There’s a paper from Hopi Hoekstra’s lab coming out in Evolution, where they look at the genetics of pigmentation in their favorite oldfield/beach mouse populations. The main point of the paper is a comparison between population history estimated from multi-locus data and the phylogeny of the causative gene that causes color variation.  In addition, take a look at the methods – see how they used a combination of sequence capture and barcoding to sequence several thousand random loci as well as a very large region surrounding Mc1R.