To be Coloured in South Africa means being all of the above

About six months ago I had a post up on the Cape Coloureds of South Africa. As a reminder, the Cape Coloureds are a mixed-race population who are the plural majority in the southwestern Cape region of South Africa. Like the white Boers they are a mostly Afrikaans speaking population who are adherents of Reformed Christianity. After the collapse of white racial supremacy many white Afrikaners have argued that it is natural and logical to form a cultural alliance with the Cape Coloureds because of the affinity of language and faith (Afrikaans speaking Coloureds outnumber Afrikaans speaking whites). For their own part, though a people of color who suffered under Apartheid, the Coloureds have an ambivalent relationship with the black majority and have supported several white dominated political movements since the end of Apartheid.

One of the reasons that the Afrikaners and Coloureds have a relationship is a genetic one: the white ancestry of the Coloureds is the same melange of Dutch, French Huguenot and German which gave rise to the Afrikaners. Though I am unaware of modern genetic studies, older genealogical research has concluded that on the order of 5% of Afrikaner ancestry is non-white, and almost certainly it is through the "passing" of Coloureds into the Afrikaner population. As the Coloureds share language and religion with the Afrikaners this would naturally not be particularly difficult if they could pass themselves off as unmixed European. Or, at least if on the frontier farms of the 18th and 19th century if the neighbors did not inquire too closely as to the provenance of an individual whose ancestry was probably mixed. It is because of the non-white genetic load, small, but not trivial, that individuals such as Sandra Laing emerged from Afrikaner pairings during the era of Apartheid.

But though the Cape Coloured derivation from Europeans and local Africans, a mixture of Bushmen, Khokhoi and Xhosa, is well known and attested, there are other groups who are in the mix, quite literally. The Cape Colony was a way station between the far flung holdings of the Dutch East Indies Company, the VOC, one of the first major joint-stock corporations in the world, and the mother country. Just as Europeans arrived from the north, so Asians were brought from the east, though in this case they were generally slaves or bonded laborers. Large numbers of Southeast and South Asians arrived to serve the Dutch and provide labor which the locals would (because they were free and outside of colonial control) or could not (they died of disease and maltreatment). The Cape Malay community, which is in some ways affinal to that of Cape Coloureds, serves as a cultural testament to the Muslims amongst those brought to Africa. But the Cape Coloureds themselves no doubt have Asian ancestry which has left fewer salient cultural marks than that of their European ancestors.

But recent genetic data is clarifying that ancestry. It seems plausible to assume now that Asian ancestry surpasses European ancestry among the Cape Coloureds, with African ancestry still retaining a plural majority. A new paper in Human Molecular Genetics confirms earlier findings, Genetic structure of a unique admixed population: implications for medical research:

Understanding human genetic structure has fundamental implications for understanding the evolution and impact of human diseases. In this study, we describe the complex genetic substructure of a unique and recently admixed population arising 350 years ago as a direct result of European settlement in South Africa. Analysis was performed using over 900 000 genome-wide single nucleotide polymorphisms in 20 unrelated ancestry-informative marker selected Coloured individuals and made comparisons with historically predicted founder populations. We show that there is substantial genetic contribution from at least four distinct population groups: Europeans, South Asians, Indonesians and a population genetically close to the isiXhosa sub-Saharan Bantu. This is in good accord with the historical record. We briefly examine the implications of determining the genetic diversity of this population, not only for furthering understanding of human evolution out of Africa, but also for genome-wide association studies using admixture mapping. In conclusion, we define the genetic structure of a uniquely admixed population that holds great potential to advance genetic-based medical research.

The name of the game again is population substructure in the service of medical research. In this case, the Cape Coloureds are relevant because of their highly diverse origins, and so their possible relevance for admixture mapping. If a genetic variant which causes disease differs greatly in frequency between two distinct populations, an admixed population would be ideal to explore that particular relationship. African Americans are a case in point, they are modeled easily as a two-way mixture between Northern Europeans and West Africans. The Cape Coloureds present a more complex case, because their admixture derives from several different very distinct groups.

Historically the Asians seem likely mostly to have been from the Indonesian archipelago, as well as from coastal southern India and Bengal. The African demographics of the Cape have changed considerably since the colonial era. The Khoisan groups, both Bushmen and Khoikhoi, have declined in numbers in relation to the Xhosa. Though the Xhosa themselves have clearly absorbed a great deal of the Khoisan, before, and after, that period. For this study the researchers used 20 Cape Coloureds, 20 Xhosa and 20 Indonesians, combined with HapMap and HGDP samples. They covered 900,0000 SNPs.

Here is a figure where they display the geographical origins of their samples:

You should be familiar with most of these; e.g., the South Asian samples are from Pakistan, from the HGDP, the Europeans are Utah Whites from the HapMap.

Below are pairwise genetic distance values:

I want to emphasize that these are pairwise values. The initials represent:

COL = Coloured
XHO = Xhosa
SAN = Bushmen
YRI = Yoruba
CEU = Utah White
CHB = Chinese (Beijing)
SAS = South Asian (Pakistan)
IND = Indonesian

The relatively close relationship between the Cape Coloureds South Asians should be viewed with caution, since there is evidence that South Asians themselves are a compound admixture between quasi-Europeans and an ancient East Eurasian population of Indians. Note the small distance between South Asians and Europeans in the table above.

