Accuracy of estimated phylogenetic trees from molecular data (original) (raw)
Summary
The accuracies and efficiencies of four different methods for constructing phylogenetic trees from molecular data were examined by using computer simulation. The methods examined are UPGMA, Fitch and Margoliash's (1967) (F/M) method, Farris' (1972) method, and the modified Farris method (Tateno, Nei, and Tajima, this paper). In the computer simulation, eight OTUs (32 OTUs in one case) were assumed to evolve according to a given model tree, and the evolutionary change of a sequence of 300 nucleotides was followed. The nucleotide substitution in this sequence was assumed to occur following the Poisson distribution, negative binomial distribution or a model of temporally varying rate. Estimates of nucleotide substitutions (genetic distances) were then computed for all pairs of the nucleotide sequences that were generated at the end of the evolution considered, and from these estimates a phylogenetic tree was reconstructed and compared with the true model tree. The results of this comparison indicate that when the coefficient of variation of branch length is large the Farris and modified Farris methods tend to be better than UPGMA and the F/M method for obtaining a good topology. For estimating the number of nucleotide substitutions for each branch of the tree, however, the modified Farris method shows a better performance than the Farris method. When the coefficient of variation of branch length is small, however, UPGMA shows the best performance among the four methods examined. Nevertheless, any tree-making method is likely to make errors in obtaining the correct topology with a high probability, unless all branch lengths of the true tree are sufficiently long. It is also shown that the agreement between patristic and observed genetic distances is not a good indicator of the goodness of the tree obtained.
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- Yoshio Tateno
Present address: Institute of Physical and Chemical Research, Rikagaku Kenkyusho, Hirosawa, Wako-shi, 351, Saitama, Japan
Authors and Affiliations
- Center for Demographic and Population Genetics, University of Texas at Houston, 77025, Houston, Texas, USA
Yoshio Tateno, Masatoshi Nei & Fumio Tajima
Authors
- Yoshio Tateno
You can also search for this author inPubMed Google Scholar - Masatoshi Nei
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Tateno, Y., Nei, M. & Tajima, F. Accuracy of estimated phylogenetic trees from molecular data.J Mol Evol 18, 387–404 (1982). https://doi.org/10.1007/BF01840887
- Received: 28 May 1981
- Revised: 28 April 1982
- Issue Date: November 1982
- DOI: https://doi.org/10.1007/BF01840887