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Uh oh, a “why?” question in biology! There are many potential, and not mutually exclusive, answers to such questions. Ultimately there is a historical, evolutionary answer that underpins it all (“ostriches evolved two kneecaps because…”). But we like ostrich knees and their funky double-kneecaps (patellae; singular = patella) so we wanted to know why they get so funky. One level of addressing that question is more like a “how?” they have them. So we started there, with what on the surface is a simple analysis. And we published that paper this week, with all of the supporting data (CT, MRI, FEA).

Stomach-Churning Rating: 6/10 because there is a gooey image of a real dissection later in the post, not just tidy 3D graphics.

First author Kyle Chadwick was my research technician for 2 years on our sesamoid evolution grant, and we reported earlier on the detailed 3D anatomy of ostrich knees (this was all part of his MRes degree with me, done in parallel with his technician post). Here, in the new paper with Sandra Shefelbine and Andy Pitsillides, we took that 3D anatomy and subjected it to some biomechanical analysis in two main steps.

Ostrich (right) knee bones. The patellae are the two knobbly bits in the knee.

First, we used our previous biomechanical simulation data from an adult ostrich (from our paper by Rankin et al.) to estimate the in vivo forces that the knee muscles exert onto the patellar region during moderately large loading in running (not maximal speed running, but “jogging”). That was “just” (Kyle may laugh at the “just”– it wasn’t trivial) taking some vectors out of an existing simulation and adding them into a detailed 3D model. We’ve done similar things before with a horse foot’s bones (and plenty more to come!), but here we had essentially all of the soft tissues, too.

Ostrich knee with muscles as 3D objects.

Second, the 3D model that the muscular forces were applied to was a finite element model: i.e., the original 3D anatomical model broken up into a mesh, whose voxels each had specific properties, such as resistance to shape change under loading in different directions. The response of that model to the loads (a finite element analysis; FEA) gave us details on the stresses (force/area) and strains (deformations from original shape) in each voxel and overall in anatomical regions.

Finite element model setup for our study. If you do FEA, you care about these things. If not, it’s a pretty, sciencey picture.

The great thing about a computer/theoretical model is that you can ask “what if?” and that can help you understand “how?” or even “why?” questions that experiments alone cannot address. Ostriches aren’t born with fully formed bony kneecaps; indeed those patellae seem to mature fairly late in development, perhaps well after hatching. We need to know more about how the patellae form but they clearly end up inside the patellar (knee extensor) tendon that crosses the knee. So we modelled our adult ostrich without bony patellae; just with a homogeneous patellar tendon (using the real anatomy of that tendon with the bony bits replaced by tendon); and subjected it to the loading environment for “jogging”.

The right knee of an ostrich hatchling. The patellae have yet to form; indeed there is little bone around the knee region at all, yet.

We then inspected our FEA’s results in light of modern theory about how tissues respond to loading regimes. That “mechanobiology” theory, specifically “tissue differentiation”, postulates that tendon will tend to turn into fibrocartilage if it is subjected to high compression (squishing) and shear (pushing). Then, the fibrocartilage might eventually be reworked into bone as it drops the compression and shear levels. So, according to that theory (and all else being equal; also ignoring the complex intermediate states that would happen in reality), the real ostrich’s kneecaps should be located in the same positions where the FEA, under the moderately large loads we applied, predicts the homogeneous tendon to have high compression and shear. But did the real anatomy match the mechanical environment and tissue differentiation theory’s predictions?

Tissue differentiation diagram displaying the theoretical pathways for transformation of tissues. If tendon (red) experiences high shear (going up the y-axis) and high compression (going toward the left), it should turn into fibrocartilage (purple). Transformation into bone (diagonally to the bottom right) would reduce the shear and compression.

Well, sort of. The image below takes some unpacking but you should be able to pick out the red areas on the bottom row where the patellae actually are, and the yellow shaded regions around some of those patellar regions are where the compression and shear regimes are indeed high and overlapping the actual patellar regions. The upper two rows show the levels of compression (or tension; pulling) and shear, but the bottom row gets the point across. It’s not a bad match overall for the first (“real”; common to all living birds) patella, located on top of the upper knee (femur). It’s not a good match overall for the second (unique to ostriches) patella, located below the first one (and attached to the tibia bone).

FEA results! (click to embiggen)

Kyle says, “Being a part of this project was exciting because of the application of engineering concepts to interesting biological (including evolutionary) questions. Also, it never gets old seeing people’s reactions when I tell them I study ostrich knees.

The study had a lot of nuances and assumptions. We only looked at one instant in slow running and only at one adult ostrich, not at the full development of ostrich anatomy and loading. That’s harder. We started simple. The tissue differentiation theory is used more for fracture healing than for sesamoid bone formation but there’s some reason to suspect that similar mechanisms are at play in both. And there’s much more; if you want the gory details see the paper.

So did we solve why, or how, ostriches have two kneecaps? We felt that the mechanical environment of our FEA was a good theoretical explanation of where the first patella forms. We originally expected the second patella, which evolved more recently and might be more mechanically sensitive as a result, to be a better match than the first one, but it was the opposite. C’est la science!

Enough models, let’s have some reality! I warned you this post would get messy, and here it is. Left leg (skinned) of an ostrich showing the muscles around the knee. The patellar region would be in the gloved hand of the lucky individual shown.

This study, for me, was a fun experience in moving toward more fusion of “evo-devo” and biomechanical analyses, a research goal of mine lately– but there’s still a ways to go with the “how?” and “why?” questions even about ostrich kneecaps.

