Archive

Archive for June, 2011

Some Things to Do, and a Progress Update

June 27, 2011 5 comments

We’ve had some good discussion and suggestions for ways to tweak the phylogeny, so keep them coming! At the bottom of this post, I have a new and improved version of the phylogeny.

In the meanwhile, we’re still trying to pull together a few last measurements for the analysis. We have gotten a few new data submissions, and these all require verification entries. There are also a few papers that can be combed for measurements. So, there is still an opportunity to make a contribution.

ODP Phylogeny Draft, 27 June 2011

ODP Phylogeny Draft, 27 June 2011

Notes on Phylogeny

Updates on non-dinosaurian archosaurs from Nesbitt 2011 analysis:

Scleromochlus – position retained from old tree (not included in Nesbitt phylogeny)
Gracilisuchus and aetosaurs resolved arbitrarily at “base” of Pseudosuchia (position of clades not resolved in Nesbitt’s analysis)
Hallopus placed as per previous version of cladogram

Other Updates:
Polacanthus is arbitrarily placed as sister to Gastonia+Tatankacephalus (i.e., made as an ankylosaurid rather than a nodosaurid; will need discrete reference to justify this decision).
Position of Tatankacephalus follows Parsons & Parsons 2009

Categories: Progress Reports

An updated (updated) phylogeny

June 24, 2011 4 comments

As mentioned in the previous post, a few papers with new or updated phylogenies for various ornithischians have appeared in the last year. Thus, I spent a few hours going through them and updating the tree topology as well as adding taxa. The phylogeny is given below, with notes on what I did at the end of the post. Note that many of the arbitrarily-resolved nodes aren’t that critical for some aspects of the analysis; they often include fragmentary taxa (sometimes only known from cranial material). We may wish to revise some of the resolutions in order to reduce ghost lineages.

I have not yet incorporated Sterling Nesbitt’s most recent phylogeny of Archosauria, because I wasn’t able to successfully download the file. It’s top of my list once I do.

If you have suggestions to revise or improve the phylogeny, please mention them in the comments.

ODP Phylogeny Draft, 24 June 2011

ODP Phylogeny Draft, 24 June 2011

Notes

General Ornithischia

General phylogeny of Ornithischia updated following 50 percent majority-rule consensus tree in Butler et al. 2011, as modified by Makovicky et al. 2011 (the latter with modifications of codings for Thescelosaurus and addition of Haya)
Position of Thescelosaurus updated following Makovicky et al. 2011, modified from Butler et al. 2011
Position of Talenkauen follows Butler et al. 2011

Updated the position of Yinlong, Micropachycephalosaurus, Stenopelix. Sister taxon relationship of Yinlong+Stenopelix follows Butler et al. 2011; relationships of Micropachycephalosaurus+Chaoyangsaurus+(Stenopelix+Yinlong)+(rest of ceratopsians) resolved arbitrarily.

Topology within Heterodontosauridae after Pol et al. 2011 and after Butler et al. 2011. Echinodon was placed as a basal heterodontosaurid heterodontosaurid (following Butler et al. 2011). The clade of Abrictosaurus+NHM A100+Heterodontosaurus+Lycorhinus was resolved arbitrarily.

Bugenasaurus and Thescelosaurus synonymized following recent work by Boyd et al. (2009).

Ceratopsia

Topology of Chasmosaurinae follows Sampson et al. 2010; placement of Ojoceratops and Eotriceratops resolved arbitrarily. Triceratops, Diceratops, and Torosaurus spp. are considered separate, following Farke 2011.

Topology of Ceratopsia follows Makovicky 2010; inclusion of Micropachycephalosaurus and Stenopelix follows Butler et al. 2011. Placement of Zhuchengceratops inexpectus follows Xu et al. 2010, with Zhuchengceratops and Udanoceratops arbitrarily placed as sister taxa (based on biogeography).

Topology of Psittacosauridae follows Sereno 2010, figure 2.23E. P. gobiensis is placed arbitrarily as sister to P. sibiricus. Psittacosaurus ordosensis is synonymized with P. sinensis, following a tentative suggestion from this paper. Psittacosaurus xinjiangensis is placed following the polytomy in Averianov et al. 2006, with its resolution arbitrary.

