Archive for the ‘Progress Reports’ Category

Some (finalish) results!

May 17, 2013 7 comments

Matt and I have been meeting weekly for the past three weeks to have ODP work days–just to crank through analyses, etc. Mostly, it’s a matter of sitting down and forcing each other to do stuff. Matt’s posting soon, but in the meantime I thought I’d throw out some “final” results. These are regressions on phylogenetically independent contrasts (PICs), with analyses considering the whole sample, unequivocal quadrupeds (following Maidment and Barrett’s assignments), and unequivocal bipeds (following Maidment and Barrett, again).

A few quick notes (all of which are going into the main article text at some point)…PICs were calculated in the PDAP package of Mesquite. Limb lengths were log-transformed prior to analyses (which helped to move things towards normality a little bit, but not entirely). Branch lengths were initially set to divergence times, but we found that these violated the assumptions of PICs, and thus some transforms were used (to be outlined in the manuscript as well as a future post, once we’ve pulled that text together).

Below, I’m including the preliminary results text for this part of the analysis, the associated table, and table caption. Enjoy! And feel free to throw in some comments if you have any.

Intra- and interlimb scaling
Analyses including all taxa as well as analyses considering only unequivocal quadrupeds showed similar scaling patterns. Forelimb length scaled with strong positive allometry relative to hind limb length, whereas the distal hind limb elements (tibia and metatarsal III) collectively scaled with strong negative allometry relative to femur length. The distal forelimb (radius and metacarpal III) scaled isometrically relative to the humerus; however, we note that the lower confidence interval for the entire sample only barely excludes positive allometry. We thus speculate that a larger sample may ultimately demonstrate positive allometry.
When considering only unequivocal bipeds, none of the slopes differed from isometry. However, we note that this subset of taxa also had some of the smallest sample sizes considered here, and a larger sample might uncover allometric scaling patterns.

Table. Results of RMA (reduced major axis) regressions of PICs (phylognetically-independent contrasts) for logged limb segment lengths in ornithischian dinosaurs. In the “Allometry” column, “0” indicates a slope indistinguishable from isometry, “+” indicates a slope consistent with positive allometry, and “-” indicates a slope consistent with negative allometry. The numbers in parentheses in the “Slope” indicate the 95 percent confidence interval for the slope.










Distal Forelimb


1.139 (0.996–1.301)





Distal Hind Limb


0.812 (0.715–0.921)







1.301 (1.198–1.413)



Quadruped Only


Distal Forelimb


1.138 (0.929–1.393)



Quadruped Only


Distal Hind Limb


0.742 (0.581–0.949)



Quadruped Only




1.237 (1.027–1.489)



Biped only


Distal Forelimb


0.829 (0.588–1.17)



Biped only


Distal Hind Limb


0.903 (0.739–1.105)



Biped only




1.009 (0.543–1.876)



Regressions for PICs including the entire sample. The blue line indicates isometry.

Regressions for PICs including the entire sample. The blue line indicates isometry.




Presentation Draft – Early Results

October 12, 2012 4 comments

On Saturday, I’ll be giving a short presentation about (very) preliminary results from the ODP, for the 1st Annual Southwest Regional Joint DVM&DCB (Division of Vertebrate Morphology and Division of Comparative Biology) meeting of SICB (Society of Integrative and Comparative Biology). This conference is a one-day event held on the campus of Cal State San Bernardino, and targets functional morphologists and their kin (including paleontologists).

The presentation is entitled “Morphological disparity, locomotion and limb proportions in ornithischian dinosaurs,” and it’s set up as a 5 minute talk. One of the cool things about DVM is the option of a 5 minute format – perfect for work that is in its nascent stages or “crazy” ideas that you just want to throw out there. Given the very preliminary nature of the analysis (and the fact that I’m co-author on three posters at the Society of Vertebrate Paleontology meetings next week), I jumped at the chance for this format. Plus, the talk was a good opportunity to kick my butt in gear and do some real analysis.

