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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:

Timeline:

  • 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.

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

Summertime, open ignorance, and finishing the project

May 25, 2011 7 comments

Hi, all. Thanks for your patience this spring. Sorry we’ve let things lie fallow for so long. Many thanks to everyone for keeping things ticking over while we were AWOL.

Like Andy said in the last post, it’s time to wrestle this thing to the ground and stick a knife through its heart (I may be paraphrasing a bit). Andy, Mike, and I have cleared some protected time in our summer schedules to finish the analyses and write the paper. The next two weeks may be a bit quiet on our end as we all work to get other things tied up and off our desks–and as Andy moves his residence!–but we should be ready to hit it hard by the second week of June.

There is a lot of work to be done, and there are lots of ways to contribute to the paper for everyone who wants to be involved, right now and continuing through the summer. I’ll give some suggestions in a minute. But first, an admission.

We don’t really know what we’re doing here. That’s obvious with the social side of the project, because nothing like this has been attempted before, at least not on this scale or with this degree of openness. But it’s also true on the scientific side. None of us (Andy, Mike, or I) has ever written a paper on this topic. There are some specific analyses that we need for the paper that we’ve never run before. So we are very much learning as we go–this is the open ignorance I alluded to in the title. This isn’t by accident. We could have chosen to do something simpler and less ambitious–perhaps repeat a project that we’d already done before with only the names of the critters changed. But we wanted to learn from the project–from you, the contributors, and alongside you–and to grow as scientists from having participated in it. And we want the final product to be a truly collaborative effort, and not to simply walk everyone through a series of moves that we already know by heart.

And it is working. We have been amazed at the level of enthusiasm and commitment that you have brought to the project, and our only regret is that we have not reciprocated with the sustained level of effort that you, and the project, deserve. So we’re committing ourselves to getting this done, starting now.

How can you contribute? Here are some suggestions:

  • Update the database. New taxa continue to be described, new descriptions of established taxa continue to be published, and older publications continue to become available. So if you have been wanting to do some (more) good old-fashioned ODP gruntwork, there’s still a little time.
  • Suggest relevant references, or read up on the ones that are already suggested. It might be a good idea to gather those references together so they can be made available to anyone who is working on the project. We’ll probably do a post specifically on this in the near future, but there’s no reason not to be pulling things together in the meantime.
  • Look at the outline of the paper, suggest improvements, and–if you are so inclined–start writing those bits that can be written right now. For now, feel free to post chunks in comments or send them to us. Jay Fitzsimmons’s paragraph on citizen science and the ODP is a good model to follow. We’ll definitely be posting more on the actual writing of the paper soon, but, as with boning up on the relevant references, there’s no reason to hold off if this is something you’re interested in working on.
  • Analyze data. Obviously there are limits to what we can do until we really finalize the database once and for all, but this is a good time for exploring the data and for test-driving analyses to be done on the finalized database. We have enough data that overall trends are not likely to change much, so anything that looks interesting now will probably still be interesting in the final version.
  • Work on a time-calibrated phylogeny for the dataset. This is a big one, again probably deserving of a post of its own. We’ll also need to update the “master tree” to include the most current phylogenetic trees for the included taxa. If you’re into trees, timelines, or both, the mothership is calling you home.
  • Figure out how to do disparity analyses. This is one of those things that we project organizers have never done before. We’re reading up on it right now, but if you know anything about it, let us know. Even when we get up to speed, we’ll still need your input. Like Project Mayhem, you can determine your own level of involvement.
  • Other stuff? The project is probably at its maximum breadth in terms of types of work to be done. Up until now we’ve focused mainly on building the database and outlining where we want to go, and in a few weeks we’ll have the database finalized and our efforts will narrow as we focus on running the analyses and writing the paper. So whether you’re brand new and want to get involved for the first time, or an old hand who wants to do something different, there is something around here that needs doing. Have a look at the tasks list, go back through the last few posts, and see what appeals to you. If in doubt, give us a shout.

That’s all for now. Stay tuned for more posts very soon. But don’t just stay tuned–keep posting ideas, data, references, bits of text, and whatever else you want to contribute. We’ll do likewise.

Categories: Housekeeping, To-Do List

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!)

