ON THE BEST EVOLUTIONARY RATE FOR PHYLOGENETIC ANALYSIS

The effect of the evolutionary rate of a gene on the accuracy of phylo geny reconstruction was examined by computer simulation. The evolution ary rate is measured by the tree length, that is, the expected total n umber of nucleotide substitutions per site on the phylogeny. DNA seque nce data were simulated using both fixed trees with specified brand le ngths and random trees with branch lengths generated from a model of c ladogenesis. The parsimony and likelihood methods were used for phylog eny reconstruction and the proportion of correctly recovered branch pa rtitions by each method was estimated. Phylogenetic methods including parsimony appear quite tolerant of multiple substitutions at the same site The optimum levels of sequence divergence were even higher than u pper limits previously suggested for saturation of substitutions, indi cating that the problem of saturation may have been exaggerated. Inste ad, the lack of information at low levels of divergence should be seri ously considered in evaluation of a gene's phylogenetic utility, espec ially when the gene sequence is short. The performance of parsimony re lative to that of likelihood, does not necessarily decrease with the i ncrease of the evolutionary rate.