title: Species delimitation in Trametes: a comparison of ITS, RPB1, RPB2 and TEF1 gene phylogenies.
abstract: Trametes is a cosmopolitan genus of white rot polypores, including the "turkey tail" fungus, T. versicolor. Although Trametes is one of the most familiar genera of polypores, its species-level taxonomy is unsettled. The ITS region is the most commonly used molecular marker for species delimitation in fungi, but it has been shown to have a low molecular variation in Trametes resulting in poorly resolved phylogenies and unclear species boundaries, especially in the T. versicolor species complex (T. versicolor sensu stricto, T. ochracea, T. pubescens, T. ectypa). Here we evaluate the performance of three protein-coding genes (TEF1, RPB1, RPB2) for species delimitation and phylogenetic reconstruction in Trametes. We obtained 59 TEF1, 34 RPB1 and 55 RPB2 sequences from 69 individuals, focusing on the T. versicolor complex and performed phylogenetic analyses with maximum likelihood and parsimony methods. All three protein-coding genes outperformed ITS for separating species in the T. versicolor complex. The multigene phylogenetic analysis shows the highest amount of resolution and supported nodes separating T. ectypa, T. ochracea, T. pubescens and T. versicolor with strong support. In addition three slineages are resolved in the species complex of T. elegans. The T. elegans complex includes three species: T. elegans (based on material from Puerto Rico, Belize, the Philippines), T. aesculi (from North America) and T. repanda (from Papua New Guinea, the Philippines, Venezuela). The utility of gene markers varies, with TEF1 having the highest PCR and sequencing success rate and RPB1 offering the best backbone resolution for the genus.
authors.affiliation: Biology Department, Clark University, 950 Main Street, Worcester, Massachusetts 01610.
authors.forename: Alexis
authors.initials: A
authors.lastname: Carlson
authors.affiliation: Biology Department, Clark University, 950 Main Street, Worcester, Massachusetts 01610.
authors.forename: Alfredo
authors.initials: A
authors.lastname: Justo
authors.affiliation: Biology Department, Clark University, 950 Main Street, Worcester, Massachusetts 01610 dhibbett@clarku.edu.
authors.forename: David S
authors.initials: DS
authors.lastname: Hibbett
mesh_terms: D001483:Base Sequence; D004271:DNA, Fungal / Q000737:chemistry / Q000235:genetics; D021903:DNA, Ribosomal Spacer / Q000235:genetics; D005656:Fungal Proteins / Q000235:genetics*; D008969:Molecular Sequence Data; D058885:Multilocus Sequence Typing; D016533:Mycological Typing Techniques; D020648:Peptide Elongation Factor 1 / Q000235:genetics; D010802:Phylogeny; D012319:RNA Polymerase II / Q000235:genetics; D017422:Sequence Analysis, DNA; D055454:Trametes / Q000145:classification* / Q000235:genetics / Q000302:isolation & purification
chemical_list: D004271:DNA, Fungal; D021903:DNA, Ribosomal Spacer; D005656:Fungal Proteins; D020648:Peptide Elongation Factor 1; D012319:RNA Polymerase II
keywords: PolyPEET; Polyporales; gene phylogenies; systematics; taxonomy