The Merina of Madagascar are Malay and Bantu

By Razib Khan | September 9, 2011 12:46 pm

A month ago I asked for a Malagasy genotype. Almost immediately I received a response from someone that was 33% Malagasy. More recently I have sent a genotyping kit to someone who is Malagasy. Those results should come in within a month or so. But a few days ago I received a contact from a person of the Merina ethnic group of highland Madagascar. So of course I ran their data.

Here are the technical logistics. I wanted to look at their genotype through an African and a Southeast Asian lens. So I created an African loaded data set with 400,000 markers. Unfortunately the Southeast Asian data set I have has only 56,000 markers, and only 18,000 in common with this genotype. I ran ADMIXTURE on the former data set, K 2 to K 11. But at only 18,000 markers I think there just isn’t enough to run ADMIXTURE and make inferences of the grain which I want to make. So I ran EIGENSOFT to generate PCA’s. I did this for the African data set too. From dimension 1 to dimension 10.

I uploaded all the files to Google Docs. You can look at the Southeast Asian weighted PCA’s there. I’m not going to post them. The Asian ancestry of the Merina individual does look to be similar to that of Malays. What you’d expect. Below are K = 10 and PC’s 1 and 4.

The African ancestry of this individual is not exotic at all, and aligns with what we saw in the ~33% Malagasy individual.

CATEGORIZED UNDER: Human Genetics, Human Genomics
MORE ABOUT: Genetics, Genomics

Comments (13)

  1. David R Bachinsky

    Are bantu homogenous? In the Congo (Peace Corps) multiple languages but genetics?

  2. #1, compared to reference of pygmies or bushmen, yes. bantu languages all have a broad family similarity. linguistic diversity can build up very fast. this is most obvious in oral societies. the point here is that this individual’s african ancestry is clearly similar to bantu/west african. there isn’t much east african or pygmy or khoisan.

  3. Insightful

    Perhaps it’s safe to say that the Bantu are the most successful of all the sub-saharan Africans, out competing East African horners, South African khoisan etc. The Bantu (coming from West Africa originally) has literally pushed all these groups to the ‘fringes’ of the continent..

  4. The proportionate similarity to the East African Bantu Luhya rather than other African populations is interesting. There had been a lot of speculation out there that Madagascar might preserve some residual genetic trace of a lost population from mainland Africa or would be distinctively East African as opposed to Bantu in composition.

    The dates for the settlement of Madgascar and the Bantu expansion are sufficient close that they can be compatible, but it is a close thing. They wouldn’t necessarily have to overlap – particularly given the uncertainty about where in Africa the Asian seafarers picked up an African contribution (although one would presume that it was somewhere on the east coast of Africa).

    This does, however, fit with the notion of the Bantu as the population through which Asian tropical plants (e.g. banannas) were incorporated into African food production.

    The PCA plot is unsurprising.

    The biggest surprise seeing the data is the small but not negligible South Asian contribution, although there are multiple historical moments when that could have come about and it would not have to have been associated with the initial colonization of Madagascar.

  5. Eze

    It’s pretty cool that you were able to get a Malagasy and a Tutsi sample so quickly! The results for this full Malagasy are interesting, I expected them to be slightly more African but from what I gather the Merina are the most Asian out of the Malagasy groups so that might explain it.

  6. #6, the merina are the most asian stereotypically. the next sample will be Betsileo, which is a very closely related group. the 1/3 malagasy individual had sakalava background, and this group is more coastal and african.

