January 17, 2011

Population differentiation in gene classes (Wu & Zhang 2011)


BMC Evolutionary Biology 2011, 11:16doi:10.1186/1471-2148-11-16

Different level of population differentiation among human genes

Dong-Dong Wu, Ya-Ping Zhang

Abstract (provisional)

Background
During the colonization of the world, after dispersal out of African, modern humans encountered changeable environments and substantial phenotypic variations that involve diverse behaviors, lifestyles and cultures, were generated among the different modern human populations.

Results
Here, we study the level of population differentiation among different populations of human genes. Intriguingly, genes involved in osteoblast development were identified as being enriched with higher FST SNPs, a result consistent with the proposed role of the skeletal system in accounting for variation among human populations. Genes involved in the development of hair follicles, where hair is produced, were also found to have higher levels of population differentiation, consistent with hair morphology being a distinctive trait among human populations. Other genes that showed higher levels of population differentiation include those involved in pigmentation, spermatid, nervous system and organ development, and some metabolic pathways, but few involved with the immune system. Disease-related genes demonstrate excessive SNPs with lower levels of population differentiation, probably due to purifying selection. Surprisingly, we find that Mendelian-disease genes appear to have a significant excessive of SNPs with high levels of population differentiation, possibly because the incidence and susceptibility of these diseases show differences among populations. As expected, microRNA regulated genes show lower levels of population differentiation due to purifying selection.

Conclusion
Our analysis demonstrates different level of population differentiation among human populations for different gene groups.

5 comments:

Andrew Oh-Willeke said...

How can such obviously talented scientists with such fascinating results write a conclusion sentence that makes the conclusions in 4th grade science fair projects look good by comparison?

Michael Abramoff said...

Exciting paper, but pretty terse. I am not been able to figure out how they got from the SNPs to the gene ontology they use in figure 1 and how complete the SNP lists where. Authors only state that they used Ensembl. Certainly there is no public list of SNP->GO. Can anyone here guess how they did that?

Michael Abramoff said...

Trying to answer my own question. I think they mean through Ensembl->Biomart. But then the query is still unclear, and an acceptable methods section should have stated that.

Keith Brabender said...

To Mr. Abramoff:

Ontogeny recapitulates phraseology.

Ponto said...

Yes I guess the paper does seem like it is stating the obvious, what we can see or measure without any knowledge of genes, dna or snps. Anthropologists of old have noted human differences over the globe.

What I got out of it was this: Chromosomes 5,6,8,11,13 and 20 are practically useless for finding differences between the human geographical groups as those chromosomes are essentially identical. Also the scientists have quantified the most varied to the least varied functions and characteristics of human geographical groups. This is good for finding those SNPs which are real indicators of ancient origins and admixture, which some of us, would like to know just for the sake of knowing.