Pachycephalosauria

Topology within Pachycephalosauria follows Longrich et al. 2010. In recognition of the probably synonymy of Pachycephalosaurus, Stygimoloch, and Dracorex, the latter two animals were removed from the matrix and the matrix was rerun in PAUP otherwise following the specifications of Longrich et al. 60 equally parsimonious trees resulted; in order to more completely resolve relationships within the clade, the 50% majority rule tree was used for the topology within Pachycephalosauria. ?Sphaerotholus brevis was arbitrarily placed at the base of the clade including all other Sphaerotholus species, and Texacephale was arbitrarily placed at the base of the clade including Stegoceras+Gravitholus+Colepiocephale.

Ankylosauria

Topology within Ankylosauria updated following Burns et al. 2011, Figure 8 (50% majority rule consensus tree).

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. Cedarpelta and Gobisaurus placed as sister taxa following this same analysis.

Dyoplosaurus is recognized as a unique taxon (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.

The polytomy between Tianzhenosaurus, Nodocephalosaurus, and Ankylosaurus was resolved arbitrarily.

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.

Placement of Crichtonsaurus was semi-arbitrary; the tree of Lu et al. with this taxon cannot be easily reconciled with the Burns et al. phylogeny. Noting that both phylogenies recover Pinacosaurus “above” Gobisaurus; Crichtonosaurus was placed between the two. Crichtonsaurus‘s placement “above” Minmi was arbitrary, based on the later geological occurrence of Crichtonsaurus.

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.

The topology of nodosaurids (including the placement of Hungarosaurus and Struthiosaurus) follows Ösi 2005, Figure 15. The monophyly of Edmontonia follows Burns et al. 2011.

Basal iguanodonts

Topology of basal iguanodonts follows McDonald 2011, Figures 1 and 2.

Genus of “Camptosaurusaphanoecetes changed to Uteodon, per McDonald 2011

Muttaburrasaurus placed in Rhabdodontidae following McDonald et al. 2010. Its resolution at the base of the clade is arbitrary, but based on the fact that it occurs much earlier in the fossil record than other rhabdodontids.

Monophyly of Zallovosaurus+Dryosaurus+Dysalotosaurus+Elrhazosaurus+Kangnasaurus+Valdosaurus follows McDonald et al. 2010. Resolution within that clade is arbitrary. Dysalotosaurus is made its own genus, following recent work.

Dollodon bampingi” and M. atherfieldensis are synonymized following McDonald 2010.

Resolution of Cumnoria and Uteodon is arbitrary relative to their polytomy.

Resolution of Cedrorestes, Dakotadon, Lanzhousaurus, and Iguanacolossus relative to their polytomy is arbitrary. Lanzhousaurus as being part of less inclusive clade follows Figure 2 of McDonald.

Position of Tethyshadros, Nanyangosaurus, and Tanius adjusted in light of McDonald figures 1 and 2. Position of Telmatosaurus as part of clade excluding Lophorothon also follows this analysis.

Levnesovia and Nanyangosaurus arbitrarily made sister taxa; also made part of clade excluding Tethyshadros, following Figure 2 of McDonald. Probactrosaurus and Eolambia were arbitrarily made sister taxa to resolve a polytomy.

Altirhinus and Equijubus were arbitrarily made sister taxa, and arbitrarily placed as part of clade excluding Jinzhousaurus+Penelopognathus in order to resolve polytomy.

Iguanodon placed outside of more derived iguanodonts+Mantellisaurus. Position of Ouranosaurus is arbitrarily resolved.

Lambeosaurinae

Topology of Lambeosaurinae modified following Evans 2010 (Hypacrosaurus paper), Figure 16A (parsimony trees, strict consensus).. Pararhabdodon+Koutalisaurus+Tsintaosaurus retained from “old” Prieto-Marquez phylogeny, because the first two taxa are not on the Evans phylogeny. Nipponosaurus was deleted, because it is an obvious juvenile and many characters cannot be scored effectively. Amurosaurus+Sahaliyania retained from previous version of phylogeny, because latter taxon is not on Evans phylogeny. Polytomy of Corythosaurus and Olorotitan resolved following Bayesian tree (Fig. 16B). Lambeosaurus laticaudatus and Velafrons are arbitrarily resolved. Velafrons placed as closer to corythosaurins follows the original Gates et al. 2007 description of the taxon (Velafrons is not in the Evans phylogeny).

