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Miadlikowska J, Kauff F, Högnabba F, Oliver JC, Molnár K, Fraker E, Gaya E, Hafellner J, Hofstetter V, Gueidan C, Otálora MAG, Hodkinson B, Kukwa M, Lücking R, Björk C, Sipman HJM, Burgaz AR, Thell A, Passo A, Myllys L, Goward T, Fernández-Brime S, Hestmark G, Lendemer J, Lumbsch HT, Schmull M, Schoch CL, Sérusiaux E, Maddison DR, Arnold AE, Lutzoni F, Stenroos S. A multigene phylogenetic synthesis for the class Lecanoromycetes (Ascomycota): 1307 fungi representing 1139 infrageneric taxa, 317 genera and 66 families. Mol Phylogenet Evol 2014; 79:132-68. [PMID: 24747130 PMCID: PMC4185256 DOI: 10.1016/j.ympev.2014.04.003] [Citation(s) in RCA: 121] [Impact Index Per Article: 12.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2013] [Revised: 03/02/2014] [Accepted: 04/02/2014] [Indexed: 11/28/2022]
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.
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Affiliation(s)
| | - Frank Kauff
- FB Biologie, Molecular Phylogenetics, 13/276, TU Kaiserslautern, Postfach 3049, 67653 Kaiserslautern, Germany
| | - Filip Högnabba
- Botanical Museum, Finnish Museum of Natural History, FI-00014 University of Helsinki, Finland
| | - Jeffrey C Oliver
- Department of Ecology and Evolutionary Biology, Yale University, 358 ESC, 21 Sachem Street, New Haven, CT 06511, USA
| | - Katalin Molnár
- Department of Biology, Duke University, Durham, NC 27708-0338, USA
| | - Emily Fraker
- Department of Biology, Duke University, Durham, NC 27708-0338, USA
| | - Ester Gaya
- Department of Biology, Duke University, Durham, NC 27708-0338, USA
| | - Josef Hafellner
- Institut für Botanik, Karl-Franzens-Universität, Holteigasse 6, A-8010 Graz, Austria
| | | | - Cécile Gueidan
- Department of Biology, Duke University, Durham, NC 27708-0338, USA
| | | | | | - Martin Kukwa
- Department of Plant Taxonomy and Nature Conservation, University of Gdańsk, ul. Wita Stwosza 59, 80-308 Gdańsk, Poland
| | - Robert Lücking
- Science and Education, The Field Museum, 1400 S. Lake Shore Drive, Chicago, IL 60605, USA
| | - Curtis Björk
- UBC Herbarium, Beaty Museum, University of British Columbia, Vancouver, BC V6T1Z4, Canada
| | - Harrie J M Sipman
- Botanischer Garten und Botanisches Museum Berlin-Dahlem, Königin-Luise-Strasse 6-8, D-14195 Berlin, Germany
| | - Ana Rosa Burgaz
- Departamento de Biologı́a Vegetal I, Facultad de CC. Biológicas, Universidad Complutense de Madrid, E-28040-Madrid, Spain
| | - Arne Thell
- Botanical Museum, Lund University, Box 117, SE-221 00 Lund, Sweden
| | - Alfredo Passo
- BioLiq Laboratorio de Bioindicadores y Liquenología, Centro Regional Universitario Bariloche, INIBIOMA, Universidad Nacional del Comahue, Bariloche, 8400RN, Argentina
| | - Leena Myllys
- Botanical Museum, Finnish Museum of Natural History, FI-00014 University of Helsinki, Finland
| | - Trevor Goward
- UBC Herbarium, Beaty Museum, University of British Columbia, Vancouver, BC V6T1Z4, Canada
| | - Samantha Fernández-Brime
- Department of Plant Biology (Botany Unit), Facultat de Biologia, Universitat de Barcelona, Av. Diagonal 643, 08028 Barcelona, Spain
| | - Geir Hestmark
- CEES, Department of Biosciences, University of Oslo, PB 1066 Blindern, 0315 Oslo, Norway
| | - James Lendemer
- Institute of Systematic Botany, The New York Botanical Garden, Bronx, NY 10458-5126, USA
| | - H Thorsten Lumbsch
- Science and Education, The Field Museum, 1400 S. Lake Shore Drive, Chicago, IL 60605, USA
| | - Michaela Schmull
- Harvard University Herbaria, Organismic and Evolutionary Biology, Harvard University, 22 Divinity Avenue, Cambridge, MA 02138, USA
| | - Conrad L Schoch
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, 45 Center Drive, MSC 6510, Bethesda, MD 20892-6510, USA
| | - Emmanuël Sérusiaux
- Evolution and Conservation Biology, University of Liège, Sart Tilman B22, B-4000 Liège, Belgium
| | - David R Maddison
- Center for Genome Research and Biocomputing, Oregon State University, 3021 Agriculture and Life Sciences Building, Corvallis, OR 97331-7303, USA
| | - A Elizabeth Arnold
- School of Plant Sciences, The University of Arizona, 1140 E. South Campus Drive, Forbes 303, Tucson, AZ 85721, USA
| | - François Lutzoni
- Department of Biology, Duke University, Durham, NC 27708-0338, USA
| | - Soili Stenroos
- Botanical Museum, Finnish Museum of Natural History, FI-00014 University of Helsinki, Finland
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Passo A, Stenroos S, Calvelo S. Joergensenia, a new genus to accommodate Psoroma cephalodinum (lichenized Ascomycota). ACTA ACUST UNITED AC 2008; 112:1465-74. [PMID: 18675347 DOI: 10.1016/j.mycres.2008.06.025] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2007] [Revised: 06/13/2008] [Accepted: 06/20/2008] [Indexed: 10/21/2022]
Abstract
The taxonomy of the genus Psoroma (lichenized Ascomycota) is currently under revision, as it has long been recognized as heterogeneous. The aim of the present study was to reconstruct the phylogeny of Psoroma and related genera. The ITS region of nu-rDNA and the mtSSU rDNA from 22 collections of Psoroma and Pannaria were amplified. Sequences from GenBank were also used. For the phylogenetic analysis, direct optimization was implemented, using the program POY, and standard MP using PAUP. Both analyses resulted in similar trees. Two main clades were obtained, one including Santesoniella and most Psoroma species and the other including Pannaria and two Psoroma species, indicating that Psoroma is polyphyletic. Based on its phylogenetic position and ascus type, P. implexum is transferred to the genus Pannaria, and the new combination P. implexa is proposed. Psoroma cephalodinum clusters with Parmeliella and Degelia as a basal group within the Pannariaceae. The ascus apex of P. cephalodinum has a strong amyloid reaction revealing a compact cap-shaped plug. This differs from most of the ascus apical structures observed in the family. Both ascus internal structure and phylogenetic position suggest that P. cephalodinum is distantly related to Psoroma or Pannaria, and thus a new genus Joergensenia is proposed.
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Affiliation(s)
- Alfredo Passo
- Centro Regional Universitario Bariloche, Universidad Nacional del Comahue, Quintral 1250, 8400 Bariloche, Río Negro, Argentina.
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