Abstract
Homology between biological objects (DNA sequences, species, etc.) can be measured by genetic distance data. A genetic distance may be computed from aligned genetic sequence data; e.g. DNA sequences. We discuss the dot-matrix plot as a possible graphical check of the goodness of the alignment. The assumption of identical distributions along the sequence positions is often inappropriate. Therefore, we discuss aspects of an heuristic which allows the combined exploration of genetic distance between the sequences and of different positional variation. A tree structure is not assumed for such an exploration. Having computed a genetic distance, phylogenetic relations may be analysed by three- and four-objects methods. The approach is illustrated by a set of tRNA sequences.
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Bibliography
Barry, D., Hartigan, J.A. (1987): Statistical analysis of hominoid molecular evolution. Statistical Science, 2, 2, 191–210.
Bock, H.H. (1989): Datenanalyse zur Strukturierung und Ordnung von Information. In: Wille, R. (ed.): Klassifikation und Ordnung, Studien zur Klassifikation 19. Indeks-Verlag, Prankfurt, 1–22.
Degens, P.O. (1983): Hierarchical cluster methods as maximum likelihood estimators. In: Felsenstein, J. (ed.): Numerical Taxanomy. Springer-Verlag, Berlin Heidelberg, 249–253.
Degens, P.O. (1988): Reconstruction of phylogenies by weighted genetic distances. In: Bock, H.H. (ed.): Classification and related methods of data analysis. North Holland, Amsterdam, 727–739.
Degens, P.O. (1989): Ansätze bei der Mathematisierung der biologischen Systematik. In: Wille, R. (ed.): Klassifikation und Ordnung, Studien zur Klassifikation 19. Indeks-Verlag, Frankfurt, 23–38.
Degens, P.O., Lausen, B., AND Vach, W. (1990): Reconstruction of phylogenies by distance data: Mathematical framework and statistical analysis. In: Deuber, W., Dress, A., AND v. Haeseler, A. (eds.): Trees and hierarchical structures, Lecture Notes in Biomathematics. Springer-Verlag, Berlin Heidelberg (to appear).
Felsenstein, J. (1988): Phylogenies from molecular sequences: Inference and reliability. Annual Review of Genetics, 22, 521–565.
Kimura, M. (1980): A simple method for estimating evolutionary rates on base substitutions through comparative studies of nucleotide sequences. Journal of Molecular Evolution, 16, 111–120.
Kruskal, J.B., Dyen, I., AND Black, P. (1971): The vocabulary method of reconstructing language trees: Innovations and large-scale applications. In: Hodson, F.R., Kendall, D.G., AND Tautu, P. (ed.): Mathematics in the archeological and historical sciences. Edinburgh University Press, Edinburgh, 361–380.
Lausen, B. (1989): Exploring homologous tRNA sequence data: Positional mutation rates and genetic distance. In: Opitz, O. (ed.): Conceptual and numerical analysis of data. Springer-Verlag, Berlin Heidelberg, 381–388.
Lausen, B., AND Degens, P.O. (1986): Variance estimation and the reconstruction of phylogenies. In: Degens, P.O., Hermes, H.-J., AND Opitz, O. (ed.): Die Klassifikation und ihr Umfeld (Classification and its Environment), Studien zur Klassifikation 17. Indeks-Verlag, Frankfurt, 306–314.
Lausen, B., AND Degens, P.O. (1988A): Bootstrap evaluation in hierarchical cluster analysis. In: Diday, E. (ed.): Data analysis and informatics V. North Holland, Amsterdam, 267–276.
Lausen, B., AND Degens, P.O. (1988B): Evaluation of the reconstruction of phylogenies with DNADNA hybridization data. In: Bock, H.H. (ed.): Classification and related methods of data analysis. North Holland, Amsterdam, 367–374.
Mccullagh, P., AND Nelder, J.A. (1989 2nd ed.): Generalized linear models. Chapman and Hall, London.
Nei, M. (1987): Molecular evolutionary genetics. Columbia University Press, New York.
Sheldon, F.H., AND Bledsoe, A.H. (1989): Indexes to the reassociation and stability of solution of DNA hybrids. Journal of Molecular Evolution, 29, 328–343.
Sibley, C.G., AND Ahlquist, J.E. (1987): DNA hybridization evidence of hominoid primates phylogeny: Results of an expanded data set. Journal of Molecular Evolution, 26, 1-2, 99–123.
Sprinzl, M., Hartmann, T., Weber, J., Blank, J., AND Zeidler, R. (1989): Compilation of tRNA sequences and sequences of tRNA genes. Nucleic Acids Research, 17, supplement, rl–rl72.
Vach, W. (1989): Least squares approximations of additive trees. In: Opitz, O. (ed.): Conceptual and numerical analysis of data. Springer-Verlag, Berlin Heidelberg, 231–238.
Vach, W., AND Degens, P.O. (1991): A new approach to isotonic agglomerative hierarchical clustering. Journal of Classification (to appear).
Weir, B.S. (1989): Building trees with DNA sequences. Biometric Bulletin, 6, 4, 21–23.
Wolf, K., AND Degens, P.O. (1989): On properties of additive tree algorithms. In: Opitz, O. (ed.): Conceptual and numerical analysis of data. Springer-Verlag, Berlin Heidelberg, 256–265.
Wolf, K., AND Degens, P.O. (1990): Variance estimation in the additive tree model, (this volume).
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Lausen, B. (1991). Statistical Analysis of Genetic Distance Data. In: Bock, HH., Ihm, P. (eds) Classification, Data Analysis, and Knowledge Organization. Studies in Classification, Data Analysis, and Knowledge Organization. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-642-76307-6_34
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DOI: https://doi.org/10.1007/978-3-642-76307-6_34
Publisher Name: Springer, Berlin, Heidelberg
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