Using X-rays to learn what walking rats can teach us about early placental mammal locomotion

In paleontology, we often infer the habits and behaviors of fossil vertebrates by reference to their skeletal shape. However, it is often difficult to appreciate what those shapes are telling us: how well does shape correlate with motion?

We are members of the eutheiran branch of the mammal family tree. Among many questions concerning mammal evolution, one is how did the earliest eutherian (so-called “placental”) mammals use their forelimbs? This question has important implications for how our earliest relatives got around. The earilest known members of our group are small and are often hypothesized to be scansorial (Luo et al., 2003, 2011), meaning that they are at home on the ground as well as clambering up trees.These inferences are drawn in large part from the form of the fossilized forelimb bones and their presumed functions.

If you’ve been following this blog, you know that I have been immersed in learning XROMM (X-ray Reconstruction of Moving Morphology), a technique that combines video fluoroscopy (X-ray movies) with registration of three-dimensional bone models to yield 3-D moving X-rays.

I am happy to report that my colleagues, two Stockton undergraduates (Radha Varadharajan and Corey Gilbert), and I have published an Open Access article in PLoS One that, for the very first time, reconstructs the three-dimensional movements of the long bones (humerus, radius, ulna) in the forelimb of rats. Why rats? Rats have a forelimb anatomy that is very similar in many ways to those of the earliest eutherian mammals, and as a plus, rats are scansorial. Rats are also relatively easy mammals to work with in the lab (although some days they out-clever the humans) and can be trained. As a fun side note, we named two of the rats Pink and Floyd.

Our setup was straightforward — at the C-arms XROMM lab at Brown University, the rats walked along a plank of wood to a darkened hide box. While traversing the plank, they made their X-ray cameos in two fluoroscopes connected to hi-speed cameras filming at 250 frames per second (your iPhone camera films at 30 frames per second in normal mode). When we were finished collecting our data, the rats were CT-scanned so that we could have exact three-dimensional models of their limb bones. The most painstaking part was the several months it took to digitize each of our good trials. That is, using animation software, we had to match the bone models up to their X-ray shadows in the two calibrated fluoroscope movies. Once this was accomplished, our task turned to watching how the bones moved in three-dimensional space as well as analyzing the joint angle data that was generated.

Our basic setup for the XROMM study -- rats were trained to walk across a plank towards a dark hide box, leading them between the two videofluoroscopes.

Our basic setup for the XROMM study — rats were trained to walk across a plank towards a dark hide box, leading them between the two videofluoroscopes.

What we found both confirms previous work on small mammal locomotion, but added some interesting new insights as well. As a general rule, small mammals have a crouched posture where the elbows and knees are bent. This type of posture may aid small mammals in maneuvering around objects and keeping a lower center of gravity, which would enhance stability, especially on branches and other narrow perches. Not surprisingly and given previous work on rat locomotion, we see that these mammals do indeed walk on crouched limbs — the elbow angle, for example, never exceeded 123 degrees in full extension. By way of comparison, your elbow can be extended to 180 degrees.

A figure from my book, The Bare Bones. Note how the rat has a more crouched posture whereas the cat is more upright.

A figure from my book, The Bare Bones. Note how the rat has a more crouched posture whereas the cat is more upright.

However, we often get the impression that mammal locomotion is similar at different scales. From cats and dogs on up, it appears that the forelimbs and hindlimbs function very much as glorified pendulums. In essence, eutherian mammal locomotion is understood as mostly two-dimensional. Although rats are small and have a crouched posture, their limb bones would be presumed to follow the pendulum model.

But what the bones were doing in three-dimensions was fascinating. Both the humerus (upper arm bone) and radius (the forearm bone that aligns with your thumb) showed they were capable of long-axis rotation. Long-axis rotation is similar to the way a lathe or axle spins. Our rats’ bones certainly weren’t spinning on their long-axis, but they did show a non-trivial range of movement. A step cycle consists of a stance phase (when the hand is on the ground and forelimb is supporting the body) and a swing phase (when the hand is off the ground and the forelimb is swinging back to support the body for the next step). We found that during stance, the humerus both moves toward the midline (adducts) and rotates on its long axis towards the body. These combined movements appear to ensure that the elbow points backwards so that the forearm maintains an upright posture. During swing, the humerus moves away from the body midline (abducts) and rotates on its long axis away from the body. These combined movements seem to allow the forelimb to clear the rat’s body as the limb is brought forward to start a new step.

