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

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