Abstract
There are many different methods of phylogenetic reconstruction for DNA sequence data, and their advantages and disadvantages are discussed by considering various factors such as the constancy of evolutionary rate, extent of sequence divergence, variation in evolutionary rate over the sequence, number of nucleotides examined, number of sequences used, etc. It is shown that the bootstrap method of testing the stability of the branching pattern of a tree is not really accurate in evaluating the probability level of the clustering of a group of sequences and that it sometimes leads to an erroneous conclusion particularly when it is applied to the maximum parsimony method. Nevertheless, it is a useful method for obtaining a rough idea of the stability of the branching pattern of a tree. Application of the neighbor-joining and maximum parsimony bootstrap methods to Gyllensten et al.’s sequence data for the DQB locus alleles from primates confirmed the trans-species polymorphism between humans and gorillas, but the trans-species polymorphism between humans and chimpanzees was ambiguous. However, sequence data for the DQA locus alleles confirmed the trans-species polymorphism among all of the humans, chimpanzees and gorillas.
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References
Cavalli-Sforza, L.L. and Edwards, A.W.F: Phylogenetic analysis: Models and estimation procedures. Amer J Hum Genet 19: 233–257, 1967
Efron, B.: The jackknife, the bootstrap and other resampling plans. Society for Industrial and Applied Mathematics, Philadelphia 1982
Felsenstein, J.: Evolutionary trees from DNA sequences: A maximum likelihood approach. J Mol Evol 17: 368–376, 1981
Felsenstein, J.: Confidence limits on phytogenies: an approach using the bootstrap. Evolution 39: 783–791, 1985
Felsenstein, J.: Phylogenies from molecular sequences: Inference and reliability. Ann Rev Genet 22: 521–565, 1988
Fitch, W.M.: Toward defining the course of evolution: minimum change for a specific tree topology. Syst Zool 20: 406–416, 1971
Fitch, W.M. and Margoliash, E.: Construction of phylogenetic trees. Science 155: 279–284, 1967
Gyllensten, U.B. and Erlich, H.A.: Ancient roots for polymorphism at the HLA-DQa locus in primates. Proc Natl Acad Sci 86: 9986–9990, 1989
Gyllensten, U.B., Lashkari, D., and Erlich, H.A.: Allelic diversification at the class II DQB locus of the mammalian major histocompatibility complex. Proc Natl Acad Sci 87: 1835–1839, 1990
Klein, J.: Origin of major histocompatibility complex polymorphism: The trans-species hypothesis. Hum Immunol 19: 155–162, 1987
Li, W.-H.: A statistical test of phylogenies estimated from sequence data. Mol Biol Evol 6: 424–435, 1989
McConnell, T.L., Talbot, W.S., McIndoe, R.A., and Wakland, E.K.: The origin of MHC class II gene polymorphism within the genus Mus. Nature 332: 651–654, 1988
Nei, M.: Molecular Population Genetics And Evolution, North-Holland, Amsterdam and NewYork 1975
Nei, M.: Molecular Evolutionary Genetics. Columbia University Press, New York 1987
Nei, M.: Relative efficiencies of different tree-making methods for molecular data. In M.M. Miyamoto and J.L. Cracraft (eds.): Recent advances in Phylogenetic studies of DNA sequences. Oxford University Press. Oxford and New York (submitted 1991)
Nei, M. and Hughes, A.L.: Polymorphism and evolution of the major histocompatibility complex loci in mammals. In R.K. Selander, A.G. Clark, and T.S. Whittam (eds.): Evolution at the Molecular Level, pp. 222–247. Sinauer Associates, Sunderland, MA 1991
Nei, M., Stephens, J.C., and Saitou, N.: Methods for computing the standard error of branching points in an evolutionary tree and their application to molecular data from humans and apes. Mol Biol Evol 2: 66–85, 1985
Saitou, N. and Imanishi, T.: Relative efficiencies of the Fitch-Margoliash, maximum- parsimony, maximum-likelihood, minimum-evolution, and neighbor-joining methods of phylogenetic tree construction in obtaining the correct tree. Mol Biol Evol 6: 514– 525, 1989
Saitou, N. and Nei, M.: The neighbor-joining method: A new method for reconstructing phylogenetic trees. Mol Biol Evol 4: 406–425, 1987
Sneath, P.H.A. and Sokal, R.R.: Numerical Taxonomy. Freeman, San Francisco 1973
Sokal, R.R. and Michener, C.D.: A statistical method for evaluating systematic relationships. University of Kansas Sci Bull 28: 1409–1438, 1958
Sourdis, J. and Krimbas, C.: Accuracy of phylogenetic trees estimated from DNA sequence data. Mol Biol Evol 4: 159–166, 1987
Sourdis, J. and Nei, M.: Relative efficiencies of the maximum parsimony and distance-matrix methods in obtaining the correct phylogenetic tree. Mol Biol Evol 5: 298–311, 1988
Tateno, Y., Nei, M., and Tajima, F.: Accuracy of Estimated phylogenetic trees from molecular data: I. Distantly related species. J Mol Evol 18: 387–404, 1982
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Nei, M., Rzhetsky, A. (1991). Reconstruction of Phylogenetic Trees and Evolution of Major Histocompatibility Complex Genes. In: Klein, J., Klein, D. (eds) Molecular Evolution of the Major Histocompatibility Complex. NATO ASI Series, vol 59. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-642-84622-9_2
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DOI: https://doi.org/10.1007/978-3-642-84622-9_2
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