Abstract
The evolutionary history of life is inscribed in the DNA and protein sequences of living organisms, and we can infer evolutionary trees from these sequences. DNAs and proteins are sequences of four types of bases and of twenty types of amino acids, respectively. At each site of a sequence, one type of base or amino acid may change to another one during evolution, and the substitutions occur independently between lineages after they separate in an evolutionary tree. These substitutions can be best regarded as stochastic, and therefore, it is appropriate to infer evolutionary trees in the framework of maximum likelihood (ML) based on a statistical model for base or amino acid substitutions.
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References
Adachi, J. and Hasegawa, M. (1992a) MOLPHY: Programs for Molecular Phylogenetics, I — PROTML: Maximum Likelihood Inference of Protein Phylogeny, Computer Science Monographs, No. 27, Institute of Statistical Mathematics, Tokyo.
Adachi, J. and Hasegawa, M. (1992b) Amino acid substitution of proteins coded for in mitochondrial DNA during mammalian evolution. Japanese Journal Genetics, Vol. 67, No. 3, 187–197.
Adachi, J., Cao, Y. and Hasegawa, M. (1993) Tempo and mode of mitochondrial DNA evolution in vertebrates at the amino acid sequence level: rapid evolution in warm-blooded vertebrates. Journal of Molecular Evolution (in press).
Akaike, H. (1974) A new look at the statistical model identification. IEEE Transactions on Automatic Control, Vol. AC-19, No. 6, 716–723.
Dayhoff, M.O., Schwartz, R.M., and Orcutt, B.C. (1978) A model of evolutionary change in proteins, Atlas of Protein Sequence and Structure (ed. M.O. Dayhoff), Vol. 5, Suppl. 3, 345–352, National Biomedical Research Foundation, Washington, D.C.
Felsenstein, J. (1981) Evolutionary trees from DNA sequences, a maximum likelihood approach. Journal of Molecular Evolution, Vol. 17, 368–376.
Felsenstein, J. (1985) Confidence limits on phylogenies, an approach using the bootstrap. Evolution, Vol. 39, No. 4, 783–791.
Felsenstein, J. (1988) Phylogenies from molecular sequences, inference and reliability. Annual Review of Genetics, Vol. 22, 521–565.
Felsenstein, J. (1990) PHYLIP, Version 3.3, University of Washington, Seattle.
Fukami-Kobayashi, K. and Tateno, Y. (1991) Robustness of maximum likelihood tree estimation against different patterns of base substitutions. Journal of Molecular Evolution, Vol. 32, 79–91.
Hasegawa, M. (1990) Phylogeny and molecular evolution in primates. Japanese Journal of Genetics, Vol. 65, No. 4, 243–265.
Hasegawa, M. (1991) Molecular phylogeny and man’s place in Hominoidea. Journal of Anthropological Society of Nippon, Vol. 99, No. 1, 49–61.
Hasegawa, M. (1992) Evolution of hominoids as inferred from DNA sequences, Topics in Primatology, Vol 1. Human Origins, (eds. T. Nishida, W.C. McGrew, P. Marler, M. Pickford, and F.B.M. de Waal), 347–357, Univ. Tokyo Press, Tokyo.
Hasegawa, M. and Fujiwara, M. (1993) Relative efficiencies of the maximum likelihood, maximum parsimony, and neighbor joining methods for estimating protein phylogeny. Molecular Phylogenetics and Evolution (in press).
Hasegawa, M. and Hashimoto, T. (1993) Ribosomal RNA trees misleading? Nature,Vol. 361, No. 6407, 23–23.
Hasegawa, M. and Horai, S. (1991) Time of the deepest root for polymorphism in human mitochondrial DNA. Journal of Molecular Evolution, Vol. 32, No. 1, 37–42.
Hasegawa, M. and Kishino, H. (1989a) Confidence limits on the maximum-likelihood estimate of the hominoid tree from mitochondrial-DNA sequences. Evolution, Vol. 43, No. 3, 672–677.
Hasegawa, M. and Kishino, H. (1989b) Heterogeneity of tempo and mode of mitochondrial DNA evolution among mammalian orders. Japanese Journal of Genetics, Vol. 64, No. 4, 243–258.
Hasegawa, M. and Kishino, H. (1991) DNA sequence analysis and evolution of Hominoidea. New Aspects of the Genetics of Molecular Evolution, (eds. M. Kimura and N. Takahata), 303–317, Springer-Verlag, Berlin.
Hasegawa, M. and Kishino, H. (1993) Simple methods for estimating bootstrap probability of a maximum likelihood tree. Molecular Biology and Evolution (in press).
