Better prediction through better measurement

One of the most successful achievements of the "post-genomic era" has been the elucidation of the genetic architecture which undergird the variation in human pigmentation. I like to point out that in 2005 the geneticist Armand Leroi observed in his book Mutants that we didn't know the genetics of normal variation in relation to the trait of skin color. In 2010 one couldn't plausibly write that. We know the genes which control the vast majority of the interpopulational variation in human complexion. This is not due to human ingenuity, but the fortuitous hand that nature dealt us. Pigmentation is a very salient phenotype, evident by the classification of genetically very distinct populations in Africa, India and Oceania as "black." But in terms of a genetic research project it has long been one of the ways to explore patterns of inheritance in model organisms such as mice, in particular in relation to coat patterns and pigment. And luckily for us, many of the genes which are implicated in pigment variation produce similar changes across diversetaxa. Additionally, the genetic architecture of human pigmentation variation is such that most of the variance is concentrated among a few loci of large effect. Concretely, it seems that well over 50% of the African-European difference in skin color as measured by reflectance of visible light is attributable to two genes, SLC24A5 and KITLG. In Europeans around 75% of the dichotomous variation between those with blue and non-blue eyes may be due to changes in the genomic region across HERC2 and OCA2 (these two genes are very near each other). These are the veritable low hanging fruit, amenable to studies with even small sample sizes and modest statistical power, so strong are the effects of the genetic variables. And why is pigment important? Obviously there are social ramifications. But pigmentation is likely a major target of natural selection as well, as I suggested in relation to Neandertals. The results are sometimes confusing, but it does seem that pigmentation related loci are enriched in relation to those genomic regions which turn up as positive in tests of natural selection. Additionally, looking at variation around those genes which are correlated with lighter skin across Eurasia it also seems that it may be that our own lineage has become somewhat paler within the last 20,000 years, perhaps even more recently. And the same may have been true for our possible Neander-kin. At the current rate in regards to pigmentation the age of revolutionary science may soon be over. Extraction of ancient DNA will probably resolve the rate and nature of evolutionary change, while further typing of current populations will flesh out our understanding of the variants responsible for normal human variation. To do that requires more than simply larger sample sizes or improved genomic techniques, it also requires better measurement. The utilization of reflectance indices in studies of study skin color are a step in the right direction, but a new paper in PLoS Genetics points the way toward the same in the study of eye color, Digital Quantification of Human Eye Color Highlights Genetic Association of Three New Loci: