title: 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.
authors.affiliation: Department of Biology, Duke University, Durham, NC 27708-0338, USA. Electronic address: jolantam@duke.edu.
authors.forename: Jolanta
authors.initials: J
authors.lastname: Miadlikowska
authors.affiliation: FB Biologie, Molecular Phylogenetics, 13/276, TU Kaiserslautern, Postfach 3049, 67653 Kaiserslautern, Germany.
authors.forename: Frank
authors.initials: F
authors.lastname: Kauff
authors.affiliation: Botanical Museum, Finnish Museum of Natural History, FI-00014 University of Helsinki, Finland.
authors.forename: Filip
authors.initials: F
authors.lastname: Högnabba
authors.affiliation: Department of Ecology and Evolutionary Biology, Yale University, 358 ESC, 21 Sachem Street, New Haven, CT 06511, USA.
authors.forename: Jeffrey C
authors.initials: JC
authors.lastname: Oliver
authors.affiliation: Department of Biology, Duke University, Durham, NC 27708-0338, USA.
authors.forename: Katalin
authors.initials: K
authors.lastname: Molnár
authors.affiliation: Department of Biology, Duke University, Durham, NC 27708-0338, USA.
authors.forename: Emily
authors.initials: E
authors.lastname: Fraker
authors.affiliation: Department of Biology, Duke University, Durham, NC 27708-0338, USA.
authors.forename: Ester
authors.initials: E
authors.lastname: Gaya
authors.affiliation: Institut für Botanik, Karl-Franzens-Universität, Holteigasse 6, A-8010 Graz, Austria.
authors.forename: Josef
authors.initials: J
authors.lastname: Hafellner
authors.affiliation: Department of Biology, Duke University, Durham, NC 27708-0338, USA.
authors.forename: Valérie
authors.initials: V
authors.lastname: Hofstetter
authors.affiliation: Department of Biology, Duke University, Durham, NC 27708-0338, USA.
authors.forename: Cécile
authors.initials: C
authors.lastname: Gueidan
authors.affiliation: Department of Biology, Duke University, Durham, NC 27708-0338, USA.
authors.forename: Mónica A G
authors.initials: MA
authors.lastname: Otálora
authors.affiliation: Department of Biology, Duke University, Durham, NC 27708-0338, USA.
authors.forename: Brendan
authors.initials: B
authors.lastname: Hodkinson
authors.affiliation: Department of Plant Taxonomy and Nature Conservation, University of Gdańsk, ul. Wita Stwosza 59, 80-308 Gdańsk, Poland.
authors.forename: Martin
authors.initials: M
authors.lastname: Kukwa
authors.affiliation: Science and Education, The Field Museum, 1400 S. Lake Shore Drive, Chicago, IL 60605, USA.
authors.forename: Robert
authors.initials: R
authors.lastname: Lücking
authors.affiliation: UBC Herbarium, Beaty Museum, University of British Columbia, Vancouver, BC V6T1Z4, Canada.
authors.forename: Curtis
authors.initials: C
authors.lastname: Björk
authors.affiliation: Botanischer Garten und Botanisches Museum Berlin-Dahlem, Königin-Luise-Strasse 6-8, D-14195 Berlin, Germany.
authors.forename: Harrie J M
authors.initials: HJ
authors.lastname: Sipman
authors.affiliation: Departamento de Biologı́a Vegetal I, Facultad de CC. Biológicas, Universidad Complutense de Madrid, E-28040-Madrid, Spain.
authors.forename: Ana Rosa
authors.initials: AR
authors.lastname: Burgaz
authors.affiliation: Botanical Museum, Lund University, Box 117, SE-221 00 Lund, Sweden.
authors.forename: Arne
authors.initials: A
authors.lastname: Thell
authors.affiliation: BioLiq Laboratorio de Bioindicadores y Liquenología, Centro Regional Universitario Bariloche, INIBIOMA, Universidad Nacional del Comahue, Bariloche, 8400RN, Argentina.
authors.forename: Alfredo
authors.initials: A
authors.lastname: Passo
authors.affiliation: Botanical Museum, Finnish Museum of Natural History, FI-00014 University of Helsinki, Finland.
authors.forename: Leena
authors.initials: L
authors.lastname: Myllys
authors.affiliation: UBC Herbarium, Beaty Museum, University of British Columbia, Vancouver, BC V6T1Z4, Canada.
authors.forename: Trevor
authors.initials: T
authors.lastname: Goward
authors.affiliation: Department of Plant Biology (Botany Unit), Facultat de Biologia, Universitat de Barcelona, Av. Diagonal 643, 08028 Barcelona, Spain.
authors.forename: Samantha
authors.initials: S
authors.lastname: Fernández-Brime
authors.affiliation: CEES, Department of Biosciences, University of Oslo, PB 1066 Blindern, 0315 Oslo, Norway.
authors.forename: Geir
authors.initials: G
authors.lastname: Hestmark
authors.affiliation: Institute of Systematic Botany, The New York Botanical Garden, Bronx, NY 10458-5126, USA.
authors.forename: James
authors.initials: J
authors.lastname: Lendemer
authors.affiliation: Science and Education, The Field Museum, 1400 S. Lake Shore Drive, Chicago, IL 60605, USA.
authors.forename: H Thorsten
authors.initials: HT
authors.lastname: Lumbsch
authors.affiliation: Harvard University Herbaria, Organismic and Evolutionary Biology, Harvard University, 22 Divinity Avenue, Cambridge, MA 02138, USA.
authors.forename: Michaela
authors.initials: M
authors.lastname: Schmull
authors.affiliation: National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, 45 Center Drive, MSC 6510, Bethesda, MD 20892-6510, USA.
authors.forename: Conrad L
authors.initials: CL
authors.lastname: Schoch
authors.affiliation: Evolution and Conservation Biology, University of Liège, Sart Tilman B22, B-4000 Liège, Belgium.
authors.forename: Emmanuël
authors.initials: E
authors.lastname: Sérusiaux
authors.affiliation: Center for Genome Research and Biocomputing, Oregon State University, 3021 Agriculture and Life Sciences Building, Corvallis, OR 97331-7303, USA.
authors.forename: David R
authors.initials: DR
authors.lastname: Maddison
authors.affiliation: School of Plant Sciences, The University of Arizona, 1140 E. South Campus Drive, Forbes 303, Tucson, AZ 85721, USA.
authors.forename: A Elizabeth
authors.initials: AE
authors.lastname: Arnold
authors.affiliation: Department of Biology, Duke University, Durham, NC 27708-0338, USA.
authors.forename: François
authors.initials: F
authors.lastname: Lutzoni
authors.affiliation: Botanical Museum, Finnish Museum of Natural History, FI-00014 University of Helsinki, Finland.
authors.forename: Soili
authors.initials: S
authors.lastname: Stenroos
mesh_terms: D001203:Ascomycota / Q000145:classification* / Q000235:genetics; D002467:Cell Nucleus / Q000235:genetics; D005800:Genes, Fungal; D050259:Genes, Mitochondrial; D016013:Likelihood Functions; D008957:Models, Genetic; D010802:Phylogeny; D012335:RNA, Ribosomal / Q000235:genetics; D016415:Sequence Alignment; D017422:Sequence Analysis, DNA; D012984:Software
chemical_list: D012335:RNA, Ribosomal
keywords: Classification; Cumulative supermatrix; Lecanoromycetes; Lichenized fungi; Multi-gene phylogeny; Systematics
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