Fig. 3.

Allele frequency covariance and fitness are accurately inferred from recovered clonal structure. a) True and b) recovered integrated allele frequency covariance matrices, and c) their difference are plotted for the simulation example in Fig. 2. The fitness of all haplotypes present in the evolution, inferred with d) the true covariance, e) covariance recovered with dxdx, and f) only variances (ignoring LD) are compared against true fitness values. Both allele frequency covariance and fitness values are accurately recovered. In this example, the fitness values inferred when ignoring LD are also strongly correlated with true values, but not as accurate as those inferred with our method.