Some limitations of ancestral character-state reconstruction with testing evolutionary hypotheses

The recent explosion of phylogenetic in-formation has had an impact far beyond the eld of systematic biology. Workers in a variety of disciplines are now interested in generating and using phylogenies for their groups (or genes) of interest (e.g., Brooks and McLennan, 1991; Harvey et al., 1995; Martins, 1996). In large part, this new inter-est has been driven by the promise of using phylogenies to reconstruct ancestral charac-ter states, usually by parsimony. The sim-plicity of testing evolutionary hypotheses by mapping characters ontoaphylogenyhas an appeal that has not been lost on the biologi-cal community. Despite its appeal, ancestral state recon-struction is an ambitious exercise. Although we are very familiar with the difculty of accurately inferring phylogenies with thou-sands of characters (reviewed by Swofford et al., 1996), the challenges associated with reconstructing ancestral character states of individual characters are correspondingl