The Open Source Paleontologist

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Ramblings on the role of open source software in paleontology, the latest and sometimes not-so-greatest ways in which we reconstruct the past, and the occasional bits of career advice and paleo news.

Andrew Farke
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  • April 8, 2011
  • 02:02 PM
  • 432 views

Life After Death At Yellowstone: An Interview with Josh Miller

by Andrew Farke in The Open Source Paleontologist

In my last post, I introduced a ground-breaking study recently published in PLoS ONE, that shows how we can infer long-term trends in animal populations just from their bones. This work has big implications for ecology, conservation, and public policy, and is also a really neat piece of science. For this post, I talked to the author of the study, Josh Miller, about his work and some of the tidbits that didn't make it into the paper.Yellowstone NP gets a lot of visitors, and you surely must have had some interactions with them during your fieldwork. How did they react to what you were doing? JM: I work in areas that are generally well off trail and in places most Yellowstone visitors just don't see. Over the years, there are have been very few times when tourists actually ever saw my teams conducting our bone work. Most of the time, conversation with the public occur in the evenings back at camp. We generally use the public campgrounds for our homebases and my research will often come up in conversation with tourists. When folks learn what my teams and I are up to, they are always very interested and ask lots of questions. Our National Parks are an important resource, and I think people like to be reminded of their biological and scientific value. At the same time, I think it gives folks a way of looking at Yellowstone in a new and exciting way. I know lots of people who talk to us one day and keep an eye out for bones the next.Miller studying bone survey data sheets on Northern Range, Yellowstone National Park. Photo by Scott Rose.You looked at hundreds of bones during your survey. Was there any particular specimen that stuck out in your mind? What about it was interesting?JM: I looked at over 20,000 bones during my work in Yellowstone. And you are right, there are a few that really stand out. Some of the most memorable bones are those of animals with severe bone maladies. In some individuals we found severe arthritis or broken bones that didn’t heal properly. Other memorable bones include rare and unusual species. One of the most exciting finds was the skull of a mountain lion. We just stumbled upon on it one afternoon walking from one transect to another. This beautiful rounded huge cat skull just lying in the grass staring up at us –a rare and amazing site.This paper focused on bones from large animals, but surely there are a lot of small animal bones out there too - rodents, bats, rabbits, etc. Do you think they would show a similar correlation over time between abundance in life and death? Or are the taphonomic effects too different between large and small animals to expect the same pattern? JM: Stay tuned! I kept careful attention to the bones of the small mammals we found. My bone survey teams were amazingly good at finding bones of all shapes and sizes (from bison skulls to limb bones of squirrels). One of the challenges, unfortunately, is the lack of high-quality data on the living populations in Yellowstone. One thing I'll say at the moment, however, is that the record of small-bones is surprisingly rich and diverse on the Yellowstone landscapes.I see that you used the open source stats program R to do your data analysis. Was this something you picked up just for your dissertation work? Why did you choose R over some of the other commercial packages that are out there?JM: I was introduced to R during the early days of my graduate work. R is a very powerful statistics language, in part, because of the large community of scientists and academics that use R and contribute to its ever-expanding utility. Another reason I use R is that I can completely control all aspects of the analysis. In canned programs, much of the analysis sits under a black box and uncovering exactly how the data were analyzed can be very difficult. But most of all, R just fits how I do science.Thank you for your time, Josh!CitationMiller, J. (2011). Ghosts of Yellowstone: Multi-Decadal Histories of Wildlife Populations Captured by Bones on a Modern Landscape PLoS ONE, 6 (3) DOI: 10.1371/journal.pone.0018057Note: I'm an academic editor at PLoS ONE, but had no role in the handling of this paper.... Read more »

Miller, J. (2011) Ghosts of Yellowstone: Multi-Decadal Histories of Wildlife Populations Captured by Bones on a Modern Landscape. PLoS ONE, 6(3). DOI: 10.1371/journal.pone.0018057  

  • April 8, 2011
  • 10:13 AM
  • 463 views

Life After Death at Yellowstone

by Andrew Farke in The Open Source Paleontologist

Taphonomy - the study of what happens to an organism after it dies - is integral to reconstructing the past. Perhaps the most important lessons come in inferring ecological interactions. Did that group of animals live and die together, or were they jumbled long after death? Were all of those shark teeth with the plesiosaur bones from a feeding frenzy, or just a fluke of currents? How closely does a set of fossils represent the relative abundance of the different species in the quarry? Such examples are numerous, and thus we commonly think of taphonomy as a study in deep time. This is certainly true, but also certainly incomplete. In fact, some of the most ground-breaking taphonomic work has been done in contemporary ecosystems. Kay Behrensmeyer, for instance, has spent decades studying bone accumulations in Kenya, and a 1927 work by Johannes Weigelt (complete with photos of dead cattle) is still considered a classic.A new study by paleontologist and taphonomist Josh Miller, just published in PLoS ONE, shows some of the great insights that can arise from looking at taphonomy in modern settings. Josh and his field assistants trekked through Yellowstone National Park (one of the western USA's oldest and best-known parks), cataloging the identity and physical condition of every animal bone sitting out on the surface (an elk skeleton from the project is shown at right; photo courtesy of and copyright Josh Miller). Using these data, Josh found that you can actually infer the major ups and downs of animal populations from their old bones. This is quite exciting, not just from a gee-whiz factor, but because it may be possible to infer population trends for areas where historical surveys are absent or spotty. Such data are important not only for ecologists, but for informed public policy. It sounds magical, so how was the study done?Based on other studies (in combination with radiometric dating), it's known that bones in excellent condition usually came from animals that died only recently, whereas bones in crummy condition are from animals that died longer ago. By using the condition of the bones as a proxy for time since death, Josh estimated how long the various bones of various animals had been around. Then, based on the bone ages, he estimated the relative population of each type of animal a given number of years ago. We have very good wildlife census data for Yellowstone, and it turns out that estimates from the bones match the "real" values quite nicely. Boom years for animals (such as elk) mean lots of bones going into the system, bust years mean few bones, and these trends shows up in bone surveys.You can read all about it at PLoS ONE, or here, here, and here. I recently talked to Josh to get a few behind-the-scenes tidbits. Stay tuned for the interview later today!CitationMiller, J. (2011). Ghosts of Yellowstone: Multi-Decadal Histories of Wildlife Populations Captured by Bones on a Modern Landscape PLoS ONE, 6 (3) DOI: 10.1371/journal.pone.0018057Note: I'm an academic editor at PLoS ONE, but had no role in the handling of this paper.... Read more »

Miller, J. (2011) Ghosts of Yellowstone: Multi-Decadal Histories of Wildlife Populations Captured by Bones on a Modern Landscape. PLoS ONE, 6(3). DOI: 10.1371/journal.pone.0018057  

  • December 13, 2010
  • 12:24 PM
  • 297 views

Back to the Late Jurassic, With Chris Noto

by Andrew Farke in The Open Source Paleontologist

If you ask the average person to imagine the Age of Dinosaurs, odds are quite good that they might envision a scene from the Morrison Formation. This Late Jurassic-aged (156 - 147 million year old) rock unit of the western United States has given us such dinosaur greats as Stegosaurus, Apatosaurus, Allosaurus, and more. Many of these animals are known from exquisitely-preserved, complete skeletons - and thus their anatomy has been described in pretty ridiculous detail. The functional morphology (how these animals moved, breathed, ate, and fought) has also gotten a lot of attention. But, this only tells us about the individual lives of the organisms. To really understand their world, we need to think bigger.Chris Noto, my friend and academic brother (we had the same Ph.D. advisor), has devoted his scientific career to a big-picture understanding of dinosaur ecology. He has a special place in his heart for the dinosaurs of the Morrison Formation, and has been chipping away at their ecology for quite awhile now. Thus, it was really exciting to see his recent co-authored paper in PLoS ONE, about that very topic. Also of note was that this paper served as Chris's contribution to the 2009 Paleo Project Challenge!Chris was kind enough to offer a little behind-the-scenes look at his project and the research results. I hope you'll find it enlightening!How did you get the idea for your project?Well, this involves going back a ways. I have always been fascinated by extinct organisms, particularly what they were like as living, breathing individuals in their environment. As an undergraduate at the University of Chicago I had the privilege of working with two really great scientists: Paul Sereno and Fred Ziegler. Paul is a well known paleontologist who has worked all over the world. Fred’s work was responsible for many of the paleogeographic and paleoclimate maps used today. Working with Paul got me thinking about how dinosaurs varied over space and time; working with Fred introduced me to global climate patterns and changes in continental arrangement.Once I got to graduate school at Stony Brook University I was taught the fundamentals of ecological theory. I started formulating an idea for looking at variation in dinosaur communities (the collection of all the different types of organisms that live in an area) and how those differences may be related to climate, but wasn’t sure how to approach it. Enter my good friend (and coauthor) Ari Grossman, who suggested applying this method, called Ecological Structure Analysis, commonly used in the study of fossil mammals. After some discussion on the appropriate way to adapt this method to the type of information available for dinosaur fossils, we agreed to work together on this project.What was the most challenging part of writing the manuscript?Like many papers, this one languished half done for many years. This was a side project of ours, and unfortunately our dissertation research had to come first. Every time I started working on it again I would realize that the data needed to be changed or updated, and this would sometimes change the results and our interpretation. I am a stickler for details and want to make sure all the data are as accurate as possible. But this project was simply too cool to let go. Once I graduated I decided to finish this manuscript as a first priority. It actually didn’t take too long after that once I put my mind to it; in the end I think that the paper was all the better for it. I learned a lot in the meantime, which contributed to making it a stronger manuscript. The hardest part by far though was actually submitting it to PLoS ONE for consideration. No one likes to be rejected, especially after putting so much work into a project! But this is the way the peer-review system works.I noticed that you used the program PAST for your statistical analyses - how did you decide on that program? Were there any particular challenges to using this software?I was attracted to PAST because it could perform the analyses I needed to do without a lot of unnecessary complication. Best of all, it was free, and I was a poor graduate student at the time. Most commercial statistics programs are expensive and difficult to use. PAST has a relatively simple interface and the results are easy to interpret, which is important. The major challenge with using PAST is in data management. If the data are not arranged in exactly the right way the analysis will not work correctly. Therefore it requires arranging the data first in a program like Microsoft Excel, and then copying and pasting it into PAST.What was the most interesting thing you learned while doing your research?First of all, I wasn’t sure what to expect when I started doing this research. No one has looked for large-scale patterns like this in dinosaurs before. One interesting thing I learned is that such patterns exist in the fossil record and are preserved over the immense spans of time between when these communities existed and when they were recovered. The most exciting result for me has to be the fact that the proportion of different “ecomorphs”, such as high-browsing herbivores vs. low-browsing herbivores or bipeds vs. quadrupeds, varies with climate. So, we can draw a connection between the climate, environment, and adaptations of organisms living in an area (see figure below). This is no surprise for any ecologist working today, but has not been shown in a terrestrial ecosystem as ancient as the Jurassic (~155 million years ago). This opens up new areas of research into the role climate change plays on the structure of ecosystems over time.Cartoon showing variation of environment and dinosaur ecomorphs. Drier conditions are on the left, where very large herbivores dominated among relatively sparse plant life. Communities under seasonal conditions are towards the center, and include a greater diversity of feeding modes among increased ground cover. To the right are moister conditions, where smaller herbivores are more prevalent within a more densely vegetated environment. Green=high browser, orange=intermediate browser, blue=low browser, red=ground forager. After Noto and Grossman 2010.Thanks, Chris! For more about his research, check out his web site.[Disclaimer: Although I am an editor at PLoS ONE, I had no role in the handling of this paper]CitationNoto, C., & Grossman, A. (2010). Broad-scale patterns of Late Jurassic dinosaur paleoecology PLoS ONE, 5 (9) DOI: 10.1371/journal.pone.0012553... Read more »

