TESTING SPECIES PHYLOGENIES AND PHYLOGENETIC METHODS WITH CONGRUENCE

We assessed the utility of congruence and multiple data sets to test s pecies relationships and the accuracy of phylogenetic methods. The ong oing controversy about whether to combine data sets for phylogenetic a nalysis was evaluated against the naturalness of different types of da ta (as commonly recognized by systematists) and character independence . We defend the recommendation that independent data sets (defined in terms of process partitions; sensu bull et al., 1993, Syst. Biol. 42:3 84-397) should rarely be combined but should be kept separate for phyl ogenetic analysis because their independence increases the significanc e of corroboration. Trees of natural taxa, well supported by many inde pendent lines of evidence, should be used in the same way as the known phylogenies of simulations and of certain laboratory and domesticated groups, i.e., as standards for evaluating the accuracy of different p hylogenetic methods. Although compromised by their imperfect reliabili ties, such tests using well-supported trees of wild taxa provide impor tant reality checks on the conclusions of the other two approaches by encompassing more of the complexity and diversity of natural systems a nd their evolutionary processes. In this way, a combination of testing with the well-supported trees of natural groups, with simulations, an d with those laboratory and domesticated taxa with known phylogenies i s most likely to prove effective in establishing the strengths, weakne sses, and assumptions of different phylogenetic methods.