Figure 2.

Probability of fixation of the second allele relative to the unlinked case, $\mathrm{\Pi },$ as a function of the first allele frequency, p. $N=10,000,$ $s_A$ = 0.01, $s_B$ = 0.005 (so $\phi =0.5$), and from bottom to top in A–E, $r=0.0001,$ 0.001, 0.01 (corresponding to $\rho =0.01,$ 0.1, 1). In F, $r=0.1$ and 0.25 results are also added (corresponding to $\rho =10$ and 25). Other parameters used are listed above each subplot. Curves correspond to solutions provided by the analytical system of differential equations (Equation 12), rescaled so they are a function of p. In F, dashed lines are analytical results using the more exact recombination rate, $r\left(1-2F+\mathrm{\Phi }\right).$ Points correspond to 5000 stochastic simulations for which the second beneficial allele has fixed. Bars represent 95% confidence intervals; if the intervals cannot be seen, they lie within the plotted points. Note that in A, simulation results are presented after rescaling fixation probability by the diffusion equation solution, to account for recessive alleles (see main text for details).