John - from a quick scan of the paper, it's a posterior density of region of origin, not for the allele, but for co-evolution of the gene and a dairy culture! Each point represents the outcome of a simulation; the heat map was generated using a kernel density estimator (presumably Gaussian), and looks smooth because kernel density estimators don't recover high frequency information. They've really created a very detailed simulation - it even contains topographic data to model the effect on mobility of terrain.