Probabilities on Phylogenetic Trees

Tom DiBenedetto tdib at UMICH.EDU
Sun Sep 14 18:17:32 CDT 1997

On Thu, 11 Sep 1997 07:50:49 -0700, Curtis Clark wrote:

>. What you want instead is an estimate of which part of the data is
>more reliable.
>That's what bootstrap, jackknife, decay indices, and the like are supposed
>to do. For reasons that are not yet clear to me, there are detractors of
>all these methods, but it seems to me that people who make these methods
>are on the right track.

How does running an analysis on a variety of randomly chosen
schemes (which is all bootstrapping amounts to) give you any sense of

the reliability of the data?

>I've recently and somewhat tongue-in-cheek suggested that nodes in a
>cladogram without at least 50% bootstrap support should be collapsed into
>polytomies, since in a sense they don't really exist.

Why tongue in cheek? A very good, and oft made suggestion. When
first discussed bootstrapping he couched the discussion in terms
which made
reference to 95% confidence limits. When I tweaked him a bit about
this (on the
systematics or evo biology newsgroups), he did admit that he felt
that bootstrap
values below 80 should be regarded with great suspicion (paraphrase).
I responded that his comment seemed to pull the rug out from under
most of the
"accomplishments" of statistical phylogenetics, he did not respond
(I didnt take it personally....)

Tom DiBenedetto       
Fish Division                                   tdib at
University of Michigan Museum of Zoology

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