Mitochondrial genome data alone are not enough to unambigously resolve the relationships of Entognatha, Insecta and Crustacea sensu lato (Arthropoda)

An analysis of the relationships of the major arthropod groups was undertaken using mitochondrial genome data to examine the<p>hypotheses that Hexapoda is polyphyletic and that Collembola is more closely related to branchiopod crustaceans than insects. We<p>sought to examine the sensitivity of this relationship to outgroup choice, data treatment, gene choice and optimality criteria used in<p>the phylogenetic analysis of mitochondrial genome data. Additionally we sequenced the mitochondrial genome of an<p>archaeognathan, Nesomachilis australica, to improve taxon selection in the apterygote insects, a group poorly represented in<p>previous mitochondrial phylogenies. The sister group of the Collembola was rarely resolved in our analyses with a significant level of<p>support. The use of different outgroups (myriapods, nematodes, or annelids + mollusks) resulted in many different placements of<p>Collembola. The way in which the dataset was coded for analysis (DNA, DNA with the exclusion of third codon position and as<p>amino acids) also had marked affects on tree topology. We found that nodal support was spread evenly throughout the 13<p>mitochondrial genes and the exclusion of genes resulted in significantly less resolution in the inferred trees. Optimality criteria had a<p>much lesser effect on topology than the preceding factors; parsimony and Bayesian trees for a given data set and treatment were<p>quite similar. We therefore conclude that the relationships of the extant arthropod groups as inferred by mitochondrial genomes are<p>highly vulnerable to outgroup choice, data treatment and gene choice, and no consistent alternative hypothesis of Collembola’s<p>relationships is supported. Pending the resolution of these identified problems with the application of mitogenomic data to basal<p>arthropod relationships, it is difficult to justify the rejection of hexapod monophyly, which is well supported on morphological<p>grounds.