The reconstruction of phylogenies using cladistic methods is a powerful and well-established tool for evolutionary biologists and paleobiologists. Indeed, the construction of rigorous phylogenetic hypotheses has become widely accepted as an essential first step in the analysis of historical patterns for both extant and extinct organisms. In the past few years, there has arisen a healthy and constructive debate as to the exact methods that will lead to the most accurate tree (for example whether statistical inference or stratigraphic information has any part to play in phylogenetic reconstruction). Although important, this debate has tended to focus on the problems of tree construction and divert attention away from the applications of tree-based research. The construction of a phylogeny is, after all, only a first step, and phylogenetic trees provide the starting point from which to address a wide range of interesting biological and geological topics.