November 08, 2009

Genetic ancestry of Coloured South Africans

Hum Mol Genet. 2009

Genetic structure of a unique admixed population: implications for medical research.

Patterson N, Petersen DC, van der Ross RE, Sudoyo H, Glashoff RH, Marzuki S, Reich D, Hayes VM.

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 approximately 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.

Link

21 comments:

Annie Mouse said...

Indonesians?

Gioiello said...

Netherlands had colonized Indonesia and many Indonesians probably were taken to South Africa. Why not?

Charles Iliya Krempeaux said...

@Gioiello, you said...

"Netherlands had colonized Indonesia and many Indonesians probably were taken to South Africa. Why not?"

Just a guess, but couldn't Madagascar be a source of "Indonesian" genes as well? People from Borneo settled in Madagascar long long ago, didn't they?

Gioiello said...

I don't know if there was a migration from Madagascar to South Africa. Certainly Malagasyans are of South-Asian language and genetically a mix with Africans, but Madagascar was a French colony and population wasn't numerous. Without reading more, I bet on a fluxus from Indonesia by Dutches.
When South Africa passed under British rule, workers began to come from India.

Maju said...

Some of their ancestry comes from Malaysia, Indonesia and seemingly also from Madagascar (I did not know that).

What I find odd is that no Khoikhoi (Hottentot) has been detected, when originally they were the offspring of white colonists and the native Khoikhoi. I wonder if this cluster is hidden in the "Xhosa" cluster somehow (as Xhosa are obviously one of the most "Khoi" of all Bantu nations - just look at Mandela's "bushman" face).

terryt said...

"I wonder if this cluster is hidden in the "Xhosa" cluster somehow".

Almost certainly so. 'a population genetically close to the isiXhosa sub-Saharan Bantu'. So I presume it includes all 'native' southern Africans.

Michael said...

Hi (Dienekes, is it?),

My name is Michael Rivera, and I'm an 18-year-old blogger, studying Anthropology in the UK right now. I'm only just starting an undergraduate course right now, so after browsing through your blog and the things you link to, I feel like I'm incredibly naive and dense in comparison.

I'm about to start a blog similar to yours, one about my readings and my research in the subject. I feel like it'll help me understand anthropology if I'm constantly writing about it, and I just wanted to let you know here that I'm reading your blog (trying to, at least), and the depth and difficulty challenges me. I actually learn a little with every post, so well done on maintaining what looks like many months of research, you are an inspiration to me.

Michael.
Do you hate it too?
"If you're going through Hell, keep going."

Ponto said...

The South African Bantu speaking population has a lot of Khoi Khoi admixture. You would be hard pressed to find any Khoi Khoi left, that is unmixed to test.

Personally the researchers used Indonesians solely because of the Dutch presence there, an easy cop out. Obviously the researchers don't know Indonesia very well. It spans many islands over a large distance with many ethnic groups. Using Indonesian is meaningless unless you quantify which Indonesians you are referring to by that nomenclature.

Actually the element was Malay, and spoke Malay and practiced Islam. Indonesians have been nominally muslim for most of their Muslim history until the advent of independence and improvements in education in the later 20th century. Indonesian is a modern language ca 1945 used by after independence as a unifying language to encompass the whole of Indonesia and its many ethnic groups and mutually incomprehensible languages.

The Indonesian thing is pure laziness on the part of the researchers. As to the Malagasy Republic, only some of its people derive from the Nusantera, probably Borneo (Kalimantan) and they did not speak Malay or Bahasa Indonesia and were not Muslims.

Saya berbicara Bahasa Indonesia. Selamat jalan.

Maju said...

Not sure how correct it is, but if you look up Coloured (notice the British "ou" spelling, "colored" brings you to a different page) in Wikipedia, they claim that all three Malay, Indonesian and Malgassy are part of their ancestry, along with Indian, European and native South African, of which I believe a good deal is Khoikhoi.

terryt said...

"As to the Malagasy Republic, only some of its people derive from the Nusantera, probably Borneo (Kalimantan) and they did not speak Malay or Bahasa Indonesia and were not Muslims".

The Malagasay language is classified as belonging to the Austronesian family, specifically closest to the languages from the western branch. So it's technically not Malay but related to it. The fact they were not Muslims is irelevant. They arrived in Madagascar long before that religion had even first evolved. Agreed that there have been a reasonable number of Africans arrive in Madagascar since the Austronesians so the population is now mixed. But, because Austronesian-speaking people reached Madagascar, it's almost inconceivable that they failed to reach the African mainland. But I have no idea if the 'Indonesian' element in this study is partly a result of such a contribution.

"Indonesian is a modern language ca 1945 used by after independence as a unifying language to encompass the whole of Indonesia and its many ethnic groups and mutually incomprehensible languages".

But most of those languages, although 'mutually incomprehensible', are classified as Austronesian. Papuan languages survive in the east, specifically on the island of New Guinea.

"Indonesians have been nominally muslim for most of their Muslim history until the advent of independence and improvements in education in the later 20th century".

Still are muslim as far as I'm aware.

Maju said...

But, because Austronesian-speaking people reached Madagascar, it's almost inconceivable that they failed to reach the African mainland.

