Thank you to everyone who commented on the first draft of the phylogeny. Based on all of this, I’ve updated the tree, incorporating most of what was recommended. As before, the rationale behind the topology is included at the end of the post. Note that I have also proposed a few taxa to cut from the end analysis. If you have any comments or suggestions, please feel free to post it in the comments!
Overall topology of Ornithischia:
From Butler et al. 2008, Figures 2, 3, and 4, with additional modifications from Butler et al. 2009, Figure S4
Contents of Thyreophora (Scutellosaurus, Emausaurus, Scelidosaurus, Stegosauria, Ankylosauria; with exception of Lesothosaurus) based on this phylogeny
Placement of Stenopelix within Pachycephalosauria based on this phylogeny (2009).
Position of Heterodontosauridae follows this reference (2008), as do positions of Stormbergia, Agilisaurus, and Hexinlusaurus.
The position of Othnielia (Othnielosaurus) follows Figures 2 (50% majority rule part), 3, and 4. (2008)
The position of Orodromeus follows Figures 3 and 4. (2008)
The position of Hypsilophodon relative to Jeholosaurus, Yandusaurus, Orodromeus, and Zephyrosaurus follows Figure 2 (50% majority rule part). (2008)
Jeholosaurus and Yandusaurus are arbitrarily placed as sister taxa. Their position basal to Hypsilophodon follows Fig. 2 (50% majority rule part), and Jeholosaurus‘s position more derived than Orodromeus follows Figure 4. (2008)
Bugenasaura is excluded from the tree following its synonymization with Thescelosaurus by Boyd et al. 2009.
The positioning of Thescelosaurus, Parksosaurus, and Gasparinisaura as more derived than Hypsilophodon and outside of the remaining ornithopods follows Figure 2 (50% majority rule part), Figure, and Figure 4. Thescelosaurus is arbitrarily placed as more derived than Parksosaurus+Gasparinisaura. (2008)
The positioning of Talenkauen follows that of Figure 2 (50% majority rule part). (2008)
The remainder of Ornithopoda is consistent across all versions of the cladogram, and this phylogeny is followed for the positions of Rhabdodontidae, Tenontosaurus, Dryosauridae, and Ankylopollexia.
The problematic taxa Zephyrosaurus, Echinodon, Lycorhinus, were excluded (and do not have postcrania, anyhow).
The placement of Lesothosaurus follows Butler et al. 2009, Figure S4.
The synonymy of Lesothosaurus and Stormbergia follows Knoll et al. 2010
The placement of Oryctodromeus and Orodromeus as sister taxa follows Varrichio et al. 2007, Figure 5
Topology of Rhabdodontidae:
Follows Weishampel et al. 2003
Topology of Stegosauridae:
From 50% Majority-Rule Consensus Tree of Mateus et al. 2009 (Miragaia paper, supplementary information, Figure S7B)
Topology of Ankylosauria:
From Vickaryous 2004, Figure 17.20 (strict consensus tree)
Pawpawsaurus, Sauropelta, and Silvisaurus were in a polytomy; their positions were assigned arbitrarily. This will not matter ultimately, because Pawpawsaurus and Silvisaurus do not have multiple postcranial elements known, and are thus excluded from the quantitative analysis. Saichania and Talarurus had polytomy arbitrarily resolved, too.
The placement of Cedarpelta as an ankylosaurid follows Lü et al. 2007 and an unpublished analysis by Nick Gardner (http://whyihatetheropods.blogspot.com/2008/12/cedarpelta-as-ankylosaurid.html). Ultimately, no postcrania for this taxon are included, so its placement is not terribly critical.
The topology of nodosaurids (including the placement of Hungarosaurus and Struthiosaurus) follows Ösi 2005, Figure 15. The monophyly of Edmontonia follows Vickaryous 2004, Figure 17.20
Dyoplosaurus is recognized as an ankylosaurid (Arbour 2009), and is arbitrarily placed as sister to Euoplocephalus.