Noto, C., & Grossman, A. (2010) Broad-scale patterns of Late Jurassic Dinosaur paleoecology. PLoS ONE, 5(9). DOI: 10.1371/journal.pone.0012553  

  • November 22, 2010
  • 07:00 AM
  • 244 views

Big Pterosaurs Really Did Fly: Interview with Mark Witton Part II

by Andrew Farke in The Open Source Paleontologist

A new paper in PLoS ONE, by Mark Witton and Mike Habib, re-evaluates claims that big pterosaurs were too big to fly. To make a long story short, multiple lines of evidence suggest that giants like Quetzalcoatlus really did take wing! One of my previous blog posts summarized the paper and featured the first part of an interview with senior author Mark Witton. That part of the interview focused on many of the scientific aspects of the research. Today, we'll highlight some of the other highlights. I think you'll find it illuminating!This paper has received a fair bit of press coverage. Is there anything about the research that you wish had received more attention?Our coverage was really good: as mentioned above, we ended up in the most unlikely of places along with getting pieces in much more familiar territory. In that respect, I can’t complain but, at the same time, the press really focused on the quadrupedal launch idea [illustrated at right, with a Pteranodon launching itself in this fashion; figure from Witton and Habib 2010] which, while still quite novel to most, was actually first proposed (in print) by Mike back in 2008. There was a fair amount of press coverage for the idea back then, too. Prior to that, though, both Mike [Habib] and Jim Cunningham, who developed the same idea independently of Mike, had given the idea considerable airing on the Dinosaur Mailing List. Bottom line: this latest paper really isn’t the first to comment on it in any capacity. We talked about it a lot, but we’re definitely not its origin. Still, the press really ran with it, despite the fact that the main thrust of our paper is that pterosaurs and birds are generally incomparable beyond very basic aspects of their flight mechanics, and that previous assumptions that they were had lead to probably incorrect assumptions about their way of life. Their disparate launch mechanisms are a particularly important part of our considerations, but they are only one part of many. It’s no big deal, really, but I’m a little concerned that some people will now associate quad launching with this paper and I really don’t want to steal the thunder away from Mike and Jim: they did the real work on it. I’m sure People in the Know will realise the score, but I’ve already had e-mails about the presentation of the quad launch in our new paper like we proposed it. Tell the world, folks: quadrupedal launch came from Mike and Jim! They’re the real geniuses here!With you in the UK and Mike in the US, the paper is a very international collaboration. What sort of challenges, if any, were particular to this sort of cross-border work?Mike and I met up twice during the work on the project at different conferences, but, that aside, we worked entirely through e-mail. Trite as it sounds, the internet is amazing: a project like this would be so much harder and longwinded without it. Throwing drafts of the MS at each other, bouncing ideas around and working on the figures was no sweat at all. We could have revisions done and sent back to each other as fast as we could turn them around. In that respect it was as efficient as working with someone in the same department, if not slightly more so, as meandering chats and tangential fieldwork anecdotes – always a risk of visiting the office of any academic – were largely kept out of our online conversations (we made up for it at conferences, though). The long duration spent putting the paper together, mentioned above, was mainly thanks to my workload with the pterosaur models, not anything to do with working internationally. The paper spent a long time sitting on my desk as my time for writing disappeared amidst a blur of fake fur, bluefoam and acrylic paints. So no, working internationally presented very few obstacles. I’m sure the story would be very different if we were working 20 years ago or so, but, today, you can work with whoever you want, wherever they are without a hitch. Well, assuming they check their in-box regularly, that is.Thank you, Mark, for an informative interview!CitationWitton, M., & Habib, M. (2010). On the size and flight diversity of giant pterosaurs, the use of birds as pterosaur analogues and comments on pterosaur flightlessness. PLoS ONE, 5 (11) DOI: 10.1371/journal.pone.0013982[full disclosure: I am an editor at PLoS ONE, the journal in which this paper appeared]... Read more »

Witton, M., & Habib, M. (2010) On the size and flight diversity of giant pterosaurs, the use of birds as pterosaur analogues and comments on pterosaur flightlessness. PLoS ONE, 5(11). DOI: 10.1371/journal.pone.0013982  

  • November 19, 2010
  • 01:09 AM
  • 257 views

Big Pterosaurs Really Did Fly: Interview with Mark Witton

by Andrew Farke in The Open Source Paleontologist

Pterosaurs - winged denizens of the Mesozoic skies - get a bum rap. It's bad enough that their name is smeared by the general public, when animals like Pterodactylus are confused with dinosaurs in the news media and in just about every cheap set of plastic dinosaurs. Lately, some scientists have suggested that the largest of these animals just couldn't fly. Is it true that Quetzalcoatlus (pictured here; image from Wikimedia Commons), with its 10 meter wingspan, had wings that were too narrow, a body that was too portly, and bones that were too weak to support flight? Some of the most recent studies have certainly suggested this!Yet, extraordinary claims require extraordinary evidence, or at least extraordinary scrutiny. Thus, a study by pterosaur experts Mark Witton and Mike Habib takes a close look at the idea of super-lame flightless giant pterosaurs. Using new body mass estimates, revised reconstructions of the wing dimensions, bone strength calculations, and many other lines of evidence, Mark and Mike argue that even the biggest Quetzalcoatlus could fly after all.This paper, published in PLoS ONE [full disclosure: I am an editor for this journal], has been featured all over the mainstream news media and blogosphere. For a slightly different take on the matter, I decided to go straight to the source. Mark Witton (pictured below; thanks to Mark for the picture, copyright him) was kind enough to answer a few questions about the study - not just on its methods, results, and conclusions, but also on some of the behind-the-scenes doings that led up to this work.I've split this interview into two parts. For starters, we'll talk about the genesis of the paper, and some of its major findings.How did this study come about? Did any particular event spur you and Mike [Habib] into working on this issue of flight in giant pterosaurs?I reckon a paper like ours has been a long time coming, really. There’s been a lot of talk in recent years that pterosaurs may not be what Greg Paul termed ‘ultralight airbeings’, and numerous blogs and internet forums have responded with comments what this may mean for their flight dynamics. It was only a matter of time before the flight of realistically massed pterosaurs was considered in the technical literature (well, beyond saying they couldn’t fly). We were kicked into action, though, when press reports of an abstract presented by Katsufumi Sato et al. were released in April 2009, saying giant pterosaurs couldn’t fly. Keen members of the palaeoblogsphere may remember this ruffled a fair few feathers when it was released, and their paper (Sato et al. 2009) followed shortly to similarly raised-eyebrows. Most folks even vaguely familiar with large pterosaurs were astonished to see them cap flight at such a low size: 41 kg and 5 m wingspans are very middling in the spectrum of pterosaur size (10.5 m spans and 250 kg body masses are considered maximum in our paper). Because plenty of clearly-flight adapted forms got much larger than this, I got to work on a response. Mike and I have fairly regular correspondence and were talking about the project soon after I started, and it wasn’t long before we realised that working together would make the project much stronger.Plus, I had giant pterosaurs on the brain at that time. I’d just started work on a massive modelling project where I had to build several models of the largest pterosaurs going. The logistics and costs of building a 13 m span pterosaur against a 10 m span animal is quite something, so I figured a little checking of the wingspans of these poorly known animals wasn’t the worst way to spend an afternoon as it would avoid having to find a bigger workshop. The timing of this was spot on for the project with Mike, too, as it meant we could ensure the size estimates for our flight analysis were as accurate as we could make them. These two events combined to form the beginnings of the paper and reminds me that we started it well over a year ago: where did that time go?What was the most surprising finding to you, and why?The most surprising? Hard to put my finger on one thing exactly: we covered quite a lot of topics, and each had their own intriguing little revelations. I mean, the 13 m span estimates of Arambourgiania, the giant pterosaur from Jordan, always seemed a little iffy to me because they were based on a single neck vertebra, but not Hatzegopteryx. Being based on forearm material, I figured the 12 m span estimate for this critter was a sound bet but, no, the material just seems distorted to appear bigger than it actually is. The numbers generated in the flight analysis for the speed of flying giant pterosaurs were impressive, too. The thought of a giraffe-sized pterosaur pumping its wings to scream overhead at 75 mph is staggering: this is real ‘if I had a time machine…’ stuff.That said, for all these little surprises, the biggest ones came from the paper’s release and press coverage: I was really blown away to see just how much interest we had. To be honest, we did want to make a splash because, following the Sato et al. abstract, the internet is awash with articles saying giant pterosaurs couldn’t fly. We wanted to balance it out a little (this is also, incidentally, why we chose PLoS ONE as our venue: we want interested people of all backgrounds to be able to see our rationale for flighted giants: open access is definitely the way forward, folks). However, I was truly taken aback when our work was quoted directly alongside some half-naked chick in the British tabloids newspaper, The Sun. How often do science stories penetrate that far into the press, let alone those dealing with relatively unimportant extinct flying reptiles? I can only assume that pterosaurs are becoming more exciting and cool with every new discovery, or it was a slow news day. Either way, I’ve not stopped telling people about that since.Next Time. . .the ins and outs of trans-Atlantic collaborations, and what the media should have mentioned.CitationsSato, K., Sakamoto, K., Watanuki, Y., Takahashi, A., Katsumata, N., Bost, C., & Weimerskirch, H. 2009. Scaling of soaring seabirds and implications for flight abilities of giant pterosaurs. PLoS ONE, 4 (4), DOI: 10.1371/journal.pone.0005400.Witton, M., & Habib, M. (2010). On the size and flight diversity of giant pterosaurs, the use of birds as pterosaur analogues and comments on pterosaur flightlessness PLoS ONE, 5 (11) DOI: ... Read more »

