Restriction site parsimony methods

Although distance methods have certain advantages for the analysis of restriction site data, notably their computational efficiency, they also have an important disadvantage. By reducing the data to pairwise distances, important information on the evolutionary history of individual restriction sites is lost. In chloroplast DNA, for example, individual sites often evolve at very different rates. A parsimony analysis of 328 restriction site mutations shared among two or more taxa in a survey of 57 taxa from the sunflower family showed that 186 of the sites had only a single mutation, whereas 6 sites showed nine or more mutations.24 A conservative statistical... 

Three different parsimony methods have been used for the analysis of restriction site data Wagner parsimony,25 Dollo parsimony,26 and weighted parsimony or generalized parsimony.27 As the names suggest, they all invoke a parsimony principle to select the best tree (or trees) from the set of all possible trees. Specifically, the trees selected are those that require the minimum amount of evolutionary change. The methods differ from one another in how the amount of evolutionary change is calculated. 

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