Computational protocol: Parallel Evolution of Metazoan Mitochondrial Proteins

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Protocol publication

[…] We obtained multiple-species alignments of 12 mitochondrial proteins of metazoans from (), and analyzed alignment columns with <1% gaps (which comprised 77% of all sites). As there is no accepted phylogenetic tree for this large and diverse set of species spanning a wide range of phylogenetic distances, we took a hybrid approach to reconstructing their phylogeny. First, we constrained the tree topology using the curated taxonomy-based phylogeny of the ITOL (Interactive tree of life) project (). By requiring the presence of each species in the ITOL database, we were left with >900 metazoan species for each protein (). The resulting topology was not fully resolved, and contained multifurcations. We then used RAxML 8.0.0 () under the GTR-Γ model to resolve multifurcations and to estimate the branch lengths. Finally, ancestral states were reconstructed using codeml program of the PAML package () under the substitution matrix and the value of the parameter alpha of the gamma distribution inferred by RAxML.Independently, using the same methods and parameters, we reconstructed a joint phylogeny of 3,586 chordate, 586 nonchordate, and 178 fungal species (for a total of 4,350 species) based on amino acid sequences of five concatenated mitochondrial genes, each of which was aligned by MUSCLE covering a total of 1,524 amino acid positions.Transmembrane and nonmembrane sites were obtained from UniProt database (http://www.uniprot.org/). […]

Pipeline specifications

Software tools iTOL, RAxML, PAML, MUSCLE
Applications Phylogenetics, Nucleotide sequence alignment
Chemicals Amino Acids