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Abstract Detail

Systematics Section / ASPT

Tippery, Nicholas P. [1], Les, Donald H. [1].

Expanding the phylogenetic utility of the internal transcribed spacer (ITS) region using predicted secondary structure.

Molecular phylogenetic methods often are based purely on the linear sequence of nucleotides for the region of interest. Methods that explore additional facets of sequence data include models of codon evolution for protein coding regions and doublet models that account for covarying sites. We have developed a method that extracts further phylogenetically-informative data from the nuclear internal transcribed spacer (ITS) region, based on predicted models of ITS secondary structure. Like their flanking ribosomal genes, the ITS regions (ITS-1 and ITS-2) have secondary structures ('stems' and 'loops') that are conserved across taxonomic groups as divergent as algae and angiosperms. In the method presented, seven conserved structural regions of ITS (three from ITS-1 and four from ITS-2) were scored for their nucleotide composition and pairwise alignment type (match or mismatch). Data for different taxa were aligned to each other under the primary criterion of structural similarity, which differed from the traditional, phenetic alignment. Rather than incurring costs simply for changes in nucleotide identity, the method penalizes changes that disrupt secondary structure. Thus, by aligning sequences based on structure and assigning costs to structural changes, the method generates phylogenetic data that are nearly independent from the simple nucleotide sequences on which they were based. In an application from the family Menyanthaceae, the method substantially improved support for nodes that were ambiguous under analysis of traditionally aligned sequences.

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1 - University of Connecticut, Ecology & Evolutionary Biology, 75 North Eagleville Road, U-3043, Storrs, Connecticut, 062693043, USA

RNA secondary structure

Presentation Type: Oral Paper:Papers for Sections
Session: CP24
Location: Continental C/Hilton
Date: Tuesday, July 10th, 2007
Time: 8:45 AM
Number: CP24004
Abstract ID:1326

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