The effectiveness of mitochondrial rRNA gene sequences for the reconstruction of the phylogeny of an insect order (Orthoptera).

We investigated the value of mitochondrial rRNA sequences for analyzing pre-Cainozoic divergence events in insects. Using small subunit and large subunit rRNA sequences from 38 orthopteroid species, we examined several aspects of sequence evolution including secondary structure, substitution rate, and base composition. Substitution matrices calculated from the two genes were very similar, though differences were detected in rates of C-T transitions between paired and unpaired positions in secondary structures. By contrast, extreme disparities between substitution frequencies at different phylogenetic levels make character-transition weighting essential in parsimony reconstruction. The analysis of base composition indicated that branch attraction of at least two important lineages was due to shared base composition biases and to long branch attraction. The importance of taxonomic sampling and sequence length for the effectiveness of phylogenetic recovery using the rRNA fragments was also assessed. Significantly, combining the two sequences seemed both justifiable and necessary for this taxonomic sample. However, for reconstructing deep branches of phylogeny, it seems that increasing either or both the number of taxa or nucleotide positions will not necessarily solve all problems. Instead, the resolution of ancient branching events using mtDNA sequences probably depends upon the development and application of better specified reconstruction methods.