Re: Benton et al.'s Supertree (long)

[Michael Bruce Habib <mbh3q@guppy.mail.virginia.edu>]

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' 
methods.

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 
phylogenetic relationships.

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 
this).

Sorry for the long ramble,
--Mike Habib 

On Sun, 19 May 2002 20:23:33 -0700 Mickey Mortimer 
<Mickey_Mortimer111@msn.com> wrote:

> 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
> relationships.