Phylogeny of noctuoid moths and the utility of combining independent nuclear and mitochondrial genes

Phylogenies based on single genes can be discordant with organismal phylogenies. One solution to this problem is to sequence independent genes and combine the data in phylogeny estimates. The mitochondrial gene ND1 was sequenced for representative noctuoid moths to complement a nuclear ribosomal RNA (rRNA) data set. Before combining the two data sets, the mitochondrial DNA (mtDNA) data were analyzed under different assumptions of character treatment (unweighted sites, transversion parsimony, third codon site omitted). Although theoretical justifications exist for differentially weighting transversions and codon sites, these approaches did not improve our phylogeny estimates of noctuoid relationships based on only the mtDNA sequences. However, the contribution of the relatively small (25% of total data) but independent nuclear rRNA data set had a substantial impact on our analysis. The trees produced from the combined data do not support the monophyly of the largest family, the cutworms (Noctuidae). We suggest that cutworms are a grade rather than a clade in the superfamily. We mapped the replacement pathways of the ND1 amino acids using transformation series analysis and the most robust noctuoid tree. The resulting cladogram characters show that different amino acid replacement pathways exist for the same set of amino acid residues at different positions in the molecule. These replacement pathways do not conform to models proposed for protein evolution.