Separate Versus Combined Analysis of Phylogenetic Evidence

There has been much discussion in the recent systematic literature over whether different data sets bearing on phylogenetic relationships should be analyzed separately or combined and analyzed simultaneously. We review arguments in favor of each of these views. Assuming that the goal is to uncover the true phylogeny of the entities in question, arguments for combining data based on the notions that one should use the total evidence available, or that the combined analysis gives the tree with the greatest descriptive and explanatory power, are not compelling. However, combining data sets can enhance detection of real phylogenetic groups. On the other hand, if there is heterogeneity