Species tree inferred by gene tree parsimony. A. The best species tree obtained using gene tree parsimony based on the maximum likelihood gene tree collection. It is identical to the accepted tree in Figure 2. B. The best species tree obtained using GTP based on the maximum parsimony gene tree collection. It differs from the accepted tree only within the legumes. Bootstrap II support values (resampling the gene trees: see text) are shown in plain text for each bipartition in the tree. Bootstrap I values (resampling the data within the original clusters) are shown in italics for tree B.