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Re: Benton et al.'s Supertree (long)
Michael Habib wrote-
> The "weighting" I mentioned is not the weighting of characters, it is
> the weighting of sources. For example, it is common practice to take
> all of the related trees from one paper, combine them into a small
> tree, and then put them in the supertree together, thus giving the
> group a single unit instead of overweighting that study.
This would indeed be better than separately including multiple trees from
the same source. There are not many examples of a source having multiple
trees in Benton et al. though, Sereno 1999 being an obvious exception. But
as Sereno divided his analyzed groups well, I don't think much phylogenetic
information is repeated between trees.
> Yes, the equal weighting has its weaknesses. However, in most cases,
> it is not clear whether one tree is better than another. A more
> common situation would be a 70 character tree versus a 65 character
> tree. Yes, one has more characters than the other, but are you really
> going to say the 70 character has to be better because it has 5 more
> traits in the matrix? Things also get messy when you try to work out
> what a "good" trait is. These types of decisions and debates
> certainly are important in phylogenetics, and equal weighting is one
> way to approach it.
Deciding whether a 65 character tree or a 70 character tree is better
(assuming they had different sets of characters and the same taxa) is indeed
difficult. And in that case, equal weighting would be fine. Looking at
Benton et al.'s references though, we have cases like Holtz's 2000 analysis,
which included just about every useful character used in published theropod
analyses before it (plus a lot more taxa). Thus, earlier analyses like
Gauthier (1986), Russell and Dong (1993), Currie (1995), Novas (1997),
Forster et al. (1998), Harris (1998) and Makovicky and Sues (1998) are
effectively "worse" than Holtz's 2000 analysis. In addition, there are many
cladograms (I count 19 just skimming through the list) not even based on
character lists. If all the examined trees were based on actual
quantitative phylogenetic analyses and used different characters, I would
support Benton et al.'s results more.
> Ah, but different morphological characters are used by different
> analyses. I agree that Benton's tree is weaker than others to some
> extent in that it lacks molecular and behavioral data (nothing he can
> do about that, of course). However, there are still different types
> of analysis going into the tree in the sense that different aspects of
> morphology are used in different studies.
The problem is different analyses on the same group almost always have a
majority of characters in common. I would say at least 80% of the
characters in any given analysis are taken directly from previous analyses.
There is a range of course, as in coelurosaur analyses
for instance, Xu et al. (2002) probably have a percentage closer to 60,
while Xu et al. (1999) have 96%. If you had different papers analyzing
different areas of the body (like Makovicky's 1995 unpublished coelurosaur
phylogeny based on vertebral anatomy), I could see the potential. As it is,
I don't think Benton et al.'s supertree utilizes this possible advantage.