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Citation: Nature Communications 5, Article number: 3163 doi:10.1038/ncomms4163



Etienne Patin has another paper out on the genomics of Central Africa, and the relationship of the Pygmies to their agriculturalist neighbors, The impact of agricultural emergence on the genetic history of African rainforest hunter-gatherers and agriculturalists. It is to a great extent expanding upon earlier work with denser marker sets, larger sample sizes, and of course ~2014 statistical genomic techniques (e.g., ALDER). As background you have to remember what Patin established before: the western and eastern Pygmy populations of the Congo rainforest seem to have diverged tens of thousands of years ago, tens of thousands of years after their divergence from the ancestors of their agriculturalist neighbors. By and large these neighbors speak Bantu languages, which have swept out of the eastern fringe of what is today Nigeria only within the last 3,000 years. The numbers alluded to the paper are separations on the order of ~20,000 years before the present for the Pygmy groups (west vs east), and then ~50,000 years for the ancestors of the agriculturalists vs. the proto-Pygmies. Think about this: diversification within Africa occurred at about the same time that the most distant of the non-African groups were starting to become isolated from each other. The Pygmies are not just interesting from an ethnological perspective, along with the Khoisan they preserve to a high degree an ancient and diverged group of populations which have largely been marginalized due to the demographic expansions of peoples speaking Niger-Congo and Nilo-Saharan languages (the Pygmy speak the languages of their agricultural neighbors, but this seems a recent development).

An interesting twist revealed in this paper is that admixtures seem to be relatively recent (on the order of 1,000 years), and, those levels are quite high indeed in many Pygmy populations. This is not the case with agriculturalists. In other words, the genes of agriculturalists seeped into the Pygmies, but far less moved in the reverse direction. As analogy, consider that the average Native American is far more European than the average European American is Native. But, as with the case of the Pygmies and their neighbors it may be that there is more Pygmy ancestry in the aggregate in their numerous neighbors, than among the relatively rare Pygmies!

Finally, I think we need to now broach the topic of genomic value for posterity. It is well known that in the Congo region today Pygmies have been the target of conscious genocide, as well as suffering from the consequences of the great wars of the past few decades (I recommend Dancing in the Glory of Monsters: The Collapse of the Congo and the Great War of Africa to anyone with a modicum of interest in this topic). But the results in this paper indicate that the Pygmies are under clear threat of being demographically absorbed by their neighbors before the passing of this century. In particular this paper reinforces what has been clear in other results: the Mbuti of the eastern regions of Congo in particular harbor unadmixed genetic variation. While the Khoisan of southern Africa reside in a quiescent zone of the continent, the Mbuti are not so fortunate. I hope that we get at least hundreds of whole-genome sequences from this population within the next decade, for the sake of all of humanity. Ancient DNA seems unlikely from most of Africa, so massive surveys of the contemporary genomic landscape of this continent is going to be essential to understanding our species’ collective past.

• Category: Science • Tags: Pygmies 
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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.

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“There were giants in the earth in those days; and also after that, when the sons of God came in unto the daughters of men, and they bare [children] to them, the same [became] mighty men which [were] of old, men of renown.”

Genesis 6:4

The Pith: Pygmies and Khoisan have admixture from a distinct population at the level of ~2%. This population diverged from the other ~98% of their ancestry ~700,000 years before the present, and the hybridization occurred ~30-40,000 years before the present. Most other African groups have only traces of this element, with some West Africans lacking it.

I have read the paper in PNAS which I referred to below. There isn’t that much I can add at this point. A lot of the guts were pushed into the supplements, which aren’t on the web yet. I was correct that the Mbuti Pygmies of the eastern Congo likely have a special place in this possible admixture event. In particular, they seem to possess the diverged variants found in the western Pygmies, the Biaka, and the Khoisan populations of southern Africa. As assumed the pattern of admixture seems to be such that the two Pygmy groups and the Khoisan exhibit elevated signatures of archaic contributions, while other African groups manifest admixture in direct proportion to their known admixture to the aforementioned populations. For example, the Bantu group with the highest proportion of admixture are the Xhosa, who also have the most Khoisan ancestry of non-Khoisan populations. The West African Mandenka seem to have trivial admixture from this archaic group. What does this mean?