Witton, M., & Habib, M. (2010) On the size and flight diversity of giant pterosaurs, the use of birds as pterosaur analogues and comments on pterosaur flightlessness. PLoS ONE, 5(11). DOI: 10.1371/journal.pone.0013982  

  • November 17, 2010
  • 10:21 AM
  • 330 views

Ancient Beavers in PLoS ONE: Interview with Josh Samuels

by Andrew Farke in The Open Source Paleontologist

An earlier post here detailed a study just published in PLoS ONE, which focused on unraveling the relationship of an extinct Chinese beaver, Sinocastor, to its modern cousins in the genus Castor. Using a combination of morphometrics (shape analysis) and good old fashioned description, a team led by paleontologist Natalia Rybczinski concluded that Sinocastor is indeed quite distinct from today's Castor.Yesterday I caught up with one of the co-authors of the study, Josh Samuels. Josh is an expert on fossil rodents (especially beavers) and morphometrics, working as a paleontologist at John Day Fossil Beds National Monument. He was kind enough to answer a few questions about his part in the project.You have quite a track record of working with beavers and other rodents. How did you get interested in this group in the first place?Ever since I was a kid, I have been interested in understanding how extinct species lived. In college I became interested in studying the evolution of mammals, particularly their dietary and locomotor specializations. I learned that rodents are the most species rich group of mammals and have amazingly diverse ecologies, with everything from semi-aquatic carnivores to gliding herbivores and blind burrowers. Despite their diversity, the evolution of rodents has not been as well studied as some other groups. Beavers, in particular, are known for their dramatic impact on ecosystems and have an excellent fossil record. Given their importance today, I find working to understand their evolution to be quite fascinating.The PLoS ONE paper certainly was a collaborative effort - what role did you play in the research?Some of my past research used geometric morphometrics to examine how skull shape in rodents relates to their ecology. Natalia approached me about the possibility of using similar techniques to examine how Sinocastor was related to living and extinct beavers. I helped design the methods and ran most of the analyses, and writing the paper was definitely a group effort. Having a group of collaborators with different skills really helped the project come together smoothly.Was there anything particularly surprising to you about the results?Given the broad geographic range of Eurasian and North American beavers today, I was surprised to find subtle, yet consistent differences in shape among species. One of the specimens in our analysis was from a peat bog in England, but its skull shape was almost identical to individuals from China and Russia. This really gives me hope that these techniques could be used an effective way to look at the phylogenetic relationships of extinct species.Thanks, Josh!CitationRybczynski, N., Ross, E., Samuels, J., & Korth, W. (2010). Re-evaluation of Sinocastor (Rodentia: Castoridae) with implications on the origin of modern beavers. PLoS ONE, 5 (11) DOI: 10.1371/journal.pone.0013990Full disclosure: I am an editor at PLoS ONEImage credits: National Park Service website... Read more »

Rybczynski, N., Ross, E., Samuels, J., & Korth, W. (2010) Re-evaluation of Sinocastor (Rodentia: Castoridae) with implications on the origin of modern beavers. PLoS ONE, 5(11). DOI: 10.1371/journal.pone.0013990  

  • November 16, 2010
  • 09:05 PM
  • 304 views

Re-Evaluating Ancient Beavers

by Andrew Farke in The Open Source Paleontologist

Beavers are some of the most distinctive (and largest) rodents around today. Two species of the extant beaver, Castor, are found throughout the northern hemisphere, and these animals have an enormous effect on their landscapes. Beavers are perhaps most famous for their dam-building activities, altering the flow of streams and generating valuable wetlands used by other animals. Surely, the impact of this group extends far back in geological time.Many early beavers were fossorial, or burrowing, with little indication of aquatic tendencies. For instance, the 25 million year old Palaeocastor produced giant spiraled burrows known as "devil's corkscrews." Perhaps the acme of beaver evolution occurred during the Miocene (~23 to 5 million years ago). At least 12 genera lived worldwide; only one of these, Castor, survived to the present day. An obvious question for paleontologists thus concerns the when and where of modern beavers' origins.Enter Sinocastor. This genus was named in 1934 by famed Chinese paleontologist C.C. Young, for several species recovered in China and Mongolia from rocks deposited during the last 5 or 6 million years. Almost immediately, other authors lumped Sinocastor into Castor, and there Sinocastor has stayed for the most part. Was this a valid opinion, or did such lumping obscure a more interesting paleontological pattern?Fortunately, the exquisitely-preserved type (first described) specimen for Sinocastor anderssoni was recently restudied by a team of paleontologists from Canada and the United States. Led by Natalia Rybczynski of the Canadian Museum of Nature, the paper describing their findings appeared this week in the open access journal PLoS ONE.The authors of the new paper used geometric morphometrics, a type of shape analysis, to see just how similar the skull of Sinocastor (at right) was to modern and recently extinct Castor. For additional comparison, the early European beaver Steneofiber castorinus was also thrown into the mix. Points on the various skulls were digitized from photographs and run through computer programs that calculated the similarity between the specimens.In the end, the skull of Sinocastor fell well outside the anatomical range for modern and even most extinct beavers. Rather substantial shape differences distinguish Sinocastor from Castor; for instance, the snout is shorter and the braincase broader in Sinocastor. Although genera are always somewhat subjective, Rybczynski and colleagues argue that the major differences between Sinocastor and the species of Castor warrants the retention of Sinocastor as its own genus.Based on several other lines of evidence (including tooth anatomy), it is suggested that Sinocastor may be the sister taxon (closest relative) to modern beavers. In concert with dated fossils, this means that the common ancestor of these two kinds of beaver may have originated in eastern Asia and then spread westward into Europe and eastward into North America. The arrival of modern beavers on that landscape must have had massive ecological consequences - only more investigation of the fossil record will tell!Stayed tuned: Tomorrow, an interview with Josh Samuels, one of the paper's authors!CitationRybczynski, N., Ross, E., Samuels, J., & Korth, W. (2010). Re-evaluation of Sinocastor (Rodentia: Castoridae) with implications on the origin of modern beavers PLoS ONE, 5 (11) DOI: 10.1371/journal.pone.0013990Full disclosure: I am an academic editor at PLoS ONE, the journal at which the paper described here was published.Image credits: Image at top from Wikimedia Commons (by Steve); fossil skull modified from Figure 14 in Rybczynski et al., 2010.... Read more »

Rybczynski, N., Ross, E., Samuels, J., & Korth, W. (2010) Re-evaluation of Sinocastor (Rodentia: Castoridae) with implications on the origin of modern beavers. PLoS ONE, 5(11). DOI: 10.1371/journal.pone.0013990  

  • September 22, 2010
  • 11:31 AM
  • 308 views

Horned Dinosaurs: When It Rains, It Pours

by Andrew Farke in The Open Source Paleontologist

2010 will surely go down as the annus mirabilis of horned dinosaur research. Between the publications of the horned dinosaur symposium volume (with its myriad new taxa and other exciting pieces of research), a "bagaceratopsid" in Europe, a true ceratopsid in Asia, the hypothesis that Torosaurus and Triceratops are growth stages of the same taxon, and more, it's really tough for a "ceratophile" (to borrow Peter Dodson's term) to keep up!Today continues the embarrassment of ceratopsian riches. With my co-authors Scott Sampson, Mark Loewen, Cathy Forster, Eric Roberts, Alan Titus, and Josh Smith, I'm pleased to introduce you to Utahceratops gettyi and Kosmoceratops richardsoni (at top and bottom, respectively, in the image at right), freshly published in PLoS ONE. Although it's been a long time coming, our hope is that these new critters will really knock your socks off!So what's so special about these two animals? Well, for one they're new dinosaurs. And new horned dinosaurs at that. On a broader note, our new critters (along with careful radiometric dating of the Kaiparowits Formation, the rock unit in southern Utah from which they originated) provide important evidence for dinosaur provincialism during the Late Cretaceous. In other words, these big, elephant-sized dinosaurs weren't traveling far. They're the same age as dinosaurs known from much further to the north, yet represent a very different part of the horned dinosaur family tree. This is strange, especially when you consider that today there is only one (or maybe two, depending on whom you ask) elephant species in all of Africa! 75 million years ago, there were three or four closely related species of horned dinosaur living simultaneously on that little strip of beachfront property that comprised western North America. And that's not counting a few more less closely-related horned dinosaurs (centrosaurines) that lived at the same time! Truly weird.There's been a lot said more eloquently elsewhere about these animals, so I'm just going to close with an answer to the question that should be at the top of many people's minds. Given the possibility that Torosaurus and Triceratops might be growth stages of a single species, how do we know that Utahceratops and Kosmoceratops aren't just growth stages of one species? After all, they lived at the same time in the same place, and end up somewhat close together on the phylogenetic analysis. Well, we certainly haven't done much in the way of histology yet, which would lay the issue completely to rest. However, as readers of the paper will note, we have obvious juveniles (based on sutural fusion and cranial element size) of both species. Although these remain to be published, in my opinion they pretty firmly demonstrate that both species of dinosaur were very different very early on in their development.So, go read the paper!Full disclosure: I am a section editor at PLoS ONE, the journal at which this new paper was published. However, I had absolutely no involvement in the handling of the manuscript (assigning the academic editor, selecting reviewers, making a publication decision, etc.).Image credit: Lukas PanzarinCitationSampson, S., Loewen, M., Farke, A., Roberts, E., Forster, C., Smith, J., & Titus, A. (2010). New horned dinosaurs from Utah provide evidence for intracontinental dinosaur endemism PLoS ONE, 5 (9) DOI: 10.1371/journal.pone.0012292... Read more »

