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

The relative efficiencies of several tree-making methods for obtaining the correct phylogenetic tree were studied by using computer simulation. The methods examined were the Fitch-Margoliash (FM), maximum-parsimony (MP), maximumlikelihood (ML), minimum-evolution (ME), and neighbor-joining (NJ) methods. We simulated the evolutionary changes of six DNA sequences each with a length of either 300 or 600 nucleotides. Both constant and varying rates of nucleotide substitution were considered. The DNA sequences generated were used to reconstruct phylogenetic trees by applying the five tree-making methods, and the trees obtained were compared with the model (correct) tree. This process was repeated 50 times for each case, and the following results were obtained: ( 1) The efficiency of obtaining the correct tree for the FM method was considerably lower than those for the other methods. (2) The NJ and ME methods showed a high performance in obtaining the correct tree, and their relative efficiencies were similar to each other. ( 3) For distance methods (NJ, FM, and ME), the results obtained by using corrected nucleotide substitutions were much better than those obtained by using nucleotide differences when the rate of substitution varied greatly among different branches. (4) The ML method was slightly inferior to the NJ and ME methods when a constant rate of nucleotide substitution was assumed, but it was slightly better than the latter two methods when the evolutionary rate varied drastically among branches. If one considers the computational time involved, the NJ method seems to be a method of choice.

[1]  M. O. Dayhoff,et al.  Atlas of protein sequence and structure , 1965 .

[2]  W. Fitch,et al.  Construction of phylogenetic trees. , 1967, Science.

[3]  L. Cavalli-Sforza,et al.  PHYLOGENETIC ANALYSIS: MODELS AND ESTIMATION PROCEDURES , 1967, Evolution; international journal of organic evolution.

[4]  T. Jukes.  CHAPTER 24 – Evolution of Protein Molecules , 1969 .

[5]  W. Fitch.  Toward Defining the Course of Evolution: Minimum Change for a Specific Tree Topology , 1971 .

[6]  Walter M. Fitch,et al.  On the Problem of Discovering the Most Parsimonious Tree , 1977, The American Naturalist.

[7]  M. Hasegawa,et al.  MAXIMUM LIKELIHOOD METHOD OF PHYLOGENETIC INFERENCE FROM DNA SEQUENCE DATA , 1984 .

[8]  W. Brown,et al.  A comparison of the small ribosomal RNA genes from the mitochondrial DNA of the great apes and humans: sequence, structure, evolution, and phylogenetic implications. , 1986, Molecular biology and evolution.

[9]  M. Nei.  Molecular Evolutionary Genetics , 1987 .

[10]  C. Krimbas,et al.  Accuracy of phylogenetic trees estimated from DNA sequence data. , 1987, Molecular biology and evolution.

[11]  N. Saitou,et al.  The neighbor-joining method: a new method for reconstructing phylogenetic trees. , 1987, Molecular biology and evolution.

[12]  J A Lake,et al.  A rate-independent technique for analysis of nucleic acid sequences: evolutionary parsimony. , 1987, Molecular biology and evolution.

[13]  P. Sharp,et al.  Reconstruction of phylogenetic trees and estimation of divergence times under nonconstant rates of evolution. , 1987, Cold Spring Harbor symposia on quantitative biology.

[14]  M. Nei,et al.  Relative efficiencies of the maximum parsimony and distance-matrix methods in obtaining the correct phylogenetic tree. , 1988, Molecular biology and evolution.