Aletopelta is tentatively given as an ankylosaurid, based on text in Ford and Kirkland 2001.
Niobrarasaurus and Nodosaurus are arbitrarily given as sister taxa, because of their general similarity. Furthermore, Coombs (1990), in The Dinosauria, suggested that Nodosaurus is close to Sauropelta and Silvisaurus (p. 478, caption for Figure 22.14, “Nodosaurus probably fits just above or just below node 8.” [i.e., either between Sauropelta and Silvisaurus, or Silvisaurus and Panoplosaurus], so this opinion is followed here. Based on geography alone, they are given as sister to Sauropelta.
Polacanthus foxii is arbitrarily given the basal position within Nodosauridae occupied by Hylaeosaurus, for Coombs 1990, Fig. 22.14.
Zhejiangosaurus is completely arbitrarily placed as more derived than Polacanthus.
Because of great uncertainty in phylogenetic position, and because no phylogenetic analysis has adequately addressed the taxa, I recommend removing Aletopelta, Niobrarasaurus, Nodosaurus, Polacanthus, and Zhejiangosaurus from the analysis.
Topology of basal Iguanodontia:
Follows Norman 2004, figures 19.21 (strict consensus) and 19.22 (single most parsimonious tree following taxon deletion).
The position of Rhabdodontidae (Rhabdodon + Zalmoxes) does not follow this analysis, but instead follows Butler 2009
Tenontosaurus is treated as monophyletic, following Figure 19.22.
Jinzhousaurus and Nanyangosaurus are arbitrarily placed as sister taxa, more basal than Probactrosaurus+Ouranosaurus.
Eolambia+Altirhinus are placed between Ouranosaurus and Protohadros, following Figure 19.21 in Norman 2004.
Topology of hadrosaurids, hadrosauroids, and other derived iguanodontians:
Placement of Tethyshadros follows Dalla Vecchia 2009, Figure 8B (50% Majority Rule Tree). Mantellisaurus and Dollodon are given as sister taxa, following this analysis. Note that Claosaurus and Lophorothon are not included in this analysis, so the position of Tethyshadros relative to them has not been tested.
Rest of tree primarily follows Prieto-Marquez and Wagner 2009 (Figure 3).
Altirhinus is placed in clade with Eolambia and Protohadros after Fig. 19.21 of Norman 2004
Additional resolution within the Saurolophinae and Lambeosaurinae of Prieto-Marquez and Wagner was determined by re-running their tree using parsimony analysis, and then using the strict consensus tree. From this run, the placements of the clades Sahaliyania+Amurosaurus, Olorotitan+Parasaurolophus+Charonosaurus, and Corythosaurus+Lambeosaurus (all recovered in the published analysis) were determined. The placements of the remaining taxa were then placed from this, also. Koutalisaurus was not shown on their Figure 3, but was coded in the appendix, so its placement was derived from my run of the data.
Nipponosaurus is placed basal to Lambeosaurus+Corythosaurus+Hypacrosaurus+Olorotitan, after Evans and Reisz, 2007, Figure 9
Prosaurolophus is split into its species, assuming monophyly.
Gryposaurus resolved arbitrarily
Topology of Pachycephalosauridae:
Follows Schott et al. 2009 (Colepiocephale description in JVP 29(3)), Figure 8B. Stygimoloch is removed, following synonymization with Pachycephalosaurus by Horner et al. 2009. Colepiocephale is arbitrarily resolved as sister taxon to Stegoceras.
