Polymorphic characters in phylogenetic systematics

The use of discrete, intraspecifically variable characters in parsimony analysis is reviewed. Seven data sets (two from morphology and five from allozymes) were analyzed to (1) compare different methods for treating polymorphic characters, (2) test for phylogenetic information in polymorphic characters, and (3) determine if there is a relationship between homoplasy and intraspecific variability. The performance of eight methods was compared using five criteria (number of characters treated as informative, number of shortest trees, phylogenetic signal, number of nodes supported by bootstrapping, and sensitivity to reduced sample size). Approaches that incorporate explicit frequency information perform best overall for all the criteria, although the “majority” method ties for best for the bootstrapping criterion. Levels of phylogenetic information in the polymorphic characters differed greatly among data sets and methods. Polymorphic characters in most data sets contained significant phylogenetic structure using most methods, but only one, the frequency method, extracted significant signal from the polymorphic characters in all seven data sets. Fixed characters appear to contain more signal than polymorphic characters, and homoplasy is significantly and positively correlated with intraspecific variability. This study supports the traditional view that polymorphic characters are less reliable ininferring phylogeny but does not necessarily support their exclusion. Systematists working with morphological data often do not report intraspecific variation, the frequencies ofdifferent traits, or how polymorphic characters are screened and analyzed; this situationshould change.