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John V Jackson wrote:

> "It is hard to deny the power of the theropod hypothesis, ..."
> People often cast the issue in the form of "theropod" vs "non-theropod", but
> there is more than one theropod theory, and most are mutually exclusive.  In
> some ways, all the wrong theories have more in common with each other than
> with the truth.

But ARE these "mutually exclusive?"  There are quantitative ways of
addressing that question.  The days when we could simply step back and
say "Wow - those trees are, like, really different and stuff" are long

It is generally thought that highly congruent results from disparate
sources suggest an approximation of truth.  But, we don't necessarily
expect different data sets to yield precisely identical signals -
nature, after all, is not clean, and one has to contend with issues of
taxon sampling, methodology, and problems that might be unique to a
given group of taxa, such as timing of divergence, rates of evolution,
or diversity.  So we are forced to ask ourselves "how different must two
trees be to really be different?," and an extensive literature has
emerged about it.  This started out from the perceived "molecules versus
morphology" debate, and it's become clear from these approaches that
molecules and morphology actually produce highly congruent results most
of the time.  

But they can be applied to different morphological data sets just as
easily, as I've suggested to one or more prominent theropod
systematists.  Sure, the trees are not identical - but there's a lot of
common ground, too.  They all agree on a basal ceratosaur-abelisaurid
assemblage, an allosauroid clade, and a close relationship among
coelurosaurian lineages.  And all agree that birds are derived
coelurosaurs - topology within Coelurosauria is labile, but given the
different taxon samplings and strategies for dealing with polymorphism
among different analyses, this isn't surprising.  

So before we declare these trees "mutually exclusive," shouldn't we
apply quantitative methods to these trees first?  We can apply these
even to trees that have not been through the peer-reviewed literature,
such as some sort of arrangement where birds are more basal members of
Theropoda.  Here are some references that describe different approaches
toward testing data set (and tree) congruence.  I think I've posted some
of these before, so I apologise for the duplication:

Templeton, A. 1983.  Phylogenetic inference from restriction
endonuclease cleavage site maps with particular reference to the
evolution of humans and the apes.  Evolution, 37:221-244.  (This was one
of the first papers on the subject - dense, but a must-read.  Our
beloved "Templeton Test" comes from here.)

Faith, D.P., 1991.  Cladistic permutation tests for monophyly and
nonmonophyly.  Systematic Zoology, 40:366-375.  (Lots of subsequent
papers on his methods, both for and against, most of which were in Syst.
Zool/Syst Biol.)

Farris, J.S., M. Kallersjo, A.G. Kluge, and C. Bult.  1994.  Testing
significance of congruence.  Cladistics, 10:315-319.  (This same group
of authors also had a short note in Syst. Zool. in 1995.)

Larson, A. 1994.  The comparison of morphological and molecular data in
phylogenetic systematics.  pp. 371-390 in B. Schierwater, B. Streit,
G.P. Wagner and R. DeSalle (ed.), Molecular Ecology and Evolution: 
Approaches and Applications, Birkhduser Verlag, Basel, Switzerland.

Poe, S. 1997.   Data set incongruence and the phylogeny of
crocodilians.  Systematic Biology, 45(4):393-414.  (I did similar things
with similar data sets in my subsequent Syst. Biol. croc paper.)

Cannatella, D.C., D.M. Hillis, P.T. Chippendale, L. Weigt, A.S. Rand,
and M.J. Rand.  1998.  Phylogeny of frogs of the Physalaemus pustulosus
species group, with an examination of data incongruence.  Systematic
Biology, 47:311-335.

Schulte, J.A., J.R. Macey, A. Larson, and T.J. Papenfuss.  1998.
Molecular tests of phylogenetic taxonomies:  A general procedure and
example using four subfamilies of the lizard family Iguanidae. 
Molecular Phylogenetics and Evolution, 10:367-376.

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