We felt that the best conclusion supported by our analyses was that, rather than have homogeneous stresses and strains throughout their knee tissues (e.g. the patellar tendon), ostriches have a lot of regional diversity in how those tissues are loaded (in the condition we modelled, which is adequately representative of some athletic exertion). Look at the complex FEA coloured results above again, the top two rows: there are a lot of different shades of compression/tension and shear; not homogeneous strains. That diversity of regional loading sets those tissues up for potential transformation throughout growth and development. And thus ONE of the reasons why ostriches might have two kneecaps is that the heterogeneous loading of their knee tendon favours formation of heterogeneous tissue types.

Another, compatible, explanation is that these different tissues might have consequences for how the muscles, tendon and joint operate in movement behaviours. In due time there will be more about that. In the meantime, enjoy the paper if this post makes you want to know more about the amaaaaaazing knees of ostriches!

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A Confuciusornis fossil; not the one from our study but prettier (more complete).

Today almost three years of collaboration come together in a publication that is a fun departure from my normal research, but also makes sense in light of it. Professor Baoyu Jiang from Nanjing University in China has been being working on the taphonomy of the Early Cretaceous Jehol biota from northeastern China (Manchuria) for a while, and he found a lovely Confuciusornis (early bird) fossil; one of thousands of them; from the volcanic pyroclastic flow-based lake deposits there.

Although at first glance the skeletal remains of that fossil are not fabulous compared with some other Confuciusornis, what makes this one lovely is that, on peering at it with multiple microscopic and other imaging techniques, he (and me, and a China-UK collaboration that grew over the years) found striking evidence of very well-preserved fossil soft tissues. Our paper reporting on these findings has gone live in Nature Communications so I can blog about it now.

Reference: Jiang, B., Zhao, T., Regnault, S., Edwards, N.P., Kohn, S.C., Li, Z., Wogelius, R.A., Benton, M., Hutchinson, J.R. 2017. Cellular preservation of musculoskeletal specializations in the Cretaceous bird Confuciusornis. Nature Communications 8:14779. doi: 10.1038/NCOMMS14779

Stomach-Churning Rating: 3/10; gooey, but fossil gooey, except for some colourful, gastrically-tolerable histology of bird tissue.

Front view of the ankle/foot of our specimen.

Back view of the ankle/foot of our specimen.

What has been fun about this collaboration is that, for one, it fits in perfectly with my prior work. Ever since my PhD thesis I’d been wondering about odd bones in the legs of birds, including a very puzzling and very, very neglected bit of bone called the tarsal sesamoid, on the outside of the upper end of the ankle joint. Furthermore, a tunnel of tissue called the tibial cartilage sits next to that sesamoid bone, and then across the ankle joint there is a bony prominence with grooves and tunnels that vary highly among bird species; that is called the hypotarsus. These structures are all known in living birds and, to a degree, in extinct fossil cousins. Our specimen seems to reveal an earlier stage in how these little features of bird ankles originated, which we concluded to be a step along the transition to the more crouched legs that modern birds have.

This study has also challenged me to broaden my horizons as a scientist. Although this was a big collaboration and thus we had several specialists to apply supercharged technological techniques to our fossil, I had to learn something about what all that meant. My kind colleagues helped me learn more about tissue histology, scanning electron microscopy, synchrotron mapping, FTIR and mass spectrometry and more. I won’t go through all of these techniques but there are some pretty pictures sprinkled here and in the paper, and a lot more detail in the paper for those who want the gory techno-detail. Basically we threw the kitchen sink of science at the fossil to crack open some of its secrets, and what we found inside was nifty.

Scanning electron micrograph image of probable tendon or ligament fibres (arrow) in cross-section, from near the ankle joint.

We found preserved cells and other parts of connective tissues including tendons and/or ligaments, fibrocartilage (the tougher kind) and articular cartilage (the softer joint-padding kind). That’s great, although not unique, but the kitchen sink also flushed out even more reductionist data: those tissues included some organic residues, including what appear to be bits of proteins (amino acids); particularly the collagen that makes up tendons.

Fibrocartilage (“fc”) from the ankle joint region.

Hopefully we’re right, and we included as much of the data as we could manage so that others can look at our findings. The specimen is crushed into nearly two dimensions, like all Jehol biota organisms, so its anatomy was hard to interpret but we think we got it right. All of the other kitchen-sinky tools have their own nuances and pitfalls but we did our best with a superb team of experts. We’ve had to wait 125 million years to uncover this specimen and a few more years to find out if we’ve looked at the right way is no greater test of patience.

I thank my coauthors, especially Baoyu Jiang for the kind invitation to participate and the very fun experience of collaborating. I think I’ll remember this study for a long time because, for me, it takes a step beyond just describing Another Case of Jaw-Dropping Fossilization (can you hear the hipsters recounting the excitement and cynicism of the 1990s when this all was dawning? I was there and maybe now I’m one of them). By combining all of those methods we learned new things about the palaeobiology of birds and the evolution of traits within birds. Confuciusornis, not shockingly, had ankles that should have functioned in ways intermediate between those of bog-standard non-avian theropods and modern birds.

Same anatomical regions in an extant bird as in the main fossil specimen. Left distal tibiotarsus (TT; below) and proximal tarsometatarsus (TMT; above) from an adult helmeted guineafowl (Numida meleagris) after formalin fixation. (from our paper’s Supp Info)

I’m hopeful that more synthesis of molecular/cellular, imaging, biomechanical and other tools (not to mention good old palaeontology and anatomy!) can wash away some more of this mystery. And it was fun to be a part of a study that adds to overwhelming evidence that was heretical ~25 years ago: some hardy biomolecules such as collagen and keratin can survive hundreds of millions of years, not just thousands. Pioneers such as Prof. Mary Schweitzer led the original charge that made reporting on discoveries like ours much easier today.

