May 09, 2011

Pygmy and non-Pygmy height

Stature is a highly heritable trait, yet association studies searching for its causative genes have generally come up short on results. A couple of years ago, I posted an article that showed that Victorian 19th century height prediction methods trumped modern genomic ones: estimating one's height by taking one's parents' average explains an order of magnitude more variation in height than the genomic method.

This article shows that admixture between Pygmies and non-Pygmies is the major contributor of height variation in Pygmy groups. Note that this is a clear case where group differences in randomly chosen loci are correlated with a phenotypic trait. It was once hoped that the notion of group differences was superfluous: we would learn everything there was to know about individual-level phenotypic variation by examining individual-level genetic and environmental variation directly. According to this paper, the correlation between admixture estimates and height for the entire sample of males/females was 0.44/0.52 respectively, so about a quarter of variance in the trait can be explained by admixture.

And, here's the interesting point: this was all done with 28 microsatellites. Why do 28 microsatellites trump hundreds of thousands of SNPs? Because different groups of mankind are not the same in their genotypic propensity to manifest specific phenotypes, and admixture proportions (the pretty colors in structure runs) do correlate with measurable physical properties.

American Journal of Physical Anthropology
DOI: 10.1002/ajpa.21512

Indirect evidence for the genetic determination of short stature in African Pygmies

Noémie S.A. Becker

Abstract

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.

Link

14 comments:

Onur said...

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... 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.

These results indeed show that the Pygmy shortness is genetic (which is something entirely expected), but that doesn't tell us anything about why genes for shortness came into prominenece in Pygmies in the first place. Was it a coincidence? Or were they selected by nature (presumably due to climate and/or forest density) or by sexual selection? Or a combination of these factors?

Jim Bowery said...

We are all eternally indebted to Edwards for debunking Lewontin. Unfortunately, the definition of a heritable particle has not been correspondingly updated in Price's equations.

DocG said...

"These results indeed show that the Pygmy shortness is genetic (which is something entirely expected), but that doesn't tell us anything about why genes for shortness came into prominenece in Pygmies in the first place."

Excellent point. But you are making an assumption. I'm wondering whether anyone here can tell what it is.

????

terryt said...

" but that doesn't tell us anything about why genes for shortness came into prominenece in Pygmies in the first place. Was it a coincidence?"

Generally people who have lived in dense forest for many generations, especially in tropical regions, are short. This is probably a product of both temperature regulation and ease of passage through dense undergrowth.

Onur said...

Generally people who have lived in dense forest for many generations, especially in tropical regions, are short.

Tropical rainforest-induced shortness is my favorite scenario. Negritos are another case in point.

DocG said...

"Generally people who have lived in dense forest for many generations, especially in tropical regions, are short."

As are people who have lived in the Kalahari desert for many generations. Or the Andes for many generations.

Andrew Oh-Willeke said...

this was all done with 28 microsatellites. Why do 28 microsatellites trump hundreds of thousands of SNPs? Because different groups of mankind are not the same in their genotypic propensity to manifest specific phenotypes, and admixture proportions (the pretty colors in structure runs) do correlate with measurable physical properties.

The study is a quite clever way of showing a genetic as opposed to environmental source for variation without actually knowning the precise mechanism for the genetic variation. But, I am left confused about why ancestry informative markers show up more often in genome wide association studies?

German Dziebel said...

"Overall, we show that a Pygmy individual exhibiting a high level of genetic admixture with the neighboring Non-Pygmies is likely to be taller."

I wonder if non-Pygmies admixed with Pygmies tend to be shorter. And what's the magnitude of height fluctuations in mutually and equally admixed Pygmy and non-Pygmy groups?

Onur said...

I wonder if non-Pygmies admixed with Pygmies tend to be shorter.

I haven't read the full paper as it is not free. But according to Razib Khan's assessment of the full paper, admixture works in both ways, thus Pygmy admixed non-Pygmies tend to be shorter (which is something entirely expected).

And what's the magnitude of height fluctuations in mutually and equally admixed Pygmy and non-Pygmy groups?

That is indeed an interesting question.

DocG said...

To answer your question, German, I think it was Colin Turnbull who observed that the Bantu farmers who interact so closely with the Pygmies he studied have been getting progressivly shorter from generation to generation.

This would be consistent with the fact that it's not unusual for Bantu men to take Pygmy wives, whose children then become integrated into the Bantu community.

DocG said...

Guess I have no choice but to answer my own question. The assumption made by Onur in the first comment is that shortness must necessarily be a derived characteristic. I see no evidence that it couldn't in fact represent the original state, if not of AMH, then MRCA.

It's much more easy to see tallness as an adaptation rather than shortness. I see nothing about the tropical forest environment that would give a short person any significant advantage over a tall person, but I do see a great many advantages tall people would have over short ones.

A tall person can always crouch or crawl if necessary, but a short one can't make his arms and legs longer to make him a more effective runner, hunter or fighter.

We find very short people living in a variety of different environments, from deserts to high mountains. What they have in common is that they are ALL indigenous peoples living in refuge areas, and in many cases hunter-gatherers, which makes it even more likely that their shortness could be inherited from their (our) common ancestor.

Onur said...

DocG, modern human hunter-gatherers (including the ones nearest in time to the MRCA) were in general taller and robuster than agriculturalists who succeeded them. So your theory lacks empirical support.

terryt said...

"And what's the magnitude of height fluctuations in mutually and equally admixed Pygmy and non-Pygmy groups?"

In most domestic animals the first cross are all much the same. It is this fact that commercial breeders use to advantage. However if the first cross individuals are then allowed to breed together the resulting progeny are all over the place. Individuals can have a surprising array of combinations from the original two breeds. I'd guess the same would be so of any two different-looking human groups.

"I see nothing about the tropical forest environment that would give a short person any significant advantage over a tall person"

You've obviously never set foot in anything remotely like 'the tropical forest environment'.

"A tall person can always crouch or crawl if necessary"

It may come as a surprise, but that is much slower than running.

"I do see a great many advantages tall people would have over short ones".

Not in tropical rainforest however.

"I see no evidence that it couldn't in fact represent the original state, if not of AMH, then MRCA".

Quite possibly so. But isn't Homo erectus as tall as the average human is today?

Onur said...

DocG, modern human hunter-gatherers (including the ones nearest in time to the MRCA) were in general taller and robuster than agriculturalists who succeeded them. So your theory lacks empirical support.

Note: This comment of mine was deleted by Blogger, so I am reposting it.