I'm mapping states (geographic regions) onto a phylogeny to estimate the number of transmissions between countries.
I'm using two methods, stochastic character mapping implemented in Phytools and parsimony implemented in Mesquite.
I was expecting parsimony to give lower results than stochastic character mapping, as it doesn't attempt any simulation along branches. This is generally true, and the number of transitions between states is generally lower estimated by parsimony. However, in a couple of cases, the number of transitions estimated by parsimony is higher than by stochastic character mapping.
I'm still developing an intuition in this type of analysis, so could someone tell me if this is feasible, or should I be looking for a technical problem somewhere?