Lateral, ventral, and radioulnar joint views of the humerus (sea green), radius (black), and ulna (red) in a typical step cycle in Rattus norvegicus. Long-axis rotation (LAR) of the radius about the ulna (radius pronation) is shown in cranial view from the perspective of the ulna (the ulna appears to be stationary in the radioulnar joint view relative to the humerus and radius). Note radius (black) LAR relative to the ulna (red). Percentages = portion of the step cycle. Black bar in ventral view = body midline based on sternum.

Lateral (side), ventral (belly), and radioulnar joint (at the elbow) views of the humerus (sea green), radius (black), and ulna (red) in a typical step cycle in Rattus norvegicus. Long-axis rotation (LAR) of the radius about the ulna (radius pronation) is shown in cranial view (the rat is walking toward you) from the perspective of the ulna (the ulna appears to be stationary in the radioulnar joint view relative to the humerus and radius). Note radius (black) LAR relative to the ulna (red). Percentages = portion of the step cycle. Black bar in ventral view = body midline based on sternum.

MOVIE 1 – All the rats walking betwixt the fluoroscopes with their CT-scanned bones registered to the frames.

MOVIE 2 – One of our rats, “Floyd,” demonstrating a typical step cycle.

What was particularly exciting to me was that we saw, for the first time in rats, the radius pivot about the ulna! In humans, we take these movements for granted: our radius pivots around our ulna with ease, directing our palms either downward (pronated) when its shaft cross over the ulna, or upward (supinated) when its shaft rotates into parallel with the ulna. Up until now, it has been unclear if the radius could move in this way to flip the hand palm-side down in rats, or whether their hand posture was maintained via positioning of the limb in general. We now know that, indeed, the radius does move and does appear to be correlated with hand placement in rats. These movements are much more subtle than in you and I (in our rats a range of 10-30 degrees of rotation), but they appear to be correlated with pronation of the hand.

MOVIE 3 – One of our rats, “Floyd,” showing how the radius pivots on the ulna during a step cycle.

Our research has two messages. The first message is that given the similarities in the forelimb skeletons of the earliest known eutherian mammals (Juramaia and Eomaia) to those of rats, it is likely that a similar range of movements were possible in these distant relatives on our family tree. Paleontologists studying these fossils, such as Zhe-Xi Luo and colleagues (Luo et al., 2003, 2011), have already suggested these early eutherian mammals were scansorial, and our data bolster their hypothesis. These sorts of insights are helpful in constraining when particular locomotor behaviors and movements became possible and how that might have effected mammalian evolution.

The second message is that small mammal locomotion is probably not as similar to those of larger mammals as we often think, a sentiment echoed by the late Farish Jenkins (e.g., Jenkins, 1971) and by Martin Fischer and his colleagues (Fischer et al. 2002; Fisher and Blickman, 2006). Moreover, our rat data show that, at least for the forelimb, long-axis rotation plays a role in normal overground movement.

We hope our study provides another perspective on small mammal locomotion and encourages new and fruitful research in our furry friends past and present.


I am grateful to my colleagues and former students for their help and work on this project. I want especially to thank Elizabeth Brainerd (Brown University). She has been a source of encouragement and a patient teacher to an old dinosaur learning new tricks, and her help with learning XROMM and on designing the experiment which led to this paper (my first foray into animal kinematics) was invaluable.

The authors of the paper (* indicates a Stockton University undergraduate)

Matthew F. Bonnan (Stockton University, Biology)
Jason Shulman (Stockton University, Physics)
*Radha Varadharajan (Stockton University, Biology)
*Corey Gilbert (Stockton University, Physics)
Mary Wilkes (Stockton University, Biology)
Angela Horner (California State University, San Berardino)
Elizabeth Brainerd (Brown University)



Fischer, M. S., and R. Blickhan. 2006. The tri-segmented limbs of therian mammals: kinematics, dynamics, and self-stabilization—a review. Journal of Experimental Zoology Part A: Comparative Experimental Biology 305A:935–952.

