How to do BPA, really

Aim Recent comparisons of different approaches to historical biogeography h ave suffered in part because Brooks Parsimony Analysis (BPA) has been chara cterized as a one-step process following protocols proposed in 1981. Subseq uent modifications have resulted in a two-step methodology. This contributi on presents the mechanics and applications of those modifications. Methods The first step, or Primary BPA, which is similar to the original BP A but with modifications proposed by Wiley (1986, 1988a, b), is used to ass ess whether or not there is support for a single general area cladogram. Th e second step, Secondary BPA, proposed by Brooks (1990), depicts exceptions to the general area cladogram explicitly by duplicating areas having a ret iculate history. Results The analytical basis of area duplication in secondary BPA is explai ned more fully than in previous accounts, and the manner in which secondary BPA explicitly depicts falsification of the null hypothesis of simple vica riance is presented for four general cases. Main conclusions BPA, as fully implemented, is capable of accounting for th e 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 t o provide a distinction between general and special distribution elements.