I don’t have a lot of time at this second to detail every aspect of the methods, but here is a sketch:

  • Data were trimmed down to one entry per taxon, choosing the largest and most complete specimen possible. In a handful of cases, missing data were interpolated via regression (to estimate tibia length from fibula length) or other specimens of the same taxon.
  • Taxa were binned into five time categories, each spanning roughly 34 million years. Any finer bins, and there just weren’t enough taxa.
  • I ran principal coordinates analyses on the data, for forelimb, hindlimb, and all limbs together. Within each temporal bin from the results, I calculated the sum of variance and nth root of variance. This gives a measure of morphological disparity in each bin – high variance, high disparity. The analyses were run with the raw data, as well as data that were standardized within each taxon by the geometric mean. This was to attempt to remove the effects of body size.
  • I plotted the data in each bin. In order to compare the raw results vs. geometric mean results, I normalized the data to the largest value in each category.
  • A few notes of caution – I did not perform any statistical tests on the data (bootstrapping, confidence intervals, etc.). So, the results should not be considered to have particular statistical significance at any level. Also, no attempt was made to accommodate for sampling effects or phylogeny. Caveat emptor.
  • In any case, there are some cool results. Looking at hind limbs, there is a big jump in disparity after the first 60 million years (or so) of evolution – not unexpected, given the explosion of forms in the mid-Jurassic. What was more interesting was the fact that the disparity stayed constant when looking at raw values, but when values were corrected for size using a geometric mean, there was a big drop in disparity during the last 60 million years or so. On first consideration, this suggests to me that body size is driving some of the disparity values. Body size stayed big after the Middle Jurassic, but overall morphological disparity (in what those large body forms looked like) decreased. I wonder if some of this is due to the extinction of stegosaurs (with their bizarro limbs) at the end of the Jurassic / early Cretaceous. Forelimb disparity (when correcting with a geometric mean) by contrast takes a big jump in the late Cretaceous – I wonder if this is due to hadrosaurs, with their conventional hind limbs but really, really weird forelimbs. Food for thought.

Tonight I put together a first draft of the slides for my presentation. Supporting data are here, and a PDF of the slides is here. I’m going to do some more editing tomorrow, so any suggestions are welcome. Keep in mind that the slides are pretty rough right now, so forgive any ugliness there. Also, remember that I’m dealing with a 5 minute format, so there’s only so much more I can add (and I think I’ll have to trim some stuff – we’ll see how much time is in the mix after I run through it once out loud).

The final version, after presentation on Saturday, will be archived at figshare.

Is there a finish line? (and how to get there)

September 12, 2012 14 comments

Yes. . .I hope there is a finish line. As with many things started with the best of intentions, the ODP (and its heads – particularly me) has gotten waylaid. That said, it would be a shame to let the numerous contributions and hours of volunteer effort go to waste. So, Matt and Mike and I have been having some serious conversations about finishing this once and for all! So, here’s the deal.

  • I want to finish this. You want to finish this. It just needs to be finished.
  • Analysis and write-up are the main things that need to be done. It requires a bit of concentrated effort (primarily on my part).
  • The way I see it, the most productive product of the analysis would be to examine limb disparity in ornithischian dinosaurs through time. This would entail binning the dinos and running the analysis. Riffing off of recent work by numerous authors, this would involve running a PCO (principal coordinates analysis) on the measurements for each bin. This can then be converted to a metric that shows overall morphological disparity. The primary question this asks is, “How did ornithischians diversify in their limb bone proportions through time?” Was it something that happened right away? Or something that happened later? A related question concerns how to accommodate phylogeny. As with many recent papers, the main thing we’re interested in here are ghost lineages. Given the incomplete nature of the fossil record, ancestral state reconstruction of some sort is probably needed. The problem, however, is that these methods are often. . .vague. . .at best. Perhaps maximum likelihood reconstruction in the relevant R packages? (see this link for an example ) Or perhaps skip trying to reconstruct stuff altogether and take the results with appropriate caution?
  • I envision three analyses: all limbs together (for all animals that are appropriately complete), forelimbs, and hind limbs. This would help account for animals that preserve only forelimbs, or only hind limbs.

