The Cladogram, Version 2

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!

Phylogeny, Version 2

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