Generalized Frequency Coding: A Method of Preparing Polymorphic Multistate Characters for Phylogenetic Analysis

A new method of coding polymorphic multistate characters for phylogenetic analysis is presented. By dividing such characters into subcharacters, their frequency distributions can be represented with discrete states. Differential weighting is employed to counter the effect of using multiple characters to represent one character. The new method, termed generalized frequency coding (GFC), is potentially superior to previously used methods in that it incorporates more information and can be applied to both qualitative and quantitative characters. The method was applied to a previously published data set that includes both types of polymorphic multistate characters, and performed well according to congruence with other studies and the g1 and nonparametric bootstrap statistics. The data set was also used to compare GFC to both gap-weighting and Manhattan distance step matrix coding. On these grounds and for philosophical reasons, GFC was found to be a better estimator of phylogeny.