Huelsenbeck et al. 2003 & Maddison & Maddison 2003

It seems the stochastic mapping procedure provides the means to estimate phylogenetic uncertainty in character reconstruction that parsimony, based on the reading of the MacClade chapter 4, does not provide (examining character reconstructions on numerous parsimonious trees can become impractical especially when dealing with polytomies). Huelsenbeck et al. make the point that parsimony works best at rates of evolution that are low and branch lengths are short, but could not the same be said for the stochastic method of mapping? MacClade does provide the means to weight characters using various transformations. To what extent does this improve the performance of parsimony at higher evolutionary rates? For example, how would the analysis of heterostyly/self incompatibility done with stochastic mapping compare with a parsimony analysis using the dollo transformation on self incompatibility (given that self incompatibility is thought to evolve slowly, but lost quickly)? Unfortunately, the Pontederiaceae data was not included in figure 19 of the Huelsenbeck paper. The outgroup analysis in MacClade seems straightforward, however it was unclear to me from the other readings how outgroup data was integrated into the alternative character evolution models.