Relevant References for the ODP

November 15, 2010 22 comments
Scelidosaurus

Olde Timey Restoration of Scelidosaurus, after Marsh

In response to a recent query on this blog, ODPer Christian Foth contributed a list of papers potentially relevant to the ODP, specifically limb posture and evolution in ornithischian dinosaurs. It’s important to recognize work that others did before and see how it relates to ours. Furthermore, a good reference list is essential for the upcoming manuscript.

What can you do?

If you think of another paper that might be added to the list (within reason, of course), drop a line in the comments section. If you are interested in providing a summary of a certain paper as a guest blog post (either here or at your own blog), that would be great, too. As always, one need not be a Ph.D’ed scientist to apply! We’re just looking for a short summary.

For my part, I added the Middleton and Gatesy reference – although it deals with theropods, I think some of the background info and analytical methods are quite relevant. Hmm. . .that might be a good one to blog about.

Reference List in Progress

Alexander R. 1985. Mechanics of posture and gait of some large dinosaurs. Zoological Journal of the Linnean Society 83: 1-25.
Bakker RT. 1968. The superiority of dinosaurs. Discovery 3 (2): 11-22.
Biewener (1983). Allometry of quadrupedal locomotion: the scaling of duty factor, bone curvature and limb orientation to body size. J. Exp. Biol. 105: 147-171.
Bonnan MF & P Senter. 2007. Were the basal sauropodomorph dinosaurs Plateosaurus and Massospondylus habitual quadropeds. Special Papers in Palaeontology 77: 139–155
Bonnan, MF, & AM Yates. 2007. A new description of the forelimb of the basal sauropodomorph Melanorosaurus: implications for the evolution of pronation, manus shape and quadrupedalism in sauropod dinosaurs. pp. 157-168 in: Paul M. Barrett and David J. Batten (eds.), Special Papers in Palaeontology 77: Evolution and Palaeobiology of Early Sauropodomorph Dinosaurs. The Palaeontological Association, U.K.
Bultynck P (1992) An assessment of posture and gait in Iguanodon bernissartensis Boulenger, 1881. Bulletin de l’Institut Royal des Sciences Naturelles de Belgique: Sciences de la Terre 63: 5-11.
Carrano MT. 2000. Homoplasy and the evolution of dinosaur locomotion. Paleobiology 26 (3): 489-512.
Carrano MT (2001) Implications of limb bone scaling, curvature and eccentricity in mammals and non-avian dinosaurs. Journal of Zoology 254: 41-55.
Dilkes DW. 2000. Appendicular myology of the hadrosaurian dinosaur Maiasaura peeblesorum from the Late Cretaceous (Campanian) of Montana. Transactions of the Royal Society of Edinburgh, Earth Sciences 90: 87-125.
Dilkes DW. 2001. An ontogenetic perspective on locomotion in the Late Cretaceous dinosaur Maiasaura peeblesorum (Ornithischia: Hadrosauridae). Canadian Journal of Earth Sciences 38: 1205-1227.
Dodson, P & JO Farlow. 1997. The forelimb carriage of ceratopsid dinosaurs. DinoFest International Proceedings 393-398.
Galton PM. 1970. The posture of hadrosaurian dinosaurs. Journal of Paleontology 44 (3): 464-473.
Garstka WR & DA Burnham. 1997. Posture and stance of Triceratops. Evidence of digitigrade manus and cantilever vertebral column. DinoFest International Proceedings 385-391.
Heinrich DE, Bruff CB & DB Weishampel. 1993. Femoral ontogeny and locomotor biomechanics of Dryosaurus lettowvorbecki (Dinosauria, Iguanodontia). Zoological Journal of the Linnean Society 108: 179-196.
