Parsimony Optimization of Discrete Traits

The principle of parsimony (i.e., Occam's razor) is widely used in the natural sciences as a method for selecting from among numerous alternative hypotheses. The principle of parsimony underlies all scientific modeling and theory building. The basic idea is that one should not increase, beyond what is necessary, the number of entities required to explain anything. In this context, parsimony means that simpler hypotheses are preferable to more complicated ones. It is not generally meant to imply that Nature itself is simple, but rather that we as observers should prefer the most simple explanations.

Maximum parsimony (MP) is a character-based method used in phylogenetic systematics to reconstruct phylogenetic trees by minimizing the total number of evolutionary transformations (steps) required to explain a given set of data. In other words, MP minimizes the total tree length. The steps may be nucleotide base or amino acid substitutions for sequence data, or gain and loss events for restriction site and morphological data. MP may also be used to infer ancestral states of a character within a phylogenetic tree (this is discussed in the following).

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