Simulation of demographic and selective parameter estimates with and without linkage.
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Simulation results for ML estimate of demographic and selective parameters assuming African American demography (τ = 0.1328, ω = 0.3034) and gamma distribution of fitness effects (α = 0.184, β = 8200). Sample sizes and mutation rates are the same as those in the African American data projected down to N = 24 chromosomes. Each panel represents 100 replicates; actual values shown with black dashed lines. (A) Simulations without linkage; each entry of the site-frequency spectrum is a Poisson variate drawn with the mean being that expected under the demographic model (synonymous sfs) or demography+selection model (nonsynonymous sfs). (B) Simulations with linkage; each entry calculated from a simulation of 11,404 genes, each with 7 linked exons (see Methods). (C) Distribution of inferred values for unlinked (blue) and linked (red) simulations.