Table 3 Proportion of loci not in HWE and LD (r2) in the population simulated under divergent selection and LD
Line 1Line 2F1
Proportion of loci not in HWE
 Markers0.050.040.11
 QTL0.040.050.13
LD
 r2 at <1 cM0.430.470.40
 r2 at 4–5 cM0.140.140.10