Sampson, S., Loewen, M., Farke, A., Roberts, E., Forster, C., Smith, J., & Titus, A. (2010) New horned dinosaurs from Utah provide evidence for intracontinental dinosaur endemism. PLoS ONE, 5(9). DOI: 10.1371/journal.pone.0012292  

  • May 6, 2010
  • 10:05 AM
  • 370 views

Tony Martin Interview, Part 2

by Andrew Farke in The Open Source Paleontologist

Yesterday, I ran the first part of this two-part interview with Anthony (Tony) Martin, senior author on a new paper in PLoS ONE. The research details a rare trace fossil (figured below) left behind by a bottom-feeding fish over 50 million years ago. Yesterday's questions focused on the science - in the final installment, we'll learn more about the publishing process. (Full disclosure: I am an editor for PLoS ONE, and was the editor who handled this manuscript.)Why did you choose PLoS ONE as a venue for the manuscript?All three of us really liked the fact that by publishing in PLoS ONE we could better share our research with both our colleagues and the general public. All too often I’ve published papers that were read by maybe two or three dozen of my colleagues (if I’m lucky), rather than a broader audience that might also find the work really interesting. I’ve also published in journals with “pay walls” erected to prevent non-subscribers from seeing articles. I know this really frustrates some science bloggers who want to write about the original research instead of just relying on press releases or news articles. So I am becoming more enamored with making sure all science enthusiasts have free access to original research results. PLoS ONE also has published some top-notch paleontological articles in the past few years, so it’s become a high-profile place to publish, while also permitting laypeople to learn from our science.We also thought this research made for an interesting “fish story” combined with a “detective story,” sort of Sherlock Holmes-meets-fishing-meets-paleontology-meets-spatial analysis. The study also has some visually interesting elements, which through publishing in an electronic journal we could better share through our new (and very cool) application of the Deep Zoom™ software (link here). Now anyone with an Internet connection can check out the same trace fossil analyzed in the study through the pan-and-zoom function of the software.Was there anything about the PLoS ONE process (good or bad) that surprised you?Not really. One of my coauthors, Gonzalo [Vazquez-Prokopec] had previously published in one of the PLoS journals and said it was a straightforward process, with timely peer review and good, thorough feedback from the reviewers and editors. I’m pleased to say that our experience was the same, and it encourages me to consider PLoS ONE for future contributions.Which of the Green River fish would have tasted best?I would have loved to try Priscacara liops, either pan-fried or steamed with ginger, garlic, scallions, and soy. I’m not so sure that Notogoneus osculus [the focus of the current paper] would have been nearly as tasty, especially considering that we’re even more certain now it was a bottom feeder.A big thank you to Tony, for taking the time for this interview. Don't forget to check out the paper, if you haven't already!ReferenceMartin, A., Vazquez-Prokopec, G., & Page, M. (2010). First known feeding trace of the Eocene bottom-dwelling fish Notogoneus osculus and its paleontological significance PLoS ONE, 5 (5) DOI: 10.1371/journal.pone.0010420Image credits: Image of the ichnofossil modified from the original paper at PLoS ONE.... Read more »

Martin, A., Vazquez-Prokopec, G., & Page, M. (2010) First known feeding trace of the Eocene bottom-dwelling fish Notogoneus osculus and its paleontological significance. PLoS ONE, 5(5). DOI: 10.1371/journal.pone.0010420  

  • May 5, 2010
  • 08:56 PM
  • 362 views

Something Fishy in PLoS ONE (and it's pretty neat!)

by Andrew Farke in The Open Source Paleontologist

The open access journal PLoS ONE has published a lot of neat paleontology articles over the last few years (see here for a reasonably comprehensive listing). Charismatic, terrestrial vertebrates (whether dinosaurs, Ice Age mammals, or prehistoric humans) seem to dominate. But what about the poor, neglected fish?

Today, PLoS ONE published a nifty article by Anthony (Tony) Martin [pictured at left] and colleagues, discussing a 50 million year old fish feeding and swimming trace fossil from Wyoming. In the build-up to the release of their paper, Tony (a paleontologist with a specialization in trace fossils, over at Emory University) was kind enough to answer a few questions about the paper. Part 1 (focusing on the science behind the paper) is posted today, and Part 2 (focusing on the open access angle) will arrive tomorrow. [Full disclosure: I was the academic editor at PLoS ONE who handled this submission]
Briefly, what is the importance of the finding described in your new paper?
Several parts of it are important, and they’re all related. One is that this is the first fish trace fossil described in detail from a formation that’s world-famous for its fish body fossils, the Green River Formation near Kemmerer, Wyoming. The Green River Formation was made by a series of lakes about 50 million years ago, and it preserved many gorgeous fossil fish, which have been collected and studied since the 1850s. However, fish trace fossils, such as trails made by their fins while swimming along the lake bottom, have been mostly neglected. Trace fossils can be extremely valuable for directly reflecting ancient behavior, and because the trace fossil we studied was extraordinarily detailed, it gave us some new insights we might not have gleaned from the fish body fossils. Secondly, we are very sure about the species of fish made the trace fossil, namely, Notogoneus osculus [figured at right]. This fish had always been interpreted as a bottom feeder, and this is the first trace fossil to confirm this behavior. Our identification of the tracemaker is unusual, because oftentimes it’s tough to tell just what animal made a particular trace fossil. This one, though, gave us some great clues about “who done it.” The trace fossil [see figure below] has beautiful sine-like waves and other marks that show it made by a fish with a downward-pointing mouth, two pelvic pins, an anal fin, and a caudal fin. What really cinched it, though, was that this same species is also found as a body fossil in the same layer as the trace fossil. So our conclusion about the tracemaker is a pretty tight fit in every respect. Thirdly, we figured out the size of the fish by applying some mathematical and spatial-analysis techniques that had never been used previously on a fish trace fossil. From these methods, we were calculated that the fish was 45 cm, or about 18 inches, which is exactly the average size of Notogoneus osculus. So not only do we know which fish did it, we know how big it was! This makes for a great fish story, because we can say that it was “the one that got away,” we can tell people what it was, and hold out our hands to say, “and it was THIS big (45 cm).” The kicker, of course, is that we’re talking about a fish from 50 million years ago, and in a lake that dried up nearly that long ago. Lastly, this trace fossil shows a fish behaving normally, swimming and feeding along the lake bottom. Yet it was made in the deepest part of Fossil Lake, which supposedly excluded live fish because of low-oxygen conditions. So this fish trace fossil, along with a few others we mention in the paper, should give future researchers a good reason to reconsider the paleoecology of Fossil Lake. We now know that fish feeding on the bottom of the deepest part of Fossil Lake was a part of its benthic ecology, giving us a new insight about this long-studied deposit. If you could share one thing about the research that didn't make it into the paper, what would that be? Is there an interesting back story to the project? Actually, two things should be mentioned, the back story and a philosophical perspective. The back story is that this may be the only paleontological paper in which the coauthors consist of an ichnologist (me), a disease ecologist (Gonzalo Vazquez-Prokopec), and a geographer (Michael Page). I know it sounds like the start of a bad (and really nerdy) joke, as in, “An ichnologist, a disease ecologist, and a geographer walked into a bar one day…”, but it was a great opportunity for the three of us, all in the same Environmental Studies department at Emory University, to work together in a creative and synergistic way. I did the primary detective work, interpreting the trace fossil in the broadest sense, Gonzalo did some spatial analysis and Fourier transform calculations, and Michael put together the Deep Zoom™ application that allows a viewer to look at a detailed digital image of the trace fossil. This shows how science can work in imaginative ways! The philosophical point I want to make is summarized by a sentence buried in the paper that refers to places where the fish’s fins lifted off the bottom of the lake and left no marks: “In other words, these breaks in the continuity of the fin trails also constitute parts of the trace fossil, and have behavioral significance.” A metaphor I will use to descr... Read more »

Martin, A., Vazquez-Prokopec, G., & Page, M. (2010) First Known Feeding Trace of the Eocene Bottom-Dwelling Fish Notogoneus osculus and Its Paleontological Significance. PLoS ONE, 5(5). DOI: 10.1371/journal.pone.0010420  

  • March 23, 2010
  • 10:11 PM
  • 392 views

Welcome, Seitaad!

