Fig. 1.

The joint allele frequency spectrum (AFS) and joint distribution of fitness effects (DFE). (A) We considered populations that have recently diverged with gene flow between them. Some genetic variants will have a different effect on fitness in the diverged population (s₂) than in the ancestral population (s₁). (B) The joint DFE is defined over pairs of selection coefficients (s₁, s₂). Insets show the joint AFS for pairs of variants that are strongly or weakly deleterious in each population. In each spectrum, the number of segregating variants at a given pair of allele frequencies is exponential with the color depth. (C) One potential model for the joint DFE is a bivariate lognormal distribution, illustrated here for strong correlation. (D) We focus on a model in which the joint DFE is a mixture of components corresponding to equality (ρ = 1) and independence (ρ = 0) of fitness effects. (E) As illustrated by these simulated allele frequency spectra, stronger correlations of mutation fitness effects lead to more shared polymorphism. Here, w is the weight of the ρ = 1 component in the mixture model.