Are past phallic phylogenies of Acridoidea fallacies?

Acridoidea (Orthoptera, Caelifera) and its closest relatives represent the most recognizable of the grasshopper families. While past orthopteran studies that have focused on morphological characters, particularly phallic structure, have found strong support for the monophyly of the higher clades, relationships within the superfamily Acridoidea are poorly understood. Mitochondria genome (mtgenome) data have proven effective in resolving deep evolutionary relationships over broad time scales in other insect groups, but have yet to be broadly applied to Acridoidea. We present results from a phylogenetic analysis of 34 complete mtgenomes, including 11 unpublished genomes, representing 9 of the 11 acridoidean families and 4 closely related families (excluding outgroups). Using these data we specifically test the monophyly of Acridoidea and hypothesize the evolutionary relationships among major lineages. We also evaluate the conservation of anti-codons across the group and elucidate patterns among the start and stop codons of the protein coding genes (PCGs). We find that anti-codons are strongly conserved across the group that there are meaningful patterns among the start and stop codons for some genes, but not others. Furthermore, we find that traditional start codons cannot be used to annotate the beginning of cox1. We propose that the tetranucleotide start codon suggested by Sheffield et al. (2010) for cox1 is the best option for annotating cox1, although we did not find that the sequence was universally conserved as was previously thought. Our topology is highly congruent with current classification schemes and we find that mtgenome data provide the first robust hypothesis for Acridoidea.