A new research paper finds that many genes involved in appearance have rather clear indications of positive selection.
Dong-Dong Wu and Ya-Ping Zhang, Different level of population differentiation among human genes. BMC 2011. Open Access.
From the Abstract:
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.
While the paper does not seem to suggest why these patterns of inter-population differentiation are stronger in the genes of appearance mostly, I'd say that the selection involved is directly social and sexual and largely the same pattern by which races appeared and are maintained (to some extent). Intuitively people tend to favor statistically more those who look like themselves of people they know and have good opinion of. That way certain looks or family air are sustainedly favored within each population (the son who looks more like the father, the person who looks more sexy according to certain parameters, largely socio-cultural, etc.) producing eventually what we call races, more apparent than the actual underlying differences between populations, which are invariably much smaller than it looks.