Reconstructing phylogeny from the multifractal spectrum of mitochondrial DNA

James A. Glazier; Sridhar Raghavachari; Cheryl L. Berthelsen; Mark H. Skolnick

doi:10.1103/PhysRevE.51.2665

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Reconstructing phylogeny from the multifractal spectrum of mitochondrial DNA

James A. Glazier, Sridhar Raghavachari, Cheryl L. Berthelsen, and Mark H. Skolnick

Department of Physics, University of Notre Dame, Notre Dame, Indiana 46556
Department of Health Information Management, University of Mississippi Medical Center, School of Health Related Professions, 2500 North State Street, Jackson, Mississippi 39216
Department of Medical Informatics, Genetic Epidemology, University of Utah, 420 Chipeta Way, Suite 180, Salt Lake City, Utah 84108

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Phys. Rev. E 51, 2665 – Published 1 March, 1995

DOI: https://doi.org/10.1103/PhysRevE.51.2665

Abstract

Conventional methods of phylogenetic reconstruction from DNA sequences require simplified models of evolutionary dynamics. We present a method based on fractal analysis to reconstruct the evolutionary history of organisms from mitochondrial DNA sequences. We map animal mtDNA into four-dimensional random walks and estimate their long range correlations using multifractal spectra. We see systematic changes in correlations in mtDNA sequences across taxonomic lines, which translate into changes in the scaling of the random walks. We use cluster analysis to group the multifractal spectra and obtain the phylogeny of the organisms. Though our method uses no a priori assumptions and is independent of gene order, it yields phylogenetic relationships broadly consistent with established results. Several recent papers have analyzed DNA using fractal analysis and have found long range correlations. However, no one has succeeded in using them to deduce biologically significant relationships.

References (13)

D. R. Wolstenholme, D. O. Clary, J. L. Macfarlane, J. A. Wahleithner, and L. Wilcox, in Achievements and Perspectives of Mitochondrial Research, edited by E. Quagliariello, E. C. Slater, F. Palmieri, C. Saccone, and A. M. Kroon (Elsevier, Amsterdam, 1985), Vol. II, pp. 61–69.
G. A. Watterson and P. Donnely, Genet. Res. Cambridge 60, 221 (1992).
C. L. Berthelsen, J. A. Glazier and M. H. Skolnick, Phys. Rev. A 45, 8902 (1992).
R. F. Voss, Phys. Rev. Lett. 68, 3805 (1992).
S. V. Buldyrev, A. L. Goldberger, S. Havlin, C-K. Peng, M. H. R. Stanley and M. Simons, Biophys. J. 65, 2673 (1993).
T. Tel, A. Fulop and T. Vicsek, Physica A 59, 155 (1989).
C. L. Berthelsen, J. A. Glazier and S. Raghavachari, Phys. Rev. E 49, 1860 (1994).
C. L. Berthelsen, Ph.D. dissertation, University of Utah, 1992, p. 128.
F. Murtagh and A. Heck, Multivariate Data Analysis (Kluwer, Dordrecht, 1987), pp. 55–109.
D.R. Wolstenholme, Int. Rev. Cytol. 141, 173 (1992).
U. Arnason and E. Johnsson, J. Mol. Evol. 34, 493 (1992).
W-H. Li, M. Guoy, P. M. Sharp, C. O'Huigin and Y-W. Yang, Proc. Nat. Acad. Sci. U.S.A. 87, 6703 (1987).
S. Raghavachari, J. A. Glazier, C. L. Berthelsen, and M. H. Skolnick (unpublished).

[c1] D. R. Wolstenholme, D. O. Clary, J. L. Macfarlane, J. A. Wahleithner, and L. Wilcox, in Achievements and Perspectives of Mitochondrial Research, edited by E. Quagliariello, E. C. Slater, F. Palmieri, C. Saccone, and A. M. Kroon (Elsevier, Amsterdam, 1985), Vol. II, pp. 61–69.

[c2] G. A. Watterson and P. Donnely, Genet. Res. Cambridge 60, 221 (1992).

[c3] C. L. Berthelsen, J. A. Glazier and M. H. Skolnick, Phys. Rev. A 45, 8902 (1992).

[c4] R. F. Voss, Phys. Rev. Lett. 68, 3805 (1992).

[c5] S. V. Buldyrev, A. L. Goldberger, S. Havlin, C-K. Peng, M. H. R. Stanley and M. Simons, Biophys. J. 65, 2673 (1993).

[c6] T. Tel, A. Fulop and T. Vicsek, Physica A 59, 155 (1989).

[c7] C. L. Berthelsen, J. A. Glazier and S. Raghavachari, Phys. Rev. E 49, 1860 (1994).

[c8] C. L. Berthelsen, Ph.D. dissertation, University of Utah, 1992, p. 128.

[c9] F. Murtagh and A. Heck, Multivariate Data Analysis (Kluwer, Dordrecht, 1987), pp. 55–109.

[c10] D.R. Wolstenholme, Int. Rev. Cytol. 141, 173 (1992).

[c11] U. Arnason and E. Johnsson, J. Mol. Evol. 34, 493 (1992).

[c12] W-H. Li, M. Guoy, P. M. Sharp, C. O'Huigin and Y-W. Yang, Proc. Nat. Acad. Sci. U.S.A. 87, 6703 (1987).

[c13] S. Raghavachari, J. A. Glazier, C. L. Berthelsen, and M. H. Skolnick (unpublished).

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Reconstructing phylogeny from the multifractal spectrum of mitochondrial DNA

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