18S rRNA secondary structure and phylogenetic position of Peloridiidae (Insecta, Hemiptera)

A secondary structure model for 18S rRNA of peloridiids, relict insects wit h a present-day circumantarctic distribution, is constructed using comparat ive sequence analysis, thermodynamic folding, a consensus method using 18S rRNA models of other taxa, and support of helices based on compensatory sub stitutions. Results show that probable in vivo configuration of 18S rRNA is not predictable using current free-energy models to fold the entire molecu le concurrently. This suggests that refinements in free-energy minimization algorithms are needed. Molecular phylogenetic datasets were created using 18S rRNA nucleotide alignments produced by CLUSTAL and rigorous interpretat ion of homologous position based on certain secondary substructures. Phylog enetic analysis of a hemipteran data matrix of 18S rDNA sequences placed pe loridiids sister to Heteroptera. Resolution of affiliations between the thr ee main euhemipteran lineages was unresolved. The peloridiid 18S RNA model presented here provides the most accurate template to date for aligning hom ologous nucleotides of hemipteran taxa. Using folded 18S rRNA to infer homo logy of character as morpho-molecular structures or nucleotides and scoring particular sites or substructures is discussed. (C) 2000 Academic Press.