An alternative construction of internodons: the emergence of a multi-level tree of life.

Internodons are a formalization of Hennig's concept of species. We present an alternative construction of internodons imposing a tree structure on the genealogical network. We prove that the segments (trivial unary trees) from this tree structure are precisely the internodons.

Coding polymorphism for phylogeny reconstruction.

The methodology of coding polymorphic taxa has received limited attention to date. A search of the taxonomic literature revealed seven types of coding methods. Apart from ignoring polymorphic characters (sometimes called the fixed-only method), two main categories can be distinguished: methods that identify the start of a new character state with the origin of an evolutionary novelty, and methods that identify the new state with the fixation of a novelty.

A Posteriori and a Priori Methodologies for Testing Hypotheses of Causal Processes in Vicariance Biogeography.

Methods used in vicariance biogeography fall into the categories of a posteriori methods (e.g., Component Compatibility Analysis and Brooks Parsimony Analysis) and a priori methods (e.

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

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.

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).