First, let’s stipulate that this is a model which infers the past from the variation we have on hand. In this way it is qualitatively a different method than that used to ascertain the Neandertal or Denisovan admixture events, which derived from comparisons of moderns with the concrete genome of these ancient lineages. The authors in the PNAS paper observe that the likelihood of ever replicating the non-African results within Africa is low because of the nature of fossil preservation. The likely region of admixture, central Africa, is simply not conducive to the preservation of fossils, let alone genetic material. Now, I have stated before that I am cautious of results from computational models because they regularly reported no admixture as well, further confirming “Out of Africa” with 100% replacement. The change here is that our expectations have been shifted by the possibility of admixture outside of Africa. By testing the power of their models on the Eurasian findings they firmed up their credibility in the absence of ancient DNA. These authors used 61 non-coding genomic regions to reach their conclusions. One presumes that these findings should become more compelling once researchers start performing full genome analyses. If not, then they may be spurious.

With that out of the way, let’s review the results and what they mean on the assumption that they’re valid. The PNAS paper supports a model where a subset of descendants of anatomically modern humans (AMH), and an unnamed archaic group, population X, hybridized relatively recently. Within the last ~40,000 years or so. It seems that this post-dates the “Out of Africa” migration. This should not be shocking, and hopefully will dispel the strange notion that Africa remained static after the emergence of AMH (which leads to some reconstructions of early Eurasians as looking like modern Africans!). It also hints at the possibility that contemporary Pygmies and Bushmen are not the ur-humans, the oldest of old, but rather novel morphs which derive from a recent hybridization event (just like non-Africans).

This brings us to why Pygmies and especially Bushmen were assumed to be ur-humans, the best exemplars of early AMH: they’re basal to other human populations, AMH fossils are found in eastern and southern Africa at a very early date, and they are the most genetically diverse. If this admixture event holds up my intuition tells me that both of these findings are in part derived from this component of the ancestry of these populations. The separation between population X and AMH occured ~700,000 years ago. If I recall my human evolution chronology correctly this is about two hundred thousand years greater than the divergence between AMH and the Neanderthal-Denisovan clade! Depending on the population genetics of the X group, they may significantly reshape a phylogenetic tree which does not incorporate the correct model of divergence and admixture (reticulation).

I assumed that the Mbuti would be special even before seeing the paper because physical anthropologists have long observed that there’s a greater phenotypic difference between them and their Bantu neighbors than the Biaka and their Bantu neighbors. Playing around with public data sets (HGDP) it’s also clear that the Mbuti are more distinctive than the Biaka from other Africans. Additionally, to my great surprise there is a “hunter-gatherer clade,” where the Pygmies and the Khoisan seem to form a cluster against other African populations. It seems implausible to me that these patterns are due purely to admixture from population X. But I think it must play a role. It may also explain the finding from some full genome analyses that West Africans are closer to non-Africans than they are to Pygmies or Khoisan. This may be a function of their lack of population X (and/or, possible back-migration from Eurasia).

At this point I feel a little strange referring to “population X.” It was nice that “X-woman” eventually become the Denisovans. What should we call these potential additions to the human family album? Greg Cochran suggested to me the term ‘Mangani’, by analogy with the use of ‘Hobbit’ for H. floresiensis. Don’t remember who the Mangani were? Here’s Wikipedia on the Mangani:

As described by Burroughs, Mangani are organized in tribal bands ruled by dominant males, or “kings,” which subsist by foraging for fruit, grubs, insects, and sometimes meat, in localized territories. Tribes are generally identified by the names of their kings. Burroughs portrays the Mangani (and indeed most jungle animals) as susceptible to occasional bouts of madness in which they will lash out violently and unpredictably at other living creatures in their vicinity. Tarzan is raised in the tribe of Kerchak, based in the coastal jungle of equatorial Africa, as shown in Tarzan of the Apes and Jungle Tales of Tarzan. As an adult he comes to lead this tribe; later, he becomes accepted in other tribes of Mangani, such as the tribe of Molak in The Beasts of Tarzan. Tarzan continued to associate occasionally with his original tribe until cast out in Tarzan and the Golden Lion, as the result of a Tarzan impersonator having murdered one of its members.

