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Me vs. Makovicky et al.- comparison and consensus

Jaime Headden wrote-

Given the number of "improbable" portions of this topology, the only part of
the tree I might even not question so far is the (carnosaur (tyrannosaur
(ornithomime + maniraptor))) generality and perhaps the bird topologies, but
that is due to a [I profess] unfamiliarity with the distinct morphologies of
these birds. Thus this entire tree is rife with improbabilities that outweighs
any of the "improbabilities" in the TWG analyses, Rauhut's topology in both
thesis and published, and Holtz's analyses.

Is Jaime right? Is my tree more improbable than either the TWG's numerous permutations, Rauhut (2003) or Holtz (2000, 2004)? Well, it's only fair to compare the taxa included in both analyses when comparing their results.

When you only compare the taxa shared between my analysis and Makovicky et al.'s, the only differences are in my analysis-
1. Compsognathus is closer to birds than to Sinosauropteryx + Huaxiagnathus.
2. Ornithomimosaurs are closer to birds, moreso than compsognathids and Ornitholestes.
3. Alvarezsaurids and enigmosaurs switch places relative to birds.
4. Incisivosaurus is closer to caenagnathoids than Caudipteryx is.
5. Avimimus is outside Caenagnathoidea instead of being a caenagnathid.
6. Microvenator is an oviraptorid instead of a caenagnathid.
7. Citipati is a caenagnathid instead of an oviraptorid.
8. Patagonykus and Alvarezsaurus switch places.
9. Dromaeosaurs are sister to birds instead of to troodontids.
10. Archaeopteryx is a troodontid instead of a bird.
11. Byronosaurus is basal to IGM 100/44.
12. Mei is a basal dromaeosaur instead of a basal troodontid.
13. Sinornithosaurus is closer to dromaeosaurids than to Microraptor.
14. Unenlagia is a dromaeosaurid instead of outside the Microraptor + Dromaeosaurus clade.
15. Buitreraptor + Rahonavis are sister to Archaeopteryx instead of the Microraptor + Dromaeosaurus clade.

1. Compsognathidae was supported by only three characters in the TWG matrix, two of which are in my analysis (mesial serrations absent on teeth, poorly developed semilunate carpal; fan-shaped dorsal neural spines not included). Compsognathus was nested within the family based on an additional character (large olecranon process), also not in my analysis. Needless to say, I don't find their evidence for placing Yixian taxa in Compsognathidae particularily strong.

2. Rauhut (2003) and Holtz (2004) both agree with my analysis on this point.

3. This varies within runs of the TWG matrix, and Holtz (2004) agrees with my analysis.

4. This was supported by three characters in the TWG matrix, all of which are in mine (coronoid prominance on surangular; toothless maxilla; crenulated dentigerous margin of premaxilla). Similarly, Senter et al. (2004) support it with three characters, two of which are in mine (toothless dentary; manual phalanx II-1/II-2 ratio), and the other which is flawed (frontal vs. parietal length, since either bone can change length independantly). I've suggested before the lack of a dorsal splenial process, extremely convex mandibular articulation, and other characters may place Incisivosaurus closer to caenagnathoids than Caudipteryx is. Especially since toothlessness is converged on so much in different maniraptoriformes. I wouldn't commit to either alternative yet.

5. I know you agree with my analysis here, as do Maryanska et al. (2002) and Osmolska et al. (2004).

6. This is generally a trichotomy, though Maryanska et al. (2002) agrees with my position. You don't think either the TWG nor I are correct, and place it outside Caenagnathoidea.

7. When Lu (2004) included more oviraptorosaur taxa in the TWG matrix, he got this same result in 93% of his mpt's. Probably a result of neither the TWG matrix nor mine (yet) being made to determine caenagnathoid topology.

8. Though universally found when tested in published analyses, this was based on one character in the TWG matrix (tibiotarsus fused). Notably, Shuvuuia must reverse its tibio-tarsal fusion (though it does have astragalo-calcaneal fusion). Even matrices made to examine alvarezsaurid phylogeny don't support this very strongly, as Chiappe's analyses (1996, et al., 1998; 2002) always support it based on only two characters- better developed procoely in sacrum, posterior sacrum with better developed keels on ventral midline. Though I have 'posterior sacral articulation convex' and 'posterior sacrum with ventral midline keel' in my analysis, neither is quantified yet to incorporate the less developed morphologies of Alvarezsaurus. Novas (1996) added supracetabular crest and fourth trochanter present to support this node. However, the fourth trochanter is absent in Parvicursor and only incipient in Shuvuuia. Also, the supracetabular crest is described and illustrated as present in Alvarezsaurus by the TWG and Bonaparte (1991), so this is controversial and I've coded it as unknown. Being a hindlimb character, fourth trochanter morphology has yet to be included in my analysis. These latter two characters are somewhat dependant on topology though, as ornithomimosaurs have supracetabular crests (as do Microvenator and basal therizinosaurs) and fourth trochanters (as do Avimimus and basal therizinosaurs), so their absence could be apomorphies of Alvarezsaurus. Plus, there are characters agreeing with my topology (e.g. coracoid bent at level of tubercle in Patagonykus, but not Alvarezsaurus or Mononykus), and Patagonykus lived earlier than Alvarezsaurus and is the largest alvarezsaurid, so some data make more sense that way. While I still favor the TWG arrangement, I don't think mine is out of the question.