Topology of Ceratopsia:
For non-ceratopsids, follows Makovicky and Norell 2006, Figure 20A (strict consensus tree). Note that Xuanhuaceratops is equivalent to IVPP V12722
Placement of Cerasinops, and its relationships with Udanoceratops, Leptoceratops, Montanaceratops, and Prenoceratops, based on Figure 6 of Chinnery and Horner 2007
Graciliceratops placed as closer to Bagaceratops+Protoceratops than the least inclusive clade containing Leptoceratops and Asiaceratops. Graciliceratops‘ position relative to Microceratus is arbitrary (and ultimately doesn’t matter, because Microceratus has no limb material)
Placement of Yinlong and Micropachycephalosaurus after Figure S4 of Butler et al. supplementary information
Topology of Psittacosaurus:
Follows Figure 6 of You et al. 2008
Topology of Ceratopsidae:
Chasmosaurinae after Figure 23.8 of Sampson et al. 2004
Centrosaurinae after Figure 12 of Ryan 2007
Placement of Avaceratops based on unpublished analysis
Placement of Turanoceratops after Farke et al. 2009
Topology of Heterodontosauridae:
Follows Figure S4 of Butler et al. 2009 supplementary information.
Abrictosaurus and Tianyulong are placed arbitrarily.
Topology of basal dinosaurs, dinosauriforms, and dinosauromorphs
After Nesbitt et al. 2010, Figure S1
Topology of saurischians
After Nesbitt et al. 2009, Figure S7
Placement of Guaibasaurus:
Follows Irmis, personal communication
Placement of Panphagia:
Follows the original description
Placement of remainder of Sauropodomorpha:
Follows Yates et al. 2010, Figure S4 and S5. The position of Gyposaurus, which is not in S4 and S5, is based upon Figures S2 and S3.
Placement of Saurosuchus and Gracilisuchus
Follows Nesbitt 2009
Placement of Scleromochlus and Smilosuchus (as a member of “Phytosauridae”)
Ffollows Benton 1999
Placement of Hallopus victor and Protosuchus richardsoni:
As sister taxa based on personal communication from Randy Irmis. Placement of these taxa as sister to Dromicosuchus (on our restricted tree) from Sues et al. 2003 (description of Dromicosuchus), Figure 11.
Recommendations for Handling Data:
- Removed all specimens represented only by a single skeletal element
- Remove Barsboldia, because it is only represented by two metatarsals and a phalanx
- Synonymize Anatotitan copei with Edmontosaurus annectens, because the former is supposed to be just a crushed E. annectens, following Dinosauria II.
- Shantungosaurus giganteus is represented just by bonebed material, so it is removed from the analysis
- Mandschurosaurus amurensis large mount and small mount from Yang et al. 1986 are removed, because they are composite skeletons
- Altirhinus kurzanovi removed, because it includes only a humerus and one manual phalanx
- Remove Podekosaurus, due to phylogenetic uncertainty and missing data
- Remove Draconyx, because it is only MT I-III
- Remove Dracopelta, because it is only known from manual phalanges
- Sellosaurus gracilis is renamed to Plateosaurus gracilis, following Yates 2003
- Remove Lexovisaurus durobrovensis and Chialingosaurus kuani, following their recognition as nomina dubia by Maidment et al. 2008
- Remove Geranosaurus atavus, based on incompleteness of material (tibia and metatarsal II and pedal phalanx) and uncertainty of phylogenetic position
- ‘Gongbusaurus‘ wucaiwanensis and Xiaosaurus dashanpensis are excluded, following the lead of Butler et al. 2008, because the known material is not diagnostic or sufficient to allow phylogenetic placement
- following Nesbitt et al. 2010 (supplemental information), Pseudolagosuchus major and Lewisuchus are synonymized
- Machaeroprosopus gregorii is called Smilosuchus gregorii
- Although the pterosaurs Dimorphodon and Eudimorphodon are on the tree, they are so derived relative to the rest (for flight) that I recommend leaving them out.
- Aletopelta is an immature individual, based on generic description
Why is it that some of the “recommendations” are incorporated into the cladogram whereas others are not? Some of these are simple taxonomic updates, and they should be enacted, rather than being “recommendations”. Some issues:
1) please use Smilosuchus gregorii – Machaeroprosopus is a problematic genus (holotype is lost) and gregorii is not the type species anyway.
2) I think you misunderstood where I was saying to put Gracilisuchus based on Nesbitt (2009). It should be its own separate branch *basal* to the split between (Revueltosaurus+aetosaurs) and all other pseudosuchians (poposaurs on up). But it should be one branch above Smilosuchus gregorii.
