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Pygmies Are Short Because Nature Made Them So
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Aka Pygmies

The Pith: There has been a long running argument whether Pygmies in Africa are short due to “nurture” or “nature.” It turns out that non-Pygmies with more Pygmy ancestry are shorter and Pygmies with more non-Pygmy ancestry are taller. That points to nature.

In terms of how one conceptualizes the relationship of variation in genes to variation in a trait one can frame it as a spectrum with two extremes. One the one hand you have monogenic traits where the variation is controlled by differences on just one locus. Many recessively expressed diseases fit this patter (e.g., cystic fibrosis). Because you have one gene with only a few variants of note it is easy to capture in one’s mind’s eye the pattern of Mendelian inheritance for these traits in a gestalt fashion. Monogenic traits are highly amenable to a priori logic because their atomic units are so simple and tractable. At the other extreme you have quantitative polygenic traits, where the variation of the trait is controlled by variation on many, many, genes. This may seem a simple formulation, but to try and understand how thousands of genes may act in concert to modulate variation on a trait is often a more difficult task to grokk (yes, you can appeal to the central limit theorem, but that means little to most intuitively). This is probably why heritability is such a knotty issue in terms of public understanding of science, as it concerns the component of variation in quantitative continuous traits which is dispersed across the genome. The traits where there is no “gene for X.” Additionally, quantitative traits are likely to have a substantial environmental component of variation, confounding a simple genotype to phenotype mapping. Arguably the classic quantitative trait is height. It is clear and distinct (there aren’t arguments about the validity of measurement as occurs in psychometrics), and, it is substantially heritable. In Western societies with a surfeit of nutrition height is ~80-90% heritable. What this means is that ~80-90% of the variance of the trait value within the population is due to variance of the genes within the population. Concretely, there will be a very strong correspondence between the heights of offspring and the average height of the two parents (controlled for sex, so you’re thinking standard deviation units, not absolute units). And yet height is at the heart of the question of the “missing heriability” in genetics. By this, I mean the fact that so few genes have been associated with variation in height, despite the reality that who your parents are is the predominant determination of height in developed societies.

The issue gets even more thorny when you talk about variation across societies. This is a simple and yet complex issue. On the one hand we know that over time people across the world have gotten taller as nutrition has gotten better. What is less well known is that human populations have been shrinking until the past few centuries since the the Last Glacial Maximum ~20,000 years ago. Why? One can posit many reasons, both genetic and environmental, but it does point us to the reality that the story of height is not monotonic. That is, it doesn’t go in one direction, and has no simple one size fits all answer.

But that’s just the dimension of time. How about space? The question of whether different populations have final different genetic potentials for height is a disputed one. And yet it seems plausible that at the extremes there are genuine differences in the gene frequencies across populations which will speak to their different distributions in trait values. This is particularly interesting in the case of very populations characterized by low median adult heights, often termed “pygmies.” Of particular note are the Pygmies of Central Africa, who exist in a state of cultural symbiosis with their Bantu and Nilotic neighbors, adopting their languages, but remaining distinct.

These populations have very low median heights, but they are clearly not dwarfs (they are proportionate). Thankfully at least the population genetics of the Pygmies of Africa are now relatively well understood. It seems that the Western and Eastern Pygmy populations are very distinct clusters, with a common ancestry perhaps on the order of tens of thousands of years in the past. And not surprisingly the genetic distance between the Pygmy groups and their non-Pygmy neighbors is very large. The Western Pygmies tend to show more evidence of admixture with their Bantu neighbors than the Eastern ones (I suspect this is due to the longer residence of Bantus in this region). But for me the hardest issue to grapple with is the reality that the Pygmies of Central Africa seem to be genetically closer to the Khoisan people of Southern Africa than their Bantu or Nilotic neighbors! I believe this is evidence of an ancient hunter-gatherer continuum within Africa which has been marginalized and overlain by the recent expansion of Bantu farmers and Nilotic pastoralists.

In any case, what does all this have to do with the genetics of height? A new paper in the American Journal of Physical Anthropology synthesizes the inferences generated from population genetics with the basic logical assumptions of quantitative genetics to adduce that the difference between Pygmies and non-Pygmies in height is actually likely to be due to heritable differences. Indirect evidence for the genetic determination of short stature in African Pygmies:

Central African Pygmy populations are known to be the shortest human populations worldwide. Many evolutionary hypotheses have been proposed to explain this short stature: adaptation to food limitations, climate, forest density, or high mortality rates. However, such hypotheses are difficult to test given the lack of long-term surveys and demographic data. Whether the short stature observed nowadays in African Pygmy populations as compared to their Non-Pygmy neighbors is determined by genetic factors remains widely unknown. Here, we study a uniquely large new anthropometrical dataset comprising more than 1,000 individuals from 10 Central African Pygmy and neighboring Non-Pygmy populations, categorized as such based on cultural criteria rather than height. We show that climate, or forest density may not play a major role in the difference in adult stature between existing Pygmies and Non-Pygmies, without ruling out the hypothesis that such factors played an important evolutionary role in the past. Furthermore, we analyzed the relationship between stature and neutral genetic variation in a subset of 213 individuals and found that the Pygmy individuals’ stature was significantly positively correlated with levels of genetic similarity with the Non-Pygmy gene-pool for both men and women. Overall, we show that a Pygmy individual exhibiting a high level of genetic admixture with the neighboring Non-Pygmies is likely to be taller. These results show for the first time that the major morphological difference in stature found between Central African Pygmy and Non-Pygmy populations is likely determined by genetic factors.

First, is there a plausible physiological reason for the difference in adult height between Pygmies and non-Pygmies? The authors review the relevant evidence:

Endocrinologists have described the physiological determination of the African Pygmies’ short stature: serum levels of Insulin-Like Growth Factor 1 (IGF1) and of Growth Hormone Binding Protein (GHBP) are abnormally low, whereas the levels of Growth Hormone (GH) and IGF2 do not differ from Non-Pygmy controls…In this context, Merimee…proposed that the short stature of African Pygmies could be attributed to the absence of a growth spurt during puberty and that the genetic factor(s) implicated in the Pygmy stature were to be found in the GH-IGF1 axis…A recent gene-expression study further showed a slight (1.8-fold) under-expression of GH and a more dramatic (8-fold) under-expression of the GH receptor in adult African Pygmies, which was not found in Non-Pygmy Bantu speakers…However, the only genetic study focusing specifically on Pygmies’ stature, failed to find allele frequency differences in the promoter region of the gene encoding IGF1 between two African Pygmy populations and Non-Pygmy controls…In this context, whether the Pygmy populations’ short stature is solely due to environmental pressures experienced by individuals during growth (i.e., phenotypic plasticity), or to a complex genetic mechanism, remains to be demonstrated.

I believe that IGF can be found in meat and milk, so there are plausible dietary reasons that one could imagine this difference. As far as looking at differences between the genes which are known to impact height within populations across populations, there simply aren’t that many genes known which could account for the large between population differences. Not to mention that many of the current studies have used European populations, and so would likely have an ascertainment bias which might miss a lot of variance which is common within African populations.

The basic method in this paper is not too difficult to understand:

1) Use STRUCTURE, a program which assigns different ancestral quanta to individuals.

2) And compare the variation in a particular Pygmy-modal quantum across the population with variation in height.

If there are many genetic variants of small effect within the Pygmy genome which are resulting in their relatively low adult median height then dollops of Pygmy genome through admixture will reduce the height of non-Pygmies and dollops of non-Pygmy admixture in Pygmies will increase their height. The presumption is that if there are strong environmental impacts on height due to social differences then the disjunction between genetic identity and anthropological identity will be informative. For example, if Pygmies are put under particular stress or deprived specific nutritional intake because of their communal identity as marginalized Pygmies then different admixture levels with non-Pygmies should not matter much (and vice versa).

