More complex than simple addition

A few months ago I posted Discrete continuity in genetics to show how the granular nature of genetic inheritance may still manifest to our perception as continuous variation (i.e., quantitative traits). I used skin color as a model trait because it is easy to relate to, and we are beginning to understand its genetics in detail as I write. To recap, it seems that 3-5 genetic loci control more than 90% of the intergroup variation across populations in complexion. That is, you have a small number of genes which generate the range between black and white skin. These genes come in various flavors, alleles, which in concert sum up to one phenotype. I used a biallelic model which posited 4 loci of independent and additive effect. If a genotype on locus 1 was Aa, I assumed that the quantitative impact would be 1/2 of AA vs. 0 for aa. And so on for each successive locus, resulting in a biological binomial distribution. But, I do not believe that additivity and independence need to be perfect. I won't address developmental and environmental variance too much because they are pretty straightforward. In industrialized societies 90% of the variation in height is genetically specified because environmental variation in regards to nutrition is not particularly important, malnutrition has been rendered rather irrelevant (obesity is a problem though). Nevertheless, there is still some environmental component of variation. An acquaintance of mine was rather short in comparison to her sisters and she attributed it to her competitive gymnastics. Additionally, there might be an element of stochasticity introduced during development as a fetus prior to birth. How does this explain skin color? Well, there is still wiggle room even outside the genes of large effect, particularly on the individual level.