High-level phylogenetic relationships within Pezizomycotina revisited

Here, we re-examine the high level phylogeny of Pezizomycotina with special attention to the recently proposed phylogenomic hypothesis (Díaz-Escandón et al. 2022) that "morphologically hyperdiverse" Candelariomycetes, Coniocybomycetes, Geoglossomycetes, Lichinomycetes, Sareomycetes and Xylonomycetes (henceforth referred to as classes sensu stricto (s.s.)) should be united in a class Lichinomycetes (henceforth referred to as Lichinomycetes sensu lato (s.l.)), based on their common origin. Our examination revealed that the orthology of the aligned character states in the data used to produce this result is questionable due to the presence of poorly-aligned, indel-rich vertical alignment partitions, missing data and heterogeneous sequences. Our analyses of a thoroughly curated phylogenomic dataset and its subset with reduced compositional heterogeneity indicated that the fungi included in the Lichinomycetes s.l. form six independent lineages, of which two correspond to Geoglossomycetes s.s. and Candelariomycetes s.s. and others do not correspond to the taxonomic delimitations of the previously defined classes. Based on the results obtained here, we propose to revise the class Lichinomycetes to include Lichinomycetes s.s., Coniocybomycetes s.s. plus some incertae sedis genera (Caeruleum, Thelocarpon, Piccolia, Sarcosagium and Vezdaea). In our analysis, Xylona (Xylonomycetes s.s.) plus Sarea (Sareomycetes s.s.) were found to form an early diverging lineage within the branch also subtending Arthoniomycetes plus Dothideomycetes, which warrants the conclusion to include these two genera in a single class, whereas Symbiotaphrina, initially assigned to Xylonomycetes s.s., was found to split off the tree backbone earlier and, thus, should be treated as a separate lineage.