Tasks to do:


  • Realistically, upcoming major events in the real world mean that I (Andy) have to get this thing off my plate by December 1 at latest. This is also best for Matt and Mike, too (and everyone, right?). This means a finished, submitted manuscript.
  • If the December 1 thing doesn’t happen, realistically we need a way to “cut the data loose.” Although we’ve had a general statement on the blog that we would rather others hold off on using our data until the paper is published, it isn’t fair to sit on the data for years at a time. So, this means that we would step aside from right of first refusal for publication with the data. This means that others are welcome to use the data without explicit permission (although the ODP should still be cited as the data source). The data would be archived at figshare, which provides a stable link, long-term archiving, and DOI for future linking.

The last of what we need

February 3, 2012 1 comment

Well, this is awkward. Once again we’ve let things lie fallow for far, far too long. We all (= Andy, Mike, and I) feel rotten about it, but more importantly, we now have a finite list of stuff that we need to finish the data haul, and then we can finally do the analyses, write the paper, and generally make good on everything we set out to do.

So rather than waste your time with more blather, here’s the tail end of the wish list:

References That Have Data That Need to be Entered a First Time [note - some may not have measurements, but should at least be checked; I don't have easy access to all papers]

Bell, PR, Evans, DC (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.

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.

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

References For Data In Need of Cross-Checking

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.

Godefroit P, Pereda Suberbiola X, Li H, Dong Z-M (1999) A new species of the ankylosaurid dinosaur Pinacosaurus from the Late Cretaceous of Inner Mongolia (P.R. China). Bulletin de l’Institut Royal des Sciences Naturelles de Belgique 69-Supp. B: 17-36.

Huene Fv (1926) Vollständige Osteologie eines Plateosauriden aus dem Schwäbischen Keuper. Geologische und Palaeontologische Abhandlungen (N. F.) 15 (2): 139-179

Longrich, NR (2011) Titanoceratops ouranos, a giant horned dinosaur from the late Campanian of New Mexico. Cretaceous Research 32: 264-276.

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.

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

Pereda-Suberbiola J, Ruíz-Omeñaca JI, Ullastre J, Masriera A (2003) Primera cita de un dinosaurio hadrosaurio en el Cretácico Superior del Prepirineo oriental (Peguera, provincia de Barcelona). Geogaceta 34: 195-198

Riabinin ANN (1945) [Dinosaurian remains from the Upper Cretaceous of the Crimea] (in Russian). Vsesoy. Nauch.-Issledov. Geol. Inst. Matl. Paleontol. Strat. 4: 4–10.

Ryabinin AN (1939) The Upper Cretaceous vertebrate fauna of South Kazakhstan, Reptilia; Part 1, the Ornithischia. Transactions of the Central Geological and Prospecting Institute 118: 1-38.

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.

Zhao X, Li D, Han G, Zhao H, Liu F, Li L, Fang X (2007) Zhuchengosaurus maximus from Shandong Province. Acta Geoscientica Sinica 28: 111-122.

A First Pass at Figures

July 5, 2011 13 comments

Even though our paper is intended for a technical audience, it is still important to ensure that a broad range of readers can access and understand the information contained within the text. For instance, not even a competent dinosaur paleontologist is necessarily familiar with all of the intricacies of ornithischian clade names like “Ankylopolexia” or “Neornithischia.” Thus, we want to provide a brief bit of background for readers of the paper.

One option, of course, is to write out brief definitions of various clades as they are introduced. This works okay in some cases – for instance, we definitely want to briefly explain what an ornithischian is – but to do this for every term can get a little unwieldy. An old adage states, “A picture is worth a thousand words,” and this is just as true in scientific writing as it is in popular writing.

So, I suggest that Figure 1 for the paper include a simplified cladogram of the major clades discussed in the paper. A first pass at this is given below (click on the image to see at full resolution):

Figure 1. Phylogeny

Figure 1. Phylogeny of Ornithischia (from multiple recent sources), showing major clades discussed in the text. Outlines show representative members of each clade; names in bold indicate clades with quadrupedal taxa.

