Phylogenetic frameworks: towards a firmer foundation for the comparative approach

The growing interest in using phylogenies to test evolutionary hypotheses has focused attention on the need for robust estimates of phylogenetic history. Whether specific branching structures are correct summaries of evolutionary history can be estimated only through the examination of congruence of many sets of characters. After consideration of practical and philosophical aspects of congruence, I conclude that taxonomic congruence (analysis of congruence of topologies produced from independent datasets) is preferable to character congruence (analysis of congruence between individual characters) for estimating accuracy of phylogenetic hypotheses. Existing methods for examining taxonomic congruence are discussed and the combinable components approach, when preceded by application of rigorous statistical manipulations (e.g. jackknifing or bootstrapping), found most appropriate. Implementation of the method of combinable components is described, and is demonstrated using published data for Menidia and Rana. The robust branching structure resulting from this analysis (a phylogenetic framework) contains those nodes (phylogenetic hypotheses) that are strongly supported by at least one dataset and are consistent with all others. This approach is the most appropriate/conservative for testing hypotheses about evolutionary history.