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RE: crocodile reversed or normal

>So, according to the PhyloCode, then if Ornithosuchus isn't in the 'clade'
>(node, stem, one of those I think) then there shouldn't be an Ornithosuchia,
>because it isn't in it?

Not quite.  IF Ornithosuchia includes Ornithosuchus, than the definition
must be based on Ornithosuchus - "Ornithosuchus and all things closer to it
than to Corvus," or whatever.  The definition applied by Gauthier was
"birds and all things closer to them than to crocs;" at that time,
Ornithosuchus was thought to be a very basal member of that group, but
based on more recent surveys (Sereno, Parrish, Gower, Juul, etc.), this may
not be the case.

I don't think crocodile reversed animals should be
>in the same group as crocodile normal ankles.

If croc-reversed and croc-normal animals share an exclusive common
ancestor, we have no choice - they belong in the same group whether we like
it or not.  Whether we choose to name this group is another matter.  This
does not mean that croc-reversed taxa don't form a cluster within this
group (or croc-normal animals, for that matter); only that if two taxa
share a common ancestor, they are part of a group.  Human desire is
irrelevant to this fact.

What about birds, do they have
>normal or reversed ankles? Can we tell?

As far as I know, dinosaur ankles (avian or otherwise) are neither reversed
nor normal from a croc's perspective - it's a simple mesotarsal hinge, and
there is no peg-and-socket motion between the astragalus and calcaneum.
The calcaneum and astragalus of theropods are tightly linked and, in mature
birds and coelophysoids, fused together; motion is between the conjoined
astragalus-calcaneum-tibia and conjoined distal tarsals-metatarsals.  In
crocs, motion is between the conjoined astragalus-tibia and conjoined
calcaneum-distal tarsals-metatarsals.

If anyone knows differently, please correct me (my expertise is based on a
very specific subset of dinosaurs).

>Also, is there a good reference or references that will have the citations
>for living crocodilia? All the people who named them?

Not sure what you mean.  "Steel's Bestiary" (Handbuch der
Palaoherpetologie, vol. 16) is a standard reference, though you should
disregard his taxonomy for fossils.