Figure 3.

Expected amounts of polymorphism and divergence contributed by nonsynonymous mutations as a function of the scaled selection coefficient of a mutation. The expected amount of polymorphism in a genomic region can be summarized as the total number of polymorphic sites for both nonsynonymous (P_n) and synonymous sites (P_s, lower horizontal line), and the number of rare mutations using, for example, the number of singletons (mutations seen only once) at nonsynonymous sites (S_n). Amounts of divergence are quantified using the number of divergent synonymous (D_s, upper horizontal line) and nonsynonymous sites (D_n) relative to an out-group sequence. For a given mutation rate and effective population size, sample size n of chromosomes resequenced and size of a genomic fragment population genetic theory and diffusion results on the Wright-Fisher model can be used to compute these quantities as a function of the scaled mutation effect S of a nonsynonymous mutation. Here for illustration, we assume 1000 synonymous neutral sites, 3000 nonsynonymous nucleotide sites with a scaled mutation rate θ = 4Nμ = 0.01, a scaled divergence to the out-group of λ = 0.05, and a sample comprising n = 10 chromosomes.