Figure 6

Example of Bootstrapping. Panel A shows two different most parsimonious inferences of four genotypes from a tetraploid species. different genotypes are represented by different coloured rings whereas different explaining haplotypes are represented by different coloured circles. In Panel B, the urn symbolises the population from which genotypes are sampled. Three bootstrap replicates are drawn with replacement, the genotypes are inferred, and the occurrences of the different haplotypes are counted (middle). Because of the parsimony criterion, the shown inference of sample 1 and sample 2 are unique. Sample 3 can alternatively be inferred with the green, red and blue haplotypes. The overall number of occurrences of the haplotypes is calculated. Finally, the two most parsimonious inferences are scored by the counts of haplotypes. The inference on the left has score 222 and the inference on the right has score 78. Inference on the left is selected for further analysis.