Methods in Vicariance Biogeography: Assessment of the Implementations of Assumptions 0, 1, and 2

As we have argued previously, for the valid derivation of general area cladograms in vicariance biogeography, two requirements should be met. First, sets of area cladograms derived under assumptions 0, 1 and 2 should be inclusive (requirement I). Second, general area cladograms should be based on area cladograms, for different monophyletic groups, derived under the same assumption (requirement II). We now assess for their actual implementation of assumptions A0, A1, and A2 and for the extent to which they meet requirements I and II, the following methods (and correlated computer programs): Component Compatibility Analysis (CAFCA), Brooks Parsimony Analysis (PAUP), Component Analysis (Component 1.5), Reconciled Tree Analysis (Component 2.0), and Three Area Statement Analysis (TAS). For this purpose we use empirical ( Heterandria, Xiphophorus, Cyttaria, Eriococcus/Madarococcus ) and theoretical data sets. All programs appear to violate, to a different degree, requirement I (deriving inclusive sets of area cladograms under assumptions) when dealing with sympatric taxa under A1 or A2. Dealing with sympatric taxa a posteriori only prevents this violation. All programs examined appear to meet requirement II (deriving general area cladograms under a single assumption).     

When simplicity is not parsimonious: a priori and a posteriori methods in historical biogeography

Despite using the same null hypothesis, a priori and a posteriori approaches in historical biogeography differ fundamentally. Methods such as Component Analysis (CA) and Reconciled Tree Analysis (RTA) may eliminate or modify input data in order to maximize fit to the null hypothesis, by invoking assumptions 1 and 2. Methods such as Brooks Parsimony Analysis (BPA) modify the null hypothesis, if necessary, to maintain the integrity of the input data, as required by assumption 0. Two exemplars illustrate critical empirical differences between CA/RTA and BPA: (1) CA rather than BPA may select the incorrect general area cladogram for a set of data (2) BPA, not RTA, provides the most parsimonious interpretation of all available data and (3) secondary BPA, proposed in 1990, applied to data sets for which dispersal producing areas with reticulate histories is most parsimonious, provides biologically realistic interpretations of area cladograms. These observations lead to the conclusion that BPA and CA/RTA are designed to implement different research programmes based on different conceptual frameworks. BPA is designed to assess the biogeographic context of speciation events, whereas CA/RTA are designed to find the best fitting pattern of relationships among areas based on the taxa that inhabit them. Unique distributional elements and reticulate (hybrid) histories of areas are essential for explaining complex histories of speciation. The conceptual framework for BPA, thus, assumes biogeographical complexity, relying on parsimony as an explanatory tool to summarize complex results, whereas CA/RTA assumes biogeographical simplicity, assuming conceptual parsimony a priori .     

Cladistic and phylogenetic biogeography: the art and the science of discovery

All methods used in historical biogeographical analysis aim to obtain resolved area cladograms that represent historical relationships among areas in which monophyletic groups of taxa are distributed. When neither widespread nor sympatric taxa are present in the distribution of a monophyletic group, all methods obtain the same resolved area cladogram that conforms to a simple vicariance scenario. In most cases, however, the distribution of monophyletic groups of taxa is not that simple. A priori and a posteriori methods of historical biogeography differ in the way in which they deal with widespread and sympatric taxa. A posteriori methods are empirically superior to a priori methods, as they provide a more parsimonious accounting of the input data, do not eliminate or modify input data, and do not suffer from internal inconsistencies in implementation. When factual errors are corrected, the exemplar presented by M.C. Ebach & C.J. Humphries (Journal of Biogeography, 2002, 29 , 427) purporting to show inconsistencies in implementation by a posteriori methods actually corroborates the opposite. The rationale for preferring a priori methods thus corresponds to ontological rather than to epistemological considerations. We herein identify two different research programmes, cladistic biogeography (associated with a priori methods) and phylogenetic biogeography (associated with a posteriori methods). The aim of cladistic biogeography is to fit all elements of all taxon–area cladograms to a single set of area relationships, maintaining historical singularity of areas. The aim of phylogenetic biogeography is to document, most parsimoniously, the geographical context of speciation events. The recent contribution by M.C. Ebach & C.J. Humphries (Journal of Biogeography, 2002, 29 , 427) makes it clear that cladistic biogeography using a priori methods is an inductivist/verificationist research programme, whereas phylogenetic biogeography is hypothetico‐deductivist/falsificationist. Cladistic biogeography can become hypothetic‐deductive by using a posteriori methods of analysis.