Summary
A mathematical theory for computing the probabilities of various nucleotide configurations among related species is developed, and the probability of obtaining the correct tree (topology) from nucleotide sequence data is evaluated using models of evolutionary trees that are close to the tree of mitochondrial DNAs from human, chimpanzee, gorilla, orangutan, and gibbon. Special attention is given to the number of nucleotides required to resolve the branching order among the three most closely related organisms (human, chimpanzee, and gorilla). If the extent of DNA divergence is close to that obtained by Brown et al. for mitochondrial DNA and if sequence data are available only for the three most closely related organisms, the number of nucleotides (m*) required to obtain the correct tree with a probability of 95% is about 4700. If sequence data for two outgroup species (orangutan and gibbon) are available, m* becomes about 2600–2700 when the transformed distance, distance-Wagner, maximum parsimony, or compatibility method is used. In the unweighted pair-group method, m* is not affected by the availability of data from outgroup species. When these five different tree-making methods, as well as Fitch and Margoliash's method, are applied to the mitochondrial DNA data (1834 bp) obtained by Brown et al. and by Hixson and Brown, they all give the same phylogenetic tree, in which human and chimpanzee are most closely related. However, the trees considered here are “gene trees,” and to obtain the correct “species tree,” sequence data for several independent loci must be used.
This is a preview of subscription content, log in via an institution to check access.
Similar content being viewed by others
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
Aquadro CF, Kaplan N, Risko KJ (1984) An analysis of the dynamics of mammalian mitochondrial DNA sequence evolution. Mol Biol Evol 1:423–434
Bianchi NO, Bianchi MS, Cleaver JE, Wolff S (1985) The pattern of restriction enzyme-induced banding in the chromosomes of chimpanzee, gorilla, and orangutan and its evolutionary significance. J Mol Evol 22:323–333
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
Eck RV, Dayhoff MO (1966) Inferences from protein sequence comparisons. In: Dayhoff MO (ed) Atlas of protein sequence and structure 1966. National Biomedical Research Foundation, Silver Spring, Maryland, pp 161–169
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
Ferris SD, Wilson AC, Brown WM (1981) Evolutionary tree for apes and humans based on cleavage maps of mitochondrial DNA. Proc Natl Acad Sci USA 78:2432–2436
Fitch WM (1977) On the problem of discovering the most parsimonious tree. Am Nat 111:223–257
Fitch WM, Margoliash E (1967) Construction of phylogenetic trees. Science 155:279–284
Gojobori T, Li W-H, Graur D (1982) Patterns of nucleotide substitution in pseudogenes and functional genes. J Mol Evol 18:360–369
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
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, Ohta T (1972) On the stochastic model for estimation of mutational distance between homologous proteins. J Mol Evol 2:87–90
Klotz LC, Blanken RL (1981) A practical method for calculating evolutionary trees from sequence data J Theor Biol 91:261–272
Koop BF, Goodman M, Xu P, Chan K, Slightom JL (1986) Primate η-globin DNA sequences and man's place among the great apes. Nature 319:234–238
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, 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 (1986) Stochastic errors in DNA evolution and molecular phylogeny. In: Gershowitz H (ed) Evolutionary perspectives and the new genetics. Alan R Liss, New York, in press
Nei M (1987) Molecular evolutionary genetics. Columbia University Press, New York (in press)
Nei M, Graur D (1984) Extent of protein polymorphism and the neutral mutation theory. Evol Biol 17:73–118
Nei M, Tajima F (1985) Evolutionary change of restriction cleavage sites and phylogenetic inference for man and apes. Mol Biol Evol 2:189–205
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
Sibley CG, Ahlquist JE (1984) The phylogeny of the hominoid primates, as indicated by DNA-DNA hybridization. J Mol Evol 20:2–15
Sneath PHA, Sokal RR (1973) Numerical taxonomy. WH Freeman, San Francisco, pp 230–234
Takahata N, Nei M (1985) Gene genealogy and variance of interpopulational nucleotide differences. Genetics 110:325–344
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
Templeton AR (1983) Phylogenetic inference from restriction endonuclease cleavage site maps with particular reference to the evolution of humans and the apes. Evolution 37:221–244
Ueda S, Takenaka O, Honjo T (1985) A truncated immunoglobulin ε pseudogene is found in gorilla and man but not in chimpanzee. Proc Natl Acad Sci USA 82:3712–3715
Author information
Authors and Affiliations
Rights and permissions
About this article
Cite this article
Saitou, N., Nei, M. 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 (1986). https://doi.org/10.1007/BF02099966
Received:
Revised:
Issue Date:
DOI: https://doi.org/10.1007/BF02099966