Fig. 2

Support for observed topological discordance in the estimated gene trees. a Support that observed gene tree topologies differs from each of the inferred species trees, i.e., phylogeny inferred from intron-set (blue), ASTRAL species tree inferred from exon-set (olive green), MP-EST species tree inferred from exon-set (dark green), and concatenated tree inferred from exon-set (gray). Bars showed the proportion of loci that reject and fail to reject the species tree topology at a Bonferroni-corrected P value of 0.05 (AU tests). b,c Pairwise distances between gene trees and MP-EST and ASTRAL species tree. Distance between each gene tree and the species tree topology was calculated as the Robinson-Foulds cluster distance (b) and matching cluster distance (c). The mean values for all pairwise gene tree-species tree distance within each category are shown. Error bars indicate the 95% confidence interval of the mean. Distances were calculated from empirically estimated gene trees and from data sets of 1500 gene trees that were simulated using coalescent branch lengths from the MP-EST and ASTRAL species trees. Values above bars for simulated data sets indicate the ratios of means for simulated data sets compared to the mean for empirically estimated gene trees