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Re: So here it is... my paper, open for discussion (very long; try to view it in maximum window breadth)

Congratulations on getting your paper published!  The aquatic hypothesis is very interesting....
David Marjanovic wrote-
> Archaeopterygidae is to mean A. and Unenlagia ?= Megaraptor ?= Unquillosaurus (possible
> synonymies after the Dinosauricon); analyses by HP Mickey Mortimer put U., at least, in the > Dromaeosaurinae.
Unquillosaurus is not synonymous with Unenlagia.  Although they both have vertical pubes with similarily angled feet, there are several important differences.  Unenlagia lacks a pubic notch, has a straighter anterior edge and thinner distal shaft, and has no anterior component to its pubic foot.  The differences are even more obvious in anterior view.  Unquillosaurus' is much more concave laterally and has an apomorphic proximomedial sulcus.  Its pubes expand mediolaterally distally into a bulbous foot, whereas Unenlagia has the narrow distal pubes typical of dromaeosaurids.  Also keep in mind Unquillosaurus is from the Los Blanquitos Formation, while Unenlagia is from the Rio Neuquen Formation.  Megaraptor cannot be compared to either Unenlagia or Unquillosaurus, although it was larger than both and is from the same formation as Unenlagia.  As for putting Unenlagia in the same family as Archaeopteryx, I'd like to know what characters they share that other deinonychosaurs lack.
> Sometime it is mentioned that the latter three taxa (troodontids and tyrannosaurs: Currie,
> 1995, oviraptorosaurs: Sues, 1997 contra Norell et al. 2000) have a separate exit for the
> cranial nerve V1, which normally exits the braincase through a large foramen together with V2 > and V3. Dromaeosaurus (Currie, 1995) and Archaeopteryx (Elzanowski & Wellnhofer, 1996)
> exhibit the primitive condition.
The derived state is also present in Allosaurus and Carpenter and Currie (2000) code oviraptorids as having the primitive condition.  This shows the character distribution is more complex than presented.
> Arctometatarsalians and oviraptorosaurs also share pneumatised quadrates and articulars not > occuring in Archaeopteryx (Elzanowski & Wellnhofer, 1996) and Dromaeosaurus (Currie,
> 1995).
Caudipteryx lacks a pneumatic quadrate, as do Shuvuuia and Confuciusornis.  This character would thus be more parsimoniously interpreted at convergently evolving in arctometatarsalians, oviraptorids and ornithurines.  Pneumatic articulars are much rarer among theropods.  They are present in Tyrannosaurus, Erlikosaurus and Bagaraatan.  They are certainly absent in Chirostenotes, Deinonychus and Gobipteryx, and probably in Archaeopteryx.  I also see no evidence of a foramen in Confuciusornis.  I'm not sure where segnosaurs or Bagaraatan go in your phylogeny, but as Chirostenotes and Gobipteryx lack this feature (and I don't know the condition in Caudipteryx and oviraptorids), the assertion oviraptorosaurs and pygostylians can be united with it is weakened.
> Andrzej Elzanowski is sometimes referred to as having discovered that some features of the
> oviraptorosaur palate are more birdlike than that of Archaeopteryx. <Has been published in
> detail in the meantime, I still haven't found the paper.>
See http://www.cmnh.org/fun/dinosaur-archive/2000Dec/msg00487.html for my opinions on that papers conclusions.
> Osmólska & Maryanska (1997) note that oviraptorid quadrates are double-headed, i. e. they
> have an additional contact to the braincase, and they are much more pneumatised than in
> arctometatarsalians (Osmólska & Maryanska, 1997).
Oviraptorids have double-headed quadrates, but the basal oviraptorosaur Caudipteryx lacks this character.  This makes it equally parsimonious for oviraptorids to have convergently evolved the character.
> Oviraptorosaurs (Sues, 1997) (including Caudipteryx <and Protarchaeopteryx?>) also share
> with alvarezsaurids (Novas, 1997) rather short tails that are not stiffened distally, a condition
> seen in no other theropods. <...>
True.  Caudipteryx has an especially short tail, only slightly longer than that of Confuciusornis.  Yandangornis and segnosaurs also have relatively short tails.
> Pneumatic features also fit this picture: Archaeopteryx is no more extensively pneumatised
> than dromaeosaurids, i. e. cervical and dorsal vertebrae as well as their ribs are pneumatised > (Britt et al., 1998). In oviraptorosaurs (Currie, 1995) and alvarezsaurids (Novas, 1997),
> pneumatic foramina (or depressions) occur as far back as the middle of the tail! (In recent
> turkeys (Britt et al., 1998), the sacral and free caudal vertebrae are pneumatised, in ostriches > (Britt et al., 1998) the caudals are not.)
There is a difference between the lateral depressions found in the dorsals (confuciusornithids, enantiornithines) and caudals (Patagonykus, enantiornithines) of some maniraptorans and the pleurocoels (pneumatic foramina) found in the sacrals and caudals of caenagnathids and oviraptorids.  Patagonykus is the only alvarezsaurid known to have such depressions, they are absent in Alvarezsaurus and Parvicursor.  No alvarezsaurid has sacral or caudal pleurocoels.  On the other hand, the dromaeosaurid Achillobator has pleurocoel-like foramina on its proximal caudals, while Variraptor and Ornithodesmus have pleurocoels in the first two sacral vertebrae.  Also, the basal oviraptorosaurs Caudipteryx and Microvenator lack caudal pleurocoels.  This again suggests parallel development to any birds which have such excavations.
> With the description of Nomingia (Keesey, 2000, /genera/nomingia.html), the pygostyle has
> joined the list of maniraptoran (see cladogram) synapomorphies (no alvarezsaurid tail end is
> known, Caudipteryx and Protarchaeopteryx could have pygostyles <just discussed>, judging
> from photographs (Ackerman, 1998), the resolution of which is too coarse to be certain)."
