How to do BPA, really

Abstract

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.

Phylogeny and biogeography of Chinese sisorid catfishes re-examined using mitochondrial cytochrome b and 16S rRNA gene sequences

“…First, we performed primary BPA using the method of Brooks (Brooks et al, 2001) based on the best phylogenetic tree and the distribution pattern (Table 3). Pseudecheneis sulcatus was used as outgroup.…”

Biogeography of Amazonian fishes: deconstructing river basins as biogeographic units

“…Lineages restricted to only one basin (autapomorphic taxa or clade), albeit uninformative about area relationships, were not excluded so that the matrix is fully reflective of the database, including information on endemic taxa for each drainage (S7-10 -Available only as online supplementary file accessed with the online version of the article at http://www.scielo.br/ni). Brooks Parsimony Analysis (BPA) was proposed by Wiley (1988aWiley ( , 1988b and subsequently modified by Brooks (1990) and Brooks et al (2001). The method is based on the ideas of Brooks (1981) to study coevolution between hosts and parasites.…”

Biogeographic analysis of Crocidiinae (Diptera, Bombyliidae): finding congruence among morphological, molecular, fossil and paleogeographical data

“…For the biogeographical analysis, we performed the Brooks Parsimony Analysis (BPA) (Brooks et al 2001) aiming to reconstruct the historical relationships among the areas of endemism inhabited by Crocidiinae taxa. Five areas were used: Chile, SW Nearctic, Southern Africa, Northern Africa and SW Asia, as well as an all zero outgroup area to root the trees.…”