Computational protocol: Morphological Examination and Phylogenetic Analyses of Phycopeltis spp. (Trentepohliales, Ulvophyceae) from Tropical China

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Protocol publication

[…] Trentrepohlialean algae were selected from GenBank (http://www.ncbi.nlm.nih.gov/) for nuclear SSU and ITS rDNA sequences analyses. The sequences were initially aligned by ClustalX (v. 1.83) [], and refined manually with Seaview (v. 4.32) []. The final alignment of SSU and ITS rDNA sequences comprised a matrix of 41 sequences and 33 sequences respectively (Supplementary materials). Mutational saturation was evaluated in the variable positions of the alignments by plotting pairwise distances against model-corrected distances for Tamura and Nei (1993) and Kimura (1980) models and estimated in MEGA (v.5.0) []. And the result showed that neither transitions nor transversions have reached saturation. The empirical base frequencies of the nuclear SSU and ITS rDNA sequences were determined by PAUP 4.0*b10 [] to test for homogeneity of base frequencies across the taxa.Phylogenetic trees were constructed using maximum parsimony (MP) with PAUP 4.0*b10 [], maximum likelihood (ML) with RAxML8.0 (http://www.exelixis-lab.org/web/software/raxml/hands_on.html) [], and Bayesian Inference (BI) with MrBayes3.1.2 []. ModelTest 3.7 [] was used to select the evolutionary best-fit model according to hierarchical likelihood ratio tests and Akaike information criterion. The best-fit models of both SSU rDNA and ITS rDNA data was GTR+I+G. Bootstrap analyses with 1000 replicates of the dataset for ML and MP was performed to estimate statistical reliability. Bayesian analyses of both SSU rDNA and ITS rDNA sequence was performed with 1.0× 107 generations of Markov chain Monte Carlo iterations and trees were sampled every 1 × 104 generations. It was assumed that the stationary distribution was reached when average standard deviation of split frequencies between two runs was lower than 0.01. The first 25% of the calculated trees were discarded as burn-in, and the remaining samples were used to construct a Bayesian consensus tree and to infer posterior probabilities. The bootstrap values and posterior probabilities were presented on the nodes. The resulting phylogenetic trees were showed and edited using Figtree1.4.2 (http://tree.bio.ed.ac.uk/software/figtree/). Only maximum likelihood trees were showed. […]

Pipeline specifications

Software tools Clustal W, SeaView, MEGA-V, PAUP*, RAxML, MrBayes, ModelTest-NG, FigTree
Applications Phylogenetics, GWAS
Organisms Pyrinioides aurea