There are a few things I should mention. First, the content of the figure is nowhere near finalized. However, there were a few principles I wanted to adhere to:

  • Keep it simple. Because this is only an overview figure, I did not deem it practical to include all of the taxa that we discuss. Instead, I just chose the “important” ones that will appear over and over again.
  • Terminology. In a few cases, such as Neornithischia, including only major named clades oversimplifies things just a little too much. For instance, there are a bunch of important neornithischians (e.g., Agilisaurus and Othnielosaurus) that don’t fit comfortably within ornithopods or marginocephalians, and I want to find ways to include such taxa. Thus, I’ve created terms like “Early neornithischians”. I realize that this may imply that they are a clade in their own right, where instead they form a comb or polytomy, but perhaps this is a simplification that just has to be made. If anyone has a suggestion for a better way to title the groups, please let me know. For now, I prefer “early neornithischians” over “basal neornithischians” and the like. “Basal” implies a ranking that just isn’t there for cladograms, but maybe other folks think this is less of a deal than I do.
  • Notation of quadrupedal taxa. Because quadrupedalism vs. bipedalism is so important for the paper, I bolded relevant taxa as outlined in the caption. The icons (discussed next) provide an additional clue. If I recall correctly (Andrew McDonald is probably most up to speed on this of anyone who follows this blog), there are probably a few non-hadrosaurid ornithopods that should be inferred to be quadrupedal, too.
  • Icons. I consider it very important to include at least a small figure for each taxon, so that readers who are not familiar with all of the terms can picture each clade in their mind. The icons that are shown here (from Mike Keesey’s Phylopic) are of generally high quality, but should be considered only temporary. Ideally, I would like to generate new images to go with our figure, if only because there has been such a hubbub over the running dinosaur pose recently.
  • Orientation. I opted for portrait rather than landscape orientation for the figure, primarily because I thought it was a more efficient and readable format. Any thoughts?
  • Time calibration. One option for the figure would be to time-calibrate it, and show the duration and estimated time of origin for each clade. I feel this might make things just a little too complex (and crowd other parts of the figure), but am open to alternative interpretations. Thoughts?

At any rate, that’s what we’ve got for now. Please chime in in the comments!

Image Sources: All images are from Phylopic, and are licensed accordingly under a Creative Commons License. Individual credits are as follows: Oscar Alcober & Ricardo Martinez (, Scott Hartman (;;;, Loewen et al. (, FunkMonk (, Lukas Panzarin (, Remes et al. (; Ville-Veikko Sinkkonen (

Categories: Figures, Progress Reports

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


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).


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.


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.


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 ( 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.


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

Outlining the Paper

December 3, 2010 13 comments

Pisanosaurus, by FunkMonk

After all of this work and data accumulation, it’s probably just about time to do the darned analyses and write the darned paper. We’ve had quite a bit of discussion over the last year or so on what this might look like. To that end, I want to outline one possibility and then solicit input from everyone. Again, this is very much a work in progress, so please comment as appropriate.

Working Title: Trends and Variation in Limb Proportions of Ornithischian Dinosaurs [please think up a more exciting, succinct, and descriptive title]

Outline of Contents

  1. Introduction
    What are ornithischian dinosaurs?
    What do we already know about their modes of locomotion and limb proportions? How are they unusual compared to other dinosaurs?
    What have other workers done with analyzing dinosaurian limb proportions?
    What is the main point of this study? [to document, describe, and interpret ornithischian limb morphology, and how it relates to function]
  2. Materials and Methods
    Jay Fitzsimmon’s very nice paragraph on citizen science and the ODP goes here.
    How specimens were selected.
    Where we got the measurements.
    How we winnowed down the data.
    How we assembled the phylogeny
    Statistical analyses performed on the data [PCA to describe overall patterns; regressions accounting for phylogeny to describe various allometric patterns {we probably only want to look at patterns that are comparable with theropods or other analyses of interest}; analyses looking at trends within clades; analysis of disparity; analysis comparing characters using phylogenetically independent contrasts]
  3. Results
    Principal components analysis – done on uncorrected data, how do we describe the limb proportions in various ornithischians. Believe it or not, this hasn’t really been done!
    Regressions accounting for phylogeny to describe allometric patterns – we might want to look at a few regressions, such as forelimb vs. hindlimb length, femur vs. tibia+MTIII, humerus vs. radius+MCIII
    Analysis documenting trends in clades –  include pretty colored images a la Padian et al’s charts of dinosaurian growth rates
    Analysis of disparity – how disparate are various groups? How rapidly did the bauplans for the various groups develop?
  4. Discussion & Conclusions
    What do these results mean?
    We’ll have more to fill in when we get some “final” results!

