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

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.

 http://blogs.discovermagazine.com/gnxp/2012/04/pygmies-old-populations-and-a-new-look/