Hypothetical Ancestors and Rooting in Cladistic Analysis

Most hypothetical ancestors that are used to root trees in cladistic analyses summarize character-state information in one or more outgroup taxa. Nonetheless, hypothetical ancestors also provide a means of rooting trees using the ontogenetic and paleontological methods of polarizing character transformations, and for incorporating the inferences of more than one of these methods into a single analysis. However, the use of one hypothetical ancestor that combines inferences based on outgroup comparison with those based on other methods of polarizing character transformations to root a cladogram is invalid. Inferences regarding plesiomorphic character states based on outgroup comparison apply to the outgroup node, whereas inferences based on either the ontogenetic or paleontological method apply to the ingroup node. These inferences cannot be combined into a single hypothetical construct. A hypothetical ancestor based on outgroup information is included in the data matrix and used to root the resulting network; however, because this ancestor places potentially problematic constraints on the analysis, the use of actual outgroup taxa is preferable in most instances. Correct use of a hypothetical ancestor inferred with the ontogenetic and paleontological methods involves the Lundberg method in which the shortest ingroup network is rooted at the internode to which the hypothetical ancestor attaches most parsimoniously. Because inferences of polarity based on outgroup comparison cannot be combined directly with those based on other polarization methods, the synthesis of information from all three methods in a single tree must involve taxonomic congruence.