Table 1. Glossary of Notation.

Symbol	Usage
N	Population size (with $2N$ haplotypes)
σ	Proportion of matings that are self-fertilizing
F	Wright’s inbreeding coefficient, probability of identity-by-descent at a single gene, equal to $\sigma /\left(2-\sigma \right)$ at steady-state
$\text{Φ}$	Joint probability of identity-by-descent at two loci (Equation 1)
$N_e$	Effective population size, equal to $N/\left(1+F\right)$ with selfing
r	Recombination rate between loci A and B
$r_{eff}$	‘Effective’ recombination rate, approximately equal to $r\left(1-2F+\text{Φ}\right)$ with selfing
R	$2Nr$, the population-level recombination rate
$p_0$	Frequency at which the derived allele at B becomes advantageous
$p_{0,A}$	Accelerated (effective) starting frequency of B appearing as a single copy, conditional on fixation
s	Selective advantage of derived allele at B
h	Dominance coefficient of derived allele at B
t	Number of generations in the past from the present day
${\tau }_{p_0}$	Time in the past when derived locus became beneficial
$p\left(t\right)$	Frequency of beneficial allele at time t
$P_c$	Probability of coalescence at time t
$P_r$	Probability of recombination at time t
$P_m$	Probability of mutation at time t
$P_{NE}$	Probability that neutral marker does not coalesce or recombine during sweep phase
$P_{R,Sw}$	Probability that neutral marker recombines during sweep phase
$P_{R,Sd}$	Probability that neutral marker recombines during standing phase
$P_{M,Sw}$	Probability that a lineage mutates during sweep phase
$P_{M,Sd}$	Probability that a lineage mutates during standing phase
$H_l$, $H_h$	‘Effective’ dominance coefficient for allele at low, high frequency
π	Pairwise diversity at site (${\pi }_0$ is expected value without a sweep)
${\pi }_{SV}$	Pairwise diversity following sweep from standing variation
${\pi }_M$	Pairwise diversity following sweep from recurrent mutation
μ	Probability of neutral mutation occurring per site per generation
${\mu }_b$	Probability of beneficial mutation occurring at target locus per generation
$\theta =4N_e\mu$	Population level neutral mutation rate
${\text{Θ}}_b=2N_e{\mu }_b$	Population level beneficial mutation rate