A multigene phylogenetic synthesis for the class Lecanoromycetes (Ascomycota): 1307 fungi representing 1139 infrageneric taxa, 317 genera and 66 families

Abstract

The Lecanoromycetes is the largest class of lichenized Fungi, and one of the most species-rich classes in the kingdom. Here we provide a multigene phylogenetic synthesis (using three ribosomal RNA-coding and two protein-coding genes) of the Lecanoromycetes based on 642 newly generated and 3329 publicly available sequences representing 1139 taxa, 317 genera, 66 families, 17 orders and five subclasses (four currently recognized: Acarosporomycetidae, Lecanoromycetidae, Ostropomycetidae, Umbilicariomycetidae; and one provisionarily recognized, ‘Candelariomycetidae’). Maximum likelihood phylogenetic analyses on four multigene datasets assembled using a cumulative supermatrix approach with a progressively higher number of species and missing data (5-gene, 5+4-gene, 5+4+3-gene and 5+4+3+2-gene datasets) show that the current classification includes non-monophyletic taxa at various ranks, which need to be recircumscribed and require revisionary treatments based on denser taxon sampling and more loci. Two newly circumscribed orders (Arctomiales and Hymeneliales in the Ostropomycetidae) and three families (Ramboldiaceae and Psilolechiaceae in the Lecanorales, and Strangosporaceae in the Lecanoromycetes inc. sed.) are introduced. The potential resurrection of the families Eigleraceae and Lopadiaceae is considered here to alleviate phylogenetic and classification disparities. An overview of the photobionts associated with the main fungal lineages in the Lecanoromycetes based on available published records is provided. A revised schematic classification at the family level in the phylogenetic context of widely accepted and newly revealed relationships across Lecanoromycetes is included. The cumulative addition of taxa with an increasing amount of missing data (i.e., a cumulative supermatrix approach, starting with taxa for which sequences were available for all five targeted genes and ending with the addition of taxa for which only two genes have been sequenced) revealed relatively stable relationships for many families and orders. However, the increasing number of taxa without the addition of more loci also resulted in an expected substantial loss of phylogenetic resolving power and support (especially for deep phylogenetic relationships), potentially including the misplacements of several taxa. Future phylogenetic analyses should include additional single copy protein-coding markers in order to improve the tree of the Lecanoromycetes. As part of this study, a new module (“Hypha”) of the freely available Mesquite software was developed to compare and display the internodal support values derived from this cumulative supermatrix approach.

Molecular analyses uncover the phylogenetic placement of the lichenized hyphomycetous genusCheiromycina

“…3) is topologically congruent with the previous analysis of Miadlikowska et al (2014). Although this topology was limited in terms of taxon sampling relative to previous studies, the relationships among families and orders within Lecanoromycetes in our phylogenetic inference were largely consistent with previous reconstructions and relationships were generally recovered with high support.…”

“…Bayesian PP >95% and ML bootstrap support values >70% are reported above branches. Clades are named according to Miadlikowska et al (2014) and represent a broad selection of taxa within the Lecanoromycetes. The newly sequenced samples (as in TABLE 1) are reported in bold. …”

“…As the National Center for Biotechnology Information (NCBI) BLAST results always output as closest matches representatives of Lecanoromycetes, and our first single-locus analyses also placed the sequences within Lecanoromycetes, we reduced the data set of the final phylogenetic analysis to Lecanoromycetes only and selected 10 species of Leotiomycetes as outgroups (TABLE S1). The selection of the outgroups and of the Lecanoromycetes ingroups was based on the recent phylogenetic analyses of Ertz et al (2013) and Miadlikowska et al (2014). For a number of specimens, we were unable to generate sequences for all the selected loci (18S, 28S, and mitochondrial 12S), and a complete set of all three sampled loci were not available in GenBank.…”

Kalbionora palaeotropica, a new genus and species from coastal forests in Southeast Asia and Australia (Malmideaceae, Ascomycota)

“…KY926780-KY926790) from the type specimen of the new species and added to an alignment used by Miadlikowska et al with over 1300 representatives in Lecanoromycetes (downloaded from https://treebase.org -study no. 156552; Miadlikowska et al 2014). In a second analysis focusing on Malmideaceae, we aligned nuLSU and mtSSU sequences from three specimens of the new species with all Malmideaceae sequences used in Ertz et al (2013).…”

Brownlielloideae, a new subfamily in the Teloschistaceae (Lecanoromycetes, Ascomycota)

“…The genus Caloplaca, previously one of the largest of all lichen genera comprising around 1,000 species, is now segregated into 42 genera spread over the entire family (Arup et al 2013a, Kondratyuk et al 2013c, 2014a, 2015. However, a number of these new genera have not been generally accepted (Miadłikowska et al 2014).…”