Return of the ODP!

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.

New ODP article in the Palaeontological Association newsletter

The new issue of the Palaeontological Association newsletter dropped through the letterbox this morning, and I was delighted to see that our article on the Open Dinosaur Project was included.  The PalAss newsletter, despite its name, is not a couple of mimeographed-and-stapled sheets, but a reasonably substantial publication (98 glossy pages in the current issue), so hopefully it will help to raise our profile, especially among more traditional professionals who get their news from dead-tree media rather than the Internet.

You can download the whole newsletter as a single PDF from the PalAss site, or just the OPD article (five pages) if you prefer.

Reference

Taylor, Michael P., Andrew A. Farke and Mathew J. Wedel. 2010. The Open Dinosaur Project. The Palaeontological Association Newsletter 73:59-63.

Sauropelta Solved!

The ever-problematic Sauropelta, as restored by John Conway.

A nagging problem in our dataset has been the issue of the Sauropelta edwardsi specimen AMNH 3032. Its tibia seems way, way too short (even for ankylosaurs), and it’s thus a bizarro outlier.

So, I finally got my behind into gear to check out the problem. Was the measurement a typo? Was the tibia incompletely preserved? Was it from a smaller individual? On p. 115, I found the answer. The tibia for AMNH 3032 is here listed as 57.5 cm (575 mm) in length. This makes much, much more sense, so we’ll go with that number. Apparently, the value given in the table was simply an error. On further looking, I was able to confirm that the table heading for Sauropelta measurements on p. 120 was actually transposed with a Tenontosaurus table (as Rob Taylor had ably picked up on some time ago)! It looks like the measurements here are all from AMNH 3032, not YPM 5456 and 5459. Mystery (finally) totally solved, and the database is fixed!

It also turns out that the tabular error has been perpetuated across a few more publications. The Tenontosaurus-turned-Sauropelta YPM 5456 makes an appearance in Ford and Kirkland 2001 as well as Maidment et al. 2008. It in no way harms the conclusions of these papers (after all, the error is in the specimen number, not the measurements). But, I have removed all references for a YPM 5456 Sauropelta from our data tables.

References
Ford TL, Kirkland JI (2001) Carlsbad ankylosaur (Ornithischia, Ankylosauria): an ankylosaurid and not a nodosaurid. In: Carpenter K, editor. The Armored Dinosaurs. Bloomington: Indiana University Press. pp. 239–260.
Maidment SCR, Norman DB, Barrett PM, Upchurch P (2008) Systematics and phylogeny of Stegosauria (Dinosauria: Ornithischia). Journal of Systematic Palaeontology 6: 367-407.
Ostrom JH (1970) Stratigraphy and paleontology of the Cloverly Formation (Lower Cretaceous) of the Bighorn Basin area, Wyoming and Montana. Bulletin of the Peabody Museum of Natural History 35: 1–234.

Image Credit: Restoration by John Conway, from 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

Analytical Software

As the past two posts have attested, we are on the cusp of doing some actual, real-life analysis. If at all possible, I want to run the analyses using freely available, open source software. Fortunately, all of the major software packages for phylogenetically-informed, quantitative analaysis are free! Here are the ones I’m looking at:

• For constructing trees and some simple analyses: Mesquite. (all of the tree plots you’ve seen have been done in this program)
• For general statistical analysis: R, along with the smatr, ape and ggplot2 packages. I will make a serious effort to post all scripts that are used to generate graphics and analyses; I would encourage all of you to do the same.
• For additional analysis of quantitative data in a phylogenetic context: COMPARE.

http://opendino.wordpress.com/2010/03/10/by-popular-demand/

Things to Do

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. 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.

Radius, Not Ulna

As you may recall from your own background knowledge or from this tutorial, the forearm includes two bones: radius and ulna. One of the core analyses we’re going to be looking at is the proportions of the forearm relative to the arm (“upper arm”). Of course, we have to use bone length as a proxy for the true length of the different limb segments. For the arm, it’s a no-brainer. There’s only one bone, the humerus. For the forearm, we can choose between the radius and the ulna. At first glance, it might seem like the bones are interchangeable. But, it’s not really that simple.

Forelimbs of Othnielosaurus (left) and Triceratops (right), modified after the Marsh 1896 originals. In each, the radius is green, the main body of the ulna is blue, and the olecranon process of the ulna is yellow.

You see, some ornithischians (especially the big ones, it seems) have this giant sticky-outey thing on the proximal end of the ulna: the olecranon process. The triceps, among other muscles, attaches here. Because our spreadsheet only records maximum length of the ulna (and this is all most researchers ever report, anyhow), we encounter a complicated situation. The olecranon sticks up past the end of the humerus – so that a naive ulna : humerus ratio doesn’t really accurately describe forearm : arm length. It actually covers forearm + a little bit of the arm : arm length.

