Property and efficiency of the maximum likelihood method for molecular phylogeny

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.