© 2007 The Authors. Journal compilation © 2007 The Norwegian Academy of Science and Letters • Zoologica Scripta, 37, 1, January 2008, pp43–56 43 Jordal, B., Gillespie, J. J. & Cognato, A. I. (2008). Secondary structure alignment and direct optimization of 28S rDNA sequences provide limited phylogenetic resolution in bark and ambrosia beetles (Curculionidae: Scolytinae). — Zoologica Scripta, 37, 43–56. 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 clade. 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. Corresponding author: Bjarte Jordal, Department of Biology, University of Bergen, Allegt 41, NO-5007 Bergen, Norway. E-mail: bjarte.jordal@bio.uib.no Joseph J. Gillespie, Department of Microbiology and Immunology, University of Maryland School of Medicine, 660 West Redwood Street, HH Room 3-24, Baltimore, MD 21201, USA Joseph J. Gillespie, Virginia Bioinformatics Institute, Bioinformatics Facility (0477), Washington Street, Virginia Tech, Blacksburg, VA 24061, USA. E-mail: pvittata@hotmail.com; jgill@vbi.vt.edu Anthony I. Cognato, Department of Entomology, Michigan State University, 243 Natural Science Bldg., East Lansing, MI 48824, USA. E-mail: cognato@msu.edu Blackwell Publishing Ltd Secondary structure alignment and direct optimization of 28S rDNA sequences provide limited phylogenetic resolution in bark and ambrosia beetles (Curculionidae: Scolytinae) BJARTE JORDAL, JOSEPH J. GILLESPIE & ANTHONY I. COGNATO Submitted: 17 May 2007 Accepted: 8 September 2007 doi:10.1111/j.1463-6409.2007.00306.x Introduction Bark beetles in the weevil subfamily Scolytinae are well known for their severe effect on boreal forest stands and particularly so on the conifers. The economical impact from a handful of tree-killing species is huge and the commercial value of cut timber is often reduced by fungal pathogens transmitted by wood-boring ambrosia beetles (including the Platypodinae). What is less known to the broader audience, however, is the enormous variation in biological and ecological characteristics in the nearly 7500 species of Scolytinae and Platypodinae (Wood & Bright 1992). A variety of reproductive behaviours, ranging from monogyny to harem polygyny and inbreeding by sibling mating, are associated with different genetic systems such as normal Xy diplodiploidy in outbreeding species, or haplodiploidy or paternal genome elimination for inbreeding species (see Jordal 2008). Resource use also goes far beyond the familiar association with inner bark and phloem, for example, there are many species from unrelated lineages that feed exclusively on fungal hyphae grown in wood tunnels (Beaver 1979). The non-reversed evolution of fungus cultivation (e.g. Farrell et al. 2001; Jordal 2002) has resulted in a tight symbiosis with highly modified cuticular modifications to carry fungal spores (Beaver 1989). The wide range of biological features across various groups of Scolytinae thus provides a highly informative system to study the evolution of important ecological traits. However,