A Recommendation:

We all will have an urge to make this paper as absolutely comprehensive as possible – in the past we have talked about many, many different kinds of analyses, hypotheses, etc. But, I think we also want to avoid getting bogged down in needless detail or bloated and waylaid by side tangents of marginal importance. (some of what I outlined above may very well fall into this category!) So, let’s keep that in mind. . .(but don’t be afraid to make suggestions, either!)

Return of the ODP!

November 11, 2010 7 comments

Mantellisaurus, a big ornithopod

It’s bAAAAaaaack!

The hiatus has been a long one (far longer than expected), but now it’s time to get the show on the road again. Life has been busy for everyone, but it’s time to make some time for the ODP. Basically, Wedel was over the other night and reminded me I should do a blog post. There’s so much to see, so much to do, so much to talk about! Here’s some highlights:

  • The dataset is pretty much all together; we just have to finish analyzing the darned thing. Stay tuned for more.
  • I (Andy) had a fun time at SVP in Pittsburgh, and got to meet a number of ODP volunteers there. Awesomeness!
  • Casey Holliday and colleagues published an interesting article on articular cartilage in dinosaur limb bones, suggesting that limb lengths may have been up to 10 percent longer than we see just from the bones. Read the paper for free at PLoS ONE – anyone interested in doing a guest post on it, perhaps?
  • We should probably start putting together a reference list of papers related to the mission of the ODP: analyzing limb proportions in ornithischian dinosaurs. I’ll probably start a thread for that, too.

As added incentive, I made the ODP one of my personal goals for the Paleo Project Challenge. If you haven’t checked out the challenge yet, please do so. The main premise: make a plan to complete a project, or else face public humiliation. Let’s see if it works. . .

That’s all for now!

Image credit: By Steveoc 86, from Wikimedia Commons.

Cladogram(s), Part III

March 8, 2010 6 comments

I think we’re now converging on a cladogram that reasonably captures the current state-of-the-art. Thank you to everyone who has contributed so far. The topology has incorporated most of the suggestions, and I think the nomenclature is finally up-to-date. As always, post something in the comments if you see anything that needs work.

A Disclaimer

The phylogeny, in general, is intended to be used for numerical analyses (e.g., phylogenetically independent contrasts) that incorporate information on the evolutionary relationships of organisms (that topic is crying out for a post, had I the time). Studies have shown that these methods are generally pretty robust, even if the phylogeny is incorrect in some details. So. . .it means that we shouldn’t sweat too much about uncertainties or the inevitable error/new data. In a handful of cases (hadrosaurs, perhaps?), we may want to run analyses with alternative trees, but we’ll worry about that when we get there. The position of some annoyingly fickle taxa (like Micropachycephalosaurus) will end up being a moot point, because we don’t have decent postcrania for them.

That said, this tree is a mutt (but a loveable one). We’ve done the best we can with the published analyses and our personal opinions. It’s pretty darned good for the most part (in my opinion), but it will never be perfect. Anyone is welcome to use it, but caveat emptor. If using the tree for other purposes, please refer to the notes given in previous posts so you have an understanding of the how’s and why’s of the tree. I am happy to send the NEXUS file to anyone who requests it (and we’ll want to include it as supplemental information when we publish).

The Current Version

The version below shows all of the taxa, with most corrections incorporated as suggested.

Cladogram, Version 3

Cladogram, Version 3 (click to enlarge)

I’ve also generated a version where taxa that aren’t in our database are trimmed out. This is what we’ll use for most of our analyses. See below:


Trimmed Cladogram, Version 3. I accidentally took Eoraptor out.


Notes from the previous version still apply.

Psittacosaurus xinjiangensis given as sister taxon to P. sinensis, following Sereno 1987, p. 267. This taxon, the measurements for which are based on a juvenile (Sereno 1988, original description), has not been included in any published phylogenetic analysis.

The species of Camptosaurus and Dryosaurus are placed so as to preserve monophyly for each genus.

Animantarx is given as sister to Edmontonia, following Hill et al. 2003, Figure 9

Both species of Postosuchus need to be shown

Edmontosaurus saskatchewanensis needs to be dealt with

Eoraptor needs to be added into the trimmed cladogram.

Categories: Progress Reports

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