How to do BPA, really

Aim Recent comparisons of different approaches to historical biogeography have suffered in part because Brooks Parsimony Analysis (BPA) has been characterized as a one-step process following protocols proposed in 1981. Subsequent modifications have resulted in a two-step methodology. This contribution presents the mechanics and applications of those modifications. Methods The first step, or Primary BPA, which is similar to the original BPA but with modifications proposed by Wiley (1986, 1988a, b), is used to assess whether or not there is support for a single general area cladogram. The second step, Secondary BPA, proposed by Brooks (1990), depicts exceptions to the general area cladogram explicitly by duplicating areas having a reticulate history. Results The analytical basis of area duplication in secondary BPA is explained more fully than in previous accounts, and the manner in which secondary BPA explicitly depicts falsification of the null hypothesis of simple vicariance is presented for four general cases. Main conclusions BPA, as fully implemented, is capable of accounting for the complexity of speciation, dispersal and extinction events in a historical biogeographic context without removing or modifying input data from basic phylogenies, so long as at least three clades are analysed simultaneously to provide a distinction between general and special distribution elements.