A) Phylogenetic tree representing the evolutionary relationships among the 60 fungal species considered in the study, as resulting from the ML analysis of the concatenated alignment of 69 widespread proteins. Numbers on the nodes indicate two different types of support values. The first number indicates the phylome support for that node, that is, the percentage of trees in the phylome that support the specific arrangement of the three or four groups of species defined by its daughter nodes (see B). An asterisk next to this number indicates that the topology obtained by the species tree is not the most common among the trees in the phylome. Whenever there is a second number (in bold), this indicates the bootstrap support when this is lower than 100. Partitions that do not have this second number have a bootstrap support of 100. Branches with dashed lines indicate evolutionary relationships that are supported by less than 50% of the trees in the phylome. B) Schematic representation of the two types of support values for the different nodes in the tree. X indicates the phylome support for the specific topology indicated by that node. Two types of nodes do exist attending to the number of partitions delimited by their daughter nodes. A first class of nodes (top), delimit relative topologies of three partitions (A, B and C), whereas a second class (bottom) delimit four partitions (A, B, C and D). Phylome support values indicate the percentage of trees that show exactly the relative grouping of the three or four groups delimited by the node. This percentage is expressed over the fraction of trees that contain at least one species from each of the partitions considered. The second number (Y) indicates the bootstrap support for the partition delimited by that node, but does not provide specific support for the specific arrangement of the sub-partitions within that partition. C) Correlation between the fungal species tree topologies recovered by the individual trees included in the concatenated alignment (Y axis) and all the trees in the phylome (X axis). In both cases the fraction of trees that are compatible with a given topology, as computed with the topology scanning algorithm, is represented.

The synteny based and manually curated orthology predictions available at YGOB database [18] is taken as a golden set to compute the number of true positives (TP), false positives (FP) and false negatives (FN) yielded by each method. For each method, the sensitivity S = TP/(TP+FN) and the positive predictive value P = TP/(TP+FP) are computed.