April 13, 2009

Origin of African Pygmies

From the paper:
Finally, our estimates of gene flow between each group of Pygmies and agricultural populations yielded contrasting values, with levels of gene flow between WPYG and AGR populations three to seven times higher than those between EPYG and AGR populations (Table 2). This result, together with those obtained with protein markers [27], mtDNA [8],[36] and autosomal microsatellites [41],[46], indicates that (i) substantial gene flow has occurred between Western Pygmies and agricultural populations, possibly during a period before the strong social barriers currently separating these two groups became established [29],[32],[33],[41],[56], and (ii) the Eastern Mbuti Pygmies (i.e., the EPYG group in the filtered population dataset) have probably been among the most isolated Pygmy populations of sub-Saharan Africa.

Here are some pictures of Mbuti Pygmies from a National Geographic article.

PLoS Genetics doi:Inferring the Demographic History of African Farmers and Pygmy Hunter–Gatherers Using a Multilocus Resequencing Data Set

Inferring the Demographic History of African Farmers and Pygmy Hunter–Gatherers Using a Multilocus Resequencing Data Set

Etienne Patin et al.


The transition from hunting and gathering to farming involved a major cultural innovation that has spread rapidly over most of the globe in the last ten millennia. In sub-Saharan Africa, hunter–gatherers have begun to shift toward an agriculture-based lifestyle over the last 5,000 years. Only a few populations still base their mode of subsistence on hunting and gathering. The Pygmies are considered to be the largest group of mobile hunter–gatherers of Africa. They dwell in equatorial rainforests and are characterized by their short mean stature. However, little is known about the chronology of the demographic events—size changes, population splits, and gene flow—ultimately giving rise to contemporary Pygmy (Western and Eastern) groups and neighboring agricultural populations. We studied the branching history of Pygmy hunter–gatherers and agricultural populations from Africa and estimated separation times and gene flow between these populations. We resequenced 24 independent noncoding regions across the genome, corresponding to a total of ~33 kb per individual, in 236 samples from seven Pygmy and five agricultural populations dispersed over the African continent. We used simulation-based inference to identify the historical model best fitting our data. The model identified included the early divergence of the ancestors of Pygmy hunter–gatherers and farming populations ~60,000 years ago, followed by a split of the Pygmies' ancestors into the Western and Eastern Pygmy groups ~20,000 years ago. Our findings increase knowledge of the history of the peopling of the African continent in a region lacking archaeological data. An appreciation of the demographic and adaptive history of African populations with different modes of subsistence should improve our understanding of the influence of human lifestyles on genome diversity.



FeministX said...

Wow. I have been fascinated by this all day after reading this. Pygmies look so different that it's not hard to see them as the beginning of a sort of speciation.

I might write about this on my blog. Dieneke, I think you might like to read it. I have been posting a lot about human biodiversity issues lately-


Etienne Patin said...

Thanks for your interest in our article! I just want to clarify a point, as FeministX mentions the word 'speciation'.

Studying the history of African Pygmies and non-Pygmies can unfortunately have some consequences at the local political scale (if political actors hear about our study, for example). Indeed, Pygmies are victims of racial discrimination by farming villagers. Providing any scientific justification to the racial thesis of local political actors could be extremely destructive for Pygmies. So I want to clarify that the idea that Pygmies are beginning to speciate is scientifically wrong.

First, ancestors of Pygmies and non-Pygmies diverged ~60 Kya. This timescale is short, compared to evolutionary times. Ancestors of Africans and non-Africans, and probably ancestors of Khoisan and non-Khoisan, diverged at the same time and you won't say that non-Africans have begun to speciate. Actually, human populations are weakly differentiated, compared to chimpanzee populations, for example.

Second, all human populations who live nearby exchange migrants, including Pygmies and non-Pygmies. This diminishes and will always diminish the genetic differentiation of these populations.

I hope I did not bother you with this, but I think it was important to clarify this issue. Thank you for your understanding!

FeministX said...


Don't worry. I don't actually think they are beginning to form their own species. Their main physical difference seems to be their height, and that could be the result very few mutations.

I did end up writing a little about the pygmies. When I write, I take the viewpoint that IQ is accurately measured in most populations and that it is highly heritable (I take the viewpoint in order to examine it). However, this does not reflect what I actually believe.

The pygmies: