Pygmies: "old" populations, and a new "look" (?)

By Razib Khan | April 30, 2012 12:32 am

Over the years one issue that crops up repeatedly in human evolutionary genetics and paleoanthropology (or more precisely, the popular exposition of the topics in the media) is the idea that is that “population X are the most ancient Y.” X will always refer to a population within a larger set, Y, which is defined by relative marginalization or retention of older cultural folkways. So, for example, I have seen it said that the Andaman Islanders are the “most ancient Asian population.” Why? The standard model for a while now has been that non-Africans derive from a line of Africans which left the ancestral continent 50 to 100 thousand years ago, and began to diversify. Presumably Andaman Islanders have ancestry which goes back to this original dispersion, just as Europeans and Chinese do (revisions which suggest that Aboriginals may have been part of an earlier wave, still put the Andamanese in the second wave). The reason that the Andaman populations are termed ancient is pretty straightforward: they’re Asia’s last hunter-gatherers, literally chucking spears at outsiders. An ancient lifestyle gets conflated with ancient genetics.

This is a much bigger problem with the hunter-gatherers of Africa, the Pygmies, Hadza, and Bushmen. The reason is that these populations are of particular interest because they seem to have diverged from the rest of humanity rather early on. Both Y chromosomes and mtDNA confirmed this, and now autosomal analyses looking across the whole genome are confirming it. In other words, they’re basal to the rest of humanity. I believe this is moderately misleading. With the Bantu Expansion much of African genetic diversity disappeared. The hunter-gatherers seem exceptional long and bare branches on the phylogenetic tree because all their relatives are gone!

But the hunter-gatherers remain, and their genetic material has been collected for scientists to study. A new paper in PLoS Genetics puts the spotlight on Western Pygmies, and their relationship to their Bantu neighors. Patterns of Ancestry, Signatures of Natural Selection, and Genetic Association with Stature in Western African Pygmies:

Africa is thought to be the location of origin of modern humans within the past 200,000 years and the source of our dispersion across the globe within the past 100,000 years. Africa is also a region of extreme environmental, cultural, linguistic, and phenotypic diversity, and human populations living there show the highest levels of genetic diversity in the world. Yet little is known about the genetic basis of the observed phenotypic variation in Africa or how local adaptation and demography have influenced these patterns in the recent past. Here, we analyze a set of admixing Bantu-speaking agricultural and Western Pygmy hunter-gatherer populations that show extreme differences in stature; Pygmies are ~17 cm shorter on average than their Bantu neighbors and among the shortest populations globally. Our multifaceted approach identified several genomic regions that may have been targets of natural selection and so may harbor variants underlying the unique anatomy and physiology of Western African Pygmies. One region of chromosome three, in particular, harbors strong signals of natural selection, population differentiation, and association with height. This region also contains a significant association with height in Europeans as well as a candidate gene known to regulate growth hormone signaling.

The method here is simple. Previous work already confirmed that the height of a given Pygmy was strongly predicted by the amount of non-Pygmy ancestry they carried within their genome. Now the authors here are focusing on regions of the genome which not only show association with the phenotype in question, but signatures of natural selection. At this point I’m cautious enough about associations and positive results from tests for natural selection to be wary of accepting this on face value, but we have some priors here which should make this plausible. That is, there are strong functional rationales, and it isn’t as if the Pygmies are not distinctive in their height phenotype.

Let’s take the likelihood of natural selection for height as a given. What fascinates me is that the authors suggest that selection post-dates the divergence of the Western and Easter Pygmy populations. Why does this matter? Because it may give us a better clue as to the nature of the “pygmy” phenotype, which is common among relic hunter-gatherers the world over. The Bushmen, Pygmy, and various “Negritos” of Asia are small. Some have suggested this is an ancestral human type, or a natural adaptation, or an adaptation to the rainforest. On the other hand, the populations of Oceania are not small. To my knowledge the Indians of the Amazon are not the size of Pygmies. To put my own cards on the table I lean toward the proposition that the “pygmoid” body plan emerges when populations are driven to the margins, or, are being buffeted by disease and stress. It seems likely now that the closest relatives of the Philippine Negritos are the people of Oceania, most of whom are not small of stature. There are non-Bushmen Khoisan populations who are not small of stature. And, reportedly the isolated Andamanese of Sentinel Island are not of small stature!

The point here is that studying marginalized hunter-gatherers has limits in telling us about the nature of the human ancestors. It may be that Pygmies are in many ways derived in their phenotypes, relatively recent adaptations to contemporary exigencies. The results above even imply that the small stature of these populations may be a byproduct of the genetic correlation between various traits, and selection in one direction resulted in a correlated response in height. I would like to make a modest proposal: simply take these people on their own terms, and stop trying to slot them into a convenient paradigm. I doubt that Pygmies are going to be the great physicists of the 21st century because of their genetic variation (this was floated by Dierdre McCloskey on Dan MacArthur’s blog), nor do I think they are a special window in the very earliest of H. sapiens sapiens. They are who they are.

Addendum: Though I do know that some people would be curious about the evolutionary origins of other traits besides height in African hunter-gatherers.

  • Maju

    “To my knowledge the Indians of the Amazon are not the size of Pygmies”.

