Computational protocol: Theissenia reconsidered, including molecular phylogeny of the type species T. pyrenocrata and a new genus Durotheca (Xylariaceae, Ascomycota)

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Protocol publication

[…] Each DNA sequence was checked for ambiguous bases, assembled using BioEdit v. 6.0.7 (), and submitted to GenBank (). Proofed sequences were then aligned using ClustalW () incorporated in BioEdit v. 6.0.7 and alignments were refined by directed examination. Parsimony and Bayesian analyses were first carried out for each gene on individual datasets. Potential conflicts were assessed by comparing individual parsimony bootstrap trees. In case two different relationships for the same set of taxa were both supported by bootstrap values greater than 70 % from different genes, it was assumed that the incongruence was signicant (). Parsimony (PAUP v. 4.0b10, Swofford 2002) and Bayesian (MrBayes v. 3.0, ) phylogenetic analyses were performed on the combined data set of the β-tubulin and α-actin genes. The maximum parsimony analysis was performed using the heuristic search, starting with trees obtained via 1000 random stepwise addition sequences, and tree-bisection-reconnection as the branch-swapping algorithm. All characters were given equal weights and gaps were treated as missing data. No topological constraints were enforced and the ‘Multrees’ option was in effect. Relative support for the branches was obtained from bootstrap proportions (BP) using 1000 heuristic searches using the aforementioned parsimony settings and 10 random sequence additions per bootstrap replicate. Prior to conducting the Bayesian analysis MrModeltest v. 2.2 () was used to determine the best nucleotide substitution model. After the best nucleotide substitution model was determined for each gene partition and combined dataset, Bayesian analysis was conducted using MCMC using a GTR+I+G model. Four default chains were sampled every 100 generations and run for a total of 2 M generations. Bayesian posterior probabilities (PP) were calculated on the posterior distribution of trees excluding the initial set of burn-in trees. […]

Pipeline specifications

Software tools BioEdit, Clustal W, PAUP*, MrBayes, MrModelTest
Application Phylogenetics