I know how the birds fly, how the fishes swim, how animals run. But there is the Dragon. I cannot tell how it mounts on the winds through the clouds and flies through heaven. Today I have seen the Dragon.“– Confucius, ca. 500 BCE.

Let’s finish with some images of a living bird’s ankle region, by co-author and PhD student Sophie Regnault. We considered these for inclusion in the paper but they didn’t fit quite right. I love them anyway so here they are:

Patchwork of histology slide images, from a guineafowl’s ankle (as per photo above). The numbered squares correspond to zoomed-in images below. The tibiotarsus is on the proximal end (bottom left); the tarsometatarsus is on the distal end (right side); and the enigmatic tarsal sesamoid is at the top. Magnification: 20x overall.

Region 1. nice (fibro)cartilage-bone inferface at ligament insertion.

Region 2: longitudinal slice through ligaments connecting the tibiotarsus to the tarsometatarsus across the ankle joint.

Region 3: front (bottom) of the tibiotarsus/upper ankle.

Region 4: tendon fibres in longitudinal section; on the back of the tibiotarsus. Some show mineralization into ossified tendons (“metaplasia”); another curious feature of modern birds.

Region 5: muscle attachment to the back of the upper tarsometatarsus bone. Small sesamoid fragment visible.

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The early, hippo-like mammal Coryphodon. I didn’t know it had a patella but it does. From Yale Peabody Museum.

I’m not shy about my fondness for the patella (kneecap) of tetrapod vertebrates, and neither are the other members of RVC’s “Team Patella”. We’ve had a fun 3+ years studying these neglected bones, and today we’ve published a new study of them. Our attention has turned from our prior studies of bird and lepidosaur kneecaps to mammalian ones. Again, we’ve laid the groundwork for a lot of future work by focusing on (1) basic anatomy and (2) evolutionary history of these sesamoid bones, with a lot of synthesis of existing knowledge from the literature; including development and genetics. This particular paper is a sizeable monograph of the state of play in the perusal of patellae in placental and other synapsids. Here’s what we did and found, focusing mostly on bony (ossified) patellae because that allowed us to bring the fossil record better to bear on the problem.

Reference: Samuels, M., Regnault, S., Hutchinson, J.R. 2016. Evolution of the patellar sesamoid bone in mammals. PeerJ 5:e3103 https://doi.org/10.7717/peerj.3103

Stomach-Churning Rating: 1/10; bones and more bones.

The short version of the story is that mammals evolved bony kneecaps about five times, with marsupials gaining and losing them (maybe multiple times) whereas monotremes (platypus and echidna) and placentals (us and other mammals) didn’t do much once they gained them, and a couple of other fossil groups evolved patellae in apparent isolation.

Evolution of the patella in mammals: broad overview from our paper. Click to zoom in.

The marsupial case is the most fascinating one because they may have started with a fibrocartilaginous “patelloid” and then ossified that, then reduced it to a “patelloid” again and again or maybe even regained it. There needs to be a lot more study of this group to see if the standard tale that “just bandicoots and a few other oddballs have a bony patella” is true for the Metatheria (marsupials + extinct kin). And more study of the development of patellae in this group could help establish whether they truly do “regress” into fibrocartilage when they are “lost” in evolution, or if other, more flexible patterns exist, or even if some of the cases of apparent “loss” of a bony patella are actually instances of delayed ossification that only becomes evident in older adults. Our paper largely punts on these issues because of an absence of sufficient data, but we hope that it is inspiration for others to help carry the flag forward for this mystery.

The higgledy-piggledy evolution of a patella in Metatheria, including marsupials. Click to zoom in.

Some bats, too, do funky things with their kneecaps, analogous to the marsupial “patelloid” pattern, and that chiropteran pattern also is not well understood. Why do some bats such as Pteropus fruit bats “lose” their kneecaps whereas others don’t, and why do some bats and other species (e.g. various primates) seem to have an extra thing near their kneecaps often called a “suprapatella”? Kneecap geeks need to know.

The short-nosed bandicoot (marsupial) Isoodon, showing a nice bony patella as typifies this group. From Yale Peabody Museum.

Otherwise, once mammals evolved kneecaps they tended to keep them unless they lost their hindlimbs entirely (or nearly so). Witness the chunky patellae of early whales such as Pakicetus and join us in wondering why those chunks persisted. The evolutionary persistence of blocky bits of bone in the knees of various aquatic animals, especially foot-propelled diving birds, may help answer why, as the hindlimbs surely still played roles in swimming early in cetacean evolution. Ditto for sea cows (Sirenia) and other groups.

Early whale Ambulocetus, showing hefty kneecaps.

But I’m still left wondering why so many groups of land vertebrates (and aquatic ones, too) never turned parts of their knee extensor tendons into bone. We know a bit about the benefits of doing that, to add leverage to those joints that enables the knee muscles to act with dynamic gearing (becoming more forceful “low gear” or more speedy “high gear” in function). Non-avian (and most early avian/avialan) dinosaurs, crocodiles, turtles, amphibians, early mammal relatives, and almost all other known extinct lineages except for those noted above got by just fine without kneecaps, it seems, even in cases where a naïve biomechanist would expect them to be very handy, such as in giant dinosaurs.

A quoll, Dasyurus, with what is probably a fibrocartilaginous “patelloid”. From Yale Peabody Museum.

