New insights into classification and evolution of the Lecanoromycetes (Pezizomycotina, Ascomycota) from phylogenetic analyses of three ribosomal RNA- and two protein-coding genes.
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.
Miadlikowska
Jolanta
J
Department of Biology, Duke University, Durham, North Carolina 27708-0338, USA. jolantam@duke.edu
Kauff
Frank
F
Hofstetter
Valérie
V
Fraker
Emily
E
Grube
Martin
M
Hafellner
Josef
J
Reeb
Valérie
V
Hodkinson
Brendan P
BP
Kukwa
Martin
M
Lücking
Robert
R
Hestmark
Geir
G
Otalora
Monica Garcia
MG
Rauhut
Alexandra
A
Büdel
Burkhard
B
Scheidegger
Christoph
C
Timdal
Einar
E
Stenroos
Soili
S
Brodo
Irwin
I
Perlmutter
Gary B
GB
Ertz
Damien
D
Diederich
Paul
P
Lendemer
James C
JC
May
Philip
P
Schoch
Conrad L
CL
Arnold
A Elizabeth
AE
Gueidan
Cécile
C
Tripp
Erin
E
Yahr
Rebecca
R
Robertson
Connie
C
Lutzoni
François
F
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
D004271:DNA, Fungal; D004272:DNA, Mitochondrial; D004275:DNA, Ribosomal; D012337:RNA, Ribosomal, 18S; D012339:RNA, Ribosomal, 28S; D012319:RNA Polymerase II