Hasegawa, M., Kishino, H. and Yano, T. (1985) Dating of the human-ape splitting by a molecular clock of mitochondrial DNA. Journal of Molecular Evolution, Vol. 22, No. 2, 160–174.
Hasegawa, M., Kishino, H. and Yano, T. (1987) Man’s place in Hominoidea as inferred from molecular clocks of DNA. Journal of Molecular Evolution, Vol. 26, No. 1–2, 132–147.
Hasegawa, M., Kishino, H., Hayasaka, K., and Horai, S. (1990a) Mitochondrial DNA evolution in primates, transition rate has been extremely low in lemur. Journal of Molecular Evolution, Vol. 31, No. 2, 113–121.
Hasegawa, M., Iwabe, N., Mukohata, Y., and Miyata, T. (1990b) Close evolutionary relatedness of archaebacteria, Methanococcus and Halobacterium, to eukaryotes demonstrated by composite phylogenetic trees of elongation factors EF-Tu and EF-G, eocyte tree is unlikely. Japanese Journal of Genetics, Vol. 65, 109–114.
Hasegawa, M., Kishino, H. and Saitou, N. (1991) On the maximum likelihood method in molecular phylogenetics. Journal of Molecular Evolution, Vol. 32, 443–445.
Hasegawa, M., Cao, Y., Adachi, J. and Yano, T. (1992) Rodent polyphyly? Nature, Vol. 355, No. 6361, 595–595.
Hasegawa, M., Hashimoto, T., Adachi, J., Iwabe, N., and Miyata, T. (1993a) Early divergences in the evolution of eukaryotes, ancient divergence of Entamoeba that lacks mitochondria revealed by protein sequence data. Journal of Molecular Evolution (in press).
Hasegawa, M., Hashimoto, T. and Adachi, J. (1993b) Origin and evolution of eukaryotes as inferred from protein sequence data, The Origin and Evolution of Prokaryotic and Eukaryotic Cells, (eds. H. Hartman and K. Matsuno), World Sci. Publ. (in press).
Hasegawa, M., Di Rienzo, A., Kocher, T.D., and Wilson, A.C. (1993c) Toward a more accurate time scale for the human mitochondrial DNA tree. Journal of Molecular Evolution (in press).
Hashimoto, T., Adachi, J. and Hasegawa, M. (1992) Phylogenetic place of Giardia lamblia, a protozoan that lacks mitochondria. Endocytobiosis and Cell Research, Vol. 9, 59–69.
Hashimoto, T., Otaka, E., Adachi, J., Mizuta, K., and Hasegawa, M. (1993b) The giant panda is most close to a bear, judged by α- and β-hemoglobin sequences. Journal of Molecular Evolution (in press).
Horai, S., Satta, Y., Hayasaka, K., Kondo, R., Inoue, T., Ishida, T., Hayashi, S., and Takahata, N. (1992) Man’s place in Hominoidea revealed by mitochondrial DNA genealogy. Journal of Molecular Evolution, Vol 35, No. 1, 32–43.
Kimura, M. (1983) The Neutral Theory of Molecular Evolution. Cambridge University Press, Cambridge.
Kishino, H., and Hasegawa, M. (1989) Evaluation of the maximum likelihood estimate of the evolutionary tree topologies from DNA sequence data, and the branching order in Hominoidea. Journal of Molecular Evolution, Vol. 29, No. 2, 170–179.
Kishino, H., and Hasegawa, M. (1990) Converting distance to time, an application to human evolution. Methods in Enzymology, Vol. 183, 550–570.
Kishino, H., Miyata, T., and Hasegawa, M. (1990) Maximum likelihood inference of protein phylogeny and the origin of chloroplasts. Journal of Molecular Evolution, Vol. 30, 151–160.
Nei, M. (1987) Molecular Evolutionary Genetics. Columbia University Press, New York.
Neyman, J. (1971) Molecular studies of evolution, a source of novel statistical problems, Statistical Decision Theory and Related Topics, (eds. S.S. Gupta and J. Yackel), 1–27, Academic Press, New York.
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© 1994 Springer Science+Business Media Dordrecht
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Hasegawa, M. (1994). Inference of Evolutionary Trees from DNA and Protein Sequence Data. In: Bozdogan, H., et al. Proceedings of the First US/Japan Conference on the Frontiers of Statistical Modeling: An Informational Approach. Springer, Dordrecht. https://doi.org/10.1007/978-94-011-0854-6_11
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DOI: https://doi.org/10.1007/978-94-011-0854-6_11
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