Razib Khan One-stop-shopping for all of my content

April 29, 2012

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 ...

September 5, 2011

Of beasts and men

“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 [...]

May 9, 2011

Pygmies are short because nature made them so


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 ...

April 6, 2011

The men of Africa


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 ...

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