Mitochondrial phylogenies in the light of pseudogenes and Wolbachia: re-assessment of a bark beetle dataset

Phylogenetic studies based on mtDNA become increasingly questioned because of potential pitfalls due to mitochondrial pseudogenes and mitochondrial selective sweeps. While the inclusion of nuclear markers should preferentially be considered for future studies, there is no need to abandon mtDNA as long as tests for the known mtDNA artefacts are performed. In this study we present additional data and test previous phylogeographical studies of Pityogenes chalcographus. We did not detect nuclear copies (numts) of the previously used mitochondrial markers by performing a combined long range/nested PCR of the COI gene and by an in silico analysis of the COI sequence data. This confirms the robustness of our previous phylogenetic study of P. chalcographus. Results of an in-situ hybridization of Wolbachia in P. chalcographus confirm the presence of this endosysmbiont in this species. However, we did not detect a correlation between infection status, geographical region and mtDNA haplotypes. The hybridisation data also support a previous hypothesis that infections do not result from parasitoids or parasitic nematodes, insect surface or laboratory contaminations and are hence a true infection of P. chalcographus. We conclude that the deep structure found in mitochondrial populations of P. chalcographus indeed represents the evolutionary history of European populations.