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

     Department of Biology, Duke University, Durham, North Carolina 27708-0338

Martin Grube
Josef Hafellner

     Institut für Botanik, Karl-Franzens-Universität, Holteigasse 6, A-8010, Graz, Austria

Valérie Reeb
Brendan P. Hodkinson

     Department of Biology, Duke University, Durham, North Carolina 27708-0338

Martin Kukwa

     Department of Plant Taxonomy and Nature Conservation, Gdansk University, A. Legionow 9, 80-441 Gdansk, Poland

Robert Lücking

     Field Museum of Natural History, 1400 South Lake Shore Drive, Chicago, Illinois 60605-2496

Geir Hestmark

     Department of Biology, University of Oslo, P.O. Box 1066 Blindern, NO-0316 Oslo, Norway

Monica Garcia Otalora

     Área de Biodiversidad y Conservación, ESCET, Universidad Rey Juan Carlos, c/ Tulipán s/n, 28933-Móstoles, Madrid, Spain

Alexandra Rauhut
Burkhard Büdel

     Fachbereich Biologie, Abt. Pflanzenökologie und Systematik, University of Kaiserslautern, Postfach 3049, 67653 Kaiserslautern, Germany

Christoph Scheidegger

     Swiss Federal Institute for Forest, Snow and Landscape Research (WSL/FNP), Zürcherstrasse 111, 8903 Birmensdorf, Switzerland

Einar Timdal

     Botanical Museum, University of Oslo, Sars’ gate 1, N-1162 Oslo, Norway

Soili Stenroos

     Botanical Museum, Finnish Museum of Natural History, University of Helsinki, P.O. Box 7, FI-00014 Finland

Irwin Brodo

     Canadian Museum of Nature, P.O. Box 3443, Station D, Ottawa, Ontario, K1P 6P4 Canada

Gary B. Perlmutter

     North Carolina Botanical Garden, University of North Carolina at Chapel Hill, CB 3375, Totten Center, Chapel Hill, North Carolina 27599-3375

Damien Ertz

     National Botanic Garden of Belgium, Department of Bryophytes-Thallophytes, Domaine de Bouchout, B-1860 Meise, Belgium

Paul Diederich

     Musée national d’histoire naturelle, 25 rue Munster, L-2160 Luxembourg, Luxembourg

James C. Lendemer

     Department of Botany, Academy of Natural Sciences of Philadelphia, 1900 Benjamin Franklin Parkway, Philadelphia, Pennsylvania 19103

Philip May

     Farlow Herbarium, Harvard University, 22 Divinity Avenue, Cambridge, Massachusetts 02138

Conrad L. Schoch

     Department of Botany and Plant Pathology, Oregon State University, Corvallis, Oregon

A. Elizabeth Arnold

     Department of Plant Sciences, University of Arizona, 1140 E. South Campus Drive, Forbes 204, Tucson, Arizona 85721

Cécile Gueidan
Erin Tripp
Rebecca Yahr
Connie Robertson
François Lutzoni

     Department of Biology, Duke University, Durham, North Carolina 27708-0338

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.

Key words: 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)