PLoS ONE's Paleontology Collection

As many of my posts over the past month have emphasized, the online open access journal PLoS ONE has been a hotbed of interesting papers relevant to paleontologists. Pterosaurs, Triceratops, whales, stromatolites, rodents and friends have been featured on the digital pages of this publication. Of course, the journal covers many other topics, too. So how is a paleontologist to find those papers immediately relevant to his or her research, among all of the other interesting papers on topics ranging from genetics to mathematics?

Enter PLoS ONE's Paleontology Collection. This is an open collection of articles--meaning that it is continually updated and augmented as new research is published in the journal. Everything the journal has ever published on paleontology is there! Right now, this includes a grand total of 26 articles, six of these in the first two months of 2009 alone. Contrast this a closed collection at PLoS ONE, which is a one-time conference proceedings or similar compendium of research.

Why should we care? Speaking selfishly, this will allow us to easily access all articles in our field. All future articles are automatically added to the collection. This means that if you don't want to wade through all of the other contributions on the PLoS ONE list (although there are some very interesting ones!), you can just keep an eye on the paleontology collection for any and all exciting developments. In a broader sense, this collection will help paleontologists to reach an even broader audience.

And once again--take advantage of the comment, note, and rating features at PLoS ONE (as outlined in my previous post). It's really a unique opportunity to interact with authors, make your thoughts known, and help science march onward. If you have that really cool piece of research, submit your manuscript!

To see what PLoS ONE has to say about the collection, point your browser here.

Image Credit: Mark P. Witton (see Witton and Naish, doi:10.1371/journal.pone.0002271)

Using the Comment, Note, and Rating Features at PLoS One

In my previous post, I highlighted some new articles from the online, open access journal PLoS ONE, and noted that the commenting feature at this journal is relatively unused for most articles. Some interesting discussion ensued on why this might be (among other issues). . .Mike Keesey suggested that maybe folks just aren't used to commenting in this format. Well then, let's do something about it!

Your Assignment:

• If you haven't already, create a user account on the PLoS website. This will allow you to post notes, make comments, and rate articles.
• Read an article that interests you on PLoS ONE (consider it part of your academic duty to keep on top of the recent literature), and make a substantive comment or note about something in the article. If you don't feel like making a specific comment (or if the article is so incredibly good as to not need comment), just rate the article.
• Feel good about contributing to a scientific discussion!
  

How It Works
Notes are for comments on specific portions of an article. For instance, maybe you think a particular sentence is well said, or relates to a very specific point that you have in mind. In this case, a note is most appropriate.

Comments are for more general thoughts on a paper--is there something particularly good, bad, or ugly? Might you have suggestions for an interesting follow-up study? Is there just something you're wondering about that you'd like the author(s) to answer?

Finally, ratings are a chance to tell folks what you really think about the paper. PLoS has three categories in which you rate an article--insight, reliability, and style. These categories are unfortunately vague in their names, but the PLoS website provides a succinct explanation of what is meant by each. Essentially, the categories rate the "importance" or "thought-provokingness" of an article, solidness of the conclusions, and technical execution and presentation of the whole package.

My First Notes, Comments, and Ratings
To check out an example, see another new paper in vertebrate paleontology published by Bates et. al:

Bates KT, Manning PL, Hodgetts D, Sellers WI (2009) Estimating Mass Properties of Dinosaurs Using Laser Imaging and 3D Computer Modelling. PLoS ONE 4(2): e4532. doi:10.1371/journal.pone.0004532

I just finished some notes, comments, and a rating of the article. (no, I did not do this just for the purpose of the blog--the topic genuinely interests me!) It's easy! Science marches on.

What are you waiting for? Go try it for yourself!

PLoS ONE strikes again!

