Computational protocol: Phylogenetic analysis of apicomplexan parasites infecting commercially valuable species from the North-East Atlantic reveals high levels of diversity and insights into the evolution of the group

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Protocol publication

[…] Sequences were checked manually using the software Geneious v4.8.5 [] and compared against the GenBank database to confirm whether they belonged within the Apicomplexa. Following the criteria of Rosenthal et al. [] only those sequences with clean chromatograms were included for analysis. All alignments were performed using MAFFT v7 [], and the software JModeltest v2.2.1 [] was used to select the appropriate model of evolution (AIC criteria). Phylogenetic reconstruction analyses based on Maximum Likelihood (ML) and Bayesian Inference (BI) were conducted using Garli v2.1 [] and MrBayes v3.2.6 [], respectively.First, a phylogenetic analysis was conducted including 40 newly generated sequences, plus 18S rRNA gene sequences of coccidians retrieved using the BLAST algorithm against the GenBank database (e.g. apicomplexans infecting corals) and sequences of piscine apicomplexans (included for example in the analyses of [–]). Separate phylogenetic analyses were conducted for subsets of related sequences identified in the preliminary analysis to improve alignment quality and outgroup choice. Two parallel runs were conducted for all analyses in MrBayes. In the first preliminary dataset runs were set to 30 million generations, and in the other subsequent analyses to 10 million. The software Tracer v1.6 [] was used to check for adequate mixing and convergence of each run. Trees from a stationary distribution (25% ‘burn-in’) were used to construct a majority rule consensus tree. For the ML analyses, 1000 bootstraps were used to evaluate branching support. Uncorrected p-distances were calculated for each group using the software MEGA6 [] to evaluate interspecific divergence and draw taxonomic conclusions. […]

Pipeline specifications

Software tools Geneious, MAFFT, jModelTest, GARLI, MrBayes, MEGA
Application Phylogenetics
Organisms Toxoplasma gondii, Danio rerio, Scyliorhinus canicula, Solea senegalensis, Dicentrarchus labrax, Sparus aurata