High-level phylogenetic relationships within <i>Pezizomycotina</i> revisited

Here, we re-examine the high level phylogeny of <i>Pezizomycotina</i> with special attention to the recently proposed phylogenomic hypothesis (Díaz-Escandón et al. 2022) that "morphologically hyperdiverse" <i>Candelariomycetes</i>, <i>Coniocybomycetes</i>, <i>Geoglossomycetes</i>, <i>Lichinomycetes</i>, <i>Sareomycetes</i> and <i>Xylonomycetes</i> (henceforth referred to as classes <i>sensu stricto</i> (<i>s.s.</i>)) should be united in a class <i>Lichinomycetes</i> (henceforth referred to as <i>Lichinomycetes</i> <i>sensu lato</i> (<i>s.l.</i>)), 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 <i>Lichinomycetes</i> <i>s.l.</i> form six independent lineages, of which two correspond to <i>Geoglossomycetes</i> <i>s.s.</i> and <i>Candelariomycetes</i> <i>s.s.</i> 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 <i>Lichinomycetes</i> to include <i>Lichinomycetes</i> <i>s.s.</i>, <i>Coniocybomycetes</i> <i>s.s.</i> plus some <i>incertae sedis</i> genera (<i>Caeruleum</i>, <i>Thelocarpon</i>, <i>Piccolia</i>, <i>Sarcosagium</i> and <i>Vezdaea</i>). In our analysis, <i>Xylona</i> (<i>Xylonomycetes</i> <i>s.s.</i>) plus <i>Sarea</i> (<i>Sareomycetes</i> <i>s.s.</i>) were found to form an early diverging lineage within the branch also subtending <i>Arthoniomycetes</i> plus <i>Dothideomycetes</i>, which warrants the conclusion to include these two genera in a single class, whereas <i>Symbiotaphrina</i>, initially assigned to <i>Xylonomycetes</i> <i>s.s.</i>, was found to split off the tree backbone earlier and, thus, should be treated as a separate lineage.