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.
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References
ELTON, R. A. (1975): Doublet frequencies in sequenced nucleic acids. J. Mol. EvoL, 4, 323–346.
FELSENSTEIN, J. (1981): Evolutionary trees from DNA sequences: a maximum likelihood approach. J. Mol. Evol., 17, 368–376.
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.
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.
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.
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.
KARLIN, S., and TAYLOR, H. M. (1975): A first course in stochastic processes. 2nd ed. Academic Press, Inc., London, pp. 558.
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.
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.
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.
SAITOU, N., and NEI, M. (1987): The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol. Biol. EvoL, 4, 406–425.
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.
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.
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.
WOESE, C. R. (1987): Bacterial evolution. Microbiol Rev., 51, 221–271
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© 1996 Springer-Verlag Berlin · Heidelberg
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Von Haeseler, A., Schöniger, M. (1996). Ribosomal RNA Phylogeny Derived from a Correlation Model of Sequence Evolution. In: Gaul, W., Pfeifer, D. (eds) From Data to Knowledge. Studies in Classification, Data Analysis, and Knowledge Organization. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-642-79999-0_41
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DOI: https://doi.org/10.1007/978-3-642-79999-0_41
Publisher Name: Springer, Berlin, Heidelberg
Print ISBN: 978-3-540-60354-2
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