So far, 2009 has been a banner year for vertebrate paleontology in the open access journal PLoS ONE. First there was the fighting Triceratops paper, followed by the Maiacetus announcement. This week brings two more offerings of the archosaurian persuasion:

Claessens LPAM, O'Connor PM, Unwin DM (2009) Respiratory Evolution Facilitated the Origin of Pterosaur Flight and Aerial Gigantism. PLoS ONE 4(2): e4497. doi:10.1371/journal.pone.0004497

Martinez RN, Alcober OA (2009) A Basal Sauropodomorph (Dinosauria: Saurischia) from the Ischigualasto Formation (Triassic, Carnian) and the Early Evolution of Sauropodomorpha. PLoS ONE 4(2): e4397. doi:10.1371/journal.pone.0004397

I don't have time right now to blog these articles (and I really, really need to get that Slicer series finished!), but do have the following thoughts:

• Is this string of papers a fluke, or is PLoS ONE becoming a more accepted, high-profile journal along the line of Science and Nature?
• PLoS ONE offers the opportunity to post comments about the article (ostensibly for "post publication peer review"). Yet, this feature really hasn't been utilized much for many of the paleontological articles. Is it that the articles are just that good? Or are paleontologists shy about posting their thoughts on this sort of thing, and saving it instead for the peer reviewed literature? Or, are the papers just not worth commenting on? Or, do paleontologists have better things to do with their time?

One Velociraptor Per Child

If you follow the open source/open access movement at all, you're probably familiar with the "One Laptop Per Child" initiative. Well. . .now there is a movement that combines the open access aesthetic with paleontology:

One Velociraptor Per Child

(I promise a real post after this week is done!)

New Paleo Paper in PLoS ONE

If you haven't seen already, the past two weeks have been great for paleontology on the pages of PLoS ONE, a high-profile open access journal. Phil Gingerich and colleagues have just published a paper on Maiacetus, a new fossil whale from Pakistan. Other bloggers have done a much more thorough job than I could of presenting the work and its importance for understanding whale evolution, so I'll just link to them and the original article.

It is good to see more paleo papers taking the open access route!

Gingerich PD, ul-Haq M, von Koenigswald W, Sanders WJ, Smith BH, Zalmout IS. (2009) New Protocetid Whale from the Middle Eocene of Pakistan: Birth on Land, Precocial Development, and Sexual Dimorphism. PLoS ONE 4(2): e4366. doi:10.1371/journal.pone.0004366

Read about it at Laelaps, Not Exactly Rocket Science, A Blog Around the Clock, The Loom, and elsewhere.

The Open Source Triceratops Paper

Wow! The past few days have been a real whirlwind. As mentioned in my last post, our long-awaited paper (well, long-awaited by my co-authors and me) on Triceratops horn use and paleopathology was unleashed by PLoS ONE on Tuesday evening. We've received some wonderful feedback through this blog and email, and are very ready to move on to the next research project.

Because this blog focuses partly on open access and open source software, I wanted to write briefly about how these issues factored into our research. This is one of the most "open" projects I've attempted to date, from start to finish. Here are the details:

• The data collection and statistical analysis were completed in OpenOffice.org Calc, with the calculations based on a spreadsheet file I found (and tested against known examples) from somewhere on the internet (but can't remember where, now!). R will also do the appropriate calculations, but I stuck with the spreadsheet because my data files were so small and straight-forward.
  
• The manuscript was written in OpenOffice.org Writer, but my co-authors and I batted it back and forth in Word format (because Darren and Ewan are using the latter program). We had no problems with this strategy, and the format conversions were a snap for the relatively simple documents we were using.
• The bibliography was compiled and formatted using Zotero. Zotero even has a readily available style file for PLoS, so this made my life very easy.
  
• The figures were edited for contrast and brightness in GIMP (no other manipulation was performed on the images) and assembled in Inkscape.
• The journal, PLoS ONE, was selected because of its high profile, high impact, and open access. Thanks to the open access policy, our article is readable by anyone who wishes to see it. I hope that the broader exposure will facilitate debate and further research on the topic--only time will tell. If I have any future articles of potentially broad interest, PLoS ONE will definitely be on my list of candidate journals.
• The popularization of the article was initiated by PLoS ONE, with follow-ups by numerous journalists and bloggers. Thanks to the wonders of the internet, many of the articles are available for free. And, I am happy to say, most of them are pretty well-done.
  

Triceratops Combat?

Exactly how did Triceratops and other horned dinosaurs use their cranial weaponry? Today, my co-authors Ewan Wolff, Darren Tanke, and I published new research in the online, open access journal PLoS ONE, giving our take on the issue. In a study spanning four years and over a dozen museums, we have marshalled what we think is the best evidence to date that Triceratops may have locked horns with their own kind.

