I don't have time to comment in detail, but I thought I'd give readers a heads up, there is a preprint in The American Journal of Human Genetics which confirms that
a few SNPs on one locus is responsible for 3/4 of the variation between blue and brown eyes in white populations
. This locus, OCA2, is the third longest haplotype in the European genome from the HapMap sequence (the European HapMap data comes from Utah Mormons). The length of this haplotype is suggestive of recent strong positive selection within the European population (the further back in time and the weaker the selective event the more power recombination has to break up associations swept up during the sweep). OCA2 seems to have a relationship to skin color as well, though it is far weaker an effect (recall that we already know another locus in Europeans has an average effect of 25-38% of the variance between Europeans and Africans).