Hutchinson JR. 2004. Biomechanical modeling and sensitivity analysis of bipedal running ability. I. Extant taxa. Journal of Morphology 262: 421-440.
Johnson RE, Ostrom JH (1995) The forelimb of Torosaurus and an analysis of the posture and gait of ceratopsian dinosaurs. In: Thomason JJ, editor. Functional Morphology in Vertebrate Paleontology. New York: Cambridge University Press. pp. 205-218.
Kilbourne BM & PJ Makovicky. 2010. Limb bone allometry during postnatal ontogeny in non-avian dinosaurs. Journal of Anatomy 217: 135-152.
Kubo T & MJ Benton. 2007. Evolution of hindlimb posture in archosaurs: limb streeses in extinct vertebrates. Palaeontology 50 (6): 1519-1529.
Lee DV & SG Meek 2005. Directionally compliant legs influence the intrinsic pitch behaviour of a trotting quadroped. Proceedings of the Royal Society B 272(1563): 567–572.
Mallinson. 2010. CAD assessment of the posture and range of motion of Kentrosaurus aethiopicus Hennig 1915. Swiss J Geosci 103: 211-233.
McMahon, T (1975) Allometry and biomechanics: Limb bones in adult Ungulates. Am. Nat. 109:547-563.
Middleton KM & S Gatesy. 2000. Theropod forelimb design and evolution. Z J Linn Soc 128: 149-187
Organ CL. 2006. Biomechnics of ossified tendons in ornithopod dinosaurs. Paleobiology 31 (4): 652-665.
Papantoniou V, Avlakiotis P & R Alexander. 1999. Control of a robit dinosaur. Phil.Trans. R. Soc. Lond. B 354: 863-868.
Paul GS & P Christiansen. 2000. Forelimb posture in neoceratopsian dinosaurs: implications for gait and locomotion. Paleobiology, 26 (3): 450–465.
Romer AS. 1923. The ilium in dinosaurs and birds. Bulletin American Museum of Natural Histroy 48: 141-145.
Raichlen DA. 2006. Effects of limb mass distribution on mechanical power outputs during quadrupedalism. The Journal of Experimental Biology 209: 633-644
Romer AS. 1927. The pelvic musculature of ornithischian dinosaurs. Acta Zoologica 8: 225-275.
Sellers WI & PL Manning. 2007. Estimating dinosaur maximum running speeds using evolutionary robotics. Proceedings of Royal Society B 274: 2711-2716.
Senter P. 2007. Analysis of forelimb function in basal ceratopsians. Journal of Zoology 273: 305-314.
Sternberg CM. 1965. New restoration of hadrosaurian dinosaur. National Museum of Canada, Natural History Papers 1-5.
Taylor CR. 1978. Why change gaits? Recruitment of muscles and muscle fibers as a function of speed and gait. American Zoologist 18: 153.161.
Tereshchenko VS. 1994. A reconstruction of the erect posture of Protoceratops. Paleontological Journal 28 (1): 104-119.
Tereshchenko VS. 1996. A reconstruction of the locomotion of Protoceratops. Paleontological Journal 30 (2): 232-245.
Tereshchenko VS. 2008. Adaptive features of protoceratopoids (Ornithischia: Neoceratposia). Paleontological Journal 42 (3): 273-286.
Thompson S & R Holmes. Forelimb stance and step cycle in Chasmosaurus irvenenesis (Dinosauria: Neoceratopsia). Palaeontologica Electronica 10 (1): 5A.
Thulborn RA. 1982. Speeds and gaits of dinosaurs. Palaeogeography, Palaeoclimatology, Palaeoecology, 38: 227-256.
Thulborn RA. 1984. Preferred gaits of bipedal dinosaurs. Alcheringa 8 (3): 243-252.
Yates, Adam M., Matthew F. Bonnan, Johann Neveling, A. Chinsamy and Marc G. Blackbeard. 2009. A new transitional sauropodomorph dinosaur from the Early Jurassic of South Africa and the evolution of sauropod feeding and quadrupedalism. Proceedings of the Royal Society B, published online. doi:10.1098/rspb.2009.1440