Categories: Progress Reports

Filling in the Blanks

June 22, 2011 7 comments

During the extended gestation/hibernation/dormancy of the ODP, a few new papers with relevant data have slipped into circulation, some with ornithischians preserving limb bones, as well as new or updated phylogenetic analyses. So, if you’re looking for a final chance at data entry, here are a few possibilities:

Open Access

Currie PJ, Badamgarav D, Koppelhus EB, Sissons R, Vickaryous. Hands, feet and behaviour in Pinacosaurus (Dinosauria: Ankylosauridae). Acta Palaeontologica Polonica in press. doi:10.4202/app.2010.0055 [link]

McDonald AT, Kirkland JI, DeBlieux DD, Madsen SK, Cavin J, et al. (2010) New basal iguanodonts from the Cedar Mountain Formation of Utah and the evolution of thumb-spiked dinosaurs. PLoS ONE 5(11): e14075. doi:10.1371/journal.pone.0014075 [link]

Closed Access

Bell, P. R. and Evans, D. C., 2010. Revision of the status of Saurolophus (Hadrosauridae) from California, USA. Canadian Journal of Earth Sciences, 47, 1417-1426.

Butler RJ, Liyong J, Jun C, Godefroit P (2011) The postcranial osteology and phylogenetic position of the small ornithischian dinosaur Changchunsaurus parvus from the Quantou Formation (Cretaceous: Aptian–Cenomanian) of Jilin Province, north-eastern China. Palaeontology 54:667-683. [link]

Cuthbertson, R. S. and Holmes, R. B., 2010. The first complete description of the holotype of Brachylophosaurus canadensis Sternberg, 1953 (Dinosauria: Hadrosauridae) with comments on intraspecific variation. Zoological Journal of the Linnean Society, 159, 373-397.

Ezcurra, M. D., 2010. A new early dinosaur (Saurischia: Sauropodomorpha) from the Late Triassic of Argentina: a reassessment of dinosaur origin and phylogeny. Journal of Systematic Palaeontology, 8, 371-425.

Langer, M. C., Bittencourt, J. S. and Schultz, C. L., 2011. A reassessment of the basal dinosaur Guaibasaurus candelariensis, from the Late Triassic Caturrita Formation of south Brazil. Earth and Environmental Science Transactions of the Royal Society of Edinburgh, 101, 301-332.

Lee, Yuong-Nam; Ryan, Michael J.; and Kobayashi, Yoshitsugo (2011). “The first ceratopsian dinosaur from South Korea”. Naturwissenschaften 98 (1): 39–49.

McDonald, A. T., Barrett, P. M. and Chapman, S. D., 2010. A new basal iguanodont (Dinosauria: Ornithischia) from the Wealden (Lower Cretaceous) of England. Zootaxa, 2569, 1-43.

Makovicky, P. J., Kilbourne, B. M., Sadleir, R. W. and Norell, M. A., 2011. A new basal ornithopod (Dinosauria, Ornithischia) from the Late Cretaceous of Mongolia. Journal of Vertebrate Paleontology, 31, 626-640.

Martinez, R. N., Sereno, P. C., Alcober, O. A., Colombi, C. E., Renne, P. R., Montanez, I. P. and Currie, B. S., 2011. A basal dinosaur from the dawn of the dinosaur era in southwestern Pangaea. Science, 331, 206-210.

Pol, D.; Rauhut, O.W.M.; and Becerra, M. (2011). “A Middle Jurassic heterodontosaurid dinosaur from Patagonia and the evolution of heterodontosaurids”. Naturwissenschaften 98 (5): 369–379. [phylogeny only – no useful postcrania] [link to free PDF]

Prieto-Marquez A. Cranial and appendicular ontogeny of Bactrosaurus johnsoni, a hadrosauroid dinosaur from the Late Cretaceous of northern China. Palaeontology (in press). DOI: 10.1111/j.1475-4983.2011.01053.x [link]

Prieto-Marquez, A. and Salinas, G. C., 2010. A re-evaluation of Secernosaurus koerneri and Kritosaurus australis (Dinosauria, Hadrosauridae) from the Late Cretaceous of Argentina. Journal of Vertebrate Paleontology, 30, 813-837. [no measurements; phylogeny only]

Wang X, Pan R, Butler RJ, Barrett PM. 2011 (for 2010). The postcranial skeleton of the iguanodontian ornithopod Jinzhousaurus yangi from the Lower Cretaceous Yixian Formation of western Liaoning, China. Earth and Environmental Science Transactions of the Royal Society of Edinburgh 101: 135-159.

Note: Most of these citations were gathered from Graeme Lloyd’s excellent compendium of dinosaur phylogenies. I’ve tracked down the links in a few cases, but otherwise you should be able to find them using a quick search on-line. Not all of the papers necessarily have usable data; the list here is a quick-and-dirty overview. I may have missed some important new contributions, too. Please feel free to flag them in the comments, and I’ll add them to the list.

