New insights into classification and evolution of the Lecanoromycetes (Pezizomycotina, Ascomycota) from phylogenetic analyses of three ribosomal RNA- and two protein-coding genes

Abstract

The Lecanoromycetes includes most of the lichen-forming fungal species (>13 500) and is therefore one of the most diverse class of all Fungi in terms of phenotypic complexity. We report phylogenetic relationships within the Lecanoromycetes resulting from Bayesian and maximum likelihood analyses with complementary posterior probabilities and bootstrap support values based on three combined multilocus datasets using a supermatrix approach. Nine of 10 orders and 43 of 64 families currently recognized in Eriksson’s classification of the Lecanoromycetes (Outline of Ascomycota—2006 Myconet 12:1–82) were represented in this sampling. Our analyses strongly support the Acarosporomycetidae and Ostropomycetidae as monophyletic, whereas the delimitation of the largest subclass, the Lecanoromycetidae, remains uncertain. Independent of future delimitation of the Lecanoromycetidae, the Rhizocarpaceae and Umbilicariaceae should be elevated to the ordinal level. This study shows that recent classifications include several nonmonophyletic taxa at different ranks that need to be recircumscribed. Our phylogenies confirm that ascus morphology cannot be applied consistently to shape the classification of lichen-forming fungi. The increasing amount of missing data associated with the progressive addition of taxa resulted in some cases in the expected loss of support, but we also observed an improvement in statistical support for many internodes. We conclude that a phylogenetic synthesis for a chosen taxonomic group should include a comprehensive assessment of phylogenetic confidence based on multiple estimates using different methods and on a progressive taxon sampling with an increasing number of taxa, even if it involves an increasing amount of missing data.

• Bayesian inference
• Lecanoromycetes
• lichen-forming ascomycetes
• maximum likelihood
• missing data
• mitochondrial ribosomal small subunit (mitSSU)
• molecular phylogenetic classification
• nuclear ribosomal large subunit (nucLSU)
• nuclear ribosomal small subunit (nucSSU)
• phenotypic characters
• photobionts
• phylogenetic confidence
• phylogeny
• RNA polymerase II largest subunit (RPB1)
• RNA polymerase II second largest subunit (RPB2)

We thank Bill Rankin, Sean Dilda and John Pormann for their assistance with the Duke C.S.E.M. computer cluster, Lutzoni’s lab members for helpful comments and suggestions, Molly McMullen (Duke University Herbarium) for curating lichen specimens and for proofreading the manuscript, William R. Buck and David M. Hillis for providing lichen specimens. ThisPUBLICation resulted from the Assembling the Fungal Tree of Life (AFTOL) project, which is supported by NSF Assembling the Tree of Life (AToL) award DEB-0228668 to FL. Additional financial support comes from NSF CAREER award DEB-0133891 to FL and from the Academy of Finland (No. 211172) to SS. We also acknowledge support from NSF 0090301, Research Coordination Network: A Phylogeny for Kingdom Fungi to M. Blackwell, J.W. Spatafora and J.W. Taylor.