9. Although recent analyses tend to support deinonychosaurian troodontids, I could see any of the three possible topologies here being true. Possible synapomorphies for dromaeosaurs + birds excluding archaeopterygids and troodontids include the medially displaced coracoid foramen (reversed in dromaeosaurids), enlarged anterior cervical epipophyses, and ossified uncinates (also in oviraptorosaurs).

10. This is pretty unique, but it's only a difference of three nodes to get from basal troodontid to basal avialan in my tree, or two nodes in Makovicky et al.'s tree (because it doesn't have Jinfengopteryx). None of the characters supporting this are particularily convincing (e.g. squamosal recess; posteriorly placed quadrate foramen; lateral dentary foramina within groove; nasolacrimal duct passes lateral to lacrimal; basisphenoid recess absent; ophthalmic branch of trigeminal nerve completely separated from main branch before exiting braincase; metotic foramen reduced to a slit or closed), partially because the latter four also occur in birds (at least in ornithurines sensu Chiappe).

11. This is only supported by one character in the TWG matrix - the enlarged otosphenoidal crest. Norell et al. (2000) added two more (basisphenoid recess absent; large axial epipophyses). All are in my analysis. Norell et al. code Byronosaurus incorrectly for both, hence their absence in diagnosis for the TWG analyses. I don't see it being very hard to overturn one character. One obvious character supporting my topology is the serrated teeth of IGM 100/44 (since Senter et al. confirmed Sinovenator lacks them).

12. This has only been tested by the TWG matrix besides mine. They support Mei as a troodontid based on eight characters, seven of which I include (the other is pedal). Normally my analysis agrees with theirs, but several of the characters are also found in basal birds and/or basal dromaeosaurs, so may actually diagnose Paraves and/or Deinonychosauria and be reversed in other clades. For instance- birds besides Archaeopteryx have dorsoventrally flattened internarial bars; birds and Sinornithosaurus lack squamosal - quadratojugal contact; Sinornithosaurus and Buitreraptor have lateral dentary grooves; Graciliraptor has dorsally grooved distal caudals; Archaeopteryx, Rahonavis and Buitreraptor have short dorsal transverse processes. The remaining characters are a robust fourth metatarsal and small tightly packed anterior dentary teeth. While I'm not throwing Mei out of Troodontidae, it isn't as definitively placed there as one might think.

13. This is sometimes found in the TWG results (e.g. Hwang et al., 2002; Makovicky et al., 2003), based on the lack of basal tooth constriction in Sinornithosaurus and dromaeosaurids. Additionally, Sinornithosaurus has mesial tooth serrations, as in dromaeosaurids. The Buitreraptor analysis found different results because three pelvic characters were added, none of which are in my analysis. Senter et al. (2004) supported Sinornithosaurus as a microraptorian based on twelve characters (only four of which are in my analysis so far), though several are seen in ornithurines (sensu Gauthier) too, so are synapomorphies of the dromaeosaur + bird clade in my latest topology. I'm inclined to agree Sinornithosaurus is a microraptorian (as I haven't included most of its suggested synapomorphies), though I don't find the alternative unlikely.

