Quest for the Malagasy genotype

By Razib Khan | July 28, 2011 11:35 am

I would like to throw out the word that I am looking for a person with Malagasy ancestry for the African Ancestry Project. To my knowledge there are no thick marker autosomal analyses of the Malagasy people. After my recent exploration of Southeast Asian genetics I think even one individual would be highly informative.

As usual I would guarantee that these data are entirely private, and I do not share it with anyone. But in this case I would like to make an exception and stipulate that Joseph K. Pickrell, a graduate student at the University of Chicago, would also be very interested in access to a Malagasy genotype for the purposes of research. Since this is an undersampled population the marginal returns to a Malagasy genotype would be enormous for science, a public good rather than just a private gain.

Also, I am still looking for a Tutsi genotype so that I can ascertain the origin of this population.

Please contact me at africanancestryproject -at- gmail -dot- com.

Je recherche une personne d’origine malgache dans le cadre du projet “l’African Ancestry Project”.

A ma connaissance, il n’existe à ce jour aucune analyse des marqueurs autosomiques du peuple malgache. Ma récente exploration de la génétique d’Asie du Sud me laisse penser que même l’étude d’une seule personne resterait très instructive.

Je garantis que ces données resteront confidentielles et ne seront pas divulguées à des tiers, à l’exception de Joseph K. Pickrell, un étudiant en thèse à l’Université de Chicago, également très intéressé par l’accès à un génotype malgache pour des fins de recherche.

Cette population étant sous-échantillonnées, les rendements marginaux d’un génotype malgache seraient énormes pour le science et d’intérêt général.

Par ailleurs, je suis toujours à la recherche d’un génotype Tutsi afin de déterminer l’origine de cette population.

Merci de bien vouloir me contacter à africanancestryproject-at-gmail-point-com.


Comments (6)

  1. What would interest me from analysis of Malagasy DNA is the African, non-Austronesian ancestry component. Is it Bantu, or is it at least partly from a different population that lived in SE Africa pre-Bantu expansion? Given that Indonesians settled Madagascar around 2000 years ago, the Bantu expansion might not have reached the SE African coast in full effect by that point.

  2. pconroy

    I predict that the African component in the Malagasy people will be more PaleoAfrican (San etc)

  3. @1 and 2

    A 2009 study of Malagasy uniparental markers, updating an earlier one from 2005, can be found here and provides strong foreshadowing of the results from the whole genome. But, even a single Malgasy whole genome could add insights impossible to discern from uniparental markers.

    For example, since Malagasy mtDNA is Austronesian biased, uniparental markers can’t resolve very accurately the extent to which Bantu Y-DNA came from a predominantly Bantu population that had demically replaced previous African populations, or a population more like the population structure of Latin American populations with Bantu male colonists having children with local non-Bantu women.

    Since Bantu Y-DNA has a very wide regional dispersal, it is hard to pin down a geographic origin for those genes within Africa. But, the extent of Bantu replacement v. admixture in different parts of Africa is fairly well established and shows strong regional variation, and in places where there is admixture there is significant regional variation, e.g., between East Africa, Mozambique, and South Africa.

    Even a single whole genome would be very informative regarding the maternal component of the African contribution to Malagasy genetics, allowing the geographic locus of the African component of the Malagasy ancestors to be determined with greater confidence and better defined.

    Even more exciting is the not implausible possibility that the African component of Malagasy genetics might preserve genetic traces of some Paleo-African population that was exterminated in the last thousand years or so, in much the way that the non-Bantu substrate in Mozambique has been determined to represent a population that is distinct from any modern African population as the Bushmen are from West Africans. Thus, a Malagasy whole genome could shed some light on the extent to which the population structure of Africa has, or has not, changed since Madagascar was first inhabited by modern humans.

    Something else that a whole genome study might reveal is a minor contribution from some place like South Asia or Arabia that could have been a port of call en route to Madagascar by Austronesian sailors (either ANI or ASI) that contributed some individuals to the colonizing population, or alternately, could rule out the possibility of some Asian or Arab admixture en route pretty definitively. If there was a contribution of that kind in the founding population of Madagascar, it would probably have reached fixation by now and appear in almost every person from Madagascar; if it was recent, it would either be much larger than uniparental markers would suggest in that individual, or not appear at all as a matter of random chance.

  4. pconroy


    The reason I hope/expect that there will be PaleoAfrican ancestry in the Malagasy, is:
    1. Based on geographical proximity – yes I know there is a trait between them and the continent
    2. Based on the distribution of H. Pylori – Ancestral African 2

    If you look at #2 above, the AA2 seems to be highest in South Africa and medium high in the Southern Cone of Africa, but medium high in Madagascar too – now this could be just an artifact of how the sampling and contour mapping was generated, but I hope not?!

    Also, off-topic, but looking at the AA2 map at max resolution, it seems that the South Western tip of India also has this at a low level – now that’s interesting?! This brings up the supposition of IIRC Kalevi Wiik, who suggested a few years ago that the First Out of Africa migration was of a pygmy-like population (aka Paleo-Africans), who evolved into Asians in South East Asia, then swept back across India and Europe as moderns…

  5. katasarka

    Madagascar population study won’t be easy. There’s african , indonesian related populations represented differently depending of the tribe studied. There has been merchandising relations and mixing with arabs, indians, chineses. The discovery of the M23 mtdna haplogroup also suggest an ancient asian (indian ?) settlement maybe before the indonesian settlement and the mixing with african.

    @pconroy H pylori study very interesting!

  6. Andry R.

    This study has already done. The Vazimba (black, and probably short) were the first peoples living there, then Sailors from Malaysia and Indonesia colonized the central part. And Arabes and Jewish occupy some parts of the Island. That is why our language is a very similar to malay and some have an arabe’s root (like name of the days, months,…). Some Jewish traditions and rituals are still kept there, like circumcision and exhibitions of the dead body (like the case of Joseph in the bible).


Discover's Newsletter

Sign up to get the latest science news delivered weekly right to your inbox!

Gene Expression

This blog is about evolution, genetics, genomics and their interstices. Please beware that comments are aggressively moderated. Uncivil or churlish comments will likely get you banned immediately, so make any contribution count!

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


See More


RSS Razib’s Pinboard

Edifying books

Collapse bottom bar