From what I recall in the films and television shows the Mangani are portrayed as rather more bestial, and ape-like, than the description above. It also made the story of Tarzan extremely implausible, more in the vein of Romulus and Remus or Mowgli. But Edgar Rice Burroughs original conception was clearly less fantastic, as the Mangani were intelligent, if profoundly different. If modern humans are the ‘third chimpanzee,’ the Mangani may have been another chimp tribe (H. floresiensis, Neandertals, and Denisovans would also be distinct tribes in this model).

At this point some of you might be alarmed. When evidence for Neandertal admixture surfaced in 2010 message boards had discussion threads with titles such as ‘White People Aren’t Human’. Whether you find this sort of joke amusing or not, it’s at least marginally acceptable to make light of scientific findings to poke fun at what is the dominant ethnic group in the developed world (e.g., see also ‘white people are mutants’). Substitute in black people, and the valence is entirely different. But these findings don’t actually imply this. Many African populations may have the highest quantum of AMH ancestry of all human groups. Rather, this new archaic element is found in Pygmies and Khoisan in particular. The ethnography is rather rich in documenting the dehumanization of these two populations at the hands of their Bantu neighbors. If you have tracked the conflict in the Democratic Republic of Congo you are also probably aware that the Pygmies in particular are targeted in the most grotesque fashion because they are perceived to be less than human. But don’t these results suggest that Pygmies are less than human?

I think on a deep level we may have to start putting this question into the “not even answerable” category. Recently I had an exchange with John Farrell in regards to how Christians, and in particular Catholics, are handling modifications to the “Out of Africa” model. I’m not expert on this obviously, but from what I can gather it seems that some Christian thinkers have taken succor in the romantic narrative of “mitochondrial Eve” and “Y chromosomal Adam” as scientific vindication of at least the general outlines of Genesis. For Roman Catholics, who otherwise can accept evolution without much qualification, the existence of these two individuals is necessary for ensoulment and the fall. Apparently some Catholics are discomfited by the opening toward polygenism implicit in the new model of admixture with archaics.

Since I don’t give much though to the religious implications of science, not being religious, I view the whole discussion with curiosity more than concern. But I think the Christian arguments about the implications of science still have something to teach secular people, because I believe we need to reconceptualize what it means to be human. The “Out of Africa” model, which is classical monogenesis on steroids, does not perturb our intuitions about ideal types and kinds. Rather, it reinforces a Platonic model of what it means to be human, as humans are all kith and kin, descendants in totality and universally from a small group of Africans who flourished ~100,000 years ago. This idea is so pervasive that it even pops up in the series finales of science fiction shows. I now believe that those of us without religious presuppositions should abandon more vigorously this model of humanity.* In a deep sense we already do, in that many of us accept without much controversy that we’re simply the product of material processes. There is nothing which makes us ineffably human. This is why many of us do not consider abortion the murder of a person. At some point the fetus becomes human in all the ways we understand to be human. The zygote’s putative descent from two individuals created in the image of God is not sufficient for us to grant it status as a person. We don’t accept the reality of this descent in the first place.

I don’t think we should be too terrified of this leap. Many of us have already abandoned a deep belief in the idea of ‘free will,’ religious and secular, and yet life goes on. For all practical purposes of decency all human populations present today are basically equivalent as humans. Whatever results we may uncover via science aren’t going to change that, because our intuitions about right or wrong don’t derive from our understanding of the latest science.