Fischer, M. S., N. Schilling, M. Schmidt, D. Haarhaus, and H. Witte. 2002. Basic limb kinematics of small therian mammals. The Journal of Experimental Biology 205:1315–38.

Jenkins, F. A. 1971. Limb posture and locomotion in the Virginia opossum (Didelphis marsupalis) and in other non-cursorial mammals. Journal of Zoology, London 165:303–315.

Luo, Z.-X., Q. Ji, J. R. Wible, and C.-X. Yuan. 2003. An Early Cretaceous Tribosphenic Mammal and Metatherian Evolution. Science 302:1934–1940.

Luo, Z.-X., C.-X. Yuan, Q.-J. Meng, and Q. Ji. 2011. A Jurassic eutherian mammal and divergence of marsupials and placentals. Nature 476:442–445.

Read the first chapter of The Bare Bones

BareBmecDue to requests for a sampler of my forthcoming book from Indiana University Press, The Bare Bones, I am now making available a PDF of the first chapter. I think this will give you a feel for the tone of the book.

Thanks to everyone for all of the interest and enthusiasm for the book. It was truly a labor of love, and I hope many of you will find it enjoyable to read and useful to those who may use it as an educational resource.

The Bare Bones, Chapter 1

I am also giving another sneak preview at one of the figures, this one from Chapter 2:

Carnivorous mammals, such as a cat, tend to have a jaw joint in line with their sharp, shearing teeth, much as the handles of a pair of scissors align with the blades.  This puts the best cutting surface towards the back of the jaws.  In contrast, herbivorous mammals such as horses have a jaw joint located above the tooth row, allowing their teeth to simultaneously contact one another like a nutcracker.

Carnivorous mammals, such as a cat, tend to have a jaw joint in line with their sharp, shearing teeth, much as the handles of a pair of scissors align with the blades. This puts the best cutting surface towards the back of the jaws. In contrast, herbivorous mammals such as horses have a jaw joint located above the tooth row, allowing their teeth to simultaneously contact one another like a nutcracker.

Also remember, you can preorder The Bare Bones through Indiana University Press or Amazon.

If you are into e-books, it can also be purchased as an e-book. See the Indiana University Press website for links to the appropriate retailers.

South Africa and the Cradle of Sauropod-Kind

Artist's reconstruction of Pulanesaura by Gina Viglietti.

Artist’s reconstruction of Pulanesaura by Gina Viglietti.

I am happy to report on a new sauropod dinosaur from the Early Jurassic of South Africa! The dinosaur, Pulanesaura, was discovered in 2004 and has been a long time coming to press. Now, she’s finally here.

When I was maybe four or five years old, I remember reading a dinosaur book with my mother. The book described for children how dinosaurs were discovered and excavated in the field, and then how the bones were reassembled back in the lab. What I don’t remember, but I have been told, was that at some point during the explanation of how dinosaurs were unearthed, I interjected, “And then they have lunch.”

I was five years old in 1978. Fast-forward to the fall of 2004, and my 31-year-old self is standing in the rain at Spion Kop farm in the Free State of South Africa marveling at the large limb bones poking out of a section of the upper Elliot Formation. I don’t recall having lunch at that moment, but I do remember being excited, and being grateful that I was part of a team, headed by Adam Yates, charged with exploring these Early Jurassic rocks. National Geographic had sponsored our grant to pursue promising bones issuing forth from these rocks, and although we did not immediately know we had a new dinosaur, there was a good possibility we did.

Matt w tibia (1)

Myself above two tibia bones (tibiae) from what would become known as Pulanesaura in 2004 … it was a less rainy day that day.

