The impact of sequence parameter values on phylogenetic accuracy

An accurately inferred phylogeny is important to the study of molecular evolution. Factors affecting the accuracy of a phylogenetic tree can be traced to several sequential steps leading to the inference of the phylogeny. I examine here the features of the sequences in the alignment which impact phylogenetic (topological) accuracy rather than any source of error during the process of sequence alignment or choice of the method of inference. Specifically, I study the implications of the following five parameters, individually and in combination: sequence length, substitution rate, nucleotide base composition, the transition-transversion rate ratio and the rate heterogeneity among the sites. It is found that the transition-transversion rate ratio or kappa has a significant impact on phylogenetic accuracy, with a strong positive interaction with accuracy at high substitution rates, contrary to general belief. This work on known expected tree has implications for the researcher in field and would enable them to choose from among the multiple genes typically available today for an accurate phylogenetic inference. In addition, the increased accuracy with increase in kappa suggest that the phylogenetic signal may be strong in the nucleotide sites that have experienced considerable number of transversion than transition substitutions and thus can be useful in inference of a meaningful phylogeny.