However, tendons don’t turn to bone unless the right stresses and strains are placed upon them, so maybe kneecaps are a “spandrel” or “exaptation” of sorts, to abuse Gould’s ghost, whose adaptive importance is overemphasized. Maybe that adaptive myopia overshadows a deeper ontogenetic story, of how tissues respond to their history of mechanical loading environment. It has been speculated that maybe (non-marsupial) mammals have broadly “genetically assimilated” their kneecaps, fixing them into semi-permanence in their genetic-developmental programmes, whereas in contrast the few studies of birds indicate more responsiveness and thus less assimilation/fixation. That “evo-devo-mechanics” story is what now fascinates me most and we’ve poked at this question a bit now, with some updates to come- watch this space! Regardless, whether an animal has a bony vs. more squishy soft tissue patella must have consequences for how the knee joint and muscles are loaded, so this kind of question is important.

Giant marsupial Diprotodon (at NHM London); to my knowledge, not known to have had kneecaps- why?

In the meantime, enjoy our latest contribution if it interests you. This paper came about when first author Dr. Mark Samuels emailed me in 2012, saying he’d read some of my old papers on the avian musculoskeletal system and was curious about the evolution of patellae in various lineages. Unlike many doctors and vets I’ve run into, he was deeply fascinated by the evolutionary and fossil components of patellae and how those relate to development, genetics and disorders of patellae. We got talking, found that we were kindred kneecap-spirits, and a collaboration serendipitously spun off from that, soon adding in Sophie. It was a blast!

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A quick heads-up that we just posted on our sister blog Anatomy To You, about a new open-access paper we’ve published on the skeletal anatomy of the tuatara Sphenodon. Lots of cool images you can’t see anywhere else are there!

In focus: The big picture of little bones in tuatara

I give it a Stomach-Churning Rating of 3/10- some picked specimens of tuatara but they’re still cute, not nasty, I’d say.

AND, like the Cool-Whip or vanilla ice cream atop your leftover pumpkin pie, there’s an added delicious bonus: a huge dataset of microCT scans from 19 tuatara specimens, free to access here:

https://osf.io/bds35/

We are VERY pumped up about getting this paper and dataset released, so we are spreading the word as wide as we can!

Sayonara.

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(Marcela with some furry friends; photo by Oliver Siddon)

(Marcela with some felid friends; photo by Oliver Siddon)

A guest post by Marcela Randau (m.randau@ucl.ac.uk)

Stomach-Churning Rating: 1/10; just bones and data plots!

It is often said that all cats are very similar in terms of their skeletal morphology (“a cat is a cat is a cat”). But is this really the case? It may be if only gross, qualitative anatomy is taken into consideration, i.e., if you just eyeball the skeletons of tigers and lions you might find yourself not knowing which one is which. But with huge advances in technology that allows for extracting detailed shape information off a structure (e.g., a skull) and for analysing this information (‘Geometric Morphometrics’), it has become more and more possible to distinguish between relatively similar forms – which may be from distinct species, separate sexes, or even just different populations of the same taxon.

And it is reasonable to think that cat skeletons might be a lot more different than what meets the eye, as for a lineage of apparently similarly built animals, with not that much variation in diet  (all cats are hypercarnivores) there is substantial variation in body mass (over 300-fold just in living species!) and in ecology across cat species. From the cursorial cheetah to the arboreal clouded leopard, felids present a wide range of locomotory adaptations. Yes, all cats can climb, but some do it better than others: think lion versus margay (yes, they do descend trees head-first). As hypercarnivores, all cats are meat specialists, but they also change with regards to how big their prey is, with a general and sometimes-not-so-black-and-white three-tier classification into small, mixed and large prey specialists. The rule of thumb is ‘if you are lighter than ~20-25 kg, hunt small stuff. If you are heavier than that, hunt BIG BIG things; bigger than yourself. And if you are in the middle ground, hunt some small-ish things, some big-ish things, and things about your size. Well, -ish’ – their prey size preference has a lot to do with energetic constraints (have a look at Carbone et al. 1999; and Carbone et al. 2007, if you’re interested in this). But the fun bit here is that form sometimes correlates quite strongly with function, so we should be able to find differences in some of their bones that carry this ecological signal.

Indeed, for a while now, we have known that the shape of the skull and limbs of felids can tell us a lot about how they move and how big their prey is (Meachen-Samuels and Van Valkenburgh 2009, 2009), but a large proportion of their skeleton has been largely ignored: we don’t know half as much about ecomorphology and evolution of the vertebral column. Well, it was time we changed this a bit! As the PhD student in the Leverhulme-funded ‘Walking the cat back’ (or more informally, “Team Cat”) project, I’ve spend a big chunk of my first two years travelling around the world (well, ok, mainly to several locations in the USA) carrying a heavy pellet case containing my working tool, a Microscribe, to collect 3-D landmarks (Fig. 1) across the presacral vertebral column of several cat species. And some of first results are just out! Check them out by reading our latest paper, “Regional differentiation of felid vertebral column evolution: a study of 3D shape trajectories” in the Organisms Diversity and Evolution journal (Randau, Cuff, et al. 2016).

cheetah-verts

Fig. 1: Different vertebral morphologies and their respective three-dimensional landmarks. Vertebral images are from CT scans of Acinonyx jubatus (Cheetah, USNM 520539)

Building from results based on our linear vertebral data from the beginning of the year (Randau, Goswami, et al. 2016), the 3-D vertebral coordinates carry a lot more information and we were able to describe how this complex shape-function relationship takes place throughout the axial skeleton (in cats at least) in much better detail than our prior study did. One of the difficulties in studying serial structures such as the vertebral column is that some clades present variation in vertebral count which makes it less straightforward to compare individual vertebrae or regions across species. However, mammals are relatively strongly constrained in vertebral count, and Felidae (cats; living and known fossils) show no variation at all, having 27 presacral vertebrae. So adaptation of the axial skeleton in mammals has been suggested to happen by modification of shape rather than changes in vertebral number.

