Figure 5. A, topological similarities between gene trees. A in Tales from the crypt: genome mining from fungarium specimens improves resolution of the mushroom tree of life

Figure 5. A, topological similarities between gene trees. A non-metric multidimensional ordination plot, based on the Robinson–Foulds (RF) distance between each pair of genes, is used to visualize the topological similarity among the 208 single gene trees. Pairs of gene trees with similar topologies are closer together in the two-dimensional space. Colours represent RF distances between individual gene trees and the extended majority-rule consensus (MRE) phylogeny. B, identifying optimal subsets of genes with the least topological incongruence. The graph shows the Tree Certainty (TC) values from Salichos & Rokas (2013). Information theory approach using the MRE phylogeny as a reference tree, where higher values represent greater congruency between the gene trees and the MRE tree. The x-axis represents the number of genes sampled, following an iterative procedure beginning with the first two genes in the respective ranking and progressively adding genes according to their order in the list. The five ranking criteria all outperformed random gene orders.