Mycologia · 2007 · 27 citations · 22 references
Life SciencesBiologyBotanyMycologyPhylogeneticsSystematicsComparative MycologyFungal ClassificationMolecular PhylogenyPhylogenetic Tree ReconstructionPlant-pathogenic FungiTaxonomic Classification16S-23s Internal Transcribed Spacer AnalysisClade DelimitationInternal Transcribed Spacer (Its) ClusteringMolecular Phylogenetics Of FungiPhylogeny Of Plant PathogensRibosomal Dna Phylogenetics
Phaeocryptopus gaeumannii, causal agent of the Douglas-fir foliar disease Swiss needle cast, is the only known pathogenic species of the genus. Current classifications place Phaeocryptopus in the Venturiaceae (Pleosporales), typified by the apple-scab pathogen Venturia inaequalis. All core members of this family have hyphomycetous anamorphs. We sought to confirm these relationships by means of phylogenetic analyses of the small (SSU) and large (LSU) subunits and internal transcribed spacer (ITS) region of nuclear ribosomal gene sequences (nrDNA). Analyses indicated that both the genus Phaeocryptopus and the family Venturiaceae, as currently defined, are unnatural groups. Phaeocryptopus nudus, type of the genus, is aligned in the Dothioraceae (Dothideales) and P. gaeumannii in the Mycosphaerellaceae (Capnodiales) near species of Mycosphaerella and Rasutoria. Core representatives of Venturiaceae formed an unambiguous clade but ordinal placement was unresolved. The family apparently is not included in the Pleosporales, Dothideales, Myriangiales or Capnodiales. Coelomycetous Rhizosphaera form-species are accepted generally as anamorphic states of Phaeocryptopus, however the relationship never has been established conclusively. Species of Rhizosphaera are closely related to P. nudus but not to P. gaeumannii, supporting an anamorphteleomorph connection between Rhizosphaera and Phaeocryptopus and providing further evidence that P. gaeumanii is not congeneric with P. nudus.
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MUSCLE: multiple sequence alignment with high accuracy and high throughput
R. C. Edgar · Nucleic Acids Research · 2004 · 46.5K citations · Full text
CONFIDENCE LIMITS ON PHYLOGENIES: AN APPROACH USING THE BOOTSTRAP
Joseph Felsenstein · Evolution · 1985 · 41.5K citations · Full text
MRBAYES: Bayesian inference of phylogenetic trees
John P. Huelsenbeck, Fredrik Ronquist · Bioinformatics · 2001 · 22.2K citations · Full text