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

Jolanta Miadlikowska, Frank Kauff, Filip Högnabba, Jeffrey C. Oliver, Katalin Molnár, Emily Fraker, Ester Gaya, Josef Hafellner, Valérie Hofstetter, Cécile Gueidan, Mónica A G Otálora, Brendan Hodkinson, Martin Kukwa, Robert Lücking, Curtis Björk, Harrie J M Sipman, Ana Rosa Burgaz, Arne Thell, Alfredo Passo, Leena MyllysTrevor Goward, Samantha Fernández-Brime, Geir Hestmark, James Lendemer, H. Thorsten Lumbsch, Michaela Schmull, Conrad L. Schoch, Emmanuël Sérusiaux, David R. Maddison, Anne E Arnold, François Lutzoni, Soili Stenroos

Research output: Contribution to journalArticle

144 Citations (Scopus)

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.

Original languageEnglish (US)
Pages (from-to)132-168
Number of pages37
JournalMolecular Phylogenetics and Evolution
Volume79
Issue number1
DOIs
StatePublished - 2014

Fingerprint

Lecanoromycetes
Ascomycota
Fungi
fungus
phylogenetics
fungi
synthesis
gene
phylogeny
Ostropomycetidae
Genes
genes
taxonomy
Acarosporomycetidae
Lecanoromycetidae
Prosopis
Lecanorales
Ribosomal RNA
Hyphae
loci

Keywords

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

ASJC Scopus subject areas

  • Ecology, Evolution, Behavior and Systematics
  • Molecular Biology
  • Genetics
  • Medicine(all)

Cite this

A multigene phylogenetic synthesis for the class Lecanoromycetes (Ascomycota) : 1307 fungi representing 1139 infrageneric taxa, 317 genera and 66 families. / Miadlikowska, Jolanta; Kauff, Frank; Högnabba, Filip; Oliver, Jeffrey C.; Molnár, Katalin; Fraker, Emily; Gaya, Ester; Hafellner, Josef; Hofstetter, Valérie; Gueidan, Cécile; Otálora, Mónica A G; Hodkinson, Brendan; Kukwa, Martin; Lücking, Robert; Björk, Curtis; Sipman, Harrie J M; Burgaz, Ana Rosa; Thell, Arne; Passo, Alfredo; Myllys, Leena; Goward, Trevor; Fernández-Brime, Samantha; Hestmark, Geir; Lendemer, James; Lumbsch, H. Thorsten; Schmull, Michaela; Schoch, Conrad L.; Sérusiaux, Emmanuël; Maddison, David R.; Arnold, Anne E; Lutzoni, François; Stenroos, Soili.

In: Molecular Phylogenetics and Evolution, Vol. 79, No. 1, 2014, p. 132-168.

Research output: Contribution to journalArticle

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 2014, 'A multigene phylogenetic synthesis for the class Lecanoromycetes (Ascomycota): 1307 fungi representing 1139 infrageneric taxa, 317 genera and 66 families', Molecular Phylogenetics and Evolution, vol. 79, no. 1, pp. 132-168. https://doi.org/10.1016/j.ympev.2014.04.003
Miadlikowska, Jolanta ; Kauff, Frank ; Högnabba, Filip ; Oliver, Jeffrey C. ; Molnár, Katalin ; Fraker, Emily ; Gaya, Ester ; Hafellner, Josef ; Hofstetter, Valérie ; Gueidan, Cécile ; Otálora, Mónica A G ; Hodkinson, Brendan ; Kukwa, Martin ; Lücking, Robert ; Björk, Curtis ; Sipman, Harrie J M ; Burgaz, Ana Rosa ; Thell, Arne ; Passo, Alfredo ; Myllys, Leena ; Goward, Trevor ; Fernández-Brime, Samantha ; Hestmark, Geir ; Lendemer, James ; Lumbsch, H. Thorsten ; Schmull, Michaela ; Schoch, Conrad L. ; Sérusiaux, Emmanuël ; Maddison, David R. ; Arnold, Anne E ; Lutzoni, François ; Stenroos, Soili. / A multigene phylogenetic synthesis for the class Lecanoromycetes (Ascomycota) : 1307 fungi representing 1139 infrageneric taxa, 317 genera and 66 families. In: Molecular Phylogenetics and Evolution. 2014 ; Vol. 79, No. 1. pp. 132-168.
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