Parsimony

One intuitive score for a phylogenetic tree is the number of changes along edges. The approach of minimizing this score is called parsimony. The logic is the basic philosophy of Okham's razor - finding the simplest explanation that works. Let us mark the vertices of a tree by V(T), and its edges by E(T). Denote the value of the jth character of vertex $v \in V(T)$ by v_j.

 

  

Figure 8.3: A most parsimonious 5-species phylogeny for 6 characters, reconstructed from the data in table 8.1. The numbers by the mutation bars indicate the changed character.

 

Table 8.1: 6 DNA site values for 5 species. This data was used to infer the phylogeny in figure 8.3.

	1	2	3	4	5	6
Aardvark	C	A	G	G	T	A
Bison	C	A	G	A	C	A
Chimp	C	G	G	G	T	A
Dog	T	G	C	A	C	T
Elephant	T	G	C	G	T	A

 

There are two levels of problems in parsimony, small parsimony and large parsimony.