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

Abstract

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