ACCURACY OF PHYLOGENETIC ANALYSIS INCLUDING AND EXCLUDING POLYMORPHICCHARACTERS

Intraspecific variation is ubiquitous in systematic characters, yet sy stematists often do not deal with polymorphism explicity. For example, morphological systematists typically exclude characters in which any or ''too much'' polymorphism is observed, and molecular systematists o ften avoid intraspecific variation by sampling a single individual per species. Recent empirical studies have suggested that polymorphic cha racters contain significant phylogenetic information but are more homo plastic than fixed characters. Given these two observations, should in cluding polymorphic characters increase or decrease accuracy? We addre ssed this question using simulated data sets that also show a strong r elationship between homoplasy and intraspecific variability. Data sets were generated with eight species, two alleles per locus, and a varie ty of branch lengths, number of led, and sample sizes (individuals sam pled per species). The data sets were analyzed using eight parsimony c oding methods (with and without a priori and successive weighting) and different variability thresholds for excluding polymorphic characters . Excluding polymorphic characters decreased accuracy under almost all conditions examined, even when only the more variable characters were excluded. Sampling a single individual per species also consistently decreased accuracy. Thus, two common approaches for dealing with intra specific variation in morphological and molecular systematics can give relatively poor estimates of phylogeny. In contrast, the unweighted f requency method, including polymorphic characters and sampling a reaso nable number of individuals per species (It greater than or equal to 5 ), can give accurate results under a variety of conditions.