Daniel Barker wrote:
> What should branch lengths on a consensus tree represent?
>
> Scott Chamberlain had written:
>
>> When making a consensus tree using ape::consensus the branch lengths are
>> lost. Is there a way to not lose the branch lengths? Or to add them
>> somehow
>> to the consensus tree after making it.
The issue of what branch lengths ought to be on a consensus tree is not simple.
If we have three rooted trees:
((A:1,B:1):1,C:2);
((A:1,B:1):1,C:2);
(A:2,(B:1,C:1):1);
the consensus tree should be the first tree, but what branch length should be
used for (say) the branch ancestral to the AB clade? 1? 0.667?
The minute you open this can of worms it becomes clear that the answer depends
on what you want that number to convey and what interpretations your audience
will tend to draw from the number. There is no "obvious" answer. So this is
not a mere technical computing question.
By the way, in my 2004 book, you will find me agonizing about this on page 526,
coming down on the side of 0.667, but not overwhelmingly convincingly. You
could argue that a branch length should be set 0 when the branch is not there,
and all the resulting values averaged, or you could argue that the average
should only be taken over those trees for which that branch is present.
One possible way to solve the problem is to take the consensus tree as if it
were a user-defined tree, use your whole data set, and infer branch lengths on
that tree. Daniel has already expressed his legitimate concerns in such a case
as to whether it takes (for example) trifurcations as if they were real rather
than an expression of our uncertainty.
J.F.
----
Joe Felsenstein j...@gs.washington.edu
Department of Genome Sciences and Department of Biology,
University of Washington, Box 355065, Seattle, WA 98195-5065 USA
(from 1 October 2012 to 10 December 2012 on sabbatical leave at)
Department of Statistics, University of California, Berkeley, 367 Evans Hall,
Berkeley, CA 94710
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