Why South Africa? As it turns out, South Africa has many exposures of Lower Jurassic rocks that record a very significant time in dinosaur evolution. The earliest true dinosaurs appeared in the Triassic period about 235 million years ago (Ma) but remained relatively small to medium-sized animals that were in competition with other vertebrate groups vying for dominance in a harsh world. During the Triassic period, all the continents were amalgamated into a single supercontinent dubbed Pangea. Although to a modern traveler the thought of Pangea sounds amazing (imagine riding a train from North America over to Europe or driving from South America into Antarctica, Africa, or Australia), ecologically this was disastrous. A huge expanse of Pangea was landlocked and nearly devoid of water, making it both hot and uninhabitable. Moreover, sea levels were also drastically lower, creating fewer areas for marine life to thrive. Thus, Pangea took a huge toll on the animals that preceded the dinosaurs. In fact, the largest mass extinction in the past 540 million years occurred just prior to the Triassic period, wiping out a majority of life on the planet.

During the Early Jurassic (starting about 200 Ma), Pangea began to unzip and break up into separate landmasses, and part of the effect of this was to bring water into regions it hadn’t been in millions of years, supporting more plants and, in turn, the animals that fed on them. It is also at this critical juncture that the sauropodomorph dinosaurs began to become larger-bodied and more diverse so that by the end of the Jurassic period (about 145 Ma), many of these herbivores were tipping the scales at 20-30 metric tons! Sauropodomorphs started out as small to medium-sized bipedal herbivores that used their long necks and grasping hands to consume foliage at different heights in their environment. Sauropods became fully quadrupedal giants with elongate necks that acted as efficient food-gathering feeding booms, sweeping across swaths of vegetation while the herbivore stayed put. And this transition from mostly bipedal herbivores eating with their hands and necks to giant quadrupeds that relied solely on long necks to feed occurred right around the Early Jurassic period about 200 Ma. So, if you want to understand the beginnings of this trend towards gigantism in the sauropodomorph dinosaurs, you need to search for fossils in Early Jurassic rocks … and that brings us back to me standing in the rain at Spion Kop on the upper Elliot Formation staring at the large bones coming out of the ground.

Those bones we were unearthing would end up being a sauropod new to science named Pulanesaura that my colleagues and I have published on this week in Nature Scientific Reports. The lead author, Blair McPhee, is a Ph.D. student at the University of Witwatersrand in South Africa who took on this dinosaur for his dissertation. Remember that we discovered Pulanesaura in 2004?  Why didn’t we publish on this animal earlier? For a number of reasons collectively called life. Between 2009 and 2011, we did publish on two other sauropodomorph dinosaurs from Spion Kop, so that took up some time. But more significantly, Adam Yates and I had major life-changing moves to new employers: Adam to the Museum of Central Australia in Alice Springs; me to Stockton University. And so poor Pulanesaura was languishing. Therefore, when Blair approached us about describing Pulanesaura for his Ph.D., we were enthusiastically supportive. I was especially pleased to see Blair at the helm of the description. I am beyond happy that a South African Ph.D. student is the lead author on the description of a native South African dinosaur. His persistence and perseverance on this project is why the world now knows about Pulanesaura.

Why Pulanesaura? Well, the name means “rain bringer” in Sesotho, which is fitting since we always seemed to get rained on during the excavation of this dinosaur. And the publication of “Rain Bringer” has finally brought home a trilogy of sauropodomorph dinosaurs and the complex story they tell of what was happening in the Early Jurassic at what is now the Spion Kop farm.

First things first – how do we know Pulanesaura is a sauropod? A number of clues point the way. For one thing, although we did not find a skull, we found teeth. The teeth of sauropods, unlike their sauropodomorph brethren, have a spoon- or spatula-like profile and have wrinkled enamel. The teeth of Pulanesaura certainly fit the bill there.

Next, being large, sauropods braced their vertebral column with extra joints in their backbones (vertebrae) – a portion of this extra joint is called the hyposphene. The body vertebrae we have of Pulanesaura only preserve their tops (the hyposphene is located on the bottom-half of the vertebra) but luckily a full tail (caudal) vertebra is preserved, and that has a hyposphene. We are also fortunate that part of the forelimb was preserved. The ulna bone in sauropods cradles the other forearm bone, the radius, by wrapping around it from behind. In sauropods, a wide, triangular depression is present on the ulna where the radius sits. Although the ulna of Pulanesaura is a bit crushed and scrappy, it was intact enough to show that, yes, indeed, such a depression for the radius was there. These features and more showed us that this dinosaur was certainly a true sauropod.

