLC24A5 in a putative Northern European population. The Afrikaners are descended from Dutch, German, and Huguenot French ancestors. In the HapMap none of the 63 “Utah White” individuals (assume these are “founders”) carried the ancestral allele.  Of the 101 Tuscans, there was one ancestral allele copy. In the paper above they report a proportion of 0.975 for the derived European variant of SLC25A5 (probably five allele copies out of 202). Very high frequency of the derived variant, but nevertheless not as high as I would have expected.  We’ve got a lot of data on this SNP, and the derived variant is pretty much fixed in Northern Europe, and nearly fixed in Southern Europe. A study of 158 Greeks yields two ancestral alleles. This is in the same range of the Tuscans, ~0.63%. The values for SLC45A2 also seem a high for a Northern Europe population, but the derived variant is not quite fixed, and the minor allele frequency is more variable across populations (the “non-European” variant is present at a less than 5% in Northern European populations, but usually more than 1%).

This question will be answered definitively soon enough. There is apparently a group working on estimating admixture of non-European ancestry in Afrikaners, and the result will probably come out in the next year or so. And there has been past genealogical work which documents the intermarriage between white men at the Cape and non-European women in the early years of the colony. But, it seems likely that this admixture was substantial enough, and enough Cape Coloureds have “passed,” that it is likely evident in the autosomal genome of contemporary Afrikaners. Neat to see that old data in light of all of the evidence we have about European populations can generate an unrelated inference.

MORE ABOUT: Genetics
  • Luis Aldamiz

    You may be right but what about SW Europeans (French, Basque, Iberians)? Huguenots were mostly from Southern France, so I would not expect any strict correlation with either SE Europeans (Tuscans, Greeks) or NW Europeans. BTW, is CEU a good enough sample for such a fine detail anyhow?
    Utah is a small place with founder effects probably playing to some extent; why not to use some other Western European samples? Just to be even more certain, you know.

    • Luis Aldamiz

      OK, I found a reference (google books’ link), where it is evident that SLC24A5 is almost totally absent not just in Europe but also West Asia and even some populations of Central Asia and Pakistan. Even in North Africa it has only minor presence, as happens with Uralics from NE Europe. So my question is answered and confirms that you seem to be quite right about admixture among Afrikaners.

  • Dmitry Pruss

    5/202 Afrikaners vs 2/156 Greeks? P-value about 0.3. Nothing significant

    • razibkhan

      i probably wouldn’t make much of it if afrikaners were not mostly northern european in heritage. also, there are other priors (e.g., slc45a2 is also on the high side). also, double the number of greeks. i was comparing out of total alleles. (158*2)

      • Dmitry Pruss

        OK still doesn’t seem significant, but it may be inching closer. Do Afrikaners have some Morisco or Sephardi ancestry? (Through refugees / escapees from Spain, the Netherland’s longtime imperial master) ? Spain’s own colonies definitely saw an enrichment in Sephardi genetic material.

        • razibkhan

          not to my knowledge, but wouldn’t seem impossible on the face of it.

  • razibkhan

    it would be preferred you speak english :-) also, please note that the indians would carry this variant to a high proportion. but i think the 10% figure is probably high. more like in the 0-5% interval. but we’ll know soon enough.


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About Razib Khan

I have degrees in biology and biochemistry, a passion for genetics, history, and philosophy, and shrimp is my favorite food. In relation to nationality I'm a American Northwesterner, in politics I'm a reactionary, and as for religion I have none (I'm an atheist). If you want to know more, see the links at http://www.razib.com


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