Journal of Molecular Evolution

, Volume 49, Issue 5, pp 691–698

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

  • Michael  Schöniger
  • Arndt  von Haeseler

DOI: 10.1007/PL00006590

Cite this article as:
Schöniger, M. & von Haeseler, A. J Mol Evol (1999) 49: 691. doi:10.1007/PL00006590


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

Copyright information

© Springer-Verlag New York Inc. 1999

Authors and Affiliations

  • Michael  Schöniger
    • 1
  • Arndt  von Haeseler
    • 2
  1. 1.Theoretische Chemie, Technische Universität München, Lichtenbergstr. 4, D-85747 Garching, GermanyDE
  2. 2.Max-Planck-Institut für Evolutionäre Anthropologie, Inselstr. 22, D-04103 Leipzig, GermanyDE