Advertisement

Ribosomal RNA Phylogeny Derived from a Correlation Model of Sequence Evolution

  • A. Von Haeseler
  • M. Schöniger
Conference paper
Part of the Studies in Classification, Data Analysis, and Knowledge Organization book series (STUDIES CLASS)

Summary

Present-day stochastic models of DNA sequence evolution assume independent and identically distributed nucleotide sites. However, it is well known that there exists correlation among nucleotides in a DNA sequence. We present a stochastic model of sequence evolution that takes into account the correlation of non—overlapping pairs of nucleotides. This model enables us to estimate the number of substitutions per nucleotide. As a biological example we re—analyze the phylogenetic tree of Metazoa based on small ribosomal subunit RNA.

Keywords

Sequence Evolution Correlation Model Rate Matrix Stem Region Compensatory Base Change 
These keywords were added by machine and not by the authors. This process is experimental and the keywords may be updated as the learning algorithm improves.

Preview

Unable to display preview. Download preview PDF.

Unable to display preview. Download preview PDF.

References

  1. ELTON, R. A. (1975): Doublet frequencies in sequenced nucleic acids. J. Mol. EvoL, 4, 323–346.CrossRefGoogle Scholar
  2. FELSENSTEIN, J. (1981): Evolutionary trees from DNA sequences: a maximum likelihood approach. J. Mol. Evol., 17, 368–376.CrossRefGoogle Scholar
  3. FIELD, K. G., OLSEN, G. J., LANE, D. J., GIQVANNONI, S. J., CHISELIN, M. T., RAFF, E. C., PACE, N. R., and RAFF, R. A. (1988): Molecular phylogeny of the animal kingdom. Science, 239, 748–753.CrossRefGoogle Scholar
  4. HASEGAWA, M., KISHINO, H., and YANO, T. (1985): Dating of the human-ape splitting by a molecular clock of mitochondrial DNA. J. Mol. EvoL, 22, 160–174.CrossRefGoogle Scholar
  5. HEDGES, S. B., MOBERG, K. D., and MAXSON, C.R. (1990): Tetrapode phylogeny inferred from 18S and 28S ribosomai RNA sequences and a review of the evidence for amniote relationships. Mol. Biol. EvoL, 7, 607–633.Google Scholar
  6. JUKES, T. H., and CANTOR, C. R. (1969): Evolution of protein molecules. In: Mammalian Protein Metabolism. H.N. Muro (ed.), pp. 21–132. Academic Press, New York.Google Scholar
  7. KARLIN, S., and TAYLOR, H. M. (1975): A first course in stochastic processes. 2nd ed. Academic Press, Inc., London, pp. 558.Google Scholar
  8. KIMURA, M. (1980): A simple method for estimating evolutionary rates of base substitutions through comparative studies of nucleotide sequences. J. Mol. EvoL,16, 111–120.CrossRefGoogle Scholar
  9. NEEFS, J. M., VAN DE PEER, Y., DE RIJK, P., CHAPELLE, S., and DE WACHTER, R. (1993): Compilation of small ribosomai subunit RNA structures. Nucl. Acids Res., 21, 3025–3049.CrossRefGoogle Scholar
  10. OHNO, S. (1988): Universal rule for coding sequence construction: TA/CG deficiency — TG/CT excess. Proc. Natl. Acad. Sci. U.S.A., 85, 9630–9634.CrossRefGoogle Scholar
  11. SAITOU, N., and NEI, M. (1987): The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol. Biol. EvoL, 4, 406–425.Google Scholar
  12. SCHONIGER, M., and VON HAESELER, A. (1994): A stochastic model for the evolution of autocorrelated DNA sequences. Molecular Phylogenetics and Evolution, 3(3), in press. Google Scholar
  13. TAVARE, S., and GIDDINGS, B. W. (1989): Some statistical aspects of the primary structure of nucleotide sequences. In: Mathematical methods for DNA sequences. M. S. Waterman (ed.), pp. 117–132, CRC Press, Boca Raton.Google Scholar
  14. VAN DE PEER, Y., NEEFS, J.-M., DE RIJK, P., and DE WACHTER, R. (1993): Reconstructing evolution from eukaryotic small-ribosomal-subunit RNA sequences; calibration of the molecular clock. J. Mol. EvoL, 37, 221–232.CrossRefGoogle Scholar
  15. WOESE, C. R. (1987): Bacterial evolution. Microbiol Rev., 51, 221–271Google Scholar

Copyright information

© Springer-Verlag Berlin · Heidelberg 1996

Authors and Affiliations

  • A. Von Haeseler
    • 1
  • M. Schöniger
    • 2
  1. 1.Institute for ZoologyUniversity of MunichMunichGermany
  2. 2.Theoretical ChemistryTechnical University MunichGarchingGermany

Personalised recommendations