A unified methodology for parsimony analysis in studies of the co-speciation of clades that co-occur in ecological associations is presented. It incorporates two methodological prescriptions proposed by Wiley with a third, namely duplication of areas when members of single or multiple clades are differentially represented. This third component eliminates the need to ignore data on widespread taxa or to weight taxa differentially. Re-analysis of Neotropical bird data demonstrates that the proposed method is sensitive to a variety of general and unique evolutionary influences in studies of historical biogeography, and is hence non-reductionist. Parsimony analysis at the level of clades is analogous to parsimony analysis at the level of ecological associations because the process invoked for homology, i.e., common history, is the same, even though the processes invoked to explain homoplasy differ, in all cases.