Supplementary Figure S3

FIGURE S3. Performance of the maximum parsimony (MP) criterion for phylogenetic estimation with UCE data. The topology of the single most parsimonious tree of 50929 steps recovered when UCE data were analyzed (A) was identical to the ML tree for those data. Minimum branch lengths for UCEs (i.e., the number of unambiguous synapomorphies) are shown above branches and bootstrap support is presented below branches. An MP analysis of combined UCEs+introns+mitochondrial data also yielded a single tree (of 59964 steps) with an identical topology. Bootstrap support for both analyses is reported as a percentage of 500 replicates. Full (100%) support is indicated using an asterisk (*). MP and ML branch lengths for the UCE data were strongly correlated (B), suggesting that the MP criterion is likely to have reconstructed character state transformations accurately. The graph was limited to internal branches.