3) Definitely use Plateosaurus gracilis. All sauropodomorph and basal dinosaur workers have been using this taxonomy since Yates (2003) proposed it, and it is borne out by the available phylogenetic analyses.
4) I forgot that Eoraptor was in the cladogram. In that case, Guaibasaurus should be on its own separate branch between Eoraptor and Tawa.
5) DO NOT synonymize Lesothosaurus and Stormbergia. I strongly agree with Richard Butler that these are separate taxa, and I have seen first-hand most of the relevant material. There is no obturator process in Lesothosaurus, despite what Knoll says. Synonymizing also makes it more difficult for you, because you have to pick which phylogenetic position to put it in, because no one has ever coded them combined in an analysis. Lesothosaurus should be its own separate branch between heterodontosaurids and Eocursor, whereas Stormbergia should be its own separate branch between Thyreophora and Agilisaurus.
Oops, forgot one more thing. You need to specify what you mean by Syntarsus. If you are talking about the African taxon, it should be listed as Coelophysis rhodesiensis. If it is the North American taxon, it should be referred to as “Syntarsus” kayentakatae (the quotes are necessary).
On a related note – I don’t know if the “PEFO Coelophysis” (has a UCMP catalog number) is in our dataset, but it is not assignable to Coelophysis bauri (see Nesbitt et al., 2007).
Ack – sorry, one more thing. Switch the positions of Saurosuchus and Batrachotomus. I just double checked this in Nesbitt 2009 (sorry I gave you the wrong info in the previous post).
I haven’t updated all of the taxonomic names yet, as you point out (as you’ll note, the “notes” on this post show the correct names for many of these, but the actual cladogram doesn’t). Yesterday was mostly a day for getting the tree topology updated. I’ll try and get a post up for some of those suggestions I didn’t incorporate – primarily it’s because alternate or updated interpretations are available.
I don’t have Nesbitt 2009 in hand, so I wasn’t able to cross-check with his trees (which I’ve done whenever possible). Thanks for the correction on my misunderstanding.
Good to have a second opinion on some of that other stuff, especially Lesothosaurus vs. Stormbergia.
Hi guys. Just browsing, and had a few comments on your topology:
1) As discussed by Butler & Sullivan (2009), Stenopelix is probably a marginocephalian but there is insufficient evidence to really support its placement within Pachycephalosauria or Ceratopsia. We considered it Marginocephalia incertae sedis.
2) Butler & Zhao (2009) redescribed Micropachycephalosaurus and concluded that it should be Cerapoda incertae sedis. It acts as a “wildcard” in analyses, and I would recommend you exclude it from your analyses. It is fragmentary in the extreme.
3) The sister-group relationship between Yandusaurus and Jeholosaurus is dubious, to say the least. Yandusaurus is extremely fragmentary, and it could go almost anywhere. You might be best excluding it.
Hi Richard – thanks for the input! The placement of Stenopelix is certainly tentative; for the types of quantitative analyses that we’re doing, uncertainty in its placement should have very little effect on the end conclusions (and we can certainly cut it out or look at the effects of alternative placements for stuff where it might matter). As for Micropachycephalosaurus, this taxon won’t be analyzed because it just doesn’t have enough measurements. On that same vein, a good percentage of the taxa on the figured cladogram will be excluded (I will post a trimmed version soon). Good point on Yandusaurus and Jeholosaurus; the former has a nice set of forelimb measurements, but we can look into tossing it for analyses where the position really, really matters.
Not in the dataset, so not a worry. . .
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For the purpose of the Project, I don’t think the exact details or placements of these taxa really matter unless they show proportions that are incredibly off the charts. =P
Still, those are some good points, Richard. =D
I’m glad that PrietoMarquez’s analysis is chosen for resolving the topology of Lambeosaurinae. I have expressed reservations numerous times on my blog about Evans and Reisz’s analysis. 😦