title: Iteratively refined guide trees help improving alignment and phylogenetic inference in the mushroom family Bolbitiaceae.
abstract: Reconciling traditional classifications, morphology, and the phylogenetic relationships of brown-spored agaric mushrooms has proven difficult in many groups, due to extensive convergence in morphological features. Here, we address the monophyly of the Bolbitiaceae, a family with over 700 described species and examine the higher-level relationships within the family using a newly constructed multilocus dataset (ITS, nrLSU rDNA and EF1-alpha). We tested whether the fast-evolving Internal Transcribed Spacer (ITS) sequences can be accurately aligned across the family, by comparing the outcome of two iterative alignment refining approaches (an automated and a manual) and various indel-treatment strategies. We used PRANK to align sequences in both cases. Our results suggest that--although PRANK successfully evades overmatching of gapped sites, referred previously to as alignment overmatching--it infers an unrealistically high number of indel events with natively generated guide-trees. This 'alignment undermatching' could be avoided by using more rigorous (e.g. ML) guide trees. The trees inferred in this study support the monophyly of the core Bolbitiaceae, with the exclusion of Panaeolus, Agrocybe, and some of the genera formerly placed in the family. Bolbitius and Conocybe were found monophyletic, however, Pholiotina and Galerella require redefinition. The phylogeny revealed that stipe coverage type is a poor predictor of phylogenetic relationships, indicating the need for a revision of the intrageneric relationships within Conocybe.
authors: Department of Microbiology, Faculty of Science and Informatics, University of Szeged, Szeged, Hungary.
authors: Annamária
authors: A
authors: Tóth
authors: Anton
authors: A
authors: Hausknecht
authors: Irmgard
authors: I
authors: Krisai-Greilhuber
authors: Tamás
authors: T
authors: Papp
authors: Csaba
authors: C
authors: Vágvölgyi
authors: László G
authors: LG
authors: Nagy
mesh_terms: D000363:Agaricales / Q000145:classification / Q000235:genetics*; D004271:DNA, Fungal / Q000737:chemistry / Q000235:genetics; D019143:Evolution, Molecular; D005656:Fungal Proteins / Q000235:genetics; D014644:Genetic Variation; D008969:Molecular Sequence Data; D020648:Peptide Elongation Factor 1 / Q000235:genetics; D010802:Phylogeny; D012339:RNA, Ribosomal, 28S / Q000235:genetics; D016415:Sequence Alignment / Q000379:methods*; D017422:Sequence Analysis, DNA; D013045:Species Specificity
chemical_list: D004271:DNA, Fungal; D005656:Fungal Proteins; D020648:Peptide Elongation Factor 1; D012339:RNA, Ribosomal, 28S