Restoration of Triceratops in horn-to-horn combat. Image copyright Lukas Panzarin, courtesy Raymond M. Alf Museum of Paleontology.

The Background
The ceratopsids, or horned dinosaurs, present a bewildering array of cranial headgear. Triceratops was one of the earliest discovered and best known, with its distinctive dual brow horns, single nose horn, and a solid frill of bone over the neck. Subsequent discoveries revealed a clade chock full of anatomical diversity - single horns, triple horns, and frills sporting all sorts of odd accessories. Consequently, a whole host of functional explanations have been dreamed up for these bones.

Defense against predators was an early, popular explanation. With threats such as Tyrannosaurus stalking the Cretaceous landscape, Triceratops and relatives surely would have used their horns for defense if they had to. Yet, this is not the primary function of the horns in modern animals. More commonly, horns, antlers, and other appendages are used for intraspecific combat and display--not against predators. A good example is the massive horns of the bighorn sheep. Careful behavioral studies have shown them to be employed in impressive visual display to other sheep, or for combat over territory, mating rights, dominance, etc. These modern analogs were quickly compared with ceratopsids.

In addition to the determination of function by analogy, some paleontologists noted odd markings on the skulls of some horned dinosaurs. Perhaps a chunk of the frill was missing, with evidence of healing. Maybe there was an abnormal, oddly positioned hole on the skull. Inevitably, these oddities were attributed to "horn gouge wounds." These alleged pathologies were interesting--but anecdotal. Without a broader context, any attempts to infer a cause for the "injuries" usually amounted to constructing a "Just So Story."

Recently, the tide has turned against the idea of horns-as-weapons in Triceratops and its relatives. Research by Kevin Padian, Jack Horner, Mark Goodwin, and others have suggested that the odd cranial ornamentation of many dinosaurs was for more peaceful purposes--specifically, species recognition (picking out members of their own kind amongst a sea of similar species). Although this idea certainly has its merits, I was never quite convinced that the horns of Triceratops were completely benign (and to be fair, I don't know that the species recognition proponents were suggesting this as the only function, either). At the same time, I wasn't exactly convinced that every single ding on a fossil skull should be considered evidence for combat.

What We Did
I've been really interested in the issue of horned combat in Triceratops for some time. Several years ago, I published a brief study, using plastic models, that demonstrated such combat was at least physically possible. I made some predictions about where we should expect injuries on the skull, noted similarities with published anecdotes of alleged injuries, and left the issue open for a follow-up study. The models were fun to play with, but I wanted to know if this combat actually happened in real life! And, I knew that paleopathology--the study of disease and injury in fossils animals--was probably the best approach. Unfortunately, I didn't know that much about the topic.

So, I teamed up with two experts. Darren Tanke works at the Royal Tyrrell Museum of Paleontology, and is an expert in both paleopathology and ceratopsian dinosaurs. Ewan Wolff recently finished his dissertation on oral pathology in archosaurs at Montana State University, and now is a student at the University of Wisconsin-Madison School of Veterinary Medicine. Ewan and Darren provided expertise in identifying and interpreting the markings we observed on the ceratopsid skulls.

Our logic was simple--if ceratopsid dinosaurs used their horns against each other in combat, evidence of this should be found in bony lesions on the skull. And, assuming that animals with different horn configurations fight differently (a fair assumption from observations of modern horned critters), we should find differing rates and patterns of lesions between different species of horned dinosaurs. If the horns were not used in combat (or specifically, patterns of horn locking that could result in injury to the skull), we should see no difference between various species.

So, we surveyed many, many specimens at over a dozen museums across North America. We looked for any evidence of pathology, and recorded its location on the skull. Two genera were the focus of our research--Triceratops (pictured at the top of the post) and Centrosaurus (pictured below this paragraph). Centrosaurus has only a single nasal horn (and no massive brow horns), so we assumed that it would be most likely to show differences from Triceratops if there were any to be found. After years of data collection, we subjected all of the numbers to statistical analysis. Lots of folks (Darren and I included) had described anecodotal reports of pathology before--but nobody had subjected them to the rigors of statistics.

One artist's concept (courtesy Wikimedia Commons) of Centrosaurus in combat.

What We Found
Briefly, we found that most bones of the skull that we examined did not show statistically significant differences (i.e., P>0.05) in rate of pathology between the two genera. Except, that is, for the squamosal bone of the frill (shown on the figure below). But what does this mean?

