159 – New Statistical Methods in Phylogenetics
A Starless Bias in the Maximum Likelihood Phylogenetic Methods
Xuhua Xia
University of Ottawa, Ottawa Institute of Systems Biology
The maximum likelihood method is the gold standard in molecular phylogenetics and accounts for nearly half of all published phylogenetic trees, but the method has a strange phylogenetic bias so far not explored. If the aligned sequences are equidistant from each other with the true tree being a star tree, then the likelihood method is incapable of recovering it unless the sequences are either identical or extremely diverged. Here I analytically demonstrate this "starless" bias and identify the source for the bias. In contrast, distance-based methods (with the least-squares method for branch evaluation and either minimum evolution or least-squares criterion for choosing the best tree) do not have this bias. The finding sheds light on the star-tree paradox in Bayesian phylogenetic inference. maximum likelihood, molecular phylogenetics, distance-based phylogenetic method, starless, star-tree paradox