Computational protocol: Phylogenetic Analysis of Ruminant Theileria spp. from China Based on 28S Ribosomal RNA Gene

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Protocol publication

[…] Phylogenetic trees of the complete 28S rRNA, D2-D3 region, and 18S rRNA were constructed using the maximum parsimony (MP) and Bayesian inference (BI). The MP trees were constructed using the PAUP4.0 []. Gaps were treated as missing data, with equal weightings for transitions and transversions, and a heuristic search was made using the TBR branch-swapping algorithm []. BI analyses of each dataset were conducted separately using the MrBayes 3.1.2 []. The Bayesian analyses were initiated using a GTR+I+Γ model with no initial values assigned to these parameters and were performed with 4 chains of 1.0×106 generations for the 28S rRNA dataset, 2.0×105 generations for the D2-D3 dataset, and 1.0×106 generations for the 18S rRNA dataset. The Markov chains were sampled at intervals of 100 generations. After discarding the burn-in samples and evaluating convergence, the remaining samples were retained for further analysis. The posterior probabilities (PP) were obtained for appropriate clades. Clades with PP ≥ 95% were considered to be highly supported. One Babesia bovis isolate was used as the outgroup. Finally, the phylogenetic trees constructed using the 2 methods were viewed using the TreeView program (version 32). […]

Pipeline specifications

Software tools PAUP*, MrBayes, TreeViewX
Application Phylogenetics
Organisms Bos taurus, Ovis aries