title: New insights into classification and evolution of the Lecanoromycetes (Pezizomycotina, Ascomycota) from phylogenetic analyses of three ribosomal RNA- and two protein-coding genes.
abstract: The Lecanoromycetes includes most of the lichen-forming fungal species (> 13500) 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.
authors.affiliation: Department of Biology, Duke University, Durham, North Carolina 27708-0338, USA. jolantam@duke.edu
authors.forename: Jolanta
authors.initials: J
authors.lastname: Miadlikowska
authors.forename: Frank
authors.initials: F
authors.lastname: Kauff
authors.forename: Valérie
authors.initials: V
authors.lastname: Hofstetter
authors.forename: Emily
authors.initials: E
authors.lastname: Fraker
authors.forename: Martin
authors.initials: M
authors.lastname: Grube
authors.forename: Josef
authors.initials: J
authors.lastname: Hafellner
authors.forename: Valérie
authors.initials: V
authors.lastname: Reeb
authors.forename: Brendan P
authors.initials: BP
authors.lastname: Hodkinson
authors.forename: Martin
authors.initials: M
authors.lastname: Kukwa
authors.forename: Robert
authors.initials: R
authors.lastname: Lücking
authors.forename: Geir
authors.initials: G
authors.lastname: Hestmark
authors.forename: Monica Garcia
authors.initials: MG
authors.lastname: Otalora
authors.forename: Alexandra
authors.initials: A
authors.lastname: Rauhut
authors.forename: Burkhard
authors.initials: B
authors.lastname: Büdel
authors.forename: Christoph
authors.initials: C
authors.lastname: Scheidegger
authors.forename: Einar
authors.initials: E
authors.lastname: Timdal
authors.forename: Soili
authors.initials: S
authors.lastname: Stenroos
authors.forename: Irwin
authors.initials: I
authors.lastname: Brodo
authors.forename: Gary B
authors.initials: GB
authors.lastname: Perlmutter
authors.forename: Damien
authors.initials: D
authors.lastname: Ertz
authors.forename: Paul
authors.initials: P
authors.lastname: Diederich
authors.forename: James C
authors.initials: JC
authors.lastname: Lendemer
authors.forename: Philip
authors.initials: P
authors.lastname: May
authors.forename: Conrad L
authors.initials: CL
authors.lastname: Schoch
authors.forename: A Elizabeth
authors.initials: AE
authors.lastname: Arnold
authors.forename: Cécile
authors.initials: C
authors.lastname: Gueidan
authors.forename: Erin
authors.initials: E
authors.lastname: Tripp
authors.forename: Rebecca
authors.initials: R
authors.lastname: Yahr
authors.forename: Connie
authors.initials: C
authors.lastname: Robertson
authors.forename: François
authors.initials: F
authors.lastname: Lutzoni
mesh_terms: D001203:Ascomycota / Q000145:classification* / Q000235:genetics*; D016000:Cluster Analysis; D019295:Computational Biology; D004271:DNA, Fungal / Q000235:genetics; D004272:DNA, Mitochondrial / Q000235:genetics; D004275:DNA, Ribosomal / Q000235:genetics; D019143:Evolution, Molecular; D010802:Phylogeny; D012319:RNA Polymerase II / Q000235:genetics; D012337:RNA, Ribosomal, 18S / Q000235:genetics; D012339:RNA, Ribosomal, 28S / Q000235:genetics; D017385:Sequence Homology
chemical_list: D004271:DNA, Fungal; D004272:DNA, Mitochondrial; D004275:DNA, Ribosomal; D012337:RNA, Ribosomal, 18S; D012339:RNA, Ribosomal, 28S; D012319:RNA Polymerase II