by Andrew Farke in The Open Source Paleontologist

I am pleased to announce the publication in PLoS ONE of Seitaad ruessi, a new sauropodomorph dinosaur from the Lower Jurassic Navajo Sandstone of southern Utah. Sauropodomorphs are (mostly) herbivorous dinosaurs that lived from the Triassic all the way until the end of the Cretaceous. Although most people know the giant quadrupedal sauropodomorphs like Brachiosaurus and Apatosaurus ("Brontosaurus"), many of the early sauropodomorphs were bipeds smaller than humans. Seitaad fits in the latter category. For reasons explained below, this is a really cool little animal and a truly rare find.I have a personal connection to this fossil on two levels. First, the authors of the article, Joe Sertich (at left, pictured with the specimen) and Mark Loewen, are good friends and colleagues of mine. So, I was really excited when they told me that they wanted to submit their manuscript to PLoS ONE (full disclosure: I am an editor there; for obvious reasons, someone else handled their submission). I'll confess that I did little to discourage them. Congratulations, Joe and Mark, on a great paper!Second, I was one of the lucky people who got to carry the block containing Seitaad from its original resting place, way back in 2005. This thing was heavy! It took a crew of 12 people (7 carrying at a time, and 5 resting for rotation back in) to haul it out. After several years of preparation and study, the new animal is finally named!I queried one of Seitaad's authors, Mark Loewen, for his thoughts on the find (Joe Sertich is out of the country, so wasn't able to contribute). Here's what Mark had to say.Briefly, what is the most significant aspect of the new find reported in PLoS ONE?Seitaad is the first dinosaur discovered from the Navajo Sandstone of Utah and one of the oldest known dinosaurs from Utah. The Navajo Sandstone is a dominant rock unit exposed all over the west. . .and is hiked by thousands of people every year. Fossils in this formation are extremely rare. Prior to its discovery our entire view of the fauna of the Navajo consisted of a partial tritylodont, three chunks of crocodylomorphs, parts of a small theropod, [and] two fragmentary sauropodomorphs. Seitaad is the most complete fossil from the Navajo and through comparisons with taxa across the world gives a much better picture of the largest herbivore in the sand seas of western North America at the same time that large true sauropods had evolved in other parts of the world.How did you choose the name that you did?Seitaad was found by Joe Pachak [pictured at left, with the specimen], a local archaeologist and artist from Bluff, Utah while hiking Comb Ridge to document petroglyphs and pictographs. He reported the specimen to the BLM, who alerted us at the Utah Museum of Natural History. We went down to check it out, and immediately started to excavate the specimen. With a crew of 12, including Andy Farke, we hauled out the jackets and began preparing them at the UMNH.The area around Comb Ridge is covered with numerous archaeological sites and cliff dwellings from the ancestral Puebloan (Anasazi) culture. In fact, Seitaad was located directly below a dwelling called the Eagles Nest. The people who lived in the area at the time would have recognized the white bones of Seitaad eroding out of the cliff if they had seen them. A nearby cliff dwelling has a slab with a dinosaur track incorporated into the window sill. I’m confident that the person who [put] this stone into the window had awareness and appreciation for the fossils preserved in the Four Corners region."Seitaad" is derived from Seit’aad, a sand-desert monster from the Navajo (Diné) creation legend that swallowed its victims in sand dunes. The skeleton of Seitaad had been "swallowed" by a fossilized sand dune. The [species name] "ruessi" is derived from Everett Ruess, the famous young artist, poet, historian, and explorer who disappeared in southern Utah in 1934. Ruess is celebrated for his love of the region, its people, and for his free-spirited and adventurous lifestyle. Everett Ruess loved the red rock country of Utah and spent a lot of time exploring the Navajo Formation, so we thought it was fitting to honor him in the taxonomic name.Why did you choose PLoS ONE as a venue for your research?We chose to submit to PLoS ONE for several reasons. The open-access format of PLoS ONE and rapid turn-around were major factors. Another factor was the opportunity to reach a broader audience and the rising impact and recognition of PLoS ONE within the paleontology academic community. Another consideration was the lack of limits to figures and unrestricted use of color. The unlimited use of color became a concern during the preparation of our manuscript, when it became clear that black and white photos were not revealing proper contrast between white bones of Seitaad and the pink sandstone of the Navajo Formation.Is there anything about this find that didn't make it into the scientific paper? When we first saw photos of the skeleton in the cliff wall we thought it was a pterosaur. The v-shaped ischia looked like dentaries. It wasn’t until UMNH preparators got into the block that we changed our identification to theropod. Then when we got to the hand, we know from the thumb claw that it was a sauropodomorph.Mark Loewen with the skeleton of Seitaad ruessi***************Check out the original article for free at the PLoS ONE website. As always, you can leave comments or rate the article there.... Read more »

Sertich, J.J.W., & Loewen, M. (2010) A New Basal Sauropodomorph Dinosaur from the Lower Jurassic Navajo Sandstone of Southern Utah. PLoS ONE, 5(3). DOI: 10.1371/journal.pone.0009789  

  • February 13, 2010
  • 04:21 PM
  • 387 views

Four-Winged, Psychedelic Dinosaurs

by Andrew Farke in The Open Source Paleontologist

When many of us think of viewing things under a "black light," we either think of those psychedelic posters from the 1960s or else the displays of fluorescent minerals that nearly every science museum has. It's also virtually mandatory to have a scene involving the use of "black light" in the popular CSI television programs - many bodily fluids show up nice and pretty under these conditions. "Black light," more properly known as "ultraviolet (UV) spectrum light", is just outside the visible light spectrum for us humans (past violet, hence the name). And, through some neat tricks of physics, many objects will brightly fluoresce under intense UV light when they wouldn't look like anything special under your standard sunlight or incandescent light bulb.Oddly enough, many fossils fluoresce under UV light (certain minerals in fossils, including phosphates, are behind this phenomenon). Thus, this technique has been used to look for otherwise hidden features of some exceptionally well-preserved fossils. Historically, it's been the domain of invertebrate paleontologists (looking at crustaceans from the Jurassic of Germany, for instance), but vertebrate paleontologists have used the technique to identify forged fossils (like Archaeoraptor), study Archaeopteryx, and much more. What might be a very subtle or invisible structure under regular light (such as a feather shaft, or antenna, or soft tissue outlines) sometimes shines nicely under UV light.Thus, Beijing paleontologist Dave Hone and colleagues applied the UV light technique to some of the spectacular fossils coming out of the Cretaceous-aged beds of China. In particular, they were interested in a little critter called Microraptor. A dromaeosaur (part of the same group including Velociraptor), Microraptor is relatively well-known as the "four-winged dinosaur." Spectacular fossils with feather impressions show the standard pair of bird-like wings on the arms and a second set of wings on the hind limbs. This suggests to some researchers that birds went through a four-winged flight phase early in their evolution, and the two-winged flight with which we are familiar only happened later.Type specimen of Microraptor gui, from the Wikimedia Commons, reproduced under a Creative Commons Attribution-Share Alike 2.5 Generic license.Although the fossil looks spectacular, many paleontologists speculated that appearances might be deceiving. Were the feathers on the legs actually in place, near their life position? Or had they gotten moved around from somewhere else on the body? A pale halo of sediment (probably from the decomposition process) obscured the contact of the feathers with the bones, so the issue remained unresolved. Either way, it had major implications for avian evolution.Hone and colleagues wondered if the full anatomy was obscured under visible light. So, they turned a UV light source against the specimen. It turns out that the feather structures fluoresce quite nicely - and can be traced right through the "halo" and up to the very edge of the leg bones. So, the feathers really are in place. Problem solved! [image, showing full skeleton, modified from Figure 2 in Hone et al. 2010]Now that we're more confident that Microraptor really was four-winged (and not just an accident of fossilization), the conversation can move forward. And, this is a great rallying cry for other researchers - who knows what structures we might discover with UV light!Close-up of hind legs of Microraptor under UV light, with arrows indicating feathers. The yellow stripes leading up to the leg bones are portions of the feathers visible only under UV. Modified from Figure 3 in Hone et al. 2010Read the full paper in the freely-available, open access journal PLoS ONE (full disclosure: I was the editor who handled this manuscript). You can post comments or ratings for the article there, too! In the blogosphere, check out Dave Hone's posting on his article, as well as ReBecca Hunt's interview with Dave.CitationD. W. E. Hone, H. Tischlinger, X. Xu, & F. Zhang (2010) The extent of the preserved feathers on the four-winged dinosaur Microraptor gui under ultraviolet light PLoS ONE 5 (2) : 10.1371/journal.pone.0009223... Read more »

David W. E. Hone1, Helmut Tischlinger, Xing Xu, & Fucheng Zhang. (2010) The extent of the preserved feathers on the four-winged dinosaur Microraptor gui under ultraviolet light. PLoS ONE, 5(2). info:/10.1371/journal.pone.0009223

  • January 28, 2010
  • 10:41 AM
  • 357 views

Where is paleontology?

by Andrew Farke in The Open Source Paleontologist

Last week, many of the leading journals in evolutionary biology - including The American Naturalist, Molecular Ecology, Journal of Evolutionary Biology, Evolution, and a number of others - announced a data archiving policy. In short, this policy states that the data behind the results of a paper should be publicly archived in well-known respositories such as Data Dryad, GenBank, or TreeBASE. Do you notice anything missing in this illustrious list of publications?Not a single one of those journals explicitly focuses on paleontology. Last time I checked, we paleontologists like to think of ourselves as evolutionary biologists. Time and time again, we lament how we're not allowed a place at "The High Table" of evolutionary thought, and how paleontology is viewed as largely irrelevant by the "people who matter." So why weren't any paleontology publications on this list? Will we see any on the list in the near future?The article in The American Naturalist gives a good run-down of the arguments for sharing data, so I'll only briefly summarize them here:It allows reproducibility of analyses.It allows others to build upon your work more easily.Papers that release their data may get cited more frequently.The data will be lost to science otherwise.It's the right thing to do.And to counter some potential objections:This would only request the release of data directly relevant to the study. Not your pages and pages of raw notes. Just that Excel spreadsheet that you already generated on your way to the analysis. Seriously. It's not a lot of extra work, if any.This is not requesting the digitization and distribution of video, CT scan, or similarly large and unwieldy data (although that would be nice in the future).No, it does not mandate the release of locality data, or similarly privileged information.The policy does not require immediate release of the data, if there's a good reason (i.e., another pending publication) to do so. I'm not sure I entirely support this (if you're publishing the analysis, you should publish the data), but I understand it as a necessary compromise to get more individuals on board. I won't let the perfect be the enemy of the good.Some of the most ground-breaking and high-profile work in paleontology is happening on account of large meta-analyses of data pulled together from the literature - largely thanks to efforts like the Paleobiology Database. This work has real implications for big questions facing our science and our world: Climate change. The pace of evolutionary radiations. The origins of modern biological diversity. These sorts of databases focus primarily on geographic, stratigraphic, and taxonomic data - but think how much more powerful they could be if all of the morphological data ever published were available! Or if the PBDB volunteers didn't always have to transcribe the information from a PDF file.Look. Amateur hour is over. If we want to play in the big leagues, we have to start acting like a real science. Real science is reproducible. Real science is data-driven. Real science involves sharing data. Yes, I know it's hard. It's new. We haven't done things this way before. There are potential problems. Not everyone is adopting it quickly. But if we always wait five years to "see what happens," we paleontologists quite frankly don't deserve a place at the High Table. Let's be leaders, not followers.ReferencesPiwowar, H. A., R. S. Day, and D. B. Fridsma. (2007). Sharing detailed research data is associated with increased citation rate. PLoS ONE 2(3):e308, DOI: 10.1371/journal.pone.0000308.Whitlock, M., McPeek, M., Rausher, M., Rieseberg, L., & Moore, A. (2010). Data archiving. The American Naturalist, 175 (2), 145-146 DOI: 10.1086/650340For previous posts on data sharing in paleontology, see here and here. Want to get involved? Spread the word. Talk to your local journal editor. Let the people who count know what you think.... Read more »

