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MBE Advance Access published online on April 20, 2005
Molecular Biology and Evolution, doi:10.1093/molbev/msi152
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© The Author 2005. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution. All rights reserved. For permissions, please e-mail: journals.permissions@oupjournals.org
Accepted April 11, 2005

Research Article

A Secondary Structural Model of the 28S rRNA Expansion Segments D2 and D3 for Chalcidoid Wasps (Hymenoptera: Chalcidoidea)

Joseph J. Gillespie 1*, James B. Munro 2, John M. Heraty 2, Matthew J. Yoder 1, Albert K. Owen 2, and Andrew E. Carmichael 2

1 Department of Entomology, Texas A&M University, College Station, TX 77843, USA
2 Department of Entomology, University of California, Riverside, CA 92521, USA

* To whom correspondence should be addressed.
Joseph J. Gillespie, E-mail: pvittata{at}hotmail.com or pvittata@gmail.com


  Abstract

We analyze the secondary structure of two expansion segments (D2, D3) of the 28S rRNA-encoding gene region from 527 chalcidoid wasp taxa (Hymenoptera: Chalcidoidea) representing 18 of the 19 extant families. The sequences are compared in a multiple sequence alignment, with secondary structure inferred primarily from the evidence of compensatory base changes in conserved helices of the rRNA molecules. This covariation analysis yielded 36 helices that are comprised of base pairs exhibiting positional covariation. Several additional regions are also involved in hydrogen-bonding, and they form highly variable base-pairing patterns across the alignment. These are identified as regions of expansion and contraction (REC) or regions of slipped-strand compensation (RSC). Additionally, 31 single-stranded locales are characterized as regions of ambiguous alignment (RAA) based on the difficulty in assigning positional homology in the presence of multiple adjacent indels. Based on comparative analysis of these sequences, the largest genetic study on any hymenopteran group to date, we report an annotated secondary structural model for the D2, D3 expansion segments that will prove useful in assigning positional nucleotide homology for phylogeny reconstruction in these and closely related apocritan taxa.

Keywords: rRNA; ribosome; chalcidoid; secondary structure; expansion segment; homology; multiple sequence alignment; 28S.
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