Journal of Molecular Evolution

, Volume 49, Issue 5, pp 691-698

First online:

Toward Assigning Helical Regions in Alignments of Ribosomal RNA and Testing the Appropriateness of Evolutionary Models

  • Michael  SchönigerAffiliated withTheoretische Chemie, Technische Universität München, Lichtenbergstr. 4, D-85747 Garching, Germany
  • , Arndt  von HaeselerAffiliated withMax-Planck-Institut für Evolutionäre Anthropologie, Inselstr. 22, D-04103 Leipzig, Germany

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We suggest a nucleotide substitution model that takes correlation between base-paired nucleotides into account. The model includes the estimation of the transition–transversion ratio and allows inference of the shape parameter of a discrete gamma distribution to include rate heterogeneity. A Cox-test statistic, applied to a diatom ribosomal RNA alignment, shows that the suggested correlation model explains evolution of the stem region better than usual independence models. Moreover, the Cox-test procedure is extended to shed some light upon the problem of assigning helical regions in a secondary structure based alignment. This approach provides an estimate of the percentage of stem positions that do not appear to be correlated.

Key words: Evolutionary models — Correlated sequence sites — Secondary structure — Alignment — Rate heterogeneity — Phylogenetic analysis — Maximum-likelihood inference — Monte Carlo simulation