Tansey Coetzee

But let’s end on a fun note, because science is fun. To the left is an image of Miss South Africa 2007, Tansey Coetzee. Ms. Coetzee has an Indian mother, and a father who is Cape Coloured. So let’s assess her ancestry. Her mother is Indian, so she is half-Indian. But what about her father? The genetics seems to indicate that the Afrikaans speaking Coloured population has ancestry from Western Europe, India, the Khoisan, the Bantu, and from Southeast Asia. From the Khoisan there will be a dollop of archaic admixture from this new population X. From the Eurasian ancestors there will be Neandertal. The Southeast Asian ancestry of the Cape Colony generally derives from what is today Indonesia (then a Dutch colony). Therefore it is not impossible that Ms. Coetzee has some Melanesian ancestry, and therefore some Denisovan! Yes, the last is a stretch, but work with me. It seems then that Ms. Coetzee may have fractions of ancestry not only from diverse modern populations, but slivers from all the known “other humans!” Above I appealed to your intuition in simply discarding the model whereby humanity is contingent on pure descent from AMH. Individuals such as Ms. Coetzee, and Desmond Tutu, Nelson Mandela, and most of the readers of this weblog, are a refutation of the Platonic model of a human essence made concrete. I know I’m human despite my Neandertal blood. You know in your heart I’m right, so let us accept the finding of science with as much equanimity as we can muster. Our understanding of the details of the human past does not alter our humanity. Just because God is dead does not mean that everything is permissible.

* I generally hold to the position that artificial general intelligence, if it ever arises, should be given the same due consideration, rights, and respect, as organic intelligence. For all practical purposes, they should be treated as we would treat humans. So this isn’t a big leap for me personally.

Image credit: Jose Rosengurtt

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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

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Khoikhoi on the move….

Dienekes mentioned today a new paper, Signatures of the pre-agricultural peopling processes in sub-Saharan Africa as revealed by the phylogeography of early Y chromosome lineages. Because of the recent comments in this space on the genetic history of Africa I was curious, but after reading it I have to say I can’t make much sense of the alphabet soup of haplogroups. Remember, there are different ways to capture and analyze the variation in one’s genes. A common activity is to sweep over the whole genome and focus on single nucleotide polymorphisms, variation at the base pair level. So my own analyses using ADMIXTURE focus on tens or hundreds of thousands of such markers. But there are other types of genomic variation, such as copy number, microsatellites, and minsatellites.

Additionally, much of the older human phylogeographic literature focused on mtDNA and Y chromosomal variance. For mtDNA it was partly a function of how easy it was to extract the genetic material (it’s copious on the cellular level). But perhaps more importantly these two types of variance aren’t subject to recombination. This means they are defined by clean phylogenetic trees which do not exhibit reticulation (recombination chops apart correlated markers and mixes & matches them) and presumably are not subject to natural selection, and so perfect for coalescent theory. So you can posit lineages related to each other by steps of sets of mutations, and also easily calculate the time until the last common ancestor for two different branches of the tree using a “molecular clock” model.

Here’s the abstract:

The study of Y chromosome variation has helped reconstruct demographic events associated with the spread of languages, agriculture and pastoralism in sub-Saharan Africa, but little attention has been given to the early history of the continent. In order to overcome this lack of knowledge, we carried out a phylogeographic analysis of haplogroups A and B in a broad dataset of sub-Saharan populations. These two lineages are particularly suitable for this objective because they are the two most deeply rooted branches of the Y chromosome genealogy. Their distribution is almost exclusively restricted to sub-Saharan Africa where their frequency peaks at 65% in groups of foragers. The combined high resolution SNP analysis with STR variation of their sub-clades reveals strong geographic and population structure for both haplogroups. This has allowed us to identify specific lineages related to regional pre-agricultural dynamics in different areas of sub-Saharan Africa. In addition, we observed signatures of relatively recent contact, both among Pygmies, and between them and Khoisan speaker groups from southern Africa, thus contributing to the understanding of the complex evolutionary relationships among African hunter-gatherers. Finally, by revising the phylogeography of the very early human Y chromosome lineages, we have obtained support for the role of southern Africa as a sink, rather than a source, of the first migrations of modern humans from eastern and central parts of the continent. These results open new perspectives on the early history of Homo sapiens in Africa, with particular attention to areas of the continent where human fossil remains and archaeological data are scant.

