We reconstructed the phylogeny for the Lepidium PI **data** set using Bayesian and likelihood analyses. For taxa that had multiple clonal PI sequences, we chose one clonal sequence from each monophyletic group of sequences representing a given taxon that was recovered in a 50% majority rule consensus tree from preliminary Bayesian analyses of all clones and that was representative of the majority of clones from a group. All other clonal sequences not forming monophyletic groups with other clones from the same taxon were included in the final analyses (Appendix 1).