Computational protocol: New Species of Boletellus Section Boletellus (Boletaceae, Boletales) from Japan, B. aurocontextus sp. nov. and B. areolatus sp. nov.

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Protocol publication

[…] After the sequences from the GenBank database were further added (), nucleotide sequences of the ITS region, RPB1, RPB2 and cox3 genes were aligned using the multiple sequence alignment program, Muscle []. The aligned sequences of the ITS region, RPB1 and RPB2 genes were cleaned using Gblocks v0.91b [], allowing smaller final blocks and gap positions within the final blocks. The resulting alignments of ITS, RPB1 RPB2 and cox3 were deposited in the TreeBASE (Study ID: 17303; http://www.treebase.org/) and were separately subjected to molecular phylogenetic inference. According the previous report [], closely related taxa of the ingroup were selected as outgroups ().The most appropriate evolutionary model was determined for each dataset by comparing different evolutionary models via the corrected Akaike information criterion (AICc) [,] using the Kakusan 4 []. Phylogenetic inference based on the maximum-likelihood (ML) method was performed using TREEFINDER 2011-March version [] with shotgun searches. Shotgun searches were repeated until no improvement was observed in the likelihood value. The confidence of the internal branches from the resulting tree was tested by bootstrap (BS) analysis [] with 1,000 replications. Bootstrapping was also performed on the basis of the maximum parsimony method (10,000 replications) using PAUP 4.0b10 (PAUP*) phylogenetic inference package []. Pairwise ML distances were calculated using the TREEFINDER based on the most appropriate evolutionary model selected by Kakusan 4. […]

Pipeline specifications

Software tools MUSCLE, Gblocks, PAUP*
Databases TreeBASE
Applications Phylogenetics, Nucleotide sequence alignment
Chemicals Nucleotides