The expected site frequency spectrum (SFS) of the derived allele (the new mutation arisen in the population) for three different demographic models: (i) a population that has been of constant size throughout history; (ii) a model previously fit to the derived allele frequency spectrum of Europeans, which includes an out-of-Africa population bottleneck and a second, more recent, population bottleneck (21); and (iii) the same two-bottleneck model of European history with the addition of recent exponential growth from a population size of 10,000 at the advent of agriculture to an extant effective population size of 10,000,000, which amounts to 1.7% growth per generation during the last 400 generations. The results presented are based on sequences of 5, 50, 500, and 5000 diploid individuals. Figures are from 10 million coalescent simulations (32); the expectation of models 1 and 2 were also validated analytically (21). In all panels, the proportions of all possible derived allele counts, ranging from 1 to 2n − 1, sum up to 1, although only those for 1 through 15 are presented. See fig. S1 for a version of this figure in which singletons are excluded and the SFS renormalized.
