Computational protocol: Molecular taxonomy of bambusicolous fungi: Tetraplosphaeriaceae, a new pleosporalean family with Tetraploa-like anamorphs

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Protocol publication

[…] Preliminary multiple alignments of sequences were conducted using MAFFT v. 6 (; http://align.bmr.kyushu-u.ac.jp/mafft/software). Final alignments were manually adjusted using BioEdit v. 7.08 (). Alignment gaps and ambiguous positions were excluded from the analyses. Alignments used in this study were deposited in TreeBASE (S2505).Two phylogenetic analyses, maximum-parsimony (MP) using a close-neighbour-interchange heuristic search with an initial tree by random addition sequence (100 replicates) and neighbour-joining (NJ) based on the Kimura 2-parameter substitution model, were carried out using MEGA v. 4 (). Characters were weighted equally and gaps were excluded. The bootstrap support (BS) values for nodes were computed from 1 000 replicates for both the MP and NJ analyses. In addition to these analyses, Bayesian analyses were done using MrBayes v. 3.1.2 (). MrModeltest v. 2.2 () in conjunction with PAUP 4.0b10 () was used to select substitution models for Bayesian analyses. On the basis of AIC (Akaike Information Criterion) of MrModeltest v. 2.2, a GTR+I+G model for the SSU+LSU nrDNA, ITS and BT, and a HKY+I+G model for TEF gene sequences were applied. Two runs with 10 chains of Markov chain Monte Carlo (MCMC) iterations were performed for 6 million and 1.2 million generations, keeping one tree every 100 generations, for a combined alignment of the SSU+LSU nrDNA sequences and the ITS+TEF+BT gene sequences, respectively. The first 5 million generations of the SSU + LSU and 200 000 generations of the ITS+TEF+BT were discarded as burn-in, and the remaining 20 002 trees were used to calculate 50 % majority rule trees and to determine the posterior probabilities (PP) for the individual branches. […]

Pipeline specifications

Software tools MAFFT, BioEdit, MEGA-V, MrBayes, MrModelTest, PAUP*
Databases TreeBASE
Applications Phylogenetics, GWAS
Organisms Eragrostis tef