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I don't understand how to sum the changes in a phylogenetic tree.

Here for example: http://www.med.nyu.edu/rcr/rcr/course/phylo-cladistic.html

How do you end up with 8 for the first and 9 for the second ?

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It seems to me that they are not summing the changes correctly in this page.

They are summing the lengths of the paths to the root (and for the fig 2, they assume that the terminal branches, from left to right are of lengths 3, 2, 1 and 1). This doesn't make sense to me.

The correct way to count changes using parsimony is to consider each site in the alignment, and try to put the minimum number of mutations on the tree to explain the states observed at the terminal branches. Then, sum the number of mutations across alignment sites.

Here, for figure 1, I get:

site 1: 1 mutation, either on the left (T->A) or on the right (A->T) internal branch.

site 2: 1 mutation on the 4th terminal branch (T->C)

site 3: 0 mutations (all terminals have C)

site 4: 1 mutation on the 2nd terminal branch (G->C)

Total: 3

for figure 2:

site 1: 1 mutation on the branch leading to the most recent common ancestor of the two right-most terminals (A->T)

site 2: 1 mutation on the right-most terminal branch (T->C)

site 3: 0 mutations (same reason as for figure 1)

site 4: 1 mutation, either on the left-most branch (G->C) or on the branch leading to the most recent common ancestor of the 3 right-most terminals (C->G)

Total: 3

The trees are equi-parsimonious.

I hope I did not make any mistakes.

There exist algorithms to do this. For instance, Wagner parsimony.

Don't trust a course on phylogeny that resides on a medical center web page.

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Ok, thanks for your time –  mwa1 Jan 7 '13 at 20:55

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