Using a variety of geometric morphometric analyses, under a phylogenetically informative methodology, we have shown that there is clear shape and functional regionalisation across the vertebral column, with vertebrae forming clusters that share similar signal. Most interestingly, the big picture of these results is a neck region which is either very conservative in shape, or is under much stronger constraints preventing it from responding to direct evolutionary pressures, contrasting with the ‘posteriormost’ post-diaphragmatic tenth thoracic (T10) to last lumbar (L7) vertebral region, which show the strongest ecological correlations.

We were able to analyse shape change through functional vertebral regions, rather than individual vertebrae alone, by making a novel application of a technique called the ‘Phenotypic Trajectory Analysis’, and demonstrated that the direction of vertebral shape trajectories in the morphospace changes considerably between both prey size and locomotory ecomorphs in cats, but that the amount of change in each group was the same. It was again in this T10-L7 region that ecological groups differed the most in vertebral shape trajectories (Fig. 2).

pta-cats

Figure 2: Phenotypic trajectory analysis (PTA) of vertebrae in the T10 – L7 region grouped by prey size (A) and locomotory (B) categories.

So in the postcranial morphology of cats can be distinguished, changing its anatomy in order to accommodate the different lifestyles we see across species. But the distinct parts of this structure respond to selection differently. The next step is figuring out how that might happen and we are working on it.

While Team Cat continues to investigate other biomechanical and evolutionary aspects of postcranial morphology in this interesting family, we’ve been able to discuss some of these and other results in a recent outreach event organised by the University College of London Grant Museum of Zoology and The Royal Veterinary College. We called it “Wild Cats Uncovered: movement evolves”. Check how it went here: (https://blogs.ucl.ac.uk/museums/2016/11/17/cheetah-post-mortem/) and here (http://www.rvc.ac.uk/research/research-centres-and-facilities/structure-and-motion/news/wild-cats-uncovered), with even more pics here (https://www.flickr.com/photos/144824896@N07/sets/72157676695634065/).

References used here:

Carbone, C., Mace, G. M., Roberts, S. C., and Macdonald, D. W. 1999. Energetic constaints on the diet of terrestrial carnivores. Nature 402:286-288.

Carbone, C., Teacher, A., and Rowcliffe, J. M. 2007. The costs of carnivory. PLoS biology 5 (2):e22.

Meachen-Samuels, J. and Van Valkenburgh, B. 2009. Craniodental indicators of prey size preference in the Felidae. Biol J Linn Soc 96 (4):784-799.

———. 2009. Forelimb indicators of prey-size preference in the Felidae. Journal of morphology 270 (6):729-744.

Randau, M., Cuff, A. R., Hutchinson, J. R., Pierce, S. E., and Goswami, A. 2016. Regional differentiation of felid vertebral column evolution: a study of 3D shape trajectories. Organisms Diversity and Evolution Online First.

Randau, M., Goswami, A., Hutchinson, J. R., Cuff, A. R., and Pierce, S. E. 2016. Cryptic complexity in felid vertebral evolution: shape differentiation and allometry of the axial skeleton. Zoological Journal of the Linnean Society 178 (1):183-202.

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It has been almost three months since my last post here, and things have fallen quiet on our sister blog Anatomy to You, too. I thought it was time for an update, which is mostly a summary of stuff we’ve been doing on my team, but also featuring some interesting images if you stick around. The relative silence here has partly been due to me giving myself some nice holiday time w/family in L.A., then having surgery to fix my right shoulder, then recovering from that and some complications (still underway, but the fact that I am doing this post is itself evidence of recovery).

Stomach-Churning Rating: 4/10; semi-gruesome x-rays of me and hippo bits at the end, but just bones really.

X-ray of my right shoulder from frontal view, unlabelled

X-ray of my right shoulder from frontal view, unlabelled

Labelled x-ray

Labelled x-ray

So my priorities shifted to those things and to what work priorities most badly needed my limited energy and time. I’ve also felt that, especially since my health has had its two-year rough patch, this blog has been quieter and less interactive than it used to be, but that is the nature of things and maybe part of a broader trend in blogs, too. My creative juices in terms of social media just haven’t been at their ~2011-2014 levels but much is out of my control, and I am hopeful that time will reverse that trend. Enough about all this. I want to talk about science for the rest of this post.

My team, and collaborators as well, have published six recent studies that are very relevant to this blog’s theme- how about we run through them quickly? OK then.

  1. Panagiotopoulou, O., Pataky, T.C., Day, M., Hensman, M.C., Hensman, S., Hutchinson, J.R., Clemente, C.J. 2016. Foot pressure distributions during walking in African elephants (Loxodonta africana). Royal Society Open Science 3: 160203.

Our Australian collaborators got five African elephants together in Limpopo, South Africa and walked them over pressure-measuring mats, mimicking our 2012 study of Asian elephants. While sample sizes were too limited to say much statistically, in qualitatively descriptive terms we didn’t find striking differences between the two species’ foot pressure patterns. I particularly like how the centre of pressure of each foot (i.e. abstracting all regional pressures down to one mean point over time) followed essentially the same pattern in our African and Asian elephants, with a variable heelstrike concentration that then moved forward throughout the step, and finally moved toward the outer (3rd-5th; especially 3rd) toes as the foot pushed off the ground, as below.

African elephant foot COP traces vs. time in red; Asian elephant in orange. Left and right forefeet above; hindfeet below.

African elephant foot COP traces vs. time in red; Asian elephant in orange-yellow. Left and right forefeet above; hindfeet below.