While Nomingia does have a pygostyle, Caudipteryx and oviraptorids do not.  Another reference (Zhou et al., 2000) can be added to the list of experts who have verified this fact (Zhou and Wang 2000, Ji et al. 1998).  Oviraptorosaurs are sort of like the basal diapsids/archosauromorphs of the birds-aren't-dinosaurs group.  Put them together (short tail and reversed hallux of Caudipteryx; pygostyle of Nomingia; elongate radius of Microvenator; caudal pneumaticity of caenagnathoids; fused jaw elements and absent coronoid of caenagnathids; double-headed quadrate and triradiate palatine of oviraptorids) and you get a perfect pygostylian sister group, but look at them separately and the picture's not so clear.
> A single bird synapomorphy, according to Elzanowski & Wellnhofer (1996), has been left to
> Archaeopteryx: the triradiate palatines. I think that it is most parsimonious to explain this
> feature by convergence <ô surprise>, though I have no idea why this should have occurred."
Well, even though my analysis currently supports Archaeopteryx as a basal deinonychosaur, I'll play devil's advocate.  Besides the reversed hallux, Archaeopteryx shares the following characters with pygostylians not seen in dromaeosaurids, oviraptorosaurs or arctometatarsalians.
- reduced olfactory lobes
- less than nine caudal vertebrae with transverse processes
- very short anterior chevrons, none taller than anteroposteriorly long
- manual digit I doesn't extend past manual phalanx II-1
- phalanges on third manual digit reduced (III-1 and III-2 sutured, not jointed; possibly ancestral to the pygostylian condition of having two non-ungual phalanges on digit III)
- proximodorsal ischial process
- tibia subequal in width and length in proximal view
As you can see, the evidence is not as weak as you claim.  While I still find it is most parsimonious to interpret these as reversed in dromaeosaurids, there's still a very good case for non-avian dromaeosaurids.
> Birds down to Alvarezsauridae have prokinesis (Chiappe, Norell & Clark, 1998);
> confuciusornithids have akinetic skulls (Hou et al., 1999), which is probably secondary
> because the jugals don’t have ascending processes.
While the akinetic skulls of confuciusornithids could very well be secondary, they do possess ascending processes on their jugals (Chiappe et al., 1999).
> '[a]nd in spite of the fact that dromaeosaurids are often proclaimed to be the most birdlike of
> the theropods <...>, they lack many of the theropod-avian synapomorphies found in other
> theropod families, and have too many specialisations to be plausible avian ancestors'
Unlike those conservative oviraptorosaurs ;-)
>         First, protofeathers evolved as a protein sink: Bird ancestors, early tetanurans,
> theropods, dinosaurs or ornithodirans in general are commonly thought to have been
> insectivorous. Insects, which radiated in the early Mesozoic, contain much more fat and
> protein than vertebrates and thus are a good reason for becoming and staying endothermic.
> (Let’s simplify the case and assume that all ornithodirans were endothermic – Paul & Leahy
> [1994] have shown excellently that even the largest ones were forced to be.) But insect
> protein contains more sulphur than small endotherms can use or excrete. So these animals
> deposited the sulphur-rich amino acids in their scales, which are made of keratin, a protein
> containing up to 3 % sulphur. The scales were enlarged and split during growth, used for
> insulation and display, and sometimes they were shed to get rid of the sulphur. This is a
> wonderful explanation for why birds moult (Reichholf 1997 <and others, which may be cited in > the published version>). Sinosauropteryx, Sinornithosaurus and, if you kindly forget its diet,
> Beipiaosaurus can be considered examples for such animals.
While I can easily picture non-dinosaurian dinosauriformes (Marasuchus, Lagerpeton) and smaller maniraptorans (Microraptor, mononykines, Archaeopteryx, enantiornithines) being at least partially insectivorous, basal theropods, sauropodomorphs and ornithischians were too large to have depended on insects as their main food source.  Also, new evidence suggests feathers may not have developed from scales, while the structure of Sinosauropteryx's integumentary filaments suggest feathers evolved by adding branching filaments, not splitting scales.
Your aquatic hypothesis is quite interesting.  Seems defendable, but on the other hand difficult to test.
>         "Arctometatarsalians did the same, but they changed to long-distance pursuing, as
> indicated by their feet. They were already present at the same time as dromaeosaurids –
> there are the troodontid Koparion, some ornithomimid teeth <and that Kimmeridgian finger
> from Great Britain -- thanks to the list I mention it in the published version>
Jurassic ornithomimid teeth?  What might the reference for this be?
>       Still true. :-( Is it likely that a mobile scapula-coracoid joint can evolve twice (or be a
> misinterpretation)? In this case Rahonavis could belong to Archaeopterygiformes... MORE
The mobile scapulocoracoid joint of Rahonavis is certainly present.  What's odd however is the absence of this character in confuciusornithids.  This could easily support a convergence or loss.
>         Neotheropoda or earlier: furcula? (not ossified – like the sternum – in e. g.
> compsognathids, attached to the scapula by ligaments and therefore frequently falling off
> before burial, which explains its rare preservation [Makovicky & Currie, 1998]; the ventral ends > of the clavicles of Sinornithoides and probably Carnotaurus are broken – perhaps the middle
> part of a furcula has broken away [Mortimer, 2000 <in the List archives, can't find it now; it is > properly cited in the published version>])
I'm actually referenced in a bibliography?  Thanks.  Adam Yates should get the real credit though, as I heard the idea from him:
I never even mentioned the Carnotaurus furcula.  That came from Thomas Holtz: http://www.cmnh.org/fun/dinosaur-archive/2000Apr/msg00635.html .
Mickey Mortimer