Trees Versus Characters and the Supertree/Supermatrix “Paradox”

In a pair of recent articles, Gatesy and colleagues (Gatesy et al., 2002, 2004; also Gatesy and Springer, 2004) have strongly criticized several recent supertree studies. In so doing, they have pointed out important, but correctable, shortcomings in how the supertree approach was applied in specific instances, and have helped to fine-tune the methodology of this comparatively young field. However, their equally strong critiques of the MRP method, if not the supertree approach as a whole, derive from a faulty basis for comparison. Gatesy et al. (2004:347) state (correctly) that primary character data are “the ultimate source data for both supertree and supermatrix analyses” (also p. 347), and use this statement to justify comparing both approaches on this level. However, because any connection between the primary character data and the supertree analysis is highly indirect—a feature of supertree construction that they also criticize—it is invalid to judge supertrees according to criteria designed for characterbased phylogenetic reconstruction. Instead, the (MRP) supertree approach should be judged with respect to the data that it uses directly, namely the phylogenetic hypotheses presented in the source trees. As I hope to show, recognizing that supertree and supermatrix analyses operate at different levels blunts most of Gatesy et al.’s criticisms of the supertree approach, thereby resolving the “paradox” they mention in their earlier paper.