Gradually, this work is moving the field toward better ability to use similar techniques to compare elephant foot mechanics among species, individuals, or over time– especially with the potential of using this method (popular in human clinical gait labs) to monitor foot (and broader musculoskeletal) health in elephants. I am hopeful that a difference can be made, and the basic science we’ve done to date will be a foundation for that.

  1. Panagiotopoulou, O., Rankin, J.W., Gatesy, S.M., Hutchinson, J.R. 2016. A preliminary case study of the effect of shoe-wearing on the biomechanics of a horse’s foot. PeerJ 4: e2164.

Finally, about six years after we collected some very challenging experimental data in our lab, we’ve published our first study on them. It’s a methodological study of one horse, not something one can hang any hats on statistically, but we threw the “kitchen sink” of biomechanics at that horse (harmlessly!) by combining standard in vivo forceplate analysis with “XROMM” (scientific rotoscopy with biplanar fluoroscopy or “x-ray video”) to conduct dynamic analysis of forefoot joint motions and forces (with and without horseshoes on the horse), and then to use these data as input values for finite element analysis (FEA) of estimated skeletal stresses and strains. This method sets the stage for some even more ambitious comparative studies that we’re finishing up now. And it is not in short supply of cool biomechanical, anatomical images so here ya go:

fig5-vonmises

Above: The toe bones (phalanges) of our horse’s forefoot in dorsal (cranial/front) view, from our FEA results, with hot colours showing higher relative stresses- in this case, hinting (but not demonstrating statistically) that wearing horseshoes might increase stresses in some regions on the feet. But more convincingly, showing that we have a scientific workflow set up to do these kinds of biomechanical calculations from experiments to computer models and simulations, which was not trivial.

And a cool XROMM video of our horse’s foot motions:

  1. Bates, K.T., Mannion, P.D., Falkingham, P.L., Brusatte, S.L., Hutchinson, J.R., Otero, A., Sellers, W.I., Sullivan, C., Stevens, K.A., Allen, V. 2016. Temporal and phylogenetic evolution of the sauropod dinosaur body plan. Royal Society Open Science 3: 150636.

I had the good fortune of joining a big international team of sauropod experts to look at how the shapes and sizes of body segments in sauropods evolved and how those influenced the position of the body’s centre of mass, similar to what we did earlier with theropod dinosaurs. My role was minor but I enjoyed the study (despite a rough ride with some early reviews) and the final product is one cool paper in my opinion. Here’s an example:

fig6a-bates-sauropod-com-evol

The (embiggenable-by-clicking) plot shows that early dinosaurs shifted their centre of mass (COM) backwards (maybe related to becoming bipedal?) and then sauropods shifted the COM forwards again (i.e. toward their forelimbs and heads) throughout much of their evolution. This was related to quadrupedalism and giant size as well as to evolving a longer neck; which makes sense (and I’m glad the data broadly supported it). But it is also a reminder that not all sauropods moved in the same ways- the change of COM would have required changes in how they moved. There was also plenty of methodological nuance here to cover all the uncertainties but for that, see the 17 page paper and 86 pages of supplementary material…

  1. Randau, M., Goswami, A., Hutchinson, J.R., Cuff, A.R., Pierce, S.E. 2016. Cryptic complexity in felid vertebral evolution: shape differentiation and allometry of the axial skeleton. Zoological Journal of the Linnean Society 178:183-202.

Back in 2011, Stephanie Pierce, Jenny Clack and I tried some simple linear morphometrics (shape analysis) to see how pinniped (seal, walrus, etc) mammals changed their vertebral morphology with size and regionally across their backbones. Now in this new study, with “Team Cat” assembled, PhD student Marcela Randau collected her own big dataset for felid (cat) backbones and applied some even fancier techniques to see how cat spines change their shape and size. We found that overall the vertebrae tended to get relatively more robust in larger cats, helping to resist gravity and other forces, and that cats with different ecologies across the arboreal-to-terrestrial spectrum also changed their (lumbar) vertebral shape differently. Now Marcela’s work is diving even deeper into these issues; stay tuned…

fig2-randau-measurements

Example measurements taken on felid vertebrae, from the neck (A-F) to the lumbar region (G-J), using a cheetah skeleton.

  1. Charles, J.P., Cappellari, O., Spence, A.J., Hutchinson, J.R., Wells, D.J. 2016. Musculoskeletal geometry, muscle architecture and functional specialisations of the mouse hindlimb. PLOS One 11(4): e0147669.

RVC PhD student James Charles measured the heck out of some normal mice, dissecting their hindlimb muscle anatomy, and using microCT scans produced some gorgeous images of that anatomy too. In the process, he also quantified how each muscle is differently specialized for the ability to produce large forces, rapid contractions or fine control. Those data were essential for the next study, where we got more computational!

mouse-mimics

  1. Charles, J.P., Cappellari, O., Spence, A.J., Wells, D.J., Hutchinson, J.R. 2016. Muscle moment arms and sensitivity analysis of a mouse hindlimb musculoskeletal model. Journal of Anatomy 229:514–535.

James wrangled together a lovely musculoskeletal model of our representative mouse subject’s hindlimb in the SIMM software that my team uses for these kinds of biomechanical analyses. As we normally do as a first step, we used the model to estimate things that are hard to measure directly, such as the leverages (moment arms) of each individual muscle and how those change with limb posture (which can produce variable gearing of muscles around joints). James has his PhD viva (defense) next week so good luck James!

mouse-simm

The horse and mouse papers are exemplars of what my team now does routinely. For about 15 years now, I’ve been building my team toward doing these kinds of fusion of data from anatomy, experimental biomechanics, musculoskeletal and other models, and simulation (i.e. estimating unmeasurable parameters by telling a model to execute a behaviour with a given set of criteria to try to perform well). Big thanks go to collaborator Jeff Rankin for helping us move that along lately. Our ostrich study from earlier this year shows the best example we’ve done yet with this, but there’s plenty more to come.

