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I'm bothered (perhaps through ignorance) about birds and theropods, and
perhaps someone on the list can put me right on a few things.
As I understand it, sorting out the relationships of modern birds based on
morphology alone is tricky, and the advent of firstly molecular data, and
more recently DNA analysis has led to some extensive revision of their
relationships. The fundamental problem is that many features in birds,
especially in their skeletal morphology, are strongly convergent.
There is a lot of traffic here dealing with dinosaur/bird relationships,
especially in recent weeks following the publication of the latest
Microraptor. It seems to be accepted without question that the various
cladograms produced exploring these relationships are true phylogenies.
If phylogenies based on the morphological analysis of the skeletons of
modern birds are so unreliable, surely the same must be true of cladistic
analyses of theropod dinosaurs, especially if they are so closely related to
modern birds that some contributors to this site make no distinction? And if
this is the case, don't we need to treat these cladograms as rather
tentative hypotheses rather than solid phylogenies?