Fig. 3

Species trees reconstructed using ASTRAL for various sets of taxa. Topologies were tested using bootstrap trees generated by PhyML. Clades observed in >85% of bootstrap replicates are not labeled, clades observed in 70 to 85% of replicates are marked with small circles, and those observed in <70% of replicates are marked with large circles. Ploidy levels are shown for non-diploid species. Branch lengths are not to scale. Species trees for datasets 1 and 5 are not shown, but they are included in the supplementary material (Additional file 4: Figure S11). Distances between topologies of reconstructed species trees are calculated as described in the text, and they are plotted in the heat map at the top left. Distance ranges are encoded as follows: XS: [0, 0.1], S: (0.1, 0.2], M: (0.2, 0.3], L: (0.3, 0.4], XL: (0.4, 0.5], XXL: (0.5, 0.6]