Wondering what to do in order to contribute data, or just need a refresher? Check out this how-to guide.

Categories: To-Do List

Disparity Notebook

June 21, 2011 1 comment

Local disparity guru and paleontologist Randy Irmis (that’s Randall B. Irmis, Ph.D., if you go by his web page) recently posted a nice long list of recommended readings on the issue of disparity – what it is, how to calculate it, etc. As a reminder, disparity is the measure of how different species are from each other in terms of shape, size, or other discrete features (not the same as diversity, which just counts how many different species exist – once again, see Randy’s eloquent post on the topics). It just so happens that documenting disparity in ornithischian dinosaurs is at the top of our list for the ODP. Hence, I decided to buckle down and read through an important recent paper on the topic (one that Randy happened to highlight in his list, too).

In the interest of getting this post out in a timely manner, I’m mainly going to be posting my unpolished notes, taken a few weeks ago in the comfort of my bed (nothing like a little light bedtime reading). I’ve made a few adjustments here and there, but otherwise you can consider this a peek into my stream of consciousness while reading the literature. Because I was mainly interested in how the work could be applied to the ODP, I didn’t really bother with summarizing the specific analyses done by the authors. Thus, without further preface:

The Citation:
Brusatte, S. L., Montanari, S., Yi, H.-Y, and Norell, M. A. 2011. Phylogenetic corrections for morphological disparity analysis: new methodology and case studies. Paleobiology 37: 1-22. [unfortunately, not openly available as a PDF] [link to abstract]

The Main Gist:
The fossil record just isn’t complete – and that’s particularly true for many of the early members of important ornithischian clades (like thyreophorans and marginocephalians). However, it’d be nice to interpolate some of these missing data in order to produce a more complete picture of the changes in a clade’s disparity over time and in morphospace (the multi-dimensional plot of the shape of an animal’s bones, in this case). Brusatte and colleagues, building on the work of many other authors, have formalized a method to fill in some of these gaps by producing a plausible reconstruction of missing ancestors.

Scutellosaurus

An early thyreophoran, Scelidosaurus; image by Nobu Tamura, used under a Creative Commons License

My Notes
[as presented here, it’s a mix of to-do tasks for the ODP, a cookbook for the analysis, and how Brusatte et al.’s method will be applied; caveat emptor]

The questions: What is the morphospace occupied by ornithischian dinosaurs over time? How does the morphospace change? How does the morphospace occupied by specific clades differ?

The tasks:

  • Assemble data matrix (taxon/measurement matrix)
  • Reconstruct ancestoral measurements following Brusatte et al. 2011
  • Calculate Euclidean distance matrix (“quantifies the pairwise dissimilarity between taxa”) – this presumably calculates dissimilarity for each taxon/measurement pair
  • Apply principal coordinates analysis (PCoA) to each analysis (better handles missing data than does PCA [principal components analysis]). Can be done in R.
  • PCoA produces scores for each taxon along n=#taxa axes. Can be done in R.
  • Examine slope of scree plot to determine where break occurs; only examine these “interesting” axes. I think this scree plot can be done in R.
  • Calculate disparity indices from the PCoAs, using different bins (categories). Can be done in R. Categories might include: 1) clade; 2) time; 3) locomotor category; 4) combination of clade/locomotor category.
  • Indices include: sum of range of values along axis 1, 2, … n (i.e., range 1+range2+range3. . .); product of range of values along axis 1, 2, n (range 1 * range 2 * range 3. . .) normalized to the nth root; and same sum and products for variance in each bin.
  • Rinse and repeat using ancestral values as calculated following Brusatte et al. 2011.

Ideal results:

  • Disparity indices that can be compared statistically (using bootstrap values) for various categories. E.g., a disparity value for Ceratopsia, Ornithopoda, Thyreophora, etc. disparity  value for quadrupeds vs. bipeds.
  • Graphs showing point clouds for various clades along various axes (e.g., PC1 vs. PC2)
  • Graphs showing trends for disparity over time, with different groups. E.g., trend line showing disparity in ornithischians as a whole, along with trend line showing disparity in thyreophorans, ceratopsians, etc. Potential sample size issues here, particularly for clades with few members or few members early in their history
  • Narrative text and / or table showing what factors are loaded on which axes
Follow

Get every new post delivered to your Inbox.