There’s a lot of statistics toward the aim of achieving significance in this paper (p-value > 0.05). And I really don’t understand the point of disaggregating males and females, for example. Just convert them to standard deviation units deviated from sex median! But in any case the major correlation is well illustrated by the two panels below. Pygmies are in red and non-Pygmies are in blue:

The y-axis is straightforward, height. You can see the Pygmies in their sample are shorter, on average. The x-axis is an ancestral component inferred from STRUCTURE which is generally found in non-Pygmies. You can see that as expected non-Pygmies have more of this than the Pygmies, but the descriptive statistic of a correlation between the non-Pygmy ancestry and height in Pygmies is evident even in this plot. Conversely, the Pygmy ancestry is correlated with lower adult height in non-Pygmies.

As a single result this particular finding isn’t too earth-shaking. If there was one population which was short due to genetic factors, I suspect that one would have to bet on the Pygmies of Central Africa. And as noted in the paper Pygmoid morphology is found among other hunter-gatherer tropical populations. This may not be a human ancestral type, but it is a type which has emerged repeatedly in our history, whether due to genetic or environmental factors. The big picture is that this same general procedure can be used to explore the differences in genetic dispositions across groups for many quantitative traits. With the coming era of cheap genotyping and sequencing I’m sure it will be done. A intrepid researcher has plenty of admixed populations in the New World to select from. There are in Brazil people who are socially identified and self-identify as white who have less European ancestry than those who are socially identified and self-identify as non-white. To compare the the social and genetic valences of African and European ancestral contributions for medical and psychological quantitative traits these sorts of populations will be of great future interest.

Link credit: Dienekes

Citation: Becker NS, Verdu P, Froment A, Le Bomin S, Pagezy H, Bahuchet S, & Heyer E (2011). Indirect evidence for the genetic determination of short stature in African Pygmies. American journal of physical anthropology PMID: 21541921

(Republished from Discover/GNXP by permission of author or representative)
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  1. This is easy to do, but somehow I think we might have to wait a while before we see results on psychological quantitative traits.

  2. How tall are pygmies? The internets tell me that peoples are classified as pygmies if the average adult male is 5’1″ or less. That actually overlaps the average height of historical poorly nourished populations elsewhere such as Japanese before 1850, or the French around 1800. I had thought that there was a separation, and that pygmies were seldom taller than 4’6″ and that normal adults could be 4′ even.

    Answer quickly because this is important to me. Adult males in my family average about 5’3 or 5’4.

  3. Razib, you said

    “I believe that IGF can be found in meat and milk, so there are plausible dietary reasons that one could imagine this difference. ”

    IGF-1 is found in meat and milk, but only in very small quantities and since it is itself a peptide, it is rapidly degraded in the GI tract, meaning you absorb very little of what you eat (which is why the only therapeutic form of IGF-1 is given via injection).
    There seem to be very few genetic defects in the IGF-1 gene itself that cause short stature. But keep in mind that the system works like this: Growth hormone circulated in the blood bound to GH binding protein, then binds to the GH receptor (interestingly, the circulating binding protein is nothing more than the extracellular part of the GH receptor). Once it binds to the receptor, it triggers a signalling cascade (the JAK-STAT pathway) that eventually increases IGF-1 production. A known, severe form of genetic dwarfism (Laron Syndrome) is usually caused by mutations in the GH receptor. But there are known (rare) defects in the JAK-STAT pathway that also cause short stature. Polymorphisms that decrease IGF-1 may occur in the IGF-1 gene itself but in this case, may be in the GH receptor (which would also decrease GH binding protein) or in the multiple genes involved in the JAK-STAT pathway. Dietary deficiency of IGF-1 would not explain this .But of course, lack of protein in the diet is a potent cause of short stature, only its not via differences in IGF-1 intake.
    Interestingly, Laron dwarfs are almost free of cancer and heart disease.

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