@article {13138,
	title = {Secondary structure alignment and direct optimization of 28S rDNA sequences provide limited phylogenetic resolution in bark and ambrosia beetles (Curculionidae: Scolytinae)},
	journal = {Zoologica Scripta},
	volume = {37},
	number = {1},
	year = {2008},
	month = {January},
	pages = {43-56},
	type = {Article},
	abstract = {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.},
	keywords = {Acanthotomicus, Cactopinus, Chramesus, Corthylina, Corthylini, Ipini, Micracini, Phloeosinini, Phloeotribus, Pityophtorina, Pseudips, Pseudochramesus, Scolytinae},
	isbn = {0300-3256},
	author = {Jordal, Bjarte and Gillespie, Joseph J. and Cognato, Anthony I.}
}
@article {8564,
	title = {Structural alignment of 18S and 28S rDNA sequences provides insights into phylogeny of Phytophaga (Coleoptera: Curculionoidea and Chrysomeloidea)},
	journal = {Zoologica Scripta},
	volume = {38},
	number = {1},
	year = {2009},
	month = {January},
	pages = {63-77},
	abstract = {We performed a comparative study of partial rDNA sequences from a variety of Coleoptera taxa to construct an annotated alignment based on secondary structure information, which in turn, provides improved rRNA structure models useful for phylogenetic reconstruction. Subsequent phylogenetic analysis was performed to test monophyly and interfamilial relationships of the megadiverse plant feeding beetle group known as {\textquoteright}Phytophaga{\textquoteright} (Curculionoidea and Chrysomeloidea), as well as to discover their closest relatives among the Cucujiformia. Parsimony and Bayesian analyses were performed based on the structural alignment of segments of 18S rRNA (variable regions V4-V5, V7-V9) and 28S rRNA (expansion segment D2). A total of 104 terminal taxa of Coleoptera were included: 96 species of Cucujiformia beetles, representing the families and most {\textquoteright}subfamilies{\textquoteright} of weevils and chrysomeloids (Phytophaga), as well as several families of Cleroidea, Tenebrionoidea and Cucujoidea, and eight outgroups from three other polyphagan series: Scarabaeiformia, Elateriformia and Bostrichiformia. The results from the different methods of analysis agree - recovering the monophyly of the {\textquoteright}Phytophaga{\textquoteright}, including Curculionoidea and Chrysomeloidea as sister groups. The curculionoid and chrysomeloid phylogeny recovered from the aligned 18S and 28S rDNA segments, which is independent of morphological data, is in agreement with recent hypotheses or concepts based on morphological evidence, particularly with respect to familial relationships. Our results provide clues about the evolutionary origin of the phytophagan beetles within the megaclade Cucujiformia, suggesting that the sister group of {\textquoteright}Curculionoidea + Chrysomeloidea{\textquoteright} is a clade of the {\textquoteright}Cucujoidea{\textquoteright}, represented in this study by species in Boganiidae, Erotylidae, Nitidulidae, Cucujidae and Silvanidae. The Coccinellidae and Endomychidae are not grouped with the latter, and the remaining terminal taxa are nested in Tenebrionoidea and Cleroidea. We propose that the combination of structurally aligned ribosomal RNA gene regions 18S (V4-V5, V7-V9) and 28S (D2) are useful in testing monophyly and resolving relationships among beetle superfamilies and families.},
	isbn = {0300-3256},
	author = {Marvaldi, Adriana E. and Duckett, Catherine N. and Kjer, Karl M. and Gillespie, Joseph J.}
}
