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RE: The cladogram from the supp. inf. of the *Anchiornis* paper

Keep in mind this is just the Epidexipteryx analysis with Anchiornis added, and 
the Epidexipteryx analysis was just Senter's (2007) analysis with Epidexipteryx 
added.  So basically everything is how it was in Senter's paper.  Anchiornis 
may very well be a troodontid, but note the matrix doesn't include Mahakala, 
Yixianosaurus, Shanag, Austroraptor, Sinusonasus or Jinfengopteryx.  The latter 
seems especially important to include, as it is another taxon which seems 
intermediate between birds and troodontids in morphology.  The original 
Anchiornis matrix from Xu et al. (2008) included Jinfengopteryx, Mahakala and 
Shanag at least, though it did not include scansoriopterygids, 
Protarchaeopteryx or basal therizinosaurs.  Also note that the original 
Anchiornis matrix included 48 characters from Xu's thesis that are useful for 
basal paravian phylogeny.  These are not present in the new Anchiornis matrix, 
though it does have 127 additional characters from all over Coelurosauria.  
These numbers are basically correct, as both matrices are modifications of the 
TWG matrix, but Senter did change and redefine several characters they share as 
well.  Thus the new assignment of Anchiornis is more complicated than just 
having cranial codings added, the analysis also lacks some relevent taxa and 
characters, while including some additional though probably less relevent taxa 
and characters.  My modified version of Senter's analysis already includes all 
of the data from both of these studies except I haven't added the new 
Anchiornis codings yet.  My site should be updated before the new year with 
those results (after the upcoming update with ornithuromorphs).
Also notice the new taxon in the supplementary info- Alvarezsauroidea.  
Unfortunately, it has an equivalent definition to previous definitions of 
Alvarezsauridae, except it uses the eponymous genus at last (the others used 
Shuvuuia).  To counter that compliment though, the authors use Deinonychus for 
Dromaeosauridae and Ornithomimus edmontonicus for Ornithomimosauria.  As an 
excellent example of why to use eponymous taxa in definitions, Ornithomimus 
edmontonicus isn't even in Ornithomimus anymore, nor should it be called 
edmontonicus.  Makovicky et al. (2004), Kobayashi et al. (2006) and Longrich 
(2008) have synonymized Dromiceiomimus with Ornithomimus edmontonicus, which 
seems correct. These authors have all used Ornithomimus edmontonicus for this 
species, but brevitertius was named seven years earlier, and given the species' 
somewhat distant relationship to Ornithomimus velox (they share a long 
metacarpal I and that's pretty much it; Anserimimus seems closer to 
Dromiceiomimus in any case), Dromiceiomimus brevitertius should be the 
combination which is used. Really how hard is it just to use the type species 
and genus in every definition?  If you worry Dromaeosaurus isn't as securely 
placed as Deinonychus, then the clade can't be called Dromaeosauridae anyway if 
Dromaeosaurus happens to fall outside it.

Mickey Mortimer
The Theropod Database- http://home.comcast.net/~eoraptor/Home.html

