We are having an ongoing discussion/disagreement in our lab about
displaying branch lengths on consensus trees derived from a parsimony
search, in other words displaying a consensus tree (ie strict consensus)
as a "phylogram". Folks in my lab (not me) sent in a manuscript with a
"consensus phylogram" and the reviewers said not to display a consensus
tree as a phylogram with no explanation as to what was wrong.
I agree with the reviewers but am having a hard time articulating why.
It's two reasons, really, that I can think of. First, polytomies in
consensus trees do not imply branches with zero length. They are
collapsed areas of multiple trees, probably with branch lengths>1.
Information is lost in consensus, and it doesn't seem right to
reintroduce that information. Second, branch lengths are character
state optimizations across a single phylogeny. Calculating steps on a
consensus tree just doesn't work for me. It would mean that the
polytomies in the consensus were true or "hard" polytomies. This is not
what is conveyed in a consensus diagram.
I'd love to hear any other thoughts or clarifications on this matter.
Michigan State University