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

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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.

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Acknowledgments

We thank two anonymous reviewers for helpful comments on the manuscript. We are grateful to Markus Friedrich and Karl Kjer for providing unpublished structural alignments for Holometabola and Odonata, respectively. Invaluable discussions with Robin Gutell and Jamie Cannone contributed greatly to the the manuscript. M.J.Y. thanks the online Perlmonks community for assistance in Perl-related questions. J.J.G. is especially grateful to Anthony Cognato for start-up funds provided by the TAMU Entomology Department. Particular thanks go to Jim Whitfield for providing supercomputer time and Andy Deans for helping to run MrBayes analyses. This project was funded in part by NSF Grant DEB-0328922 awarded to R.A.W. and DEB-0328920 awarded to Anthony Cognato.

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  1. Department of Entomology, Texas A&M University, College Station, TX, 77843, USA

    Joseph J. Gillespie, Matthew J. Yoder & Robert A. Wharton

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  1. Joseph J. Gillespie
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Correspondence to Joseph J. Gillespie.

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Access to on-line data: http://hymenoptera.tamu.edu/rna; username, ichs; password, ichzzz

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Gillespie, J.J., Yoder, M.J. & Wharton, R.A. Predicted Secondary Structure for 28S and 18S rRNA from Ichneumonoidea (Insecta: Hymenoptera: Apocrita): Impact on Sequence Alignment and Phylogeny Estimation. J Mol Evol 61, 114–137 (2005). https://doi.org/10.1007/s00239-004-0246-x

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