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Sunday, April 12, 2009

Study suggests single origin for Pygmies.

E. Patin et al., Inferring the Demographic History of African Farmers and Pygmy Hunter–Gatherers Using a Multilocus Resequencing Data Set. PLoS Genetics, 2009.

The autors analyzed autosomal DNA samples from Western and Eastern Pygmies, as well as of a variety of agriculturalist peoples of Tropical Africa. They conclude that Pygmies separated from other Tropical Africans as a single population at the estimated time of some 60,000 BP and that they split into two groups, Eastern and Western, c. 20,000 BP.

Fig. 2. A is regular K-means clustering and B represents "filtered" populations after exclusion of individuals with more than 20% admixture at K=4.


Kosmo said...

Hey! I saw this article, too, and almost posted about it on my blog. :) I'm glad to see you beat me to it.

Very interesting stuff.

Maju said...

That I posted doesn't mean that you can't post too. We probably reach out to different audiences. I really have no problem even taking stuff from other blogs (with due reference) when I find it really interesting.

Very interesting stuff.Indeed, especially because Africa is not the best studied genetical province at all. So this stuff adds a lot to our knowledge.

I am a little unsatisfied with the "filtered" graph (B) anyhow, because in fact most Mozambicans make a separate cluster at K=4, cluster largely shared with some Pygmies (both eastern and western - yellow color). B "filtered" graph is therefore a biased idealist oversimplification which may appear to support the single origin model the authors defend but that in fact shows (by comparison with the real K=4) the kind of brutal axing of data needed to reach to such conclussion.

Etienne Patin said...

Hi Maju and Kosmo, thanks for your interest and comments on our article.
Indeed, the filtered graph is an oversimplification of the current genetic diversity of these populations. Our aim with the B graph was not to show the real structure of the studied populations, but rather to represent the artificial 'filtered' dataset, which was studied to test the influence of observed admixture rates on our estimation method (see estimations of migration rates and times of divergence considering the A dataset and the B dataset, in Table 2). Also, the datasets from A and B reached the same conclusions concerning the common origin of Pygmies.

Maju said...

Thanks to you for posting here, Etienne.

I realize perfectly that the filtered dataset is intentionally simplified but I'm anyhow wondering about the yellow cluster shared by Mozambicans and some Pygmie populations. IMO, it must mean something but not sure what: it maybe an East African specific component, in which case one wonders how it reached the Bakola.

A more strict filtered graph would have shown Mozambicans and Twa Pygmies clustering together maybe, as they are dominated by this yellow component. Not totally sure about the Twa but it's very clear about Mozambicans (so filtering them into the orange cluster is what really raised my eyebrows, as they look clearly distinct from other Bantus at K=4).