Supplementary Figure 3

The effect of two forms of mutation-disruption in causing allelic dropout in simulations. Single digest (restriction recognition site length = 4, 6, or 8 bp; grey) and double digest (ezyme1 recognition length = 4, 6, or 8, and enzyme2 recognition length = 4; black) differ in the number of loci retained. (a) When only mutations occurring within cut sites cause disruption (dashed lines) longer cutters recover fewer data than short cutters. When only mutations giving rise to new cut sites within sequences cause disruption (solid lines) shorter cutters recover fewer data than long cutters. In both cases, the double digest data recover fewer loci than single digest, due to the greater opportunity for disruption. (b) When both forms of disruption cause dropout simultaneously the length of a single cutter (4, 6, or 8 bp) has little effect on the amount of data loss, while adding a second independent cutter causes the rate of mutation-disruption to approximately double.