March 25, 2009

Selection in the human genome with HGDP samples

Genetic Future points me to a new paper on signatures of selection in the human genome. Also Gene Expression and John Hawks on the subject, in which he responds to criticism in the paper about his accelerated evolution theory. Go ahead and read these sources for commentary on the paper (which is open view anyway).

I would like to comment on this interesting bit:
In general, we find the evidence for selection on disease risk is not as conclusive as that for selection on pigmentation traits. One parsimonious explanation for this is that However, the role of the genetic architecture of a trait (the number of loci underlying a trait and their effect sizes and frequencies) in how it responds to selection remains largely unexplored. Since the genetic architecture of pigmentation is relatively simple (compared with other complex traits), perhaps a selection signal on this trait is more readily detected because it is selection on disease risk, assuming disease risk is under selection at all, is much weaker than selection on pigmentation.spread across fewer loci. On the other hand, this explanation may confuse cause and effect. Perhaps skin pigmentation has a simpler genetic architecture than other complex traits because it has been subject to recent strong selection—the first moves to a new phenotypic optimum are predicted to be on mutations of large fitness
effect (Orr 2002). So assuming a positive correlation between the effects of an allele on fitness and on a trait, it is also plausible that the relatively simple genetic architecture of skin pigmentation is actually a consequence of the strong selection that has acted on this phenotype. Further work on the interplay between genetic architecture and natural selection is needed to clarify these issues.
In my opinion, there is a fairly clear dependence of pigmentation with environment (exposure to solar radiation) and with geographical latitude. While disease load varied with time and social organization, natural selection for skin pigmentation has been fairly constant: it has always been "better" to possess a dark phenotype in Africa than it is in Europe or Asia.

Depigmentation of Caucasoids and Mongoloids was thus -in all likelihood- a continuous process which invariably resulted in lighter phenotypes compared to the original dark standard. This process initially involved response to reduced solar radiation, but may have been shaped at a later stage by other factors, such as ready access to vitamin D from milk products, or sexual selection for rare phenotypes that seems to have taken hold in northern Europe.

Genome Research doi:10.1101/gr.087577.108

Signals of recent positive selection in a worldwide sample of human populations

Joseph K. Pickrell et al.


Genome-wide scans for recent positive selection in humans have yielded insight into the mechanisms underlying the extensive phenotypic diversity in our species, but have focused on a limited number of populations. Here, we present an analysis of recent selection in a global sample of 53 populations, using genotype data from the Human Genome Diversity-CEPH Panel. We refine the geographic distributions of known selective sweeps, and find extensive overlap between these distributions for populations in the same continental region but limited overlap between populations outside these groupings. We present several examples of previously unrecognized candidate targets of selection, including signals at a number of genes in the NRG–ERBB4 developmental pathway in non-African populations. Analysis of recently identified genes involved in complex diseases suggests that there has been selection on loci involved in susceptibility to type II diabetes. Finally, we search for local adaptation between geographically close populations, and highlight several examples.


1 comment:

Maju said... has always been "better" to possess a dark phenotype in Africa than it is in Europe or Asia.

Totally in agreement. But, besides, I just happened to read this news item on albino elephants (BBC). What called my attention was that:

While albinism is thought to be fairly common in Asian elephants, it is much less common in the larger African species.

While albinism is a extreme and always harmful case of depygmentation, the higher apparent survivality of such animals and the trait in Asia than in Africa made me think that similar factors were almost without doubt behind the variable but rather general depygmentation experienced by humans in Eurasia.