THE MEASUREMENT OF HOMOPLASY: A STOCHASTIC VIEW

This chapter attempts to formulate a probabilistic measure of homoplasy. The concept of homoplasy or some measurement of the “degree of homoplasy” seems to be widely used in systematics as a measure of the reliability of a phylogenetic estimate obtained from a collection of characters. Measures of homoplasy based on the maximum parsimony length of characters are poor estimators of probabilities because they ignore the possibility of multiple events within phyletic lineages. Some well known indices of homoplasy derived from the maximum parsimony procedure are not direct estimators of levels of homoplasy in this stochastic sense. Construction of an appropriate measure of homoplasy requires a determination of uncertainty in the estimated tree and a stochastic model of the phyletic character change process. One possible estimator of probability based on a simple Poisson model of evolution for binary characters is presented in this chapter.