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Mol Phylogenet Evol. 2014 Oct;79:132-68. doi: 10.1016/j.ympev.2014.04.003. Epub 2014 Apr 18.

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

Author information

1
Department of Biology, Duke University, Durham, NC 27708-0338, USA. Electronic address: jolantam@duke.edu.
2
FB Biologie, Molecular Phylogenetics, 13/276, TU Kaiserslautern, Postfach 3049, 67653 Kaiserslautern, Germany.
3
Botanical Museum, Finnish Museum of Natural History, FI-00014 University of Helsinki, Finland.
4
Department of Ecology and Evolutionary Biology, Yale University, 358 ESC, 21 Sachem Street, New Haven, CT 06511, USA.
5
Department of Biology, Duke University, Durham, NC 27708-0338, USA.
6
Institut für Botanik, Karl-Franzens-Universität, Holteigasse 6, A-8010 Graz, Austria.
7
Department of Plant Taxonomy and Nature Conservation, University of Gdańsk, ul. Wita Stwosza 59, 80-308 Gdańsk, Poland.
8
Science and Education, The Field Museum, 1400 S. Lake Shore Drive, Chicago, IL 60605, USA.
9
UBC Herbarium, Beaty Museum, University of British Columbia, Vancouver, BC V6T1Z4, Canada.
10
Botanischer Garten und Botanisches Museum Berlin-Dahlem, Königin-Luise-Strasse 6-8, D-14195 Berlin, Germany.
11
Departamento de Biologı́a Vegetal I, Facultad de CC. Biológicas, Universidad Complutense de Madrid, E-28040-Madrid, Spain.
12
Botanical Museum, Lund University, Box 117, SE-221 00 Lund, Sweden.
13
BioLiq Laboratorio de Bioindicadores y Liquenología, Centro Regional Universitario Bariloche, INIBIOMA, Universidad Nacional del Comahue, Bariloche, 8400RN, Argentina.
14
Department of Plant Biology (Botany Unit), Facultat de Biologia, Universitat de Barcelona, Av. Diagonal 643, 08028 Barcelona, Spain.
15
CEES, Department of Biosciences, University of Oslo, PB 1066 Blindern, 0315 Oslo, Norway.
16
Institute of Systematic Botany, The New York Botanical Garden, Bronx, NY 10458-5126, USA.
17
Harvard University Herbaria, Organismic and Evolutionary Biology, Harvard University, 22 Divinity Avenue, Cambridge, MA 02138, USA.
18
National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, 45 Center Drive, MSC 6510, Bethesda, MD 20892-6510, USA.
19
Evolution and Conservation Biology, University of Liège, Sart Tilman B22, B-4000 Liège, Belgium.
20
Center for Genome Research and Biocomputing, Oregon State University, 3021 Agriculture and Life Sciences Building, Corvallis, OR 97331-7303, USA.
21
School of Plant Sciences, The University of Arizona, 1140 E. South Campus Drive, Forbes 303, Tucson, AZ 85721, USA.

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.

KEYWORDS:

Classification; Cumulative supermatrix; Lecanoromycetes; Lichenized fungi; Multi-gene phylogeny; Systematics

PMID:
24747130
PMCID:
PMC4185256
DOI:
10.1016/j.ympev.2014.04.003
[Indexed for MEDLINE]
Free PMC Article

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