Table 1. Glossary of Notation.

Symbol	Usage
$2N$	Number of haplotypes in the population (of size N)
$A,B$	Locus at which first, second beneficial allele arises
r	Recombination rate between two loci
$s_A,$ $s_B$	Fitness coefficients of original and new advantageous alleles
$h_A,$ $h_B$	Dominance coefficients of original and new advantageous alleles
p	Frequency of first advantageous allele at time point
q	Frequency of second advantageous allele at time point (if $s_A<s_B$)
σ	Proportion of matings that are self-fertilizing
F	Wright’s (1951) inbreeding coefficient, $\sigma /\left(2-\sigma \right)$
$\mathrm{\Phi }$	Probability of identity by descent at two loci (Roze 2009)
$P_A\left(p\right),$ $P_B\left(p\right)$	Fixation probability of original and new allele if unaffected by linkage (Equation 1)
$P_{AB}^{\ast }$	Fixation probability of both mutants in absence of interference
$P_{AB}\left(p\right)$	Actual fixation probability of both mutants, after accounting for interference
${\overline{P}}_{AB}$	Average $P_{AB}$ over one or several selected substitutions at locus A
$R\left(p\right)$	Ratio of actual to noninterference double-allele fixation probability, $P_{AB}/$$P_{AB}^{\ast }$
$\overline{R}$	Average R over one or several selected substitutions at locus A
$P_{\mathrm{HH}}$	Fixation probability of second allele with wild-type background
$P_d\left(q\right)$	Fixation probability of haplotype carrying both sweeps
τ	Time taken for first sweep to reach frequency p
T	Scaled time, $s_{A}t$
$\mathrm{\Pi }\left(p\right)$	Average fixation probability of second allele if it does not replace the first sweep
${\mathrm{\Pi }}_{\mathrm{rep}}\left(p\right)$	Probability that second sweep replaces first if $s_B>s_A$
$Q_0\left(p\right),$ $Q_1\left(p\right)$	Fixation probability of novel allele if appearing on neutral or already beneficial genetic background
${\theta }_1\left(p\right),$ ${\theta }_0\left(p\right)$	Relative selective advantage of second allele if residing on either beneficial or neutral background
${\theta }_d\left(q\right)$	Relative selective advantage of recombinant haplotype carrying both alleles
$\mathrm{\Delta }$	Difference in fixation probability between different backgrounds, $Q_1-Q_0$
φ	Scaled advantage of new beneficial allele, $s_B/s_A$
ρ	Scaled recombination rate, $r/s_A$
${\lambda }_A$	Rate of selected substitution at locus A
$\mathrm{\Theta }$	Population rate of beneficial mutation at single locus, $4N{u}_a$