 

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  • Tereshchenko VS. 1994. A reconstruction of the erect posture of Protoceratops. Paleontological Journal 28 (1): 104-119.

  • Tereshchenko VS. 1996. A reconstruction of the locomotion of Protoceratops. Paleontological Journal 30 (2): 232-245.

  • Tereshchenko VS. 2008. Adaptive features of protoceratopoids (Ornithischia: Neoceratposia). Paleontological Journal 42 (3): 273-286.

  • Thompson S & R Holmes. Forelimb stance and step cycle in Chasmosaurus irvenenesis (Dinosauria: Neoceratopsia). Palaeontologica Electronica 10 (1): 5A.

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Return of the ODP!

November 11, 2010 7 comments
Mantellisaurus

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.

Behold, The Mighty Cladogram

March 5, 2010 23 comments

It’s taken awhile, but I finally put together a basic phylogeny to provide the evolutionary backbone for our phylogenetically-informed analyses. References (in very abbreviated format – we’ll have to flesh it out more for the paper) are given at the end of this post.

I created a “pseudo-supertree”, based on a number of what I (in my opinion) consider to be some of the better and more up-to-date published cladistic analyses. The vast majority of our species of interest are included here, and a draft is shown later in the post. But, we need your help in order to get to the final product.

Here’s What You Can Do
Below is a list of taxa that are not yet placed on the cladogram. In all cases, they were not featured in any of the cladistic analyses I looked at for my first pass. In order to incorporate them into the analysis effectively, though, we need to figure out where they belong. So. . .I’m looking for anything – a reference, personal opinion, cladogram I missed – to place them on the tree. Please mention it in the comments, and we’ll be able to get the tree updated! At the minimum, a reference would be helpful, so that we can be as explicit as possible in our reasoning for the paper. I focused my efforts so far on just ornithischians, so many of the problematic taxa are recently-published animals that are outside Ornithischia.

Also, if you see anything in the tree that you consider to be in gross error, please put a note in the comments section, and we can talk about it. We want the best phylogeny possible. But at the same time, studies have shown that some phylogeny – any phylogeny – is better than no phylogeny at all, so we don’t have to sweat things too much if new data later force us to revise.

Taxa to Place
Ankylosauria:
Aletopelta coombsi, Dracopelta zbyszewskii, Dyoplosaurus acutosquameus, Hungarosaurus tormai, Niobrarasaurus coleii, Nodosaurus textilis, Polacanthus foxii, Zhejiangosaurus lishuiensis
Ceratopsia: Graciliceratops mongoliensis, Psittacosaurus major, Psittacosaurus mongoliensis, Psittacosaurus neimongoliensis, Psittacosaurus ordosensis, Psittacosaurus sibiricus, Psittacosaurus sinensis, Psittacosaurus xinjiangensis, Xuanhuaceratops niei
Crurotarsi: Gracilisuchus stipanicicorum, Hallopus victor, Protosuchus richardsoni, Saurosuchus galilei, Pseudolagosuchus major, Scleromochlus taylori
Hadrosauroidea: Anatotitan copei (is there a consensus that this is just Edmontosaurus?), Barsboldia sicinskii, Claosaurus affinis, Edmontosaurus saskatchewanensis (how does it relate to other Edmontosaurus species?), Hadrosaurus foulkii, Mandschurosaurus amurensis, Shantungosaurus giganteus
Basal ornithischians: Eocursor parvus, Geranosaurus atavus
Ornithopods: Draconyx loureiroi, Gongbusaurus wucaiwanensis, Oryctodromeus cubicularis, Xiaosaurus dashanpensis
Parasuchia: Machaeroprosopus gregorii
Sauropodomorpha: Aardonyx celestae, Gyposaurus sinensis, Panphagia protos, Pantydraco caducus, Sellosaurus gracilis
Stegosauria: Chialingosaurus kuani, Lexovisaurus durobrivensis
Theropoda: Guaibasaurus candelariensis, Podokesaurus holyokensis

The Phylogeny

The Phylogeny, as of 4 March 2010. Click to see it in all of its glory.

Logic Behind the Tree
In the interest of Open Notebook Science, I have provided full references and justifications (if any) for the topology of the illustrated tree. All of this should go into the final paper, so that others can reproduce our work.

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 (Lesothosaurus, Scutellosaurus, Emausaurus, Scelidosaurus, Stegosauria, Ankylosauria) 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).

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.

Topology of basal Iguanodontia:
Follows Norman 2004, figures 19.21 (strict consensus) and 19.22 (single most parsimonious tree following taxon deletion).
Tenontosaurus is treated as monophyletic, following Figure 19.22.
Euijuubus is arbitrarily treated as more basal than Lurdusaurus.
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 basal hadrosaurids, hadrosauroids, and other derived iguanodontians:
Follows Dalla Vecchia 2009, Figure 8B (50% Majority Rule Tree). Bactrosaurus and Gilmoreosaurus are arbitrarily resolved from their polytomy with more derived hadrosauroids. Mantellisaurus and Dollodon are given as sister taxa, following this analysis.