It doesn’t make much of a difference for some dinosaurs – for one Psittacosaurus, for instance, we’re talking ratios of 0.66 vs. 0.67. But what about an animal like Triceratops? In some specimen, it’s a matter of 0.99 vs. 0.71!  Obviously, we would get very different results if we apply this across the board.

For this reason, I would propose that we’ll want to use radius:humerus instead of ulna:humerus. In a quick look through the data, it also looks like we wouldn’t really lose out on any specimens, either; radius length is reported just as frequently as ulna length, if not more! And, of course, radius:ulna would be an interesting way to (indirectly) examine the relative size of the olecranon process in various bipedal and quadrupedal species. Which is an important issue in its own right. . .

Notes on Data Processing

I’ve begun the process of paring down the database into the form for final analysis (but remember, of course, that the full, unaltered data live on). So far, I have deleted entries that fit into the following categories:

• Extraneous entries for “combined” specimen data sets. In other words, only the combined entry will be used for analysis. One specimen, one data point.
• Specimens comprising isolated elements (e.g., isolated humeri or femora). Because we’re analyzing skeletal proportions primarily, isolated elements aren’t terribly useful.
• Individual measurements with a “+” have been removed, as they represent measurements “as preserved” rather than estimates of original length.

Very soon we will want to make a final decision on what to do with species represented by multiple specimens. One strategy (which I think was used by Carrano 2006, if I remember correctly) is to use only the largest specimen. Here, the benefits are that juvenile specimens are pretty automatically excluded. The downside is that the largest specimens may not be the most complete.

A second strategy is to average all of the entries together. Of course, we would have to be careful on this. For instance, when we’re using ratios, we’ll want to calculate the ratio first, and then average the ratio. We don’t want to calculate, for instance, a humerus:femur ratio from the averaged measurements. Here’s why.

Let’s pretend we have specimens A and B. Specimen A has a humerus and femur length of 100 and 50, respectively. This gives a humerus:femur ratio of 2.0. Specimen B has a humerus and femur length of 50 and 100, respectively, for a humerus:femur ratio of 0.50. If we were to average the humeri and femora first, we would get average lengths of 75 each, which then results in a ratio of 1! Obviously (I hope), it is apparent that this “ratio of averages” doesn’t accurately reflect what’s going on. Furthermore, it’s quite different from the “average of ratios,” which weighs in at 1.25.

The advantage of averaging values for all specimens in a species is that we can better incorporate individual variation, and also better deal with incomplete specimens. We need to be cautious of averaging in cases of extreme size variation for a single species (hence, part of why it’s desirable to use ratios). Here, it may be worthwhile still to discard known juveniles.

Want to see the work in progress? Check it out here.

Thoughts? Let’s hear from you in the comments section!

The Analyses Ahead

Scutellosaurus, a presumably bipedal thyreophoran, unusual in a clade that was almost entirely quadrupedal

As we finish up combining the data, it’s time to start thinking about the specific analyses that we’re going to do. What are the specific questions we’re asking? What are the techniques that we need to address the questions? Some excellent discussions between ODPers have been happening in one of the recent posts, and I was hoping to continue that here. In particular, I wanted to refocus the discussion on the project’s essential questions, and consider the types of analyses that we can use to answer each question. I’m just thinking out loud here (this is open notebook science, after all), and invite suggestions and discussion in the comments section. In particular, I’m referencing the “big questions” outlined in one of our first posts.

Why did ornithischians evolve quadrupedality multiple times?
I think this one is going to have to simply rely upon our interpretation of the data. After all, we can perhaps answer “how,” but the “why” can’t really be answered in this setting. So, it’s something to consider in the “discussion” section of the paper. But, see the next question. . .

Was the evolution of quadrupedality consistently associated with an increase in body size?
Here, we’re basically looking at evolutionary trends. In other words, can we detect a trend in body size within various ornithischian lineages? The more I think about this, the less I’m convinced we can directly answer the question (if you disagree, and have a solution, pipe up in the comments, please). One problem is the difficulty in knowing whether or not certain taxa were truly quadrupedal. So, where do you make the cut-off for quadrupedal vs. bipedal vs. both? In many cases we just don’t know. There’s a danger in circular reasoning, too (the limb bones look like it’s quadrupedal, so we call it quadrupedal, and then use it as an example of a quadrupedal taxon for analysis of limb bones).

