# High-level phylogenetic relationships within Pezizomycotina revisited

## TL;DR

This paper revisits the classification of certain fungal classes, finding that some previously grouped fungi actually belong to separate lineages.

## Contribution

The study proposes a revised classification of Lichinomycetes and related classes based on improved phylogenomic data.

## Key findings

- Fungi in Lichinomycetess.l. form six independent lineages, not a single class.
- Xylona and Sarea form an early diverging lineage and should be grouped in a single class.
- Symbiotaphrina diverges earlier and should be considered a separate lineage.

## Abstract

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 Lichinomycetessensu 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 Lichinomycetess.l. form six independent lineages, of which two correspond to Geoglossomycetess.s. and Candelariomycetess.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 Lichinomycetess.s., Coniocybomycetess.s. plus some incertae sedis genera (Caeruleum, Thelocarpon, Piccolia, Sarcosagium and Vezdaea). In our analysis, Xylona (Xylonomycetess.s.) plus Sarea (Sareomycetess.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 Xylonomycetess.s., was found to split off the tree backbone earlier and, thus, should be treated as a separate lineage.