THE RECONSTRUCTION OF ANCESTRAL CHARACTER STATES

The problem of error in the phylogenetic reconstruction of ancestral c haracter states is explored by developing the model of Frumhoff and Re eve (1994). Information about the evolutionary rate of change within a character is inferred from the distribution of its character states o n a known phylogeny, and this information is used to impose confidence limits on the error associated with ancestral state inference. Ancest ral state inference is found to be remarkably robust under the model a ssumptions for a wide range of parameter values; however, the probabil ity of error increases when the number of species within a clade is sm all and/or state-transition probabilities are strongly skewed in favor of the non-ancestral state. The rationale for expecting such a skew, a hypothesis of parallelism, is shown to rely on assumptions of low ra tes of change in at least two phylogenetically inherited characters: t he tendency to occupy a particular ecological niche and the tendency t o respond in a particular way to selection. A means for judging the re lative likelihoods of parallelism vs. straightforward homology as expl anations for a given character-state distribution is suggested. Genera l problems with the model are discussed, as are methods for making it more realistic.