The impact of sequence parameter values on phylogenetic accuracy
An accurately inferred phylogeny is important to the study of evolution. Factors affecting the accuracy of an inferred tree can be traced to several sequential steps leading to the inference of the phylogeny. We have examined here the impact of some features of nucleotide sequences in alignments on phylogenetic (topological) accuracy rather than any source of error during the process of sequence alignment or choice of the method of inference (as is usually done). Specifically, we have studied (using computer simulation) the implications of changing the values of the following five parameters, individually and in combination: sequence length (l), nucleotide substitution rate (r), nucleotide base composition (?), the transition-transversion rate ratio (?), and the substitution rate heterogeneity among the sites (?). An interesting, and unexpected, result was that ? has a strong positive relationship with phylogenetic accuracy, especially at high substitution rates. This simulation-based work has implications for empirical researchers in the field and should enable them to choose from among the multiple genes typically available today for a more accurate inference of the phylogeny being studied.