Don't get things wrong, proto-Malagasy people did reach the African mainland (East Africa specifically, where there is brief archeological record of their presence). But it was a mere stop in their long journey to Madagascar. But they did not reach South Africa. The alleged Malagasy ancestry among Cape Coloureds seems to be part of the process of import of migrant workers or slaves into South Africa.

I would not make a big deal of this because Malagasy ancestry, as you say, is either Austronesian or East African, so genetically the markers and components should cluster with either group.

But I am becoming aware as we talk that I know of no paper on Malagasy genetics as of now. It seems like nobody has even bothered surveying the island. True that in general Africa is under-researched...

...

As a side note, being Muslim is not what defines if one is ethnic Indonesian or not. For example Balinese are normally Hinduist, and there are other groups that keep their pre-Muslim religions.

quantum_physics said...

Actually, there is no archeological evidence of Austranesian presence in Africa. And also genetic studies have been done on the Malagasy showing that they are 50% Austronesian and 50% Bantu, with a bit of sexual bias in this distribution.

On the other hand the first dutch settlers relied on a lot of slave labour for their settlement and most of the slaves came from SE Asia. They exist as a community in South Africa today known as Cape Malay.

Maju said...

Actually, there is no archeological evidence of Austranesian presence in Africa.

Seems I was wrong in that one. I misinterpreted more generalistic comments on the presence of Austronesian-style cultural elements, like boats, in East Africa as fossil evidence but it's not.

Mark Royer said...

Interesting discussion. For a good look at the original inhabitants of Madagascar, check out President Andry Rajoelina and his wife Mialay in this link. Clearly Indonesian, and with little or no Bantu in the mix. http://r1lita.files.wordpress.com/2009/03/andry-rajoelina-mialy-rajoelina.jpg

terryt said...

"Actually, there is no archeological evidence of Austranesian presence in Africa".

And that is interesting because they certainly reached Madagascar. As far as I know no SE Asian Y or mtDNA haplogroups have been found on the African mainland. Perhaps the numbers that reached the African mainland were so few that they were rapidly absorbed.

Maju said...

Clearly Indonesian, and with little or no Bantu in the mix.

It is known that the inhabitants of the plateau, and specially aristocrats are less biologically African, while the peoples of the west coast and plebeians are more.

The African fraction does not need to be Bantu, as probably the Malagassy are over that area before the Bantu arrived and anyhow East Africa has many non-Bantu groups.

Perhaps the numbers that reached the African mainland were so few that they were rapidly absorbed.

Absolutely! The early malagassy colonization was very limited, to a few coastal areas. This an the huge distance travelled implies they were quite few. They only had an impact in Madagascar because it was desert at the time.

They must have gone via Africa because they left no colonies in other, then desert, Indian Ocean islands, like the Mascarenes or Seychelles.

By the way, Malagassys would be a good scenario to test real mutation frequency hypothesis: there must have been some founder effects and drift because of the small initial population, the age of colonization is very recent: some 2-3 thousand years ago, just the kind Dienekes and Vizachero find ideal for all kind of haplogroups in Europe.

quantum_physics said...

"Interesting discussion. For a good look at the original inhabitants of Madagascar, check out President Andry Rajoelina and his wife Mialay in this link. Clearly Indonesian, and with little or no Bantu in the mix."

There are differences depending on which tribe you come from. The highland tribes are the most asian looking and have the most asian genes. A 2005 paper found little difference btwn the tribes in haplogroup frequency. A recent paper "On the origins and admixture of Malagasy: new evidence from high resolution analyses of paternal and maternal lineages" does find tribe specific differences in ancestry. How much I can't say. I only read the abstract.

quantum_physics said...

Madagascar is a big mystery to historians and this research could really shed some light on the peopling of the island demonstrating the utility of haplotyping. Also the sexual bias is such that there are more asian female lineages than Bantu and more Bantu male lineages than asian, Demonstrating natural selection for asian MTDNA due to the environment being similar to asia. Instead of similar amounts expected for a late arriving population.

Maju said...

Demonstrating natural selection for asian MTDNA due to the environment being similar to asia. Instead of similar amounts expected for a late arriving population.

What a naive explanation! They took local wives or concubines obviously.

Anyhow the paper is on Coloured South Africans, not Malagassys.

Katie said...

More indonesian and indian slaves were taken to cape town than african in the 17th century, cape town is where the majority of coloureds come from [both my parents are coloureds] they are a mix of northern european,various indonesian groups,san,indian and bantu african slaves and non slaves.

My half a million snps at 23andme gave me closest similarity with east asians,oceanians and northern europeans.My 1/2 million markers at decode me had me closest to Ugyhurs.

catatwork said...

Read the history! 'Malays' is a sloppy colonial term - most Cape 'Malays' did in fact come from Indonesia - especially Sulawesi, Java - and some ethnically Indonesian may also have come from Madagascar. The first Cape Malays arrived in the 1690s as political prisoners from Bantam in Java but led by Sheikh Yusuf who originally came from Indonesia. He brought 12 children with him.

Cape Malays pride themseleves on maintaining their culture but if people are willing to convert to join the culture are quite relaxed about ethnic origin so I would expect their genetic ancestry to be as mixed as stated here.