Evolution of gene orders in Pezizomycotina. A: Single ML tree (log likelihood: -50,671.86) constructed from 12 OXPHOS proteins for selected ascomycetes with complete mt genomes (see Table 2). The tree was used to map gene order rearrangements of 14 OXPHOS proteins, Rps3, and the rRNAs. Thick branches indicate bootstrap support values ≥90% in ML analysis and posterior probabilities ≥0.95 in BI. Candida albicans served as outgroup. Group numbering given on the right indicates groups of species with identical gene orders for the gene set analyzed. Ancestral gene orders are indicated next to the nodes as G followed by the group index if the gene order is identical to the gene order of a given group or as A for the gene order reconstructed by treerex (see B), except for the root node. Boxes on the braches indicate mapped rearrangements as analysed by crex and treerex. Numbers in boxes refer to the rearrangement given in C. B: Reconstructed ancestral gene orders for the Eurotiomycetes, Sordariomycetes and the Leotiomycetes. C: Evolutionary scenarios to deduce one gene order of the other for each change indicated in Figure 4A are given (trp, transpositions; tdrl, tandem-duplication-random-loss). Only the mt regions included in the operation are indicated in the Figure.