Computational protocol: Hidden diversity in Thyridaria and a new circumscription of the Thyridariaceae

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Protocol publication

[…] For phylogenetic analyses, a combined matrix of ITS-LSU, SSU, rpb2 and tef1 sequences was produced. According to results of BLAST searches of the LSU and the tree topology of , GenBank sequences of selected Pleosporales () were included to reveal the phylogenetic relationships of the taxa treated here. In addition, selected members of the families Occultibambusaceae (), Paradictyoarthriniaceae () and Torulaceae () were added. Karstenula rhodostoma was included as a member of Didymosphaeriaceae according to . Two species of Massaria (Massariaceae) were selected as outgroup according to and . All alignments were produced with the server version of MAFFT 7 (http://mafft.cbrc.jp/alignment/server/), using the default settings for the SSU rDNA and the rpb2; for the ITS-LSU and the tef1 the E-INS-i and the G-INS-i iterative refinement methods were implemented, respectively, with a gap opening penalty of 1.0. The resulting alignments were checked and refined using BioEdit v. 7.0.4.1 (). For phylogenetic analyses, all sequence alignments were combined. After exclusion of ambiguously aligned regions from the ITS1 (the first 262 characters) and tef1 introns (418 characters) and large insertions from the SSU, the final matrix contained 1 484 nucleotide characters from the ITS-LSU rDNA, 995 from the SSU rDNA, 1082 from rpb2 and 1316 from tef1.Maximum parsimony (MP) bootstrap analysis was performed with PAUP v. 4.0a149 (), with 1 000 bootstrap replicates using 5 rounds of heuristic search replicates with random addition of sequences and subsequent TBR branch swapping (MULTREES option in effect, steepest descent option not in effect) during each bootstrap replicate, with each replicate limited to 1 million rearrangements. All molecular characters were unordered and given equal weight; analyses were performed with gaps treated as missing data; the COLLAPSE command was set to minbrlen.Maximum likelihood (ML) analyses were performed with RAxML () as implemented in raxmlGUI 1.3 (), using the ML + rapid bootstrap setting and the GTRGAMMAI substitution model with 1 000 bootstrap replicates. The matrix was partitioned for the individual gene regions, and substitution model parameters were calculated separately for them. Bootstrap support of <70 % was considered low, between 70–90 % medium, and > 90 % high. […]

Pipeline specifications

Software tools MAFFT, BioEdit, PAUP*, RAxML, raxmlGUI
Application Phylogenetics