Topology of lambeosaurines:
Follows Evans and Reisz 2007, Figure 9
Corythosaurus arbitrarily resolved as closer to Hypacrosaurus than Olorotitan
Pararhabdodon as a basal lambeosaurine after Dalla Vecchia 2009

Topology of hadrosaurines:
Follows Fig. 16 of Gates and Sampson 2007
Edmontosaurus, Prosaurolophus, and Saurolophus are split into their species, assuming that each genus is monophyletic

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)
Placement of Cerasinops, and its relationships with Udanoceratops, Leptoceratops, Montanaceratops, and Prenoceratops, based on Figure 6 of Chinnery and Horner 2007
Placement of Yinlong and Micropachycephalosaurus after Figure S4 of Butler et al. supplementary information

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

Things to Do

March 4, 2010 4 comments

We’re edging ever closer to a real, live analysis! In the meantime, there are four big tasks that remain for all of us:

  1. Double-check the taxonomic assignments of specimens, and make sure that they are up-to-date.
  2. Create a full listing of the ages of all included taxa.
  3. Finish the phylogeny.
  4. Weed out composite, juvenile and taxonomically indeterminate specimens.

You can help out with any of those – right now! I’ll write about each topic in more detail below, including what you can do to help.

But first, I would like to thank ODP volunteer Dave Dreisigmeyer for some major-time database coding work that he has done. Many of our specimens have measurements for individual elements identified as right, left, or unspecified. For instance, a specimen of Iguanodon might have published measurements for both the left and right humeri. We need to average those out to get a single value for just the humerus as a whole. This could have been time-consuming (and error-prone) work, but Dave wrote  a nifty little script to do this automagically. The result is available for download here.

On to the tasks. . .

Taxonomic Assignments

Psittacosaurus_major

Psittacosaurus. This genus is a mess!

The original version of the database only used the published genus and species for each specimen. As taxonomy changes, these identifications must be updated.  In some cases, it’s straight-forward. For instance, the animal formerly known as Yandusaurus multidens is now called Hexinlusaurus multidens. But, some areas are pretty messy – there are almost certainly too many named species of Psittacosaurus, but there isn’t a good published summary of the up-to-date taxonomy for this genus. In the end, it will require personal opinion (unfortunately).
What to do to help: I’ve started the work for some of this, but now we need to get it polished up a bit more. To make things easier, please use the Google document posted here (it’s the same one we’ll use for noting ages, too). If a name needs to be fixed, just mark it in the appropriate column. The project heads (Farke, Wedel, and Taylor) will have ultimate authority in the event of any disputes.

Geologic Ages
For the analysis focusing on morphological disparity (i.e., how different are the dinosaur limbs from each other), we will also want to look at the time component (see Randy Irmis’s guest post for more on this). So, we need to know how old all of our dinosaurs are. Fortunately, Rob Taylor has gotten a great head-start on the issue, and we’ve posted his file for you to add to it. Use published references whenever possible (see the document for more instructions).
What to do to help: Using the peer-reviewed literature (with references and page numbers, please), help fill out the table posted here (Google Document). The Dinosauria (2004 edition) is quite helpful. Also, many of the papers that published the original specimen descriptions can also help (especially for newer taxa).

Finish the Phylogeny
I spent my spare moments today drafting a phylogeny on which to hang our analysis. In an upcoming post, I’ll provide a few more details on what/how to contribute to this effort.

Weed Out Composite/Juvenile/Indeterminate Specimens
I’ve already removed specimens based on isolated elements (because they’re not a lot of good for comparison). For various statistical reasons (and because animals change body proportions as they grow), we also want to remove most of the juveniles from our analysis (although we may keep a few key players in there, especially if they’re from poorly represented portions of the family tree). Composite specimens (e.g., those made of multiple individuals, as happen in some museum mounts from bonebeds) also need to be excluded, because we have no idea if they accurately represent individual proportions. Finally, if we can’t identify a specimen (i.e., it’s listed just to the family level), it should also be removed.
What to do to help: Take a look at the trimmed-down spreadsheet of measurements (available here as an Excel spreadsheet). If you see a specimen that you think should be excluded, please mention it in the comments for this post.

THANK YOU!!!

Image credits: Original by Nobu Tamura, as posted at Wikimedia Commons. This file is licensed under the Creative Commons Attribution ShareAlike 3.0 License. In short: you are free to share and make derivative works of the file under the conditions that you appropriately attribute it, and that you distribute it only under a license identical to this one. Official license

NOTE: Co-authorship on the first major resulting full paper is offered for those who contributed measurement data, and also will be offered for other contributions at the discretion of the project heads (Farke, Taylor, and Wedel). However, those who help but do not have co-authorship will receive a place in the acknowledgments for the final paper. Please make sure you mark your contributions in the appropriate place, in order to receive credit.

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