  7. David JOHNSTONE

    I am an Australian married to a Tandroy and living in Fort Dauphin in the extreme South of Madagascar. Your study and the possibility of unintended bias concerns me greatly. The Imerina represent no more than 15% (at best) of Madagascar’s population. There are, in fact, 18 different ethnic groups and their roots are similarly diverse, although most are I beleive a mixture predominantly of African and Malay. However, you should know that something very akin to apartheid exists within Malagasy society, the iMerina holding virtually all key posts, academic seats, etc. and the wealth not being distributed to others (“mainty” – or blacks) whom many iMerina shun/regard as their ethnic inferiors. Thiss is an unfortunate fact, although your iMerina contacts will poo-hoo this saying this is how it used to be but all has changed now. It hasn’t! The iMerina hold nearly all diplomatic and academic posts and are at great pains to promote their culture as THE unique culture of the island and themselves as the only indigenes (therefore possessing a superior claim to all the assets etc. of the island). For their own economic interests they have been abetted in this by the colonial (and subsequent) French administration. All, therefore, is NOT as it seems at first glance on this island, where I have now been living for 5 long years. You, sir, are a scientist I beleive. To have a balanced and unbiased view, therefore, of the true origins of the Malagasy people, you would need to analyse also the DNA of costal folk (cotiers) like my Tandroy family (we would gladly provide you with samples if you could facillitate this), their cousins the Tanosy, the Vezo from Tulear, The Betsimaraka from the Mananjary region, The Barra from the savannah region north east of Tulear etc.etc.etc. Your iMerina contacts will tell you that the ethnic variations you will find are the results of slavery and/or blow ins. Maybe … but they have a hidden agenda in claiming this. In a previous incarnation I lived for 12 years with a woman from Tonga, a cousin of the late king Tupou in fact. I was amazed when I came here to find more than a few words in the Tandroy dialect wwhich are strangely similar, aand sometimes identical. Could this point to immigration here from Polynesia too as well as from Asia and Africa …. both of which stains are imeadiately apparent in the population at large? I would be interested to hear from you sir.

  8. #8, polynesians and malagasy are both austronesian. the first malagasy i looked at was west coastal fyi, at least in part. i assume that all malagasy are primarily different proportional mixtures of malay and bantu, though other components would be a nice surprise (indian seems the most probable).

  9. Robert

    Hello Razib, have you seen the following paper?

    ß-Globin Haplotype Analysis Suggests That a Major Source of Malagasy Ancestry Is Derived from Bantu-Speaking Negroids

    Rachel Hewitt,’ Amanda Krause,’ Andrea Goldman,1 Gwyn Campbell,2 and Trefor Jenkins’
    ‘Department of Human Genetics, School of Pathology, The South African Institute for Medical Research and University of the Witwatersrand, and 2Department of Economic History, University of the Witwatersrand, Johannesburg

    Am. J. Hum. Genet. 58:1303-1308, 1996

  10. Robert

    Interesting samples would be from the Makoa in the southwest who are descendents of Mozambique slaves to see if they have Indonesian genetics. And, to look for the most light skin, straight hair Merina from Tana to see if there are any pure Indonesian Malagasy.

  11. prettyzoely

    David JOHNSTONE Says “However, you should know that something very akin to apartheid exists within Malagasy society, the iMerina holding virtually all key posts, academic seats, etc. and the wealth not being distributed to others (“mainty” – or blacks) whom many iMerina shun/regard as their ethnic inferiors.”

    Je vais parler en français, les propos de Monsieur David Johnstone me choquent profondément. Je suis originaire des Hauts Plateaux et donc Merina mais c’est vous les Vazaha qui divisent les Malgaches. Peu importe d’où je suis originaire, quand on me le demande, je réponds que je suis malgache, point final.

    As @malagasy says when he twitted your post (he is not malagasy, I think) : malagasy Merina #genetics are bantu and malay says @razibkhan . I believe he will find all malagasy to be the same.
    I completely agree with him. So please stop saying b*** Mr David JOHNSTONE

    @Razib Khan : I have a lot of respect of your work, I’m not scientist and I apologise about my comment to Mr David JOHNSTONE but I couldn’t let him saying what he said.

    Thank you very much

  12. FranckRR

    Just a few comments.
    The problem of your study must be to have the right sample. Let me explain. Every tribe in Madagascar has casts. It means that every marriage were arranged so people from the same cast marry only the same type (same physical looking : skin color, straight hair…). The history (unofficial) says that there were at least 2 big wave of indonesian/malay with a stop near Ceylan. That these people had more technical tools so they dominate the locales which may have same african-alike ancestor – (pygme mostly). When you build yuour sample, you must take care of that. Even Imerina is so wide in variety (from a almost pure asian to an almost pure african) that all the statements above may be wrong.

    In every big country history, there are battles and winners usually spread their culture, norms etc. David must take a closer look to what happen to the native Australian (their language is not official, I can’t see any of their kind in any administration… It’s well known that Imerina realm has finished “unifying” the whole island and was about to normalize the whole island when the French colonized us. This is history so we can’t judge if it’s good or bad, it’s done ! let’s take the good side of it : same language or almost, nearly the same cultural background. It’s suppose to ease creating an unified country.

    So I have one question : what is the purpose of such study of yours ? How have you built your sample to be able to state such affirmation ?


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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


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