Abstract
A method, based on the bootstrap procedure, is proposed for the estimation of branch-length errors and confidence intervals in a phylogenetic tree for which equal rates of substitution among lineages do not necessarily hold. The method can be used to test whether an estimated internodal distance is significantly greater than zero. In the application of the method, any estimator of genetic distances, as well as any tree reconstruction procedure (based on distance matrices), can be used. Also the method is not limited by the number of species involved in the phylogenetic tree. An example of the application of the method in the reconstruction of the phylogenetic tree for the four hominoid species—human, chimpanzee, gorilla, and orangutan—is shown.
This is a preview of subscription content, log in via an institution to check access.
Similar content being viewed by others
References
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
Churchill GA, von Haeseler A, Navidi WC (1992) Sample size for a phylogenetic inference. Mol Biol Evol 9:753–769
Efron B (1982) The jackknife, the bootstrap and other resampling plans. Society for Industrial and Applied Mathematics, Philadelphia
Efron B, Gong G (1983) A leisure look at the bootstrap, the jackknife and cross-validation. Am Star 37:36–48
Efron B, Tibshirani R (1991) Statistical data analysis in the computer age. Science 253:390–395
Farris JS (1981) Distance data in phylogenetic analysis. In: Funk VA, Brooks DR (eds) Advances in cladistics. Proceedings of the first meeting of the Willi Hennig Society. New York Botanical Garden, New York, pp 3–23
Felsenstein J (1984) Distance methods for inferring phylogenies: a justification. Evolution 38:16–24
Felsenstein J (1985) Confidence limits on phylogenies: an approach using the bootstrap. Evolution 39:783–791
Felsenstein J (1988) Phylogenies from molecular sequences: inference and reliability. Annu Rev Genet 22:521–565
Felsenstein J (1990) PHYLIP manual version 3.3. University Herbarium, University of California, Berkeley
Fitch WM, Margoliash E (1967) Construction of phylogenetic trees. Science 155:279–284
Jukes TH, Cantor CR (1969) Evolution of protein molecules. In: Munro HN (ed) Mammalian protein metabolism, vol III. Academic Press, New York, pp 71–123
Kimura M (1980). A simple method for estimating evolutionary rate of substitution through comparative studies of nucleotide sequences. J Mot Evol 16:111–120
Kimura M (1981) Estimation of evolutionary distances between homologous and non homologous nucleotide sequences. Proc Natl Acad Sci USA 78:454–458
Li W-H (1989) A statistical test of phylogenies estimated from sequence data. Mol Biol Evol 6:424–435
Li W-H, Gouy M (1990) Statistical tests of molecular phylogenies. Methods Enzymol 183:645–659
Li W-H, Tanimura M, Sharp PM (1987) An evaluation of the molecular clock hypothesis using mammalian DNA sequences. J Mol Evol 25:330–342
Mueller L, Ayala FJ (1982) Estimation and interpretation of genetic distance in empirical studies. Genet Res 40:127–137
Nei M, Jin L (1989) Variance of the average numbers of substitutions within and between populations. Mol Biol Evol 6:290–300
Nei M, Sthepens JC, Saitou N (1985) Methods for computing the standard errors of branching points in an evolutionary tree and their application to molecular data from human and apes. Mol Biol Evol 2:66–85
Pamilo P (1990) Statistical tests of phenograms based on genetic distances. Evolution 44:689–697
Rodríguez F, Oliver JL, Marfín A, Medina JR (1990) The general stochastic model of the nucleotide substitution. J Theor Biol 142:485–501
Rzhetsky A, Nei M (1992) A simple method for estimating and testing minimum-evolution trees. Mol Biol Evol 9:945–967
Saitou N, Nei M (1987) The neighbour-joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol 4:406–425
Sneath PHA, Sokal RR (1973) Numerical taxonomy. Freeman, San Francisco
Swofford DL, Olsen GJ (1990) Phylogeny reconstruction. In: Hillis DM, Moritz C (eds) Molecular systematics. Sinauer Associates, Sunderland, MS, pp 411–501
Tajima F (1992) Statistical method for estimating the standard errors of branch lengths in a phylogenetic tree reconstructed without assuming equal rates of nucleotide substitutions among different lineages. Mol Biol Evol 9:168–181
Tajima F, Nei M (1984) Estimation of evolutionary distance between nucleotide sequences. Mol Biol Evol 1:269–285
Takahata N (1991) Overdispersed molecular clock and the major histocompatibility complex loci. Proc R Soc Lond (Biol) 234:13–18
Takahata N, Kimura M (1981) A model of evolutionary base substitutions and its application with special reference to rapid change in pseudogenes. Genetics 98:641–657.
Takahata N, Tajima F (1991) Sampling errors in phylogeny. Mol Biol Evol 8:494–502
Zharkikh A, Li WH (1992) Statistical properties of bootstrap estimation of phylogenetic variability from nucleotide sequences. I. Four taxa with a molecular clock. Mol Biol Evol 9:1119–1147
Author information
Authors and Affiliations
Additional information
Correspondence to: J. Dopazo
Rights and permissions
About this article
Cite this article
Dopazo, J. Estimating errors and confidence intervals for branch lengths in phylogenetic trees by a bootstrap approach. J Mol Evol 38, 300–304 (1994). https://doi.org/10.1007/BF00176092
Received:
Revised:
Issue Date:
DOI: https://doi.org/10.1007/BF00176092