A Based on 105 Trials of 10Kb Loci with Θ = 0.001 / Bp and Ρ = 0.0006 / Bp

Supplementary Table S1. Comparison of distributions of summary statistics for data simulated using ms and MaCSa

n = 100 / ms
Mean / Var / MaCS h = 10000
Mean / Var / MaCS h = 1
Mean / Variance
Sb / 51.8 / 133 / 51.8 / 135 / 51.8 / 128
πc / 10.0 / 13.8 / 10.0 / 14.0 / 10.0 / 13.3
Hd / 29.1 / 18.1 / 29.1 / 18.0 / 29.1 / 18.1
r2 e / 0.077 / 0.032 / 0.077 / 0.032 / 0.077 / 0.031
D’ f / 0.951 / 0.028 / 0.951 / 0.028 / 0.952 / 0.028
RM g / 3.34 / 1.96 / 3.35 / 1.97 / 3.34 / 1.95
lb h / 6.45 / 12.2 / 6.43 / 12.3 / 6.46 / 11.9
n = 30
S / 39.6 / 118 / 39.7 / 120 / 39.6 / 113
π / 10.0 / 14.6 / 10.0 / 14.7 / 10.0 / 13.9
H / 16.1 / 6.68 / 16.1 / 6.64 / 16.1 / 6.66
r2 / 0.128 / 0.051 / 0.128 / 0.051 / 0.127 / 0.050
D’ f / 0.943 / 0.035 / 0.943 / 0.034 / 0.943 / 0.034
RM g / 2.34 / 1.54 / 2.34 / 1.54 / 2.34 / 1.52
lb h / 7.41 / 16.3 / 7.39 / 16.4 / 7.36 / 15.3

a Based on 105 trials of 10Kb loci with θ = 0.001 / bp and ρ = 0.0006 / bp

b Number of segregating sites per locus

c cf. Tajima 1983

d Number of distinct haplotypes per locus

e Average r2 value for pairs of sites ~ 5 Kb apart

f Average D’ value for pairs of sites ~ 5 Kb apart

g Minimum number of inferred recombination events, cf. Hudson and Kaplan (1985)

h cf. Wall (2000)