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Re: Benton et al.'s Supertree (long)
As someone working on supertree construction and analysis
as we speak, I have to disagree to some extent with your
comments. I agree that supertrees are not ideal, but they
offer coverage across large groups not possible in a
reasonable time-frame (or at all) using 'traditional'
Keep in mind that using multiple trees that include the
same data implies, in part, that multiple researchers agree
with that tree topology. That is, this implies some kind
of consensus between those researchers, and this is
essentially the point to begin with. That being said,
there are still some concerns in repeating data as it were,
and this can be compensated for if one wishes. Regardless,
it is likely that this repetition does not affect the
resulting topology. Weighting schemes of that type often
produce the same supertree (or nearly so).
Second, part of the point in putting together a supertree
is that it is not always known what is a "good" tree or
"good" phylogenetic information. They are supposed to
include all opinions, not just the most recent papers. Yes,
including information from taxonomies or older phylogenies
may seem a bit strange, but this information could be
useful. I, for one, am not willing to say that I always
know what trees are good and which are not; that is one
area where supertrees come in handy.
Lastly, supertrees can, in fact, give valuable information.
They give wider coverage (in terms of how much of the given
group is represented) than most trees; this is required for
some types of analysis. They show where disagreement is
rampant, as well as where agreement in the literature is
strong. Finally, supertrees give the result of using
several types of characters/phylogenetic information.
Since supertrees usually include a unique assortment of
taxa (ie. more than other trees) and present a new
combination of phylogenetic information (ie. include
trees based on many different methods or characters), I
would argue that they present new information on
This is not to say that supertrees do not have flaws. They
certainly have some problems, as does virtually any
phylogenetic analysis. However, there are cases where they
seem to be the best choice. (I, for example, am working
with a supertree because the questions that interest me
require a fully dated, species-level tree of an entire
Order. A supertree is the most reasonable way for me to do
Sorry for the long ramble,
On Sun, 19 May 2002 20:23:33 -0700 Mickey Mortimer
> I reiterate my dislike for supertrees. They are inherently flawed by the
> inclusion of multiple cladograms that use much of the same data. In fact,
> Benton et al. used several cladograms specifically based on previously
> published data, with an extra taxon added (eg. Charig and Milner's 1997
> cladogram which was basically Holtz's 1994 analysis with Baryonyx added).
> This particular supertree also used cladograms that weren't even based on a
> phylogenetic analysis (such as all those in The Dinosauria). Supertrees
> constructed this way are not even accurate consensuses of current opinion,
> as both recent and outdated trees are used (eg. Holtz 1994 and Holtz 2000).
> They certainly can't give us new information as to phylogenetic