IUBio Biosequences .. Software .. Molbio soft .. Network News .. FTP

consensus trees with branch lengths?

Dianosaur dmf_52 at hotmail.com
Fri Nov 19 11:35:21 EST 1999


Hi all,
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.
Thanks,
Diane Ferguson
Michigan State University








More information about the Mol-evol mailing list

Send comments to us at biosci-help [At] net.bio.net