I did a search under the parsimony criterion and got two trees that look just alike. Why does PAUP consider them to be different?
The answer involves how PAUP collapses zero-length branches. The default collapsing rule is that a branch is retained if it is supported under at least one most-parsimonious reconstruction (MPR) of the ancestral states, for at least one character. Here is a simple data matrix that will generate this result. characters taxa 1 23 45 —————– A 0 00 00 B 0 11 11 C 0 11 11 D 1 00 11 E 1 00 00 F 1 00 11 Analysis of this matrix using PAUP gives two most-parsimonious trees: : A B C D F E : \ \ / \ / / : \ * * / : \ \ / / : \ \ / / : tree1 \ * / : \ | / : \|/ : * : : A B C D F E : \ \ / / / / : \ * / / / : \ \ / / / : \ * / / : \ \ / / : tree2 \ * / : \ | / : \|/ : * An MPR on tree1 for character 1 requires two steps, and there are two of them: : A B C D F E A B C D F E : 0 0 0 1 1 1 0 0 0 1 1 1 : \ \ / \ / / \ \ / \ / / : \ 0 1 / \ 0 1 / : \ \ / / \ \ / / : \ \ / / \ \ / / : \ 0 / \ 1 / : \ | / \ | / : \|/ \|/ : 0 1 Because one of these two MPRs assigns a change leading to the group
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