Table 1. Modes of balancing selection and their effects on population differentiation. Balancing selection regimes simulated in this study are shared and divergent overdominance. The last column shows the effects of those regimes on population differentiation measured by F${}_{\text{ST}}$, as well as our predictions of the effects other balancing selection regimes (local and frequency-dependent selection) on F${}_{\text{ST}}$. $F_{ST}sel$ refers to F${}_{\text{ST}}$ under balancing selection and $F_{ST}neu$ refers to F${}_{\text{ST}}$ under neutrality. A and a represent two different alleles at a biallelic locus. M and m represent the major and minor allele at a biallelic locus, at any given time, respectively. p represents the frequency of the most frequent allele (M). s and t are selection coefficients, and h is the dominance coefficient. Subscripts 1 and 2 represent population specific parameters.

Mode of balancing selection (reference)	Population 1 fitness			Population 2 fitness			Difference in F${}_{\text{ST}}$ between selected and neutral SNPs
	AA	Aa	aa	AA	Aa	aa
Shared overdominance (Figure 7A)	$1-s$	1	$1-t$	$1-s$	1	$1-t$	$F_{ST}sel<F_{ST}neu$
Divergent overdominance (Figure 7B)	$1-s_1$	1	$1-t_1$	$1-s_2$	1	$1-t_2$	$F_{ST}sel>F_{ST}neu$ at low divergence times and $F_{ST}sel<F_{ST}neu$ at high divergence times, if $s_1\ne s_2$ and/or $t_1\ne t_2$.
Local selection (Charlesworth et al. 1997)	1	$1-hs$	$1-s$	$1-s$	$1-hs$	1	Prediction: $F_{ST}sel>F_{ST}neu$
	MM	Mm	mm	MM	Mm	mm
Frequency-dependent (Charlesworth et al. 1997)	$2\left(1-p\right)$	$1.5-p$	1	$2\left(1-p\right)$	$1.5-p$	1	Prediction: $F_{ST}sel<F_{ST}neu$