Secondary structure alignment and direct optimization of 28S rDNA sequences provide limited phylogenetic resolution in bark and ambrosia beetles (Curculionidae: Scolytinae)

Phylogenetic relationships in Scolytinae were reconstructed from 107 DNA sequences that spanned the D2 and D3 expansion segments, and related core regions of the nuclear large ribosomal subunit (28S). Sequences were analysed by parsimony and Bayesian analyses of aligned sequences aided by a new secondary structure model for the D2-D3 domains. Direct optimization was performed on ambiguous alignment regions in combination with fixed states optimization of unambiguous regions, but performed poorly compared to the Bayesian and parsimony analyses. Generally, the phylogenetic signal mainly resolved relationships within tribes, while deeper divergences were either not resolved or received marginal support. In addition to confirming several previously established clades, we found that Micracini formed the sister group to Cactopinus, a group of mainly cactus feeding scolytine beetles. Furthermore, Ipini was monophyletic with Pseudips and Acanthotomicus subtending to the most basal node of that Glade. The monophyly of Corthylini, which consists of the bark and cone feeding Pityophtorina and the ambrosia fungus-feeding Corthylina, was supported in some of the analyses. A close relationship was found between Phloeotribus and the two Phloeosinini genera Chramesus and Pseudochramesus, suggesting an evolutionary trajectory for the origin of a lamellate antennal club in Phloeotribus.