Whitlock, M., McPeek, M., Rausher, M., Rieseberg, L., & Moore, A. (2010) Data Archiving. The American Naturalist, 175(2), 145-146. DOI: 10.1086/650340  

  • October 28, 2009
  • 10:18 AM
  • 476 views

A Happy Family of Pachycephalosaurus

by Andrew Farke in The Open Source Paleontologist

Distinguishing the skulls of juveniles and adults of the same species, and sometimes different species, can be a prickly thing in the fossil record. The result is that paleontology is littered with juvenile fossils that have been considered adults at some time or another. The crested duck-billed dinosaur Corythosaurus has also been known under names like Procheneosaurus, the famous Monoclonius is actually a juvenile of adult Centrosaurus, Styracosaurus, and kin, and the debate still continues on whether Nanotyrannus is a juvenile Tyrannosaurus.Yesterday in the open access journal PLoS ONE, paleontologists Jack Horner and Mark Goodwin published a long-awaited paper positing synonymy for a trio of iconic (and melodiously-named) dinosaurs. The bone-headed dinosaurs Pachycephalosaurus, Stygimoloch, and Dracorex are all one and the same animal, according to their work. The latter two are juvenile stages, whereas Pachycephalosaurus represents a full adult.Skulls of Pachycephalosaurus (top), Stygimoloch (middle; the front of the skull is missing), and Dracorex (bottom; the skull is crushed from top to bottom). In particular, note the changes in skull size and similarities in spike placement. Modified after the original in Horner and Goodwin 2009.How is this possible? The animals look so different, right? Pachycephalosaurus has this big bowling ball on top of its head, which the other two lack. Stygimoloch has a uniquely-shaped, narrow dome, and Dracorex has a completely flat head. Furthermore, Pachycephalosaurus lacks the elongated spikes that make the other two look so fearsome.Well, it turns out that this can all be attributed to ontogenetic changes (i.e., change as the animals get older). Horner and Goodwin assemble multiple lines of evidence for this hypothesis.First, the skulls of Dracorex, Stygimoloch, and Pachycephalosaurus form a size gradation from smallest to largest--exactly what one would expect for a growth series. By itself, this is not irrefutable proof, of course--it could just be that Dracorex had a small adult size compared to Pachycephalosaurus.Second, many of the knobs and bumps on the skulls can be matched up one for one between individuals of the various specimens. Alternatively, one would also expect that closely related (but different) species might have similar patterns of bumps. As Horner and Goodwin admit, there is some variation between individuals of the different "species"--but, the authors also note that this sort of variation is entirely expected and occurs even within undisputed adult Pachycephalosaurus.Third, specimens of Stygimoloch, both in CT scans and physically cut specimens, show an open suture between the two frontal bones of the dome. Pachycephalosaurus domes are completely fused up. Open sutures are often strong indications that an animal is still growing--and, it's particularly intriguing that a small "species" has them but a large "species" doesn't!Finally, microscopic examination of the bones in two of the three "species" (Stygimoloch and Pachycephalosaurus; there weren't any Dracorex available for cutting up) shows that Stygimoloch was still growing (and thus not a full adult)--but Pachycephalosaurus specimens weren't growing much at all (and therefore were probably full adults).Any one of these lines of evidence might be interesting, but not completely convincing. Taken together, however, they make a pretty compelling case that Dracorex and Stygimoloch are juvenile Pachycephalosaurus. Because Pachycephalosaurus was named first, the first two become junior synonyms. It's a shame, because they're such cool names!As for duckbilled dinosaurs, horned dinosaurs, and even modern crested birds like the cassowary, the story in the pachycephalosaurs suggests that weird ornaments on the skull were something that happened only as the animals approached full size. The domes practically appeared overnight! The teenage years must have been a real headache for these dinosaurs.Thanks to the wonders of open access, the article is freely available for all to read. Additionally, it is worth taking advantage of the rating and comment features at PLoS ONE [disclaimer: I am a section editor for that journal]. . .few other scientific publications allow the readers to annotate the papers directly!CitationHorner, J., & Goodwin, M. (2009). Extreme cranial ontogeny in the Upper Cretaceous dinosaur Pachycephalosaurus. PLoS ONE, 4 (10) DOI: 10.1371/journal.pone.0007626... Read more »

Horner, J., & Goodwin, M. (2009) Extreme cranial ontogeny in the Upper Cretaceous dinosaur Pachycephalosaurus. PLoS ONE, 4(10). DOI: 10.1371/journal.pone.0007626  

  • July 3, 2009
  • 02:34 AM
  • 728 views

An Australian Dinosaur Extravaganza

by Andrew Farke in The Open Source Paleontologist

The Cretaceous of Gondwana - the formerly connected southern landmasses of Antarctica, Australia, South America, Africa, India, Madagascar, and Arabia - is a sticky problem. The terrestrial fossil record is spotty at best in most locations, and tremendous geographic and temporal gaps remain. As a consequence, there is considerable debate about the sequence of the tectonic breakup of Gondwana and even the very identity and relationships of some of its dinosaurs and other Mesozoic beasts. Once in a great while, some intrepid field paleontologists take a chance and make discoveries that move our knowledge ahead by leaps and bounds. Areas of Gondwana such as Madagascar and Argentina have had fossils rolling out of the Cretaceous hills, doing wonders for paleontological knowledge. Today, a new paper in PLoS ONE has done such a thing for Australia.Historically, paleontologists working in the Cretaceous of Oz have had to make do with pretty fragmentary material. With the exception of Muttaburrasaurus (a plant eating ornithopod known from reasonably complete skulls and skeletal material) and Minmi (an armored ankylosaur known from a relatively complete skeleton), most of the other named taxa from this time are known only from scrappy elements (e.g., Kakura, a theropod known from an isolated, opalized tibia). This poor fossil record has resulted in some odd, and highly unlikely, claims. For instance, it has been suggested that ceratopsians (otherwise known only from the northern hemisphere) lived in Australia (based on isolated ulnae that admittedly do look rather ceratopsian - although other assignments haven't necessarily been ruled out effectively), and that Allosaurus (a late Jurassic theropod from North America) survived into the early Cretaceous here. When it comes to the meat-eating theropods and the long-necked sauropods, the material is pretty frustrating. Without better specimens, it's virtually impossible to know how Australia's animals compared to those elsewhere!For this reason, the new paper is so very important. A team of paleontologists from the Queensland Museum and the Australian Age of Dinosaurs Museum of Natural History here describe three completely new dinosaur species. Two are sauropods, the third is a theropod, and all come from the Winton Formation of Queensland. The portion of the Winton Formation hosting the dinosaurs is estimated as late Albian in age (based on fossil pollen, an important criterion in the absence of radiometric dates), or roughly 100 million years old.The two sauropods belong to a group called titanosaurs. Titanosaurs were the dominant sauropods of the Cretaceous, with a virtually global distribution. Diamantinasaurus matildae (the sauropod at the top in the illustration, charmingly named after "Waltzing Matilda") and Wintonotitan wattsi (bottom) are both known from partial skeletons, whose owners might have measured 50 feet in total length (~14.8 m) when alive. Unfortunately, the phylogenetic position of the two animals is somewhat uncertain. The authors chose to put the animals into two very different datasets for their cladistic analysis (in terms of characters and taxon selection), so it's tough to know where the things actually fall out. It would be informative to merge the two datasets as much as possible and see how that affects tree topology. The incongruent trees also complicate any biogeographic conclusions that might be drawn. Regardless, it looks like Wintonotitan is a relatively basal titanosauriform (what some folks might call "primitive"), and Diamantinasaurus falls out within a group called Lithostratia, close to or within the saltasaurids (many of these animals are well-known for the armor studding their backs).There is a slim possibility that one or both new species of sauropod are synonymous with Austrosaurus mckillopi, a taxon based on poorly preserved, incomplete vertebrae from a roughly contemporaneous formation. There is some overlap with Wintonotitan, but the vertebrae from the two animals are apparently pretty different. Diamantinasaurus doesn't preserve any vertebrae, so we can't directly compare it with Austrosaurus. But because the type of Austrosaurus is so incomplete, it might be safely ignored as a nomen dubium. I'll leave it to the sauropod experts to decide that!Our third beast is a theropod (meat-eating dinosaur) named Australovenator wintonensis. It was perhaps a third of the body length of the two sauropods and is represented by a partial skeleton including a complete hindlimb, partial forelimbs, and a portion of the lower jaw. For Australian theropods, this is simply dumbfounding material (remember Kakura, only known from a fragmentary leg bone?). Heck, for theropods anywhere this is pretty darned good. Australovenator falls out as an allosauroid (a pretty common group of predators from the Jurassic and Cretaceous) just outside of carcharodontosaurids. With Australovenator thrown into the mix, allosauroids had a nearly global distribution.Open Access NerdinessThis paper is a fantastic example of the real benefits of an on-line, open access journal like PLoS ONE. Without page limitations, the authors were allowed to truly monograph the heck out of the bones. Virtually every element is illustrated from multiple angles (with high resolution photos downloadable from the website!) and accompanied by thorough text descriptions and measurements. The editors of most journals would freak out over such a "waste" of precious space - but I have a feeling that future researchers are going to thank the authors for their thoroughness. As a PDF, the paper weighs in at 51 pages - and this doesn't include the supplementary information!The authors (perhaps at the editors' behest) also make very explicit statements about the nomenclatural availability of the names, a direct result of the Darwinius fallout. Hopefully this will satisfy the requirements ICZN.On the rather nitpicky side, I would note that the minimal post-processing of the manuscripts employed by PLoS ONE shows up here and there. For instance, the term "phalange" is used as the singular instead of the correct "phalanx" (one of my few pet peeves), among a few other oddities. These are rather minor bones to pick in an otherwise weighty manuscript.As always, if you have something to say, post a comment here and then go provide your comments, notes, and ratings of the article at the PLoS ONE website.The Bottom LineSo what's so important about this paper? Well, we finally have good sauropod material from the Cretaceous of Australia, and an excellent theropod specimen to go along with it. No doubt--these specimens are going to be critical for future studies on the evolution and biogeography of both groups, as well as greatly filling in our understanding of Australia's geo... Read more »