How do we know Pulanesaura is new to science? Using a method called cladistics, the suite of features for Pulanesaura was compared to other sauropodomorphs and sauropods from South Africa and around the globe. Its unique combination of features show that it is not a member of previously known sauropodomorph or sauropod dinosaurs, but falls along its own branch of the dinosaur family tree near the common ancestor of all sauropod dinosaurs. At the moment, it is very difficult to tell the difference between a true early sauropod and a sauropodomorph very close to the common ancestor of sauropods. Given the data we have for Pulanesaura, we find it most likely to be a very early sauropod. Certainly, future studies and perhaps more material of Pulanesaura will clarify this picture.

How big was Pulanesaura? We certainly don’t have a complete skeleton of this herbivore, but we have enough bones from enough areas of the body to infer that this animal stretched nearly 8 meters (about 26 feet) long and stood about 2 meters (about 6.5 feet) high at the hip. That may seem big, but it’s small for a sauropod.

Why is Pulanesaura significant? The traditional picture of sauropodomorph evolution is that when true sauropods came onto the scene, the other sauropodomorphs were pushed aside, their small body size and “inferior” anatomy undone by the larger herbivores. But Pulanesaurua turns this notion on its head because, living alongside it at Spion Kop were other sauropodomorph dinosaurs with very different anatomies. Adam, Johann, myself, and others have described two of these other sauropodomorphs, both also from Spion Kop. One, Aardonyx, was a 7 meter long sauropodomorph capable of assuming both a bipedal and quadrupedal posture; and another, Arcusaurus, was a small, juvenile sauropodomorph with a hold-over of more primitive features. And one of the things these other sauropodomorphs had going for them was that they could feed at different heights and use their forelimbs to direct foliage to the mouth. In contrast, the anatomy of Pulanesaura shows that it was an obligate quadruped (it could not stand bipedally on its hind legs), which would have restricted its vertical reach for vegetation compared with these other sauropodomorphs. However, the single neck (cervical) vertebra we have for Pulanesaura has joints that were spaced and angled (much like those of other sauropods) such that they would have allowed for a larger range of neck motion than in other contemporaneous sauropodomorphs. In other words, although Pulanesaura could not rear up and extend its neck into the trees, it could stand still and more efficiently crop foliage over a wider range. We suggest Pulanesaura shows us the incipient stages of what sauropods became very good at: they stood in one place and swept their tiny heads across a sea of vegetation. As the Jurassic period wore on, and vegetation became larger and more widespread, the advantages conferred by a body which conserved energy by standing still and sweeping a long neck across swaths of plants would ultimately select for sauropods and not their bipedal cousins.

It would have been difficult to explain to my five-year-old self that it would be many lunch breaks from the initial discoveries at Spion Kop to their final reveal to the public. But it has been worth the wait. I consider myself to be very fortunate to have the privilege of working with so many enthusiastic and talented people. Moreover, it is important to stress that cooperation with the farmers at Spion Kop was invaluable. Partnerships with farmers are a great benefit to paleontology in South Africa. Farmers know their land well, and they’re always spotting interesting things. It’s such a pleasure to work with people who value their heritage and to help them learn more about it. Because of such mutual respect and interest in South Africa’s prehistory, we now have a much richer picture and appreciation of a pivotal moment in sauropod dinosaur history that would not otherwise be possible.

And my inner five-year-old most certainly approves!

Jurassic World: Not About Science

As a dinosaur paleontologist, I was perhaps duty-bound to see Jurassic World … that and my 10-year-old daughter was keen to see it as well. I am teaching a freshman-only seminar on dinosaurs this fall, and that also made the choice to see the movie a no-brainer. I had only seen one or two brief previews of the movie and had avoided reading reviews of the plot so I could go into the movie with as few preconceptions as possible. Here are my thoughts.

Before I start, let me say that this is not a review of the story or much about the accuracy of the science. That has already been done in multiple ways by many of my colleagues in the dinosphere. There is not much new I could add there.  Therefore, there are no spoilers here unless you consider what is shown in the movie previews as spoilers.