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> Date: Sun, 11 Oct 2009 21:36:53 +0200
> From: david.marjanovic@gmx.at
> To: dinosaur@usc.edu
> Subject: The cladogram from the supp. inf. of the *Anchiornis* paper
> The recent Nature paper that finds *A.* as a troodontid has 52 pages of
> supplementary information. For those who haven't downloaded it yet
> (unlike some other journals, Nature does not put its supp. inf. behind a
> paywall), I have retyped the cladogram (fig. S5) below.
> First in general terms, because it's so large (87 taxa, 363 characters;
> CI = 0.34):
> --+--*Allosaurus fragilis*
> `--+--*Sinraptor*
> `--+--Tyrannosauroidea
> `--+--Compsognathidae
> `--+--Ornithomimosauria
> `--+--*Ornitholestes*
> `--+--Segnosauria
> `--+--Alvarezsauridae
> `--+--Oviraptorosauria
> `--+--what they call Avialae
> `--+--Troodontidae
> `--Dromaeosauridae
> The position of *Sinraptor* probably means that the outgroup was
> erroneously restricted to *Allosaurus*. (If you don't designate an
> outgroup, PAUP* uses the first OTU in the list as the outgroup.)
> Then in detail:
> Tyrannosauroidea
> |--+--*Tanycolagreus*
> | `--*Coelurus*
> `--+--*Dilong*
> `--+--*Eotyrannus*
> `--+--*Tyrannosaurus*
> `--*Gorgosaurus*
> Jurassic tyrannosaurs all over the place, even though *Guanlong* and
> *Proceratosaurus* are not in the matrix.
> Compsognathidae
> |--*Huaxiagnathus*
> `--+--*Compsognathus*
> `--*Sinosauropteryx*
> Ornithomimosauria
> |--*Harpymimus*
> `--+--*Deinocheirus*
> `--+--*Shenzhousaurus*
> `--+--*Pelecanimimus*
> `--+--*Garudimimus*
> `--+--*Archaeornithomimus*
> `--+--*Gallimimus*
> `--+--*Struthiomimus*
> `--+--*Anserimimus*
> `--*Ornithomimus*
> Weird positions for *Pelecanimimus* and *Anserimimus*.
> Segnosauria
> |--*Falcarius*
> `--+--*Beipiaosaurus*
> `--+--*Alxasaurus*
> `--+--*Nothronychus*
> |--*Erliansaurus*
> |--*Nanshiungosaurus*
> `--+--*Neimongosaurus*
> `--+--*Segnosaurus*
> `--+--*Erlikosaurus*
> `--*Therizinosaurus*
> Alvarezsauridae
> |--*Alvarezsaurus*
> `--+--*Patagonykus*
> `--+--*Mononykus*
> `--*Shuvuuia*
> Perhaps a bit small, this taxon sample... but the biggest omission is
> not the author's fault. I'll send the SVP abstract next: the place where
> *Guanlong* and *Limusaurus* come from has now yielded an Oxfordian
> alvarezsaurid.
> Oviraptorosauria
> |--*Caenagnathus*
> |--*Avimimus*
> |--+--*Protarchaeopteryx*
> | `--*Incisivosaurus*
> `--+--*Caudipteryx*
> `--+--*Microvenator*
> `--+--*Oviraptor*
> `--+--+--+--*Khaan*
> | | `--*Conchoraptor*
> | `--+--*Ingenia*
> | `--*Heyuannia*
> `--+--+--*Rinchenia*
> | `--IGM 100/42
> `--+--*Citipati*
> `--+--*Elmisaurus*
> |--*Hagryphus*
> `--*Chirostenotes*
> *Caenagnathus* and *Chirostenotes* as far apart as at all possible! Wow.
> Nice confirmation for the position of *Oviraptor* as the sister-group to
> all other oviraptorids including "elmisaurids". Interesting confirmation
> for the tendency of dinosaurologists to resist any lumping of sister
> species into the same genus (*Incisivosaurus* is still there).
> Avialae
> |--+--*Epidendrosaurus*
> | `--*Epidexipteryx*
> `--+--+--*Archaeopteryx*
> | `--*Wellnhoferia*
> `--+--*Jeholornis*
> `--+--*Sapeornis*
> `--+--*Confuciusornis*
> `--+--*Protopteryx*
> `--*Yanornis*
> Avialae is defined on page 2 of the supp. inf. as "the most inclusive
> clade including Neornithes but not *Deinonychus antirrhopus* and
> *Troodon formosus*". Aves is defined right below as "the least inclusive
> clade including *Archaeopteryx* and Neornithes".
> I still don't believe in *Wellnhoferia*. :-)
> *Epidendrosaurus* probably includes *Scansoriopteryx*, and *Jeholornis*
> *Shenzhouraptor*.
> I wonder how much this topology can be trusted, because among the
> autapomorphies of Avialae that *Anchiornis* lacks is "reversed hallux".
> Ehem.
> Troodontidae
> |--*Sinovenator*
> `--+--*Anchiornis*
> `--+--*Mei*
> `--+--*Byronosaurus*
> `--+--*Sinornithoides*
> |--IGM 100/44
> `--+--*Troodon*
> `--+--*Saurornithoides junior*
> `--*S. mongoliensis*
> Note that, although it is the oldest troodontid in this matrix and has
> plesiomorphies like {widely spaced teeth except at the jaw tips},
> *Anchiornis* is not the basalmost one. There are two ghost lineages high
> up into the Early Cretaceous.
> Dromaeosauridae
> |--+--*Rahonavis*
> | `--+--*Unenlagia*
> | `--*Buitreraptor*
> `--+--+--*Bambiraptor*
> | `--+--*Sinornithosaurus*
> | `--+--*Microraptor*
> | `--NGM C91
> `--+--*Adasaurus*
> `--+--IGM 100/1015
> `--+--+--*Velociraptor*
> | `--*Saurornitholestes*
> `--+--*Deinonychus*
> `--+--*Atrociraptor*
> `--+--*Achillobator*
> `--+--*Dromaeosaurus*
> `--*Utahraptor*
> So *Deinonychus* is a dromaeosaurine, but *Adasaurus* is not... 
> But at least *Rahonavis* is here to stay, 4 to 6 nodes away from
> *Anchiornis*, *Archaeopteryx* and *Jeholornis*.