An easy way to visualize relationships are principal component scatter plots. These plots show independent dimensions of variation within data, in this case genetic data. The points are individuals, and in 2-dimensional plots generally the x-axis illustrates the first component of variation while the y-axis the second component. These are respectively the independent dimensions which explain the most variation in the data set.

In this paper they constructed a series of PC scatter plots where the axes display between group variation, upon which later groups are mapped upon. Below I've repurposed figure 2 a bit to fit on the screen. Here is the legend:

Figure 2. Principal components scatter plots. Indicating (A) our Coloured and isiXhosa samples across an African versus non-African axis, (B) a Bantu versus Bushmen axis, (C) European versus Asian (Han Chinese, Indonesian and South Asian) axis, (D) Chinese versus Indonesian axis and (E) European versus South
Asian axis.

In other words, what you're seeing are the Cape Coloureds being projected onto PC scatter plots where the axes are constructed from populations which resemble their putative parental populations.

And finally, bringing it all together:

The scatter of Cape Coloureds in the domains between these populations dovetails well with what intuition would suggest if they were in fact an admixture between all of these continental populations. But one issue is that because South Asians and Europeans are relatively close on a continental scale of genetic variation PC plots can only be somewhat definitive in establishing a contribution from that group, though figure 2E above comes close (showing that in relation to South Asian groups Cape Coloureds are shifted toward white Europeans).

To confirm a possible contribution from South Asians they used a regression method whereby the allele frequencies in the admixed population can be modeled as a combination of the frequencies from the non-admixed populations. Table 4 shows the results:

These align well with earlier results. But again there is an issue with the fact that South Asians and Europeans exhibit relatively small between population difference in gene frequencies (the methods rely in part on taking the difference between allele frequencies). They divided the Coloured genome into blocks and used a model where they included South Asians and left them out; the model with South Asians had much greater predictive value than that without South Asians. As I noted above the South Asians who were ancestral to the Cape Coloureds were likely Bengalis and South Indians, not the Pakistanis in the HDGP. Therefore using the model of some of the researchers in this paper the ancestors probably had an "Ancestral North Indian" (quasi-European ANI) component closer to 50% as against 70-80% in the case of the South Asian populations in the HGDP. Though even the ANI was at some genetic distance from modern Europeans, the fact that South Asians themselves can be modeled as an admixture of two populations, one very similar to Europeans, and one more similar to Indonesians than Europeans ("Ancestral South Indians", ASI), though still at a much further remove from Indonesians than the ANI from Europeans, I think explains the relatively modest Fst values between South Asians and Cape Coloureds. The Cape Coloureds in to some extent recapitulate an aspect of an the admixture event which produced South Asians (ANI:ASI::European:Indonesian).

One final dynamic confirmed by these results is that there was "female mediated Asian gene flow" and "male mediated European gene flow" in the emergence of a mixed-race group in South Africa. It is especially striking in the case of Indonesian ancestry, and to me surprisingly small in the case of the African ancestry. In the text the authors note that many marriages were contracted between whites and freeborn Africans, so what we may be seeing here is simply that sociological reality, prior to the further crystallization of a racial caste system African males were able to join the mixed-race community. By contrast Asians, disproportionately slaves, could not marry free whites. This resulted in much greater asymmetrical gene flow between white owners and female slaves.

I'll let the authors conclude:

In conclusion, using a novel method for computing degree of admixture, we demonstrate clear evidence of African (genetically close to isiXhosa), Indonesian, European and South Asian contributions in our recently ( 350 years) admixed Coloured samples. This agrees well within the historical evidence. Therefore the Coloured people represent a new class of unique genomes created from a divergent genetic background, including more than one of the described six major ancestral human genetic clusters...This admixture holds strong potential to offer new insights into complex gene-gene and gene-environment interactions, insight into human evolution and human disease evolution, and enabling medical research efforts unparalleled by any other population.

To those who assume that racial mixture leads to an indistinct and homogeneous mass, here is an extended family of Cape Coloureds:

One issue that a researcher on this paper pointed out to me is that there is a difference between the mix of populations ideally used to predict allele frequencies in populations, and the actually admixing proportions. This makes some sense when you note the difficulties involved in separating South Asian from European contributions because the two groups are the relatively similar in relation to the others. The Fst between the Bushmen and Xhoas is 3 times greater than between the South Asians and Europeans!

A final thought. We don't need to go South Africa for a very admixed population. How about Hawaii? At least 20% of the population in Hawaii apparently exhibits some sort of mixed ancestry (probably an underestimate because of various political issues related to Native Hawaiians).

Citation: Nick Patterson , Desiree C. Petersen , Richard E. van der Ross , Herawati Sudoyo , Richard H. Glashoff , Sangkot Marzuki , David Reich , and Vanessa M. Hayes
Genetic structure of a unique admixed population: implications for medical research
Human Molecular Genetics Advance Access published on November 18, 2009, DOI 10.1093/hmg/ddp505.