Measures of Clade Confidence Do Not Correlate with Accuracy of Phylogenetic Trees

Metrics of phylogenetic tree reliability, such as parametric bootstrap percentages or Bayesian posterior probabilities, represent internal measures of the topological reproducibility of a phylogenetic tree, while the recently introduced aLRT (approximate likelihood ratio test) assesses the likelihood that a branch exists on a maximum-likelihood tree. Although those values are often equated with phylogenetic tree accuracy, they do not necessarily estimate how well a reconstructed phylogeny represents cladistic relationships that actually exist in nature. The authors have therefore attempted to quantify how well bootstrap percentages, posterior probabilities, and aLRT measures reflect the probability that a deduced phylogenetic clade is present in a known phylogeny. The authors simulated the evolution of bacterial genes of varying lengths under biologically realistic conditions, and reconstructed those known phylogenies using both maximum likelihood and Bayesian methods. Then, they measured how frequently clades in the reconstructed trees exhibiting particular bootstrap percentages, aLRT values, or posterior probabilities were found in the true trees. The authors have observed that none of these values correlate with the probability that a given clade is present in the known phylogeny. The major conclusion is that none of the measures provide any information about the likelihood that an individual clade actually exists. It is also found that the mean of all clade support values on a tree closely reflects the average proportion of all clades that have been assigned correctly, and is thus a good representation of the overall accuracy of a phylogenetic tree.: The construction of phylogenetic trees, which depict past relationships between groups of DNA or protein sequences, has valuable application in many fields of study, most commonly evolutionary and population biology. Before drawing conclusions from phylogenetic trees, it is important to assess how accurate those reconstructions are. This is typically accomplished by examining measures of “clade credibility” (such as bootstrap or posterior probability values), which represent how reproducible relationships are within the tree based on the parameters of the phylogenetic analysis. However, such measures do not necessarily reflect how likely inferred relationships are to have actually occurred in nature. Therefore, using simulated data where relationships are known, we have determined how well several measures of clade credibility correlate with the likelihood that a deduced phylogenetic grouping actually exists in reality. Surprisingly, we found no such correlation, and that the inferred relationships were correctly assigned about as often in cases where clade credibility values were very low as where they were high. This finding suggests that current measures of phylogenetic tree reliability are not useful in predicting whether specific inferred relationships have actually occurred.