Schematic showing rates of pathology (number of pathological elements/total elements examined) for Triceratops (top) and Centrosaurus (bottom). The squamosal rates, highlighted here, were different from each other at P<0.05.

Did Triceratops Fight Each Other?
As you can probably guess by now, we postulate that the differences in rates of pathology between Triceratops and Centrosaurus were caused by behavioral differences. In other words, because Triceratops were locking horns with either other, they got injured. However Centrosaurus used its horns (whether for combat or display, or whatever), they didn't commonly cause injury to the squamosal bone. We do consider some alternative explanations for the lesions (predator attack, microbial origin, etc.), but generally discount these (read the paper for a full explanation).

As a reminder, if the horns were only being used for display (species recognition, or whatever), we wouldn't expect to have seen these differences in pathology rates between the two species. Thus, I am reasonably comfortable saying that the horns weren't "just for looks."

What Does This Mean for Dinosaur Research?
The statistical study presented here is some of the best evidence to date (in our opinion) for intraspecific combat in Triceratops. Centrosaurus may well have done the same, just in a very different manner (flank butting, or something like that). Or, maybe Centrosaurus was a more peaceful taxon--we just don't know yet. Lots more research is needed in this area.

Another big question is why these animals were fighting. Mating rights? Sexual dimorphism hasn't been demonstrated in the taxon, so it doesn't seem like males and females are set up any differently in terms of horn configuration (but further study may change this). Territory? Who knows (and good luck investigating this with fossils!). General bad temper? Your guess is as good as mine. We may never know the why in this case.

Centrosaurus came from an ancestor with big old brow horns--perhaps this ancestor lost the horns in favor of a kinder, gentler approach. The latest centrosaurines (living millions of years after Centrosaurus), such as Pachyrhinosaurus, ditched their horns altogether in favor of big bony pads on the skull. So, did centrosaurines evolve towards less risky forms of combat? Again, this is another hypothesis that should be tested more thoroughly. There's lots more work to do!

On a more methodological note, we hope that more studies of dinosaurian paleopathology will adopt a statistical approach. Anecdotes are interesting, and can be very informative in some cases, but they only tell part of the story. There is strength in numbers!

What Aren't We Saying?
Because cranial function is a contentious issue, I just want to make clear on what we aren't claiming. (I am speaking for myself here--my co-authors are probably largely in agreement)

• All injuries on ceratopsid skulls are attributable to combat. No, no, no. Just because there is a ding on the skull doesn't mean it's a combat wound. Almost certainly, some non-combat injuries are included in our sample--this is why we looked at overall patterns, rather than anecdotal cases. I would be willing to say, though, that the overall pattern of lesions (at least on the squamosal) suggests that most of them were caused by the horns of other ceratopids.
• Ceratopsid horns were only for combat. Again, no. This isn't the case in modern animals, and it likely wasn't the case for ceratopsids. As I (and Darren) have said elsewhere, ceratopsid horns were probably like Swiss Army Knives--multi-purpose tools. Fighting, defending, showing off, cooling off, you name it. I am just saying that now we shouldn't exclude fighting as a function.
• All ceratopsids used their horns identically. No. Different horn morphologies suggest different uses--and I would be willing to believe (as others have suggested) that animals such as Pachyrhinosaurus focused on flank-butting behavior (rather than head-to-head combat). Again, this will need more work.
  

Parting Thoughts
This has been a really, really fun study, and one that I hope will spur more research on the possibilities for skull function in horned dinosaurs. We haven't heard the last on this issue, rest assured. There are lots more specimens, new species to describe and discover, and many other people working to better understand these magnificant animals. I would also like to publicly thank my co-authors--I have learned so much about paleopathology and ceratopsids from you! Finally, a big thank you to our artist, Lukas Panzarin, who skillfully brought to life a long-vanished Triceratops battle.

Farke AA, Wolff EDS, Tanke DH (2009). Evidence of Combat in Triceratops. PLoS ONE, 4 (1):e4252. DOI: 10.1371/journal.pone.0004252
Read and download it for free at: http://dx.plos.org/10.1371/journal.pone.0004252

Coming soon. . .other goodies related to this paper, including the open source software used in the research, the open access publishing experience, and much more!