Summary
The maximum likelihood (ML) method for constructing phylogenetic trees (both rooted and unrooted trees) from DNA sequence data was studied. Although there is some theoretical problem in the comparison of ML values conditional for each topology, it is possible to make a heuristic argument to justify the method. Based on this argument, a new algorithm for estimating the ML tree is presented. It is shown that under the assumption of a constant rate of evolution, the ML method and UPGMA always give the same rooted tree for the case of three operational taxonomic units (OTUs). This also seems to hold approximately for the case with four OTUs. When we consider unrooted trees with the assumption of a varying rate of nucleotide substitution, the efficiency of the ML method in obtaining the correct tree is similar to those of the maximum parsimony method and distance methods. The ML method was applied to Brown et al.'s data, and the tree topology obtained was the same as that found by the maximum parsimony method, but it was different from those obtained by distance methods.
Article PDF
Similar content being viewed by others
Avoid common mistakes on your manuscript.
References
Anderson S, Bankier AT, Barrell BG, de Bruijn MHL, Coulson AR, Drouin J, Eperon IC, Nierlich DP, Roe BA, Sanger F, Schreier PH, Smith AJH, Staden R, Young IG (1981) Sequence and organization of the human mitochondrial genome. Nature 290:457–465
Brown WM, Prager EM, Wang A, Wilson AC (1982) Mitochondrial DNA sequences of primates: tempo and mode of evolution. J Mol Evol 18:225–239
Cavalli-Sforza LL, Edwards AWF (1967) Phylogenetic analysis: models and estimation procedures. Am J Hum Genet 19:233–257
Chakraborty R (1977) Estimation of time of divergence from phylogenetic studies. Can J Genet Cytol 19:217–223
Eck RV, Dayhoff MO (1966) Atlas of protein sequence and structure 1966. National Biomedical Research Foundation, Silver Spring MD
Faith DP (1985) Distance methods and the approximation of most-parsimonious trees. Syst Zool 34:312–325
Farris JS (1972) Estimating phylogenetic trees from distance matrices. Am Nat 106:645–668
Farris JS (1977) On the phenetic approach to vertebrate classification. In: Hecht MK, Goody PC, Hecht BM (eds) Major patterns in vertebrate evolution. Plenum, New York, pp 823–850
Felsenstein J (1973) Maximum likelihood and minimum-steps methods for estimating evolutionary trees from data on discrete characters. Syst Zool 22:240–249
Felsenstein J (1978) Cases in which parsimony or compatibility methods will be positively misleading. Syst Zool 27:401–410
Felsenstein J (1981) Evolutionary trees from DNA sequences: a maximum likelihood approach. J Mol Evol 17:368–376
Felsenstein J (1984) The statistical approach to inferring evolutionary trees and what it tells us about parsimony and compatibility. In: Duncan T, Steussy TF (eds) Cladistics: perspectives on the reconstruction of evolutionary history. Columbia University Press, New York, pp 169–191
Fitch WM (1977) On the problem of discovering the most parsimonious tree. Am Nat 111:223–257
Fitch WM (1981) A non-sequential method for constructing trees and hierarchical classifications. J Mol Evol 18:30–37
Fitch WM, Margoliash E (1967) Construction of phylogenetic trees. Science 155:279–284
Gojobori T, Ishii K, Nei M (1982a) Estimation of average number of nucleotide substitutions when the rate of substitution varies with nucleotide. J Mol Evol 18:414–423
Gojobori T, Li W-H, Graur D (1982b) Patterns of nucleotide substitution in pseudogenes and functional genes. J Mol Evol 18:360–369
Hasegawa M, Yano T (1984) Maximum likelihood method of phylogenetic inference from DNA sequence data. Bull Biometric Soc Jpn 5:1–7
Hasegawa M, Kishino H, Yano T (1985) Dating of the human-ape splitting by a molecular clock of mitochondrial DNA. J Mol Evol 22:160–174
Hixson JE, Brown WM (1986) A comparison of the small ribosomal RNA genes from the mitochondrial DNA of the great apes and humans: sequence, structure evolution, and phylogenetic implications. Mol Biol Evol 3:1–18
Jukes TH, Cantor CR (1969) Evolution of protein molecules. In: Munro HN (ed) Mammalian protein metabolism, vol III. Academic Press, New York, pp 21–132
Kashyap RL, Subas S (1974) Statistical estimation of parameters in a phylogenetic tree using a dynamic model of the substitutional process. J Theor Biol 47:75–101
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
Kimura M (1981) Estimation of evolutionary distances between homologous nucleotide sequences. Proc Natl Acad Sci USA 78:454–458
Klotz LC, Blanken RL (1981) A practical method for calculating evolutionary trees from sequence data. J Theor Biol 91:261–272
Le Quesne WJ (1969) A method of selection of characters in numerical taxonomy. Syst Zool 18:201–205
Li W-H (1981) Simple method for constructing phylogenetic trees from distance matrices. Proc Natl Acad Sci USA 78:1085–1089
Li W-H (1986) Evolutionary change of restriction cleavage sites and phylogenetic inference. Genetics 113:187–213
Li W-H, Wu C-I, Luo C-C (1984) Nonrandomness of point mutation as reflected in nucleotide substitutions in pseudogenes and its evolutionary implications. J Mol Evol 21:58–71
Nei M (1987) Molecular evolutionary genetics. Columbia University Press, New York
Nei M, Stephens JC, Saitou N (1985) Methods for computing the standard errors of branching points in an evolutionary tree and their application to molecular data from humans and apes. Mol Biol Evol 2:66–85
Saitou N, Nei M (1986) The number of nucleotides required to determine the branching order of three species with special reference to the human-chimpanzee-gorilla divergence. J Mol Evol 24:189–204
Saitou N, Nei M (1987) The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol 4:406–425
Sattath S, Tversky A (1977) Additive similarity trees. Psychometrika 42:319–345
Sokal R, Sneath PHP (1963) Principles of numerical taxonomy. WH Freeman, San Francisco
Tajima F, Nei M (1984) Estimation of evolutionary distance between nucleotide sequences. Mol Biol Evol 1:269–285
Takahata N, Kimura M (1981) A model of evolutionary base substitutions and its application with special reference to rapid change of pseudogenes. Genetics 98:641–657
Tateno Y, Nei M, Tajima F (1982) Accuracy of estimated phylogenetic trees from molecular data. I. Distantly related species. J Mol Evol 18:387–404
Author information
Authors and Affiliations
Rights and permissions
About this article
Cite this article
Saitou, N. Property and efficiency of the maximum likelihood method for molecular phylogeny. J Mol Evol 27, 261–273 (1988). https://doi.org/10.1007/BF02100082
Received:
Revised:
Issue Date:
DOI: https://doi.org/10.1007/BF02100082