    There are some Maya tribes who are Pygmy-sized. I helped to interview some of them years ago for a community radio (they were touring Europe explaining their problems in Guatemala or Mexico can’t recall) and their stature, who nobody had mentioned beforehand, truly surprised me (Pygmy sized, just like that picture above: their heads were below my shoulders like those of rather young children but were fully grown adults). We usually say just “Mayas” but they are a very complex network of tribes and languages, possibly not even mutually intelligible, and I do not know the peculiarities well enough to explain.

    I imagine that for some reason this particular tribe (maybe more ancient than others in the jungle?) re-evolved this short stature. Or maybe retained the relevant genetics? Both?

  • Julian O’Dea

    To put my cards on the table, it seems pretty clear to me that dark-skinned people who take to living in rainforest end up with short stature. It is a local adaptation to a particular environment.

    I gave my ideas on the physiology behind the low stature of Pygmies and Negritos in a paper cited here, together with some data on UV light levels in the rainforest:

    It is important to note that living in a rainforest is a very different proposition if you are an agriculturalist to being a hunter-gatherer. Only the latter actually live under the rainforest canopy and are subjected to low UV levels. Also, it is the combination of living under the canopy as hunters and having dark skin which produces low stature.

    Wikipedia seems to think that the Sentinelese are Negritos.

  • Julian O’Dea

    People want to explain the distinctive body size of Negritos and Pygmies on the basis of all sorts of things. Lack of food, generalised stress, short life span, heat stress. But the only thing which is unique to the rainforest is shortage of UV light. That is what I focussed on.

  • Miguel Madeira

    “There are some Maya tribes who are Pygmy-sized. I helped to interview some of them years ago for a community radio (they were touring Europe explaining their problems in Guatemala or Mexico can’t recall) and their stature, who nobody had mentioned beforehand, truly surprised me (Pygmy sized, just like that picture above: their heads were below my shoulders like those of rather young children but were fully grown adults).”

    «In the early nineteen-seventies, when the anthropologist Barry Bogin first visited Guatemala, the country’s two main ethnic groups seemed to live on different social planes. The Ladinos, who claimed primarily Spanish ancestry, were of average height. The Maya Indians were so short that some scholars called them the pygmies of Central America: the men averaged only five feet two, the women four feet eight. The Ladinos and the Maya shared the same small country, so their differences were assumed to be genetic.
    But when Bogin, who now teaches at the University of Michigan, began taking measurements he soon found another cause. “There was an undeclared war going on,” he says. The Ladinos, who controlled the government, had systematically forced the Maya into poverty. Whether they lived in the city or in the countryside, the Maya had less food and medicine, and they had much higher rates of disease.

    A decade and a half later, after civil war had erupted and up to a million Guatemalans had fled to the United States, Bogin took another series of measurements. This time, his subjects were Mayan refugees, between six and twelve years old, in Florida and Los Angeles. “Lo and behold, they were much taller than the Maya in Guatemala,” Bogin says. By 2000, the American Maya were four inches taller than Guatemalan Maya of the same age, and about as tall as Guatemalan Ladinos. “As far as I know, it’s the biggest increase of its kind ever measured,” Bogin says. “It shows that they weren’t genetically small. They weren’t pygmies. They were suffering.”»

  • Miguel Madeira

    About the Andamaneses (not necessarly the Sentineleses), Sir Arthur Conan Doyle apparently was convinced that they were pygmies:

  • Karl Zimmerman

    Aren’t there historic accounts of pygmies? IIRC, Rome seemed to have a vague knowledge that pygmy populations existed somewhere far upriver in the Nile Valley (admittedly, this may be one of the few cases of a legend that happened to be right by accident). Still, this seems to suggest their short height is at least 2,000 years old, meaning (assuming it was post-agricultural stress) you’d be looking at only around 1,000 years for the diminutive stature to develop.

  • Amanda S

    Australia also had some populations of short people living in the tropical rainforest nears Cairns. This is an article about them.

    This is an article about their rather taller modern descendents.

  • Maju

    #4 @Miguel Madeira: I have seen Mayas before in film and real life and they were not so extremely small, just somewhat short. Also I’m familiar with short size because of malnutrition: for example Galicians were decades ago the shortest population of Iberia by far and now the younger generations are the tallest ones. But short Galicians were never that much short: they were (still are the older generation, often) short but not Pygmy.

    There seem to be some Mayas who have some Pygmy-like genetics. I can’t say much more but it’s something more than just malnutrition and stress. Height have both environmental and genetic components: Japanese did not grow Nordic-like in size with development and improved nutrition: genetic elements also matter.

  • Audacious Epigone

    LOL at the addendum. Please don’t ban me for making such a frivolous comment, but that really did make me laugh out loud.

  • Julian O’Dea

    I hope Razib will not object if I note that some of the issues raised here in comments have already been traversed here:

  • Daninthai

    Is there any record of these African Pygmies growing up (no pun intended) in Europe or the USA (i.e. developed country), where they’ve had access to nutrition and medicine, and either keeping the small stature or having a increase compared to their kin in Africa?
    My Google search keeps linking me to pygmy pets.

  • TGGP

    I tried searching MacArthur’s blog for the McCloskey incident but came up short. Of course there are comments at the old gnxp site inaccessible nowadays.


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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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