Computational protocol: Sex Pheromone Evolution Is Associated with Differential Regulation of the Same Desaturase Gene in Two Genera of Leafroller Moths

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Protocol publication

[…] Sequences were analysed using Geneious Pro v5.3.4 (Biomatters). Sequences were aligned using ClustalX and codon aligned nucleotide alignments were produced using RevTrans version 1.4.1 (www.cbs.dtu.dk/services/RevTrans/). For phylogenetic analyses, explicit models of evolution were determined using Modeltest and GTR+I+Γ was implemented for likelihood and Bayesian analyses. Parsimony and maximum likelihood analyses were performed in PAUP v4.0b (Sinauer Associates, Sunderland, Massachusetts), and Bayesian inference was implemented in MrBayes v3.0b4 . Evidence for selection was tested by looking for deviations from neutral expectations using the CODEML program in the PAML package . Multiple models were run (M0, M3, M7, M8 and M8a) to assess selection pressures. Comparisons of nested models were used to assess heterogeneous selective pressure amongst sites (M0–M3) or positive selection (M7–M8). Nested models were compared by the implementation of a likelihood-ratio test (LRT), where the LRT is twice the log-likelihood difference of the nested models. Significance was tested using a χ2 test with degrees of freedom equal to the difference in the number of parameters between the two models. […]

Pipeline specifications

Software tools Geneious, Clustal W, RevTrans, ModelTest-NG, PAUP*, MrBayes
Applications Phylogenetics, Nucleotide sequence alignment
Organisms Ilex paraguariensis, Saccharomyces cerevisiae