14. This has been in every TWG result until Makovicky et al's latest modification. Dromaeosaurid characters of Unenlagia include the anteriorly concave preacetabular process (also seen in Shenzhouraptor, which is a dromaeosaur in my tree), and dorsal neural spine tables (also seen in ornithurines, but not basal troodontids, Buitreraptor, Archaeopteryx or Rahonavis; so this fits my topology). It's placed by Rahonavis and Buitreraptor in the TWG matrix due to four characters, only one of which is in mine (supracetabular crest). Achillobator has three of these (dorsally concave postacetabular process; elongate obturator process; mesopuby), yet is a dromaeosaurid in Makovicky et al.'s tree and mine (it's miscoded for the first two in Makovicky et al.'s matrix). Unenlagia is sister to Rahonavis in Makovicky et al.'s tree based on five characters, three of which are in mine. Three of these (all dorsals pleurocoelous; six sacrals; lateral cuppedicus ridge extending posteriorly) are found in some dromaeosaurids too. The other two (elongate preacetabular process; large proximodorsal ischial process) and the supracetabular crest support Makovicky et al.'s hypothesis, but the support for a dromaeosaurid Unenlagia isn't much worse. I'm willing to go either way. One might argue placing Achillobator in Unenlagiinae would decrease the reasons for placing Unenlagia in Dromaeosauridae, but then you'd have to explain the dromaeosaurid characters of Achillobator (large serrated teeth; short cervicals; highly elongate distal caudal prezygapophyses and chevrons; etc.).

15. You may have noticed that Archaeopteryx has six of the unenlagiine and Rahonavis + Unenlagia characters suggested by Makovicky et al. (all dorsals pleurocoelous; short dorsal transverse processes; lateral cuppedicus ridge extending posteriorly; supracetabular crest; mesopuby; elongate preacetabular process), and is polymorphic for three (dorsally concave postacetabular process; large proximodorsal ischial process; elongate obturator process). The only one it lacks is six sacral vertebrae. So it's not surprising Rahonavis and Buitreraptor come out next to Archaeopteryx in my tree. Of the seven characters placing them by dromaeosaurs in Makovicky et al.'s tree, my analysis has five. The sinusoidal supratemporal fossa edge is only known in Buitreraptor among unenlagiines, and is also present in the basal Ukhaa Tolgod troodontid and Troodon, though absent in Mei and Saurornithoides. So it has a somewhat ambiguous distribution among deinonychosaurs, though Archaeopteryx does lack it. I don't feel comfortable coding any non-dromaeosaur paravian for paraquadrate foramen size, including Mei and Archaeopteryx (the only two coded for it by TWG). In Mei, the dorsal quadratojugal process is missing, while Archaeopteryx never has the two bones visible posteriorly. Buitreraptor does have unconstricted tooth roots, but Microraptor doesn't. If Microraptor is outside Sinornithosaurus + dromaeosaurids as in my tree, this would be an ambiguous synapomorphy of Buitreraptor + Microraptoria + Dromaeosauridae at best. Distally placed cervical epipophyses are actually present in pygostylians, Archaeopteryx and most troodontids (Mei, Sinornithoides, Byronosaurus). Of these, Makovicky et al. only coded Mei for the character. So this doesn't support placing Buitreraptor with dromaeosaurids. Stalked dorsal parapophyses are found in Buitreraptor and dromaeosaurs, but also in Confuciusornis and Mei (and further down, alvarezsaurids). They are thus possibly diagnostic for Paraves or Eumaniraptora instead, and lost in Archaeopteryx and derived troodontids. The posteriorly bifurcated chevrons that supposedly join Buitreraptor, Rahonavis and dromaeosaurids (Velociraptor, Graciliraptor, Microraptor) are also found in the troodontids Jinfengopteryx and Sinornithoides, as well as Shenzhouraptor. They are absent in Achillobator, Saurornitholestes, Mei, Sinovenator, derived troodontids and Archaeopteryx. So they could support a basal troodontid or basal ornithurine (sensu Gauthier) position as well. Finally, the ginglymoid metatarsal II of Rahonavis, Neuquenraptor and Buitreraptor is seen not only in dromaeosaurids, but also in scansoriopterygids, the basal troodontid IGM 100/44 and Confuciusornis (the latter two miscoded by Makovicky et al.). So it works in my topology where Rahonavis and Buitreraptor are in a clade with scansoriopterygids.

While writing this post, I've noticed several characters miscoded in Makovicky et al.'s (2004) matrix, most of which I've commented on above (under 12, 14 and 15). After correcting those codings and rerunning it, the resulting tree is different from the published one. The Paraves portion is-

|  |--Achillobator
|  |--Utahraptor
|  |--Dromaeosaurus
|  |--Saurornitholestes
|  |--IGM 100/1015
|  `--+--Velociraptor
|     `--Deinonychus
     |  |--Unenlagia+Neuquenraptor
     |  `--+--Rahonavis
     |     `--+--Archaeopteryx
     |        `--Confuciusornis
        |  `--Sinovenator
                 `--+--Saurornithoides mongoliensis
                    `--Saurornithoides junior

IGM 100/44 has an unstable position within the troodont+bird clade, but is never inside Archaeopteryx+Confuciusornis, Mei+Sinovenator or Sinornithoides+derived troodontids.

