Computational protocol: Blue blood on ice: modulated blood oxygen transport facilitates cold compensation and eurythermy in an Antarctic octopod

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Protocol publication

[…] To illustrate phylogenetic relationships of Pareledone charcoti, Octopus pallidus and Eledone moschata, we performed Bayesian phylogenetic analysis using five genes, the mitochondrial genes cytochrome oxidase subunit I and III and the nuclear genes rhodopsin, octopine dehydrogenase and 16S rDNA of 16 octopodiform species (GenBank accession numbers in Additional file ). Sequences for each gene were aligned separately using the MUSCLE plugin of Geneious 7.1.7 []. The resulting alignments were curated using GBlocks 0.91b [,] tolerating gap positions within final blocks and concatenated to one data set. Based on the Akaike Information Criteria [], JModeltest 2.1.5 [], identified the GTR + I + G model as the best substitution models for the concatenated data set. Bayesian trees were constructed using MrBayes (v. 2.0.3) [] as implemented in Geneious running at least two independent Monte Carlo Markov Chain (MCMC) analysis with 2,000,000 generations sampled every 2,000 generations. The appropriate burnin was chosen based on the resulting traces, which showed a stationary distribution before 10% of the MCMC chain. Vampyroteuthis infernalis and Argonauta nodosa were used as outgroups. […]

Pipeline specifications

Software tools MUSCLE, Geneious, Gblocks, jModelTest, MrBayes
Applications Phylogenetics, Nucleotide sequence alignment
Diseases Fish Diseases
Chemicals Oxygen