Phylogenetic uncertainties and sensitivity analyses in comparative biology

Abstract Phylogenetic comparative analyses combine information on character states and phylogenetic relationships of taxa to test hypotheses regarding character evolution. These studies encounter uncertainties at various steps, including uncertainty in the topology of phylogenetic trees, the scoring of characters, and the addition of taxa that have not explicitly been included in phylogenetic analyses. Here we highlight a variety of sensitivity tests designed to explore the robustness of comparative conclusions to changes in underlying assumptions. These include the examination of character correlations on a set of plausible phylogenetic hypotheses (including alternative rootings and ‘neighbouring’ trees), as well as under alternative character codings. TreeBASE -a prototype relational database of phylogenetic data - should prove useful in accessing alternative hypotheses.