On the Best Evolutionary Rate for Phylogenetic Analysis

The effect of the evolutionary rate of a gene on the accuracy of phylogeny reconstruction was examined by computer stimulation. The evolutionary rate is measured by the tree length, that is, the expected total number of nucleotide substitutions per site on the phylogeny. DNA sequence data were simulated using both fixed trees with specified branch lengths and random trees with branch lengths generated from a model of cladogenesis. The parsimony and likelihood methods were used for phylogeny reconstruction, and the proportion of correctly recovered branch partitions 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 upper limits previously suggested for saturation of substitutions, indicating that the problem of saturation may have been exaggerated. Instead, the lack of information at low levels of divergence should be seriously considered in evaluation of a gene's phylogenetic utility, especially when the gene sequence is short. The performance of parsimony, relative to that of likelihood, does not necessarily decrease with the increase of the evolutionary rate.