Hocknull, S., White, M., Tischler, T., Cook, A., Calleja, N., Sloan, T., & Elliott, D. (2009) New mid-Cretaceous (Latest Albian) dinosaurs from Winton, Queensland, Australia. PLoS ONE, 4(7). DOI: 10.1371/journal.pone.0006190  

  • June 5, 2009
  • 02:13 AM
  • 794 views

How Big (Dead) Mammals Respond(ed) to Global Warming: Paleontology and Our Climate Crisis

by Andrew Farke in The Open Source Paleontologist

After all of the commotion over "Ida," I'm happy to point out a new, thought-provoking paper in PLoS ONE that perhaps has more relevance to modern humans than any old primate of debated affinity. This new contribution ties two rather cool issues together: charismatic megafauna and global warming. And what might they have to do with each other?Within the scientific community, our current cycle of climate change ("global warming") is pretty well-supported by numerous lines of evidence. In light of this change, many biologists, conservationists, and policy-makers want to know exactly how this change will affect living things (humans and wildlife alike). Will animals adapt to the new conditions? Will they die out? Will different animals cope in different ways? Models, simulations, and short-term studies are all useful, but only provide one small piece of the puzzle. Short-term studies (by short-term, I mean on the scale of months, years or decades) provide useful ground-truthing for the models, but in matters of conservation and policy, they may come too late for imperiled ecosystems. It's like having your house burn down around you before you can see the smoke.An oft-overlooked source of data comes from the fossil record. Earth's climate has changed numerous times over the millenia, and by studying previous warming or cooling episodes we may be able to understand our own times. This is where a new study, led by Larisa R. G. DeSantis in collaboration with Robert Feranec and Bruce MacFadden, comes in.Ice Age AnticsBeginning around 2.58 million years ago, in the late Pliocene, our planet has been in an Ice Age. This ice age is characterized by cooling periods (glacial periods, in which the ice sheets advance) and warming periods (interglacial periods, in which the ice sheets retreat). For the last 10,000 years or so, we've been in an interglacial period (and our present climate change is above and beyond this). As a neat natural experiment, DeSantis and colleagues decided to look at how large animals reacted (in terms of diet, etc.) to the switch from a cool period to a warm period.Grind Up Fossils in the Name of ScienceThe team focused on two sites from Florida: one from a glacial period, between 2.0 and 1.6 million years old, and another from an interglacial period, between 1.6 and 1.3 million years old. Using a little drill, the researchers sampled tooth enamel from a variety of Ice Age organisms, including horses, deer, tapirs, elephants, and other herbivorous critters that roamed Florida during that interval. And why grind up fossil specimens? It turns out that you can run the enamel powder through a spectrometer that measures the proportions of various isotopes of carbon and oxygen.And what do these isotopes tell us? Simply put, you are what you eat. Different plants use different pathways of carbon fixation (C3 and C4 were investigated here). Animals eating lots of C4 plants (primarily "warm season grasses") have one isotopic signature for carbon, and animals eating C3 plants ("cool season grasses," trees, and shrubs) have another. Furthermore, oxygen isotopes are different for arid environments and relatively wet environments. So, by looking at oxygen and carbon isotopes in concert, you can get an idea of the relative aridity of the area as well as the diet of a given animal.And now the modern tie-in: According to DeSantis and colleagues, many studies and models have concluded that under environmental change, animals tend to try to be pretty consistent in what they eat. In other words, if you start out at a grass-eater, you will try and stay a grass eater. So, mammals don't really do much in response to warming (or cooling). Of course, this has pretty important implications for conservation: once the grass disappears in the face of a changing climate (whatever the cause), our grass-eaters are toast.The ResultsInterestingly, it turns out that different mammals had different stories over the course of the glacial cycle. Based on the isotopic data, the types of plants changed over time, with C3 plants dominating the cooler cycle (as would be expected) and C4 plants predominating in the warm interval. And, many of the same animals are found in both the "warm" and the "cool" study sites. Although some apparently maintained similar diets (e.g., tapirs), most other animals (e.g., deer and horses) showed very different isotopic signatures over time. They were eating different foods. . .thus, these animals were quite adaptable!What It All MeansA striking implication of the study is that some animals may not be as vulnerable to climate change as previously thought. These Ice Age species changed their ecological niches in the face of climate change. So, if large modern animals can adapt their diets relatively easily, they may be able to escape extinction too. The bottom line still is that previous assumptions of do-or-die dietary stability for large mammals are not valid in all cases. Here we have yet another cool example of how paleontology can provide important information for "real-world" problems!Parting ThoughtsThe paper, posted at PLoS ONE, covers much more than the little bit I've highlighted here. There are some interesting tidbits on changes in rainfall and ecological partitioning, among other things. It's a quick and very accessible read (weighing in at 7 PDF pages, including figures and references), and even this non-geochemist followed the text pretty easily. So, go check it out! As always, you can rate the paper or make comments at the PLoS ONE website.The CitationDeSantis, L., Feranec, R., & MacFadden, B. (2009). Effects of global warming on ancient mammalian communities and their environments PLoS ONE, 4 (6) DOI: 10.1371/journal.pone.0005750... Read more »

DeSantis, L., Feranec, R., & MacFadden, B. (2009) Effects of global warming on ancient mammalian communities and their environments. PLoS ONE, 4(6). DOI: 10.1371/journal.pone.0005750  

  • May 19, 2009
  • 09:33 PM
  • 751 views

About That Adapid. . .Or, Hype In the Digital Age

by Andrew Farke in The Open Source Paleontologist

Today's PLoS ONE includes an article on a new primate from the Eocene of Germany, Darwinius masillae. Poor Darwinius has suffered heaps of abuse over her existence (we know the specimen is probably a she, based on the lack of a baculum). She died young, possibly suffocating during a belch of noxious gas from a volcanic lake. She got squashed ("lightly crushed," as her describers euphemistically say) under tons of rock, and then was rudely given a split personality upon her discovery. Each half of Darwinius was sold privately to a different collector, and eventually one half made it as far as a museum in Wyoming. This half received a little bit of creative restoration somewhere in between. The other, more intact half eventually made it to a museum in Norway. But, the fun was only beginning!Our friend was described by a multi-national team of scientists, who teamed up with the History Channel, BBC, and other outlets to create a media blitz the likes of which the world has never seen before. Not only a peer-reviewed article, but press conferences, book deals, television programs, interviews, and much more.Why is there such a fuss over such a little specimen (weighing in at approximately a kilogram while alive)?First off, this is a spectacular fossil. The Messel Beds of Germany have produced truckloads of spectacular specimens with exquisite soft tissue preservation (everything from bats to birds to rodents), but primates are exceedingly, exceedingly rare. Nobody would debate the tremendous scientific value of the find. People are debating the authors' interpretation of the find.The authors claim that Darwinius is a haplorhine primate. That is, Darwinius (and other members of its clade, the adapoid primates) is more closely related to anthropoid primates (including monkeys of all sorts, apes, humans, etc.) than to strepsirrhine primates (the group including lemurs). It's hard to believe for those of us who study dinosaurs, but this is a ridiculously contentious claim. To put it into context for you dinosaur nerds, this would be similar to someone claiming that Compsognathus is more closely related to birds than Velociraptor. Oh, the humanity!The claim of Darwinius and other adapoids as a haplorhine is contentious for two reasons: 1) most recent, widely accepted cladistic analyses place adapoids as closer to lemurs (strepsirrhines) than to monkeys (haplorhines); and 2) there is no real cladistic analysis to support the claim made by the present paper. Instead, the authors give a list of characters that they believe to support the assignment to the haplorhine clade. Unfortunately, there is little or no discussion as to what these characters (including absence of a "toilet-claw" and "tooth comb," features found within, but not universally across, lemurs and kin) mean, including the possibility of convergence or mosaic evolution.So, it appears that some extraordinary claims are made about Darwinius, but the supporting analyses are non-existent. Given the wonderful preservation of the skeleton, it should be relatively straight-forward to code this specimen and present a cladistic hypothesis. Darwinius is an important fossil. The problem is that the interpretation of this specimen is highly debateable. The authors may very well be right. . .but the burden of proof is still upon them.As always with articles in PLoS ONE, the paper is free for everyone. Judging by the blogosphere today, there are some very strong opinions about this specimen - if you have thoughts on the little critter, please post a comment or note over at PLoS ONE!Further Reading in the BlogosphereBrian Switek presents an excellent, in-depth analysis of Darwinius over at Laelaps.ReferenceFranzen, J., Gingerich, P., Habersetzer, J., Hurum, J., von Koenigswald, W., & Smith, B. (2009). Complete Primate Skeleton from the Middle Eocene of Messel in Germany: Morphology and Paleobiology PLoS ONE, 4 (5) DOI: 10.1371/journal.pone.0005723Image at top from the original article at PLoS ONE.... Read more »

Franzen, J., Gingerich, P., Habersetzer, J., Hurum, J., von Koenigswald, W., & Smith, B. (2009) Complete Primate Skeleton from the Middle Eocene of Messel in Germany: Morphology and Paleobiology. PLoS ONE, 4(5). DOI: 10.1371/journal.pone.0005723  

  • April 29, 2009
  • 11:28 PM
  • 780 views

Albatross vs. Pterosaur

by Andrew Farke in The Open Source Paleontologist

Today, there was a paper tangentially related to pterosaurs in the open access journal PLoS ONE. A team of investigators wired up albatrosses and petrels with accelerometers, in order to measure the percentage of time these animals spent flapping their wings and soaring. They found two main styles of wing flapping (as inferred from the accelerometer measurements): 1) high frequency flapping during take-off; and 2) low-frequency flapping during soaring. Interestingly, the frequencies scale with body mass in such a way that a maximum possible body size for the albatross-like body plan that still allows flight is extrapolated to a body mass of 41 kg and wingspan of 5.1 m (with the requisite error bars, of course).The authors then go on to discuss the implications for pterosaur paleobiology, essentially suggesting that albatross-style soaring was physically impossible for pterosaurs such as Quetzlcoatlus (assuming that it also had albatross-style wings). Frustratingly, there is little discussion of the alternative possibilities of wing shape in pterosaurs, among other things. Furthermore, the underlying data for the analysis only focus on four species of birds with limited morphological diversity. As suggested by the authors of the current paper, data on thermal-soaring birds such as condors (which have a decidedly un-albatross-like form) are sorely needed.So, kudos to Sato et al. for collecting some interesting morphological data. This sort of information is invaluable for verifying and refining existing models of vertebrate flight. However, the relevance of the data to pterosaurs should probably be reviewed by someone who knows the group better than I do - so if you're one of those people, hop (or soar) on over to PLoS ONE and comment on the article!ReferenceSato, K., Sakamoto, K., Watanuki, Y., Takahashi, A., Katsumata, N., Bost, C., & Weimerskirch, H. (2009). Scaling of soaring seabirds and implications for flight abilities of giant pterosaurs. PLoS ONE, 4 (4) DOI: 10.1371/journal.pone.0005400... Read more »

