Journal of Molecular Evolution

, Volume 61, Issue 1, pp 114–137 | Cite as

Predicted Secondary Structure for 28S and 18S rRNA from Ichneumonoidea (Insecta: Hymenoptera: Apocrita): Impact on Sequence Alignment and Phylogeny Estimation

  • Joseph J. Gillespie
  • Matthew J. Yoder
  • Robert A. Wharton
Article

Abstract

We utilize the secondary structural properties of the 28S rRNA D2–D10 expansion segments to hypothesize a multiple sequence alignment for major lineages of the hymenopteran superfamily Ichneumonoidea (Braconidae, Ichneumonidae). The alignment consists of 290 sequences (originally analyzed in Belshaw and Quicke, Syst Biol 51:450–477, 2002) and provides the first global alignment template for this diverse group of insects. Predicted structures for these expansion segments as well as for over half of the 18S rRNA are given, with highly variable regions characterized and isolated within conserved structures. We demonstrate several pitfalls of optimization alignment and illustrate how these are potentially addressed with structure-based alignments. Our global alignment is presented online at (http://hymenoptera.tamu.edu/rna) with summary statistics, such as basepair frequency tables, along with novel tools for parsing structure-based alignments into input files for most commonly used phylogenetic software. These resources will be valuable for hymenopteran systematists, as well as researchers utilizing rRNA sequences for phylogeny estimation in any taxon. We explore the phylogenetic utility of our structure-based alignment by examining a subset of the data under a variety of optimality criteria using results from Belshaw and Quicke (2002) as a benchmark.

Keywords

rRNA Ribosome Hymenoptera Braconidae Ichneumonidae Secondary structure Expansion segment Variable regions Homology Phylogeny Multiple alignment 18S 28S 

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Copyright information

© Springer Science+Business Media, Inc. 2005

Authors and Affiliations

  • Joseph J. Gillespie
    • 1
  • Matthew J. Yoder
    • 1
  • Robert A. Wharton
    • 1
  1. 1.Department of EntomologyTexas A&M UniversityCollege StationUSA

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