Measures for Obtaining Inclusive Sets of Area Cladograms under Assumptions Zero, 1, and 2 with Different Methods for...

We present modifications to computer programs of a posteriori and a priori methods for vicariance biogeography that enable them to obtain inclusive sets of area cladograms under assumptions zero, 1, and 2. With CAFCA (Component Compatibility Analysis) an upper limit for area cladogram selection by the number of steps is not always sufficient for inclusive sets. CAFCA needs additionally a lower limit for the number of components used to derive area cladograms when noninclusion arises because CAFCA selects area cladograms with different resolutions. PAUP (Brooks Parsimony Analysis) derives inclusive sets when it selects area cladograms under assumptions zero, 1, and 2 by using an upper limit for the number of steps and not collapsing unsupported nodes. For the computer programs Component 1.5 (Component Analysis), Component 2.0 (Reconciled Tree Analysis), and TAS (Three Area Statement Analysis) we suggest a two-step procedure for inclusive sets. The first step involves dealing with widespread taxa a priori under assumptions zero, 1, or 2. The second step involves dealing with sympatric taxa "as is" (Component 1.5 and TAS) or by tree reconciliation using an upper limit for the number of losses (Component 2.0).