I was not surprised and kind of disappointed by I what I saw. In a sentence: it was a monster movie and not a movie about dinosaurs or science. There were no paleontologist characters in the movie, and the dinosaurs were there to devour people and cause mayhem or serve as background. As anyone would know from the movie previews, this is again a retread of technology gone wrong and hubris. No one should be surprised by the basic plot and its outcome.

So here is my question: since this movie is clearly not about science and is, like the original Jurassic Park, yet another Frankenstein story, why should we as scientists care how accurate is? And I ask this question because we dinosaur paleontologists suffer from a public image problem. We are often considered to be kids who never grew up, but not “real” scientists. I am the first to admit that my fascination with dinosaurs started early, and that many of us have a friendly competition to see who was interested in dinosaurs the earliest. It does come with a certain badge of honor. But I think that outside of our small group, this doesn’t often help us be taken seriously.

I suppose, for example, one could point to someone like Neil DeGrasse Tyson, arguing that he engages the public with his take on science-fiction movies. But even here astronomy and physics have more science “street cred” than dinosaur paleontology. Tyson can let his nerd flag fly, so to speak, without much “damage” to the reputation of physics because his science is “the” science in the mind of the public. Nobody (sane) argues about gravity. Everyone, though, is happy to argue with dinosaur experts about what they think dinosaurs were like … perhaps in part because we all know the science is done by big kids who aren’t real scientists.

I agree and empathize with many of my colleagues that dinosaur movies often miss an opportunity to educate the public about science as a process as well as entertain. But I also think we tread a fine line here — one that may inadvertently only reinforce the stereotype of the nerdy (read “child-like” and “out-of-touch”) dinosaur paleontologist when we engage the “science” of a movie that is clearly not about science at all. This stereotype of the “big kid” dino-nerd is more damaging than just reputation. For example, the recent attempt to sell the privately-owned “Dueling Dinosaurs” was predicated on the identity of one of the dinosaurs as Nanotyrannus. Even when an expert on tyrannosaurids like Thomas Carr pointed out in great detail why Nanotyrannus is not real, it is perhaps easier to ignore his expertise in favor of profit partly because of the “big kid” stereotype.

My suggestion would be, rather than engaging the press in the predictable “this and that were wrong” conversation, why not simply say, “this is science fiction and a monster movie and it doesn’t represent paleontology.” Jurassic World is about as close to dinosaur paleontology as Star Wars is to astronomy. These movies can be inspiring to children and adults, but their main focus is a story, its plot, climax, and resolution, not scientific accuracy. And the sad part about Jurassic World is that the missed opportunity is less about the science (which is relatively non-existent) and more about the tired re-hashing of gender stereotypes and hubris/comeupance plot lines.

Dinosaur paleontology, for those of us who are experts, is a rigorous science with many insights to offer us in the present. And, yes, many of us have been enraptured with this science since childhood. There is nothing wrong with that. But understanding how stereotypes about our science and about us as scientists play in the larger world are equally important to recognize. We have an important message about the past and our future to impart to the public. Let’s not dilute our energies on the trivial details of an expensive and silly monster movie.

Bearded Dragon Runs for Science!

Bonnan Lab Lizard TreadmillA brief post to show our progress in the BFF Locomotion Lab. We’re learning our equipment and training our lizards to walk and run. The lizards are rewarded with a cricket as a treat. The lizard you see in the video is Graybeard, a juvenile bearded dragon (Pogona vitticeps). This video is comprised of two synched cameras and is a test video and not yet the “real” thing. But we’ll be capturing real data and more soon enough.

As always, stayed tuned and there will be more reptiles running in the near future!

New interview on Prehistoric Pub

Just a brief post to point those interested to my interview with Jersey native and paleontology enthusiast Gary Vecchiarelli:

Thanks for the interview, Gary!


The NAMS Research Symposium at Stockton University – Friday, April 17

Just a brief announcement that the NAMS Research Symposium, which features research by NAMS students with faculty, is this Friday, April 17 in the C/D Atrium on the Main Campus of Stockton University. Students will be at their posters between 3-5PM.

You can see the research our students are doing by downloading the NAMS Research Symposium Abstract Booklet 2015.

You can tweet about the event with the hashtag #OspreySci

You can also join us on Facebook.