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consensus trees with branch lengths?

Jack Sullivan sullivan at onyx.si.edu
Sun Nov 21 15:00:52 EST 1999

Here's my take on branch lengths on consensus trees (for what it's worth).
I basically agree with the reviewers, but there's certainly room for
disagreement. Because the mp (or ml or me, whaterver) trees are point
estimates of the true tree the consensus (i.e. treating polytomies as hard)
may not be a significantly worse estimate than any of the fully resolved
trees. This is the whole point of estimating nodal support, and the same
question pertains to figures for 50% bootstrap trees. So, what I typically
do (again, for what it's worth) is pick one of the optimal trees (mp,
ml...whatever), depict it as a phylogram (for the reasons Doug gave, among
others), use a scale bar to indicate branch lengths and put estimates of
nodal support (bootstrap/jacknife values, decay indices) on each node. If a
node receives <50% bootstrap support, I still show it as resolved unless
there's a zero-length internal branch in all optimal trees. With the low
support value indicated, it's plain as day that the data don't support that
bifurcation well. Nodes that collapse in the consensus of equally optimal
trees get a decay index of zero in the figure. I then usually discuss
alternative equally optimal resolutions in the text. All the info is there,
and no one is misled.


Jack Sullivan				Phone: (208) 885-9049
Department of Biological Sciences	Fax: (208) 885-7905
Box 443051				e-mail: sullivan at onyx.si.edu
University of Idaho
Moscow, ID 83844-3051

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