The authors posit that the connections between southern African Bushmen and the Pygmies of central Africa which they find in the Y chromosomal lineages might have been mediated by the peregrinations of Khoikhoi pastoralists, who possibly diffused from a central-southern African ur-heimat in advance of the Bantu expansion. This seems plausible to me.

The main issue which I’m curious about in regards to all these results are the connections between Pygmies and Bushmen set against the Bantus. I certainly had no expected it, and it has been repeated several times. There is now a lot of weird evidence that demands a hypothesis.

Image credit: Wikipedia

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

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.

Most people know the standard Out of Africa model. ~50-10,000 years before the present modern humans left the African continent, therefore extant human populations today are descendants of this migration event. The main argument on the margins is only about the possibility of introgression of genetic variants from other non-African lineages into the human gene pool as a supplementary assimilation to the dominant dynamic of replacement. But the story in Africa did not end with that. It is famously well known that Africans have the most genetic diversity of human populations, arguably more than all other populations combined (from mtDNA, Y lineages and more recent autosomal studies). There is population structure, Africa did not remain in stasis after the ancestors of non-Africans left ~75,000 years ago. This paper addresses some of the deeper questions about African structure.

pygmyfig5.pngThe hypotheses being tested by the researchers in this paper are outlined in Figure 5. To the left you can see the 4 models. “AGR” = Agricultural, “WPYG” = Western Pygmies and “EPYG” = Eastern Pygmies. The usage of a cultural term like “Agricultural” is due to the fact that the Pygmies are distinctive in their language, as they speak the dominant dialects of their region, but their lifestyle, which is dissimilar from that of their neighbors. The Pygmies still engage hunter-gathering, while other populations do not. Additionally they are characterized by the physical peculiarity of relatively short stature, ergo the name “Pygmy.”
Pygmies have been of intense scholarly interest, most famously the work of Colin Turnbull, but also by the geneticist L. L. Cavalli-Sforza in his book African Pygmies. While the cultural details of the Pygmies were of interest to anthropologists, the short stature naturally would pique the curiosity of geneticists. Additionally the Pygmy groups could not be understood except in light of a relatively recent event, the Bantu Expansion. As I noted above Africa has not been in stasis. Genetically adaptations to malaria are relatively recent, and almost certainly due to ecological changes wrought by the rise of agriculture as the dominant mode of life across much of the continent. The spread of the Bantu seems to fall into L. L. Cavalli-Sforza’s classic demic diffusion, whereby a population which adopts farming begins to rapidly increase in population up to the Malthusian limit, and then advance as a demographic wave which carries their cultural toolkit forward at a rapid clip. From Cameroun these peoples swept east across the savanna, then south along the littoral of the Indian ocean until they reached the margins of the Cape of Good Hope, where a Mediterranean climatic regime renders the Bantu agricultural techniques relatively inefficient. Another group pushed south through central Africa and the Congo basin down into what is today Angola. All the while these peoples admixed with the local populations, as evidenced by the obvious Khoisan phenotypes among the Xhosa people (e.g., Nelson Mandela) who were along the leading edge of the demographic advance. But they retained their language, whose relatively recent diversification is indicated by the similarities of the Bantu languages from the margins of West Africa all the way into modern South Africa (I have read that most Bantu languages are intelligible, though obviously can not attest to this personally).
Culturally the Pygmies were swept up in the Bantu Expansion, as they speak Bantu languages. This is not exceptional for indigenous peoples, the Vedda of Sri Lanka speak Sinhalese. The similarites and interdependencies between the agriculturalists and Pygmies in a given region have of course given rise to models which suggest that the Pygmies are not autochthonous at all, but rather instances of convergent evolution across the forest zone of Central Africa which were shaped by local adaptation to the hunter-gatherer lifestyle. The recurrent physical motif of Pygmy and Pygmoid peoples across Island Southeast Asia without any suggestion of a phylogenetic closeness between these groups opens up this as a plausible option. The geographic separation between the West Africa and East African Pygmies is not trivial, on the order of 1,000 miles or 1/3 the distance across of the United States. And the terrain across the interval is fragmented by forests and river systems. In fact the Congo river serves as the north-south division line between Bonobos and the Common Chimpanzee, suggesting the power of geography in driving speciation.