But, I think we can detect trends across Ornithischia as a whole, and within specific lineages. For instance, is there a trend for increasing body size across Ornithiscians? Is there a trend for increasing body size within Ornithopoda? Ceratopsia? Thyreophora? In fact, Matt Carrano found a consistent and statistically significant increase in body size within ornithischians (and indeed, within most dinosaurs) when considering femoral measurements (go here to download a free PDF of Carrano, 2006).  So, that makes this question a little less interesting (and indeed, less publishable, because it’s already been done). Do you think we should move it to the back burner? Or should we spin it in another way? Thoughts are welcome.

Did different groups of quadrupedal ornithischians arrive at this body form in similar ways, or did they have different strategies?
Here (as far as I know) is a genuinely novel question, and I think it’s the core of the ODP’s current phase. What we’re really saying (I think) is this: We know that thyreophorans, hadrosaurs, and ceratopsids independently evolved quadrupedal locomotion. Did each group have similar limb proportions, or were they different? I think this is where we’ll want to look at principal components analysis, at least as a starting point for data visualization. And, we’ll have to do that within a phylogenetic context. A recent paper by Liam Revell (2009) addressed how to do this (thanks to ODPer Randy Irmis for bringing up this paper; you can download it for free here – it’s well worth a read).

A second way to look at this question is to look for trends in certain structures – for instance, do the metacarpals tend to get elongated in each group (relative to the rest of the arm) as different clades became quadrupedal? Here, we might use a simple non-parametric correlation of the ratio with patristic distances (see the Carrano paper, again, and references therein, for a brief introduction to this method), to investigate that question within different lineages. Basically, patristic distance estimates the distance of a particular species from the base of the tree (by the number of branching points leading up to it). A taxon that split off early in a group’s evolution would have a low patristic distance, and vice versa for one that split off late in a group’s evolution. So, we might look at the correlation of metacarpal:arm length ratio to patristic distance for thyreophorans, hadrosaurs, and ceratopsians.

I think I’ll end here for now! Please add thoughts, suggestions, corrections, and anything else you think relevant in the comments. Next time, I’ll move on to the final issue, quantifying morphological disparity in ornithischian evolution.

References
Carrano, M. T. 2006. Body-size evolution in the Dinosauria. In M. T. Carrano , R. W. Blob, T. J. Gaudin & J. R. Wible (eds.), Amniote Paleobiology: Perspectives on the Evolution of Mammals, Birds, and Reptiles. University of Chicago Press, Chicago:225-268. Freely available here.
Revell, L. J. 2009. Size-correction and principal components for interspecific comparative studies. Evolution 63: 3258-3268. Freely available here.

Image at beginning of post by Pavel Riha, licensed under the Creative Commons Attribution ShareAlike 3.0 License.

Found an Error? Have a Change to Suggest?

In order to streamline things during this time in the project (and in order to keep important notes from getting lost in other comment threads or email inboxes), I’ve created an “Errata” page. As it says there, this is an excellent place to post taxonomic suggestions, museum abbreviation updates, potential typos in the data, duplicate entries, etc. You can access it on the side bar, under Resources, with the link name of “Tasks: Found an Error“?

Thanks to contributor David Dreisigmeyer for the suggestion!

The ODP in the Spotlight #scio10

As I catch up after ScienceOnline2010, I wanted to share a few things that I learned there.

1. People love what we’re doing with this project. The response I received was nearly uniformly positive, and a number of people provided leads for future funding possibilities.
2. We’re not the only folks doing open notebook science. But, it’s still a pretty small niche in the broader profession. Will it become the dominant model? Or just a toy for a few crazy individuals? Only time will tell.
3. Our project is unusual among many citizen science projects in the depth to which participants are encouraged to contribute beyond data collection. We don’t want just data monkeys – we want folks who think about the process, contribute ideas, and (hopefully) help us craft the best research paper possible. Of course, we don’t think any less of you if you just want to submit data – but don’t feel limited to data entry alone if you desire more participation!
4. Our project is also unusual among citizen science projects in the stated publication goals. There seems to be a sense out there (I don’t know how accurate it truly is) that many of these sorts of efforts end in a nice pile of data, but no real published results. That’s all the more incentive to bring our paper through to its logical conclusion!

I have no word yet on the YouTube video of my presentation. Did anyone catch it live?

The ODP Around the Blogosphere
We’ve got a few new links to mention. These include:

• Desafiando a Nomenklatura Científica has a short blog post on the project.
• Sarah Dowdey, writing for Discovery News, discusses the ODP as egalitarian science. The Guild of Scientific Troubadours reblogged that story.
• Andria Krewson, on the PBS blog MediaShift, gives us a brief shout-out.
• Jeremy Yoder, writing at Denim and Tweed, talks about his impressions of the ODP from his attendance at ScienceOnline2010.
• Jean-Claude Bradley, writing at Useful Chemistry, has some nice things to say about the ODP presentation at ScienceOnline2010.

If you know of any others, please feel free to post the link in the comments section.