Complex evolutionary history of the fungal order Hymenochaetales revealed by analyses of trait evolution and diversification

Supplementary Figure 1 – The phylogenetic tree of Hymenochaetales generated by maximum likelihood algorithm. Bootstrap values are indicated at the nodes. Supplementary Figure 2 – The time-calibrated ultrametric supertree with a 99.6% sample proportion of all known species in Hymenochaetales. The mean divergence times of clades (crown ages) were labeled at the nodes. Supplementary Figure 3 – The ultrametric phylogenetic tree of Hymenochaetales with trait evolution of basidiomes. The posterior probability distribution for the most recent common ancestor of each node was shown as a pie chart. Supplementary Figure 4 – The ultrametric phylogenetic tree of Hymenochaetales with trait evolution of hymenophores. The posterior probability distribution for the most recent common ancestor of each node was shown as a pie chart. Supplementary Figure 5 – The ultrametric phylogenetic tree of Hymenochaetales with trait evolution of trophic modes. The posterior probability distribution for the most recent common ancestor of each node was shown as a pie chart. Supplementary Figure 6 – The ultrametric phylogenetic tree of Hymenochaetales with trait evolution of hosts. The posterior probability distribution for the most recent common ancestor of each node was shown as a pie chart. Supplementary Figure 7 – The numbers of transition events of all nodes and tips between different forms of each trait were shown by arrows with different thicknesses; the absence of arrows between forms indicates no transition event. (A) basidiomes. (B) hymenophores. (C) trophic modes. (D) hosts. Supplementary Figure 8 – The nine most probable transition configurations inferred by Bayesian Analysis of Macroevolutionary Mixtures. These nine most probable configurations are remarkably stable with little different marginal shift probabilities. Supplementary Figure 9 – Net diversification rate through time of the six clades showing significant diversification rate shifts (A–F, respectively, correspond to the clades 1–6 in Fig. 3A) and the net diversification rate of Hymenochaetales through time after removing the clade 5 corresponding to the Phylloporia clade in Fig. 3A (G). Supplementary Figure 10 – Correlation coefficients of net diversification rate and paleotemperature. (A) The entire Hymenochaetales. (B) The clade 5 corresponding to the Phylloporia clade in Fig. 3A. (C) The entire Hymenochaetales after removing the Phylloporia clade. The mean correlation coefficient and an estimate of the standard error inferred with Pearson’s cross-correlation analysis are shown. Supplementary File 1 – The concatenated alignment for constructing the ML phylogenetic tree. Supplementary Table 1 – Information for species used in phylogenetic and evolutionary analyses of Hymenochaetales.