pygmystructure.pngThe data reported here do not support the position that the Pygmies evolved recently from agricultural populations. Here is a reedit of Figure 1 from the paper (so it can fit on the screen easily). You see the agricultural populations the researchers used, as well as the two Pygmy groups, and where they are located. The second set of figures shows how the results are displayed using Structure. Assuming a number of populations defined by K you see where individuals within these populations sort out. Admixed individuals exhibit the admixture in their genotypes, while those who are not do not. At K = 2 you see immediately that there is a difference between Pygmies and non-Pygmies. Additionally the researchers observe that the two Pygmy populations which are sometimes termed “Pygmoid” because of their comparative acculturation to Bantu populations among whom they live show the greatest evidence of admixture and gene flow. Then at K = 3 the two Pygmy groups separate out. In other words, the agriculturalists are the outgroup to the Pygmies, and Pygmies are a phylogenetically supported group, though one with two branches. This does not prove that Pygmy stature is necessarily a common derived feature inherited from the ancestral population, for that you would need to look closely at the genetic architecture of the trait in question and the phylogeny of the haplotypes on the implicated loci. In any case the second set of Structure results are filtered for individuals with less than 20% admixture, and so the between group differences are even starker. It seems likely then that whatever the origin of the Pygmy phenotype, they are the descendants of the pre-Bantu substrate which was extant across Central Africa before the great expansion, and these pre-Bantu populations had a common ancestry.
Now the relationship the populations in question is established, the temporal dynamics are next up. Using a standard molecular evolutionary method, Tajimas D, they infer that the agricultural populations have been through a demographic expansion recently. Going back to the Bantu Expansion this gels well with what we know from non-genetic disciplines. Farming populations expand fast up to the Malthusian limit. But what about the Pygmies? If the model of Pygmies as non-farmers is true, combined with their long residence in their localities, one would assume less evidence of a recent expansion. The carrying capacity for a hunter-gatherer lifestyle is lower, the rapid expansion of farmers is due to their switch to that lifestyle, or their emigration to “virgin land.” Neither of these would hold for hunter-gatherers who are indigenous of long standing. Though classical tests implied constant population size, putting more assumptions into the model (ones which are likely or supported, such as gene flow between populations and so forth) gives a more nuanced result:

A bottleneck beginning 2,500-25,000 years ago with an 80% decrease in population size, followed by a recovery starting 125 years later with a size increase of between 100% and 400% (Figure 4), fitted the WPYG data significantly better than the constant-sized population model (P = 0.04, see Materials and Methods). For the EPYG group, a bottleneck starting 250-2,500 years ago with a 90 to 95% decrease in population size (Figure 4) fitted the observed genetic diversity significantly better than the constant-sized population model

I wouldn’t get too caught up in the specific numbers here, but the evidence of a population bottleneck is suggestive in light of what we know from history and anthropology when farmers and hunter-gatherers come into contact: the latter are often decimated by disease and warfare due to the appearance on the scene of the former. The genetic data opens up the a more detailed historical narrative which would be impossible otherwise because there are no extant records from this period in this region, and archaeological evidence is difficult to extract due to the unfavorable ecology for preservation. The bounce-back of the Pygmy population could be because after the initial shock of contact with the relatively rapacious agricultural societies the hunter-gatherers retreated to the regions where their lifestyle was still at a comparative advantage and eventually established a symbiotic mondus vivendi whereby both groups might benefit. But that’s just a story, more numbers. Using a combination of the molecular genetic data, demographic assumptions and simulations they come up with some time frames for separation of the populations:

…finding that the ancestors of AGR and PYG populations diverged ca. 60 Kya is consistent with our recent single-locus estimation based on the mtDNA diversity of African farmers and Western Pygmies…Most of the large waves of population expansion and migration, both within and out of Africa, have been dated at ca. 50-80 Kya, based on several genetic markers…It has been suggested that these early population movements within and out of Africa may have been triggered by rapid environmental changes. During this period, sub-Saharan Africa witnessed a major episode of climatic change: a sharp oscillation towards a drier climate, with annual rainfall decreasing by up to 50%…In this context, our estimated date of the initial divergence between the ancestors of present-day farmers and Pygmies implies that this period was characterized not only by major human movements, but also by early episodes of population differentiation within the African continent.
Our evidence for a separation of the ancestors of Western and Eastern Pygmy groups ca. 20 Kya is also consistent with a previous mtDNA study, dating the time of separation of these two Pygmy groups to at least 18 Kya…These estimates coincide with another period of major climatic change, the Last Glacial Maximum, which led to a massive retreat of tropical forests in Central Africa…Our genetic results thus support the anthropological hypothesis that the ancestors of present-day forest specialists — Western and Eastern Pygmies — began to diverge at the same time as the rainforest retreated into refugia, ~20 Kya…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…

These data suggest the intriguing possibility that concurrently with the Out of Africa event the seeds for the structure in modern African populations was already being laid. No doubt there were many populations between the ancestors of the Bantus and the Pygmies whom they enveloped, but as I suggest above it may be that the Pygmy groups we see are trivial remnants of the extant populations which were pushed aside by the agriculturalists as they expanded. The Western and Eastern Pygmies may have had the good luck to be in close proximity to ecological domains where their lifestyle was at a comparative advantage and so were able to maintain some sort of demographic and population genetic integrity in the face of the agricultural onslaught. Ergo, the genetic discontinuity might be an outcome of these details of history, as the groups which span the gap between the proto-Bantu and the Pygmies left very few descendants.
I wonder therefore the need to appeal to refugia ~20,000 years ago, as opposed to the Western and Eastern Pygmy simply being the western and eastern edges of a continuous population of which they are the last fragments. I do know that there are data which suggest that the speciation of some African monkeys is a function of the fragmentation of the rainforest during the Last Glacial Maximum, but most monkeys are by nature forest animals, while humans are not. Therefore I am skeptical of the thesis that ecological fragmentation is the reason behind the genetic differences between the two Pygmy groups dating to ~20,000 before the present. Much more likely that the Pygmy populations retreated to regions where hunter-gathering was still viable, and their genetic distance is simply an echo of population structure since erased by the Bantu demographic expansion. On the other hand, if subsequent data showed that the Pygmy phenotype is of very ancient pedigree, then perhaps the concept of perpetually forest resident populations might seem more plausible.
Hopefully there will be some examination of the other pre-Bantu populations of Southern Africa in the near future, the Hadza and Khoisan.
Citation: Patin E, Laval G, Barreiro LB, Salas A, Semino O, et al. (2009) Inferring the Demographic History of African Farmers and Pygmy Hunter-Gatherers Using a
Multilocus Resequencing Data Set. PLoS Genet 5(4): e1000448. doi:10.1371/journal.pgen.1000448

• Category: History, Science • Tags: Africa, Evolution, Genetics, Human Evolution, Pygmies 
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There was some talk about Pygmies on the post about Jerry Coyne’s weblog. PLoS Genetics has a new paper up on the topic of Pygmy origins and their relationship to non-Pygmy populations. I’ve blogged it over at ScienceBlogs.

• Category: Science • Tags: Evolution, Genetics, Population Genetics, Pygmies 
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