I am incredibly excited that, now that my team has the tools and expertise built up to do what I’ve long wanted to do, we can finally deliver the goods on the aspirations I had back when I was a postdoc, and which we have put enormous effort into pushing forward since then. In addition to new analyses of horses and mice and other animals, we’ll be trying to push the envelope more with how well we can apply similar methods to extinct animals, which brings new challenges– and evolutionary questions that get me very, very fired up.

Here we are, then; time has brought some changes to my life and work and it will continue to as we pass this juncture. I suspect I’ll look back on 2016 and see it as transformative, but it hasn’t been an easy year either, to say the least. “Draining” is the word that leaps to mind right now—but also “Focused” applies, because I had to try to be that, and sometimes succeeded. I’ve certainly benefited a lot at work from having some talented staff, students and other collaborators cranking out cool papers with me.

I still have time to do other things, too. Once in a while, a cool critter manifests in The Freezers. Check out a hippo foot from a CT scan! It’s not my best scan ever (noisy data) but it shows the anatomy fairly well, and some odd pathologies such as tiny floating lumps of mineralized soft tissue here and there. Lots to puzzle over.

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Last year we finally, after about 14 years of slow work, released our biomechanical model of an ostrich’s hindleg. We showed how it informed us about the potential leverages (moment arms; contributions to mechanical advantage of the joints) of all of the muscles. It was a satisfying moment, to understate it, to finally publish this work from my postdoc at Stanford. Today, we begin to deliver on that model’s promise. And it only took 4 years or so, roughly? The journal Royal Society Interface has published our study of how we used this musculoskeletal model to simulate walking and running dynamics. Those simulations join an intimidatingly broad and complex literature using similar models to study human (and some other primate) locomotion or other functions at the level of individual muscles (for whole limbs/bodies) in vast detail and growing rigor. I have Dr. Jeffery Rankin, a research fellow finishing up his post with me after ~6 years of hard work on many projects, to thank for driving this work forward, and Dr. Jonas Rubenson (now at PennState) for his patient collaboration that has continued since the early 2000’s.

Stomach-Churning Rating: 2/10; computer models of muscle actions. The underlying anatomical data are goopy, as prior ostrich-dissection-focused posts show!

Our model; in right side view (on the left) and frontal view (on the right), with muscles in red and the leg's force as the blue arrow; frozen at the middle of a step.

Our model; in right side view (on the left) and frontal view (on the right), with muscles in red and the leg’s force as the blue arrow; frozen at the middle of a running step.

Simulations like these predict things that we can’t easily measure in living animals, such as how much force muscles and tendons generate, how quickly those tissues change length, how much mechanical energy they thus contribute to the joints, limbs and whole body, how much metabolic energy their actions cost, and much more. There are more ways to use these tools than I have space or time to explain, but simply put we forced our ostrich simulation to match experimental measurements of the motions and forces of a representative walking and running ostrich stride, from contact of one foot until the next time that foot hit the ground. It then used optimization methods (minimizing target criteria like muscle stress) to estimate how the muscles and tendons were used to generate those motions and forces. This is a ways ahead of some prior ostrich simulations such as this one that I recall from classes during my PhD studies.

Any modeller worth their salt knows that their models and simulations are wrong at some level. This is much as most science is “wrong”; i.e. a simplification of reality with some errors/noise introduced by assumptions, variation, methods and such. But generally these kinds of musculoskeletal dynamic simulations hold up pretty well against experimental data. A standard “validation” is to test how closely the simulations’ predictions of muscle activity match the “real” (measured in life, also with some uncertain error) activity of muscles. Science still lacks those data for ostriches, but fortunately measurements from other birds (by Steve Gatesy and colleagues) indicate that muscles tend to follow fairly conservative patterns. Grossly speaking, avian leg muscles tend to either be active mainly when the foot is on the ground (stance phase) or off the ground (swing phase). Some studies acknowledge that this is an oversimplification and other muscles do act across those two phases of a stride, either in multiple pulses or as “transitional” (stance-to-swing or swing-to-stance) switch-hitters in their activations. Our ostrich predictions matched the qualitative patterns for avian muscle activations measured to date, so that’s good. The results also reinforced the notion of transitional or multi-phasic muscle activation as still having some importance, which bears more study.

Yet what did the simulations with our ostrich model tell us that other ostrich experiments or other bird species didn’t? Three main things. First, we could calculate what the primary functions of muscles were; they can act as motors (generating energy), brakes (absorbing energy), springs (bouncing energy back and forth) or struts (just transmitting force). We could then sum up what whole muscle groups were doing overall. The image below shows how these broad functions of groups vary across the stance phase (swing phase is harder to condense here so I’ve left it out).

Positive work can speed things up; negative work can slow things down.

Positive work can speed things up; negative work can slow things down. Solid bars are running; striped bars are walking. (from our Fig. 13) You may need to click to em-broaden this image for the gory biomechanical details.

There’s a lot going on there but a few highlights from that plot are that the hip extensor (antigravity) muscles (biarticular hip/knee “hamstrings”) are acting like motors, the knee extensors (like our quadriceps) are mainly braking as in other animals and the ankle is fairly springy as its tendons (e.g. digital flexors; gastrocnemius) suggest. We often characterize birds as “knee-driven” but it’s more accurate biomechanically to say that their hips drive (power; i.e. act as motors) their motion, whereas their knees still act as brakes — in both cases as in many other land vertebrates. Thus in some ways bird legs don’t work so unusually. Birds like ostriches are, though, a little odd in how much they rely on their hamstring muscles to power locomotion (at the hip) rather than their caudofemoral muscles, which are reduced. Zooming in on some particular muscles such as parts of the hip or knee extensors, the functions sometimes weren’t as predictable as their similar anatomy might suggest. Some muscles had parts that turned on during swing phase and other parts used during stance phase. Neural control and mechanics can produce some unexpected patterns.