- You'll notice troodontids are now sister to birds instead of to dromaeosaurs. The third possibility, not seen in the usual TWG matrix or my latest run. I noted under #9 that I consider this plausible, and this is proof it's not to hard to recover.
- Byronosaurus and Sinornithoides switched places, which is unsurprising since this varies between TWG runs.
- Microraptorians aren't necessarily monophyletic. I noted under #13 that this wasn't unlikely.
- Microraptorians are sister to troodontids + birds, which is quite an odd result. This is based on- posteriorly placed maxillary fenestra; squamosal-quadratojugal contact absent; carotid processes; lobate preacetabular process; proximodorsal ischial process; obturator process placed at distal end of ischium; subarctometatarsus; posterior or lateral metatarsal IV flange; elongated obturator process. The only relevent coding I changed was Sinornithosaurus' lack of squamosal-quadratojugal contact (Xu and Wu, 2001).
- There's a clade consisting of Buitreraptor, Unenlagia, Rahonavis, Archaeopteryx and Confuciusornis. This is sort of a blend between Makovicky et al.'s results and mine. It's very similar to mine, except Unenlagia gets moved from Dromaeosauridae (agreeing with Makovicky et al.) and Confuciusornis (and presumably other birds) gets moved from being sister to dromaeosaurs. It recovers the Unenlagiinae of Makovicky, except it includes his two birds, Archaeopteryx (agreeing with my analysis) and Confuciusornis. It's not surprising considering what I wrote above under #14 and #15. Note there is no Unenlagiinae exclusive of birds though, as Unenlagia and Buitreraptor are in a polytomy with a Rahonavis + birds clade. The latter are united by - reduced pubic apron; metatarsal III not reduced proximally; posterior or lateral metatarsal IV flange absent; mid-dorsal ischial process; elongate ulna. None of these are in my analysis yet. In my analysis, Rahonavis is sister to Buitreraptor exclusive of Archaeopteryx based on enlarged dorsal hypapophyses, and three distal chevron characters. So I'd favor combining Rahonavis and Archaeopteryx to the exclusion of Buitreraptor, as in the modified Makovicky matrix. Unenlagia shares an enlarged proximodorsal ischial process with Rahonavis + birds; Buitreraptor shares an elongate humerus with them; Unenlagia and Buitreraptor share a lobate postacetabular process to the exclusion of Rahonavis + birds. So assuming Unenlagia really is part of this clade, how exactly it relates to Buitreraptor and Rahonavis + birds seems unresolved.
Are birds a member of this clade though, or are they somewhere else (like sister to dromaeosaurs, or sister to dromaeosaurs + troodontids)? The TWG matrix can't test this very well, as it only includes Confuciusornis among ornithurines sensu Gauthier. Of the 'unenlagiine' synapomorphies, pygostylians lack dorsal pleurocoels, short dorsal transverse processes (ornithuromorphs at least), a supracetabular crest, mesopuby, dorsally concave postacetabular processes, and elongate obturator processes. They are polymorphic for elongate cuppedicus fossae, and they have elongate preacetabular processes, large proximodorsal ischial processes, and more than five sacrals. They do have four of the five Rahonavis + Archaeopteryx found by the TWG though. Although twelve characters are found to place Confuciusornis sister to Archaeopteryx in Makovicky et al.'s matrix, Archaeopteryx lacks two (reversed hallux; proximodorsal lips on manual unguals absent), all birds except archaeopterygids and confuciusornithids lack a fused scapulocoracoid, other 'unenlagiines' may have two (unfused parietals; splenial not exposed broadly laterally), and other basal paravians have three (asymmetrical remiges; reduced number of caudals; reduced number of caudals with transverse processes). Four may be good (biceps scar on deltopectoral crest; distal tarsals fused to metatarsus; metatarsus fused; sickle claw absent), though I've examined none of them, and only the Wellnhoferia specimen has fused metatarsals. Opposing these, there are some characters suggesting Rahonavis is closer to birds than Archaeopteryx is - trochanteric crest; fibula doesn't reach tarsus; m. iliofibularis tubercle faces posteriorly; proximal tarsals fused together. At the moment, I accept birds as part of the Archaeopteryx + Rahonavis clade, but the evidence for placing them closer to either taxon seems about even. This assessment could use a lot more work though.

At the moment, I find the following most likely, but I'm just as iffy on basal paravian topology as ever.

|  `--Dromaeosauridae
  |  `--other Troodontidae

Additional studies would be needed to judge the position of Shenzhouraptor et al. and Jinfengopteryx.

Mickey Mortimer