Fig S1. Mismatch in expected number of alleles in bottlenecked and equilibrium populations, estimated
with 10,000 coalescent simulations of a single locus. When θ = 1 prior to the bottleneck (a), all observed
alleles numbers occur in both equilibrium and bottlenecked (Ne = 25 or 100) populations. However, when
θ = 5 prior to the bottleneck (b), bottlenecked populations can have <3 alleles, but even with 10,000
simulations, non-equilibrium populations never had <3 alleles. This mismatch makes comparing
expected heterozygosity between bottlenecked and equilibrium populations conditional on the number of
alleles computationally problematic in certain parameter spaces.
0.4
a) θ = 1
Ne == 25
Ne
25
Ne ==100
Ne
100
0.3
No BN
bottleneck
No
Proportion of Simulations
0.2
0.1
0
1
0.4
2
3
4
5
6
7
8
9
10 11 12 13 14+
4
5
6
7
8
9
10 11 12 13 14+
b) θ = 5
0.3
0.2
0.1
0
1
2
3
Number of Alleles