Second, we looked at one important methodological issue. Simulations of musculoskeletal dynamics can vary from simple static (assuming each instant of a motion is independent from the others; e.g. ignoring acceleration, inertia, tendon effects, etc.) to more complex grades of fully dynamic flavours (e.g. assuming rigid or flexible tendons). We looked across this spectrum of assumptions, for both walking and running gaits, with the expectation that more static assumptions would work less well (vs. more dynamic ones; by various criteria) for running vs. walking. This also showed us how much tendons influence our simulations’ estimates of muscle mechanics—a fully rigid tendon will make the muscle do all of the work (force times length change) whereas a flexible tendon can literally take up some (or even all) of that slack, allowing muscles to remain closer to their isometric (high force-generating, negligible length change) quasi-optimum.

Nicely, our predicted muscle functions weren’t influenced much by these methodological variations. However, static assumptions  clearly were in some ways less appropriate for running than for walking, as were flexible tendons. Somewhat surprisingly, making the simulations more dynamic didn’t lower the levels of activation (and thus presumably the metabolic costs) of muscles, but actually raised those levels. There are good reasons why this might be realistic but it needs further study. It does muddy the waters for the issue of whether assuming that rapid locomotion can be modelled as static is a “bad” thing such as for estimating maximal speeds—yes, tendons can do more (elastic energy storage, etc.) if more dynamic models are used, but co-contraction of antagonistic muscles against each other also brings in some added costs and might lead to slower speed estimates. We’ll see in future work…

Finally, one often overlooked (sometimes even undiscussed!) aspect of these simulations is that they may silently add in extra forces to help muscles that are struggling to support and move their joints. The justification is typically that these extra “reserve actuators” are passive tissues, bony articular forces and other non-muscular interactions. We found that the hip joint muscles of ostriches were very weak at resisting abduction (drawing the thigh away from the body) and this needed resisting during the stance phase, so our simulations had very high reserve actuators switched on there. That fits the anatomy pretty well and needs more investigation.

Want to know more? Happily, not only is the paper free for anyone to view but so are all of the data including the models (modified slightly from our last paper’s). So, although the software (Opensim) isn’t ideal for 4-year-olds to play with (it is fancy engineering stuff), if you have the interest and dilligence it is there to play with and re-use and all that. But also watch this space for future developments, as there is more to happen with our steadily improving models of ostriches and other beasties. Anyway, while this paper is very technical and challenging to explain I am not too bashful to say it’s one of the finer papers from my career; a big stride forward from what we’ve done before. I have been looking forward for a long time to us getting this paper out.

P.S. Our peer reviewers were splendid- tough but constructive and fair. The paper got a lot better thanks to them.

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Seeking adaptations for running and swimming in the vertebral columns of ancient crocs

A guest post by Dr. Julia Molnar, Howard University, USA (this comes from Julia’s PhD research at RVC with John & colleagues)

Recently, John and I with colleagues Stephanie Pierce, Bhart-Anjan Bhullar, and Alan Turner described morphological and functional changes in the vertebral column with increasing aquatic adaptation in crocodylomorphs (Royal Society Open Science, doi 10.1098/rsos.150439). Our results shed light upon key aspects of the evolutionary history of these under-appreciated archosaurs.

Stomach-Churning Rating: 5/10; a juicy croc torso in one small photo but that’s all.

Phylogenetic relationships of the three crocodylomorph groups in the study and our functional hypotheses about their vertebrae. * Image credits: Hesperosuchus by Smokeybjb, Suchodus by Dmitry Bogdanov (vectorized by T. Michael Keesey) http://creativecommons.org/licenses/by-sa/3.0

Phylogenetic relationships of the three crocodylomorph groups in the study and our functional hypotheses about their vertebrae. * Image credits: Hesperosuchus by Smokeybjb, Suchodus by Dmitry Bogdanov (vectorized by T. Michael Keesey) http://creativecommons.org/licenses/by-sa/3.0

As fascinating as modern crocodiles might be, in many ways they are overshadowed by their extinct, Mesozoic cousins and ancestors. The Triassic, Jurassic, and early Cretaceous periods saw the small, fast, hyper-carnivorous “sphenosuchians,” the giant, flippered marine thalattosuchians, and various oddballs like the duck-billed Anatosuchus and the aptly named Armadillosuchus. As palaeontologists/biomechanists, we looked at this wide variety of ecological specializations in those species, the Crocodylomorpha, and wanted to know, how did they do it?

Of course, we weren’t the first scientists to wonder about the locomotion of crocodylomorphs, but we did have some new tools in our toolbox; specifically, a couple of micro-CT scanners and some sophisticated imaging software. We took CT and micro-CT scans of five fossil crocodylomorphs: two presumably terrestrial early crocodylomorphs (Terrestrisuchus and Protosuchus), three aquatic thalattosuchians (Pelagosaurus, Steneosaurus, and Metriorhynchus) and a semi-aquatic modern crocodile (Crocodylus niloticus). Since we’re still stuck on vertebrae (see, e.g., here; and also here), we digitally separated out the vertebrae to make 3D models of individual joints and took measurements from each vertebra. Finally, we manipulated the virtual joint models to find out how far they could move before the bones bumped into each other or the joints came apart (osteological range of motion