Computational protocol: The Covert World of Fish Biofluorescence: A Phylogenetically Widespread and Phenotypically Variable Phenomenon

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Protocol publication

[…] A majority of the DNA sequence data used in this study is from , but additional sequences were obtained from many studies –; the GenBank accession numbers for these sequences as well as our added GenBank accession numbers (KF768155-KF768177) can be found in . Mitochondrial and nuclear genes were aligned using the program MAFFT v6.0 with default parameters . The phylogenetic analysis presented herein had a total of 5,238 base pairs including: one mitochondrial gene (cytochrome oxidase I, 812 bps), and five protein-coding genes (glycosyltransferase gene, 732 bps; myosin heavy chain 6 alpha gene, 737 bps; pleiomorphic adenoma protein-like 2-like gene, 659 bps; recombination activating gene 1, 1403 bps; zic family member protein, 890 bps). For each maximum likelihood analysis, the dataset was partitioned by individual gene fragments. A model of molecular evolution was chosen by the program jMODELTEST v.2.1 with the best fitting model under the Akaike information criteria (AIC) for each individual gene partition assigned, including: cytochrome oxidase I (GTR+I+Γ), glycosyltransferase (GTR+ Γ), myosin heavy chain 6 alpha (GTR+I+Γ), pleiomorphic adenoma protein-like 2-like gene (GTR+I+Γ), recombination activating gene 1 (SYM+I+Γ), and zic family member protein (GTR+I+Γ). Maximum likelihood analyses were performed in GARLI v2.0 . Ten separate analyses were conducted, and the tree having the best likelihood score is presented here (, ) to evaluate evolutionary relationships. […]

Pipeline specifications

Software tools MAFFT, jModelTest, GARLI
Application Phylogenetics
Organisms Danio rerio, Dipturus trachyderma