Character Based Methods: Parsimony

Abstract

Maximum Parsimony (MP) methods were originally developed for comparing morphologies. However, they are increasingly being used on molecular data for inferring species trees from gene trees. In MP methods, four or more aligned nucleotide or amino acid sequences are considered. The parsimony analysis for each site in the aligned sequence is performed for each possible tree, where the tree that produces the alignment with the minimal number of transformations is considered to be the one with maximum parsimony. The theoretical basis for the method is Occam’s razor which states that the explanation of any phenomenon should make as few assumptions as possible, eliminating, or “shaving off,” those that make no difference in the observable predictions of the explanatory hypothesis or theory. Thus, the simplest explanation is the one that is most likely correct.