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. This program carries out the Dollo and polymorphism parsimony methods. The method is named after Louis Dollo since he was one of the first to assert that in evolution it is harder to gain a complex feature than to lose it. The characters are evolving independently.
Different lineages evolve independently.
The lengths of the segments of the true tree are not so unequal that two changes in a long segment are as probable as one in a short segment. One problem can arise when using additive binary recoding to represent a multistate character as a series of two-state characters. Unlike the Camin- Sokal, Wagner, and Polymorphism methods, the Dollo method can reconstruct ancestral states which do not exist. An example is given in my 1979 paper. It will be necessary to check the output to make sure that this has not occurred.