Sato, K., Sakamoto, K., Watanuki, Y., Takahashi, A., Katsumata, N., Bost, C., & Weimerskirch, H. (2009) Scaling of soaring seabirds and implications for flight abilities of giant pterosaurs. PLoS ONE, 4(4). DOI: 10.1371/journal.pone.0005400  

  • March 24, 2009
  • 10:52 PM
  • 913 views

Bone-ing Up on Allometry

by Andrew Farke in The Open Source Paleontologist

Allometric scaling - roughly defined, when different parts of an organism grow at different rates - is an important factor in biology. In part, allometry describes how babies have relatively larger heads than adults (we exhibit negative allometry in this trait, because our skulls don't grow as quickly as the rest of the body) or how some crabs have gigantic claws (an example of positive allometry, in which the claw grows much faster than the rest of the body). Allometry (and its counterpart isometry, in which proportions don't change at all) can be examined on an intraspecific level, such as the example in humans, or on an interspecific level.It's not cute - it's allometric! Toronja Azul, Chihuahua Puppy, 5 August 2007 via Wikimedia Commons, Creative Commons Attribution 2.0For paleontologists and biologists, allometry and isometry are particularly interesting when it comes to understanding groups with large ranges in body size. When you grow a Tyrannosaurus from an Eoraptor-like ancestor, what has to change in order to support the body mass? Sometimes it's postural - big animals tend to have more "columnar" posture (with the supporting legs straight beneath the body) and small animals tend to have more "flexed" posture. In other cases, it's allometric - big animals might tend to have relatively thicker bones than small animals. Sometimes, it might even be both. And sometimes, none of these comfortable patterns seem to fit perfectly.Looking at CatsRegardless of the patterns (and often because of them), scaling studies of limb bones have attracted a lot of ink over the years. A recent contribution, authored by Michael Doube and colleagues, appeared the other week in the open access journal PLoS ONE. Their paper, entitled "Three-dimensional geometric analysis of felid limb bone allometry," takes a novel peek at how different limb bones scale within cats. Cats are a particularly interesting study subject, because they span a range of adult body masses - from as little as 3 kg in the domesticated cat to 306 kg in the largest tiger.Domesticated cat (left) and lion skeletons, scaled to roughly the same height at the shoulders.Limb bone allometry in its own right is an interesting, but rather conventional, topic. Most studies are content to take some linear measurements, or perhaps a cross-section or two, for a range of species. Doube and colleagues did something unique - they examined the three-dimensional properties of entire limb bones, as well as two-dimensional properties in series along the entire bone, using CT scans coupled with custom-written software macros.The macros (which are one of the really cool things about this paper, and a big reason for why I'm highlighting it here) calculate a variety of cross-sectional properties automatically from CT scan data. Previous macros (such as the very useful MomentMacroJ) required a human operator to do things one slice at a time. Believe me, this can take forever for a limb bone data set of 200 CT slices. The authors of the paper in question were able to quickly and efficiently assemble data sets for a variety of measurements from a variety of limb bones for a variety of felid species - over 16,000 CT slices in total! So, this allowed compilation of a database for measurements throughout the bone - not just at the boring old mid-shaft. Furthermore, they calculated joint geometries (through a sphere-fitting routine, to approximate surface area of certain joints) as well as moments of inertia for entire bones.This data set allowed the authors to get one of the the most complete pictures of limb bone properties ever assembled. In general, cross-sectional properties at mid-shaft (a standard location for measurement) did not differ significantly from isometry (i.e., big cat bones look the same as little cat bones). Of course, a larger sample might achieve statistical significance at P less than 0.05 (results are suggestive, but don't differ significantly from isometry). Interestingly, joint surfaces and moments of inertia tend to scale with positive allometry. In other words, big cats have relatively bigger joints and beefier bones (a more thorough and accurate explanation of moments of inertia is beyond the scope of this post) than do small cats.So why are these results interesting? Well, it appears that cats "get big" differently from other animals. Whereas comparably sized mammals tend to change from flexed limb postures to more columnar limb postures as body size increases, cats apparently maintain a relatively flexed posture across their size range. Instead, cats compensate for the change in body mass by beefing up their bones. Skeletal and postural responses to increased body size are pretty darned diverse, and there is no "one size-fits-all" solution. It will be very interesting to see broader applications of this methodology.Open Source SolutionsThe authors used ImageJ, an open source image processing system (detailed in a previous post here) for much of their data collection. The macro they wrote and used is also freely available with their paper--so feel free to try it out with your own data. Their massive datafiles were collated with MySQL, and the statistical analysis was conducted within R, using the SMATR package for regression analysis. So, it was an open source project from start to finish! As the cherry on top of the cake, publication in PLoS ONE means that the paper is easily and freely accessible to all. I've already made a few notes on the paper, with quick and gracious responses from one of the authors. If you have anything to add to the discussion, don't be shy!Further ReadingIf you're interested in more open source solutions to these sorts of problems, check out lead author Michael Doube's web page. He's got lots of macros, pretty pictures, and other goodies for enjoyment and download.The CitationDoube, M., Conroy, A., Christiansen, P., Hutchinson, J., & Shefelbine, S. (2009). Three-dimensional geometric analysis of felid limb bone allometry. PLoS ONE, 4 (3) DOI: 10.1371/journal.pone.0004742... Read more »

Doube, M., Conroy, A., Christiansen, P., Hutchinson, J., & Shefelbine, S. (2009) Three-Dimensional Geometric Analysis of Felid Limb Bone Allometry. PLoS ONE, 4(3). DOI: 10.1371/journal.pone.0004742  

  • March 4, 2009
  • 12:50 AM
  • 935 views

Crouching Theropod, Hidden Dragon

by Andrew Farke in The Open Source Paleontologist

Fossil footprints (falling in the general category of "ichnofossils") reveal a wealth of information about dinosaur biology, such as speed, posture, and behavior. These traces are particularly useful when offering information independent from, but consistent with, hypotheses derived from purely anatomical studies.Today, a new paper in the open access journal PLoS ONE presents an unusual set of theropod (meat-eating dinosaur) ichnofossils from the Early Jurassic-aged Moenave Formation of southwestern Utah. The tracks are preserved within the St. George Dinosaur Discovery Site at Johnson Farm, a massive facility housing thousands of footprints (for additional scientific publications and background on the site, refer to this page). But, if there are thousands of footprints known at the site (in addition to the thousands known from other sites throughout the world), what makes the fossils featured in the paper so special?Theropods were bipedal animals, and known ichnofossils typically only preserve evidence of the hindlimb. But, one specimen in particular at the St. George locality preserves impressions of the hind feet, forefeet, and the rear end of a lazy carnivore. A resting trace!Artist's conception of the St. George trackmaker at rest. Note in particular the resting posture and the orientation of the hands. From Milner et al. 2009; painting by Heather Kyoht Luterman.Yet, even resting traces aren't completely unheard of for theropod dinosaurs. The really interesting thing here is that the specimen preserves relatively unambiguous impressions of the hand posture. The animal was resting with its hands turned inward, and the outer surfaces of the fingers and wrist (rather than the palms) touching the substrate.Why does this matter? Well, it all has to do with reconstructions of forelimb mobility and posture. Old reconstructions of theropod dinosaurs showed them walking around with palms down (think of an alligator dragged upright); later work has strongly suggested that the palms faced inward, more like birds.Traditional restoration of two theropods, by Charles R. Knight. Note the palm-down, rather than palm-in, posture of the hands.So, the new St. George tracks are the first good ichno-evidence of forelimb posture in theropod dinosaurs. Furthermore, and perhaps most importantly, it suggests that this posture evolved pretty early on, in some of the first theropod dinosaurs.As the authors note, anatomical reconstructions of forearm movement have primarily focused on more "derived" theropods (animals from the Late Jurassic and beyond). It would be really, really nice to get additional studies on the anatomical structures of the forelimb in animals like Dilophosaurus and Coelophysis (Ken Carpenter did get a good start on this a few years back; see his 2002 paper, "Forelimb biomechanics of nonavian theropod dinosaurs in predation." Senckenbergiana Lethaea 82: 59-76). Also, paleontologists will want to be on the lookout for similar traces. Is the specimen described here typical, or an individual anomaly? The authors reviewed other alleged resting traces from theropods, but considered that most of them were either misidentified or too poorly preserved to offer usable information. Finally, does resting posture of the forelimbs necessarily reflect what the animals were doing the other 99 percent of the time?Congratulations to the authors on a stimulating paper. If you have an opinion on this research, don't just post it in the blog's comment section (although please do that, too). Head over the the PLoS ONE website, and register your own comments, notes, and ratings on the article!The ReferenceAndrew R. C. Milner, Jerald D. Harris, Martin G. Lockley, James I. Kirkland, Neffra A. Matthews (2009). Bird-Like Anatomy, Posture, and Behavior Revealed by an Early Jurassic Theropod Dinosaur Resting Trace. PLoS ONE, 4 (3) DOI: 10.1371/journal.pone.0004591... Read more »

Andrew R. C. Milner, Jerald D. Harris, Martin G. Lockley, James I. Kirkland, & Neffra A. Matthews. (2009) Bird-Like Anatomy, Posture, and Behavior Revealed by an Early Jurassic Theropod Dinosaur Resting Trace. PLoS ONE, 4(3). DOI: 10.1371/journal.pone.0004591  

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