Written by Joseph Felsenstein. Permission is granted to copy this document provided that no fee is charged for it and that this copyright notice is not removed. PARS is a general parsimony program which carries out the Wagner parsimony method with multiple states. Wagner parsimony allows changes among all states. The criterion is to find the tree which requires the minimum number of changes.
Different characters evolve independently.
Different lineages evolve independently. These changes are a priori improbable over the evolutionary time spans involved in the differentiation of the group in question. Other kinds of evolutionary event such as retention of polymorphism are far less probable than these state changes. Rates of evolution in different lineages are sufficiently low that two changes in a long segment of the tree are far less probable than one change in a short segment. In fact, one can use different symbols in different columns of the data matrix, although it is rather unlikely that you would want to do that.