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I haven't had a chance to carefully read (much less digest) your post,
but will make a few comments just to get a discussion going.
The topology of your tree seems to indicate that you believe that the
"separate exit for cranial nerve V1" only evolved once. I know nothing
about this character, but just to play devil's advocate, I wonder how likely
it would be that this separate exit developed at least twice. Has anyone
discussed this in the literature?
The parts on feather evolution look very interesting to me, but not
enough time to digest it today. However, I would agree that your tree
topology is another example of how phylogenetic taxonomy can run into very
serious difficulties. It would certainly complicate what groups belong to a
cladistically-defined Aves (at least those anchored on Archaeopteryx). And
having a Eumaniraptora more inclusive than Maniraptora is also troubling (as
you pointed out), so if you maintain this tree topology, I definitely would
scrap the name Eumaniraptora. I am tempted to throw in some comments about
PhyloCode, but I will bite my tongue and end this post here.
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