Molecular phylogeny of non-endopterygote Hexapoda: Do new data from 30 genes solve the interordinal puzzle?

The higher phylogeny of Hexapoda has been a topic of intense debate for decades, in particular the interordinal relationships. Different morphological and molecular characters frequently yield different topologies, but statistical tests of conflict are seldom used with morphological characters, while the repeated analyses of incrementally expanded ribosomal and mitochondrial DNA data have failed to provide a robust phylogenetic hypothesis. Statistically well supported phylogenies of early hexapod and of endopterygote insect orders based on nuclear, protein-coding genes were recently published, but many relationships between the remaining insect orders are still contentious.

Here we present new data from 30 nuclear, protein-coding genes for 71 taxa (plus outgroup taxa) representing all orders of non-endopterygote Hexapoda. Maximum likelihood and Bayesian analyses of non-synonymous nucleotide substitutions robustly resolve most interordinal relationships. The resulting topology is congruent with those higher taxa that were well supported in previous studies, but provides additionally supported hypotheses for previously unresolved groupings. Particular attention is paid to the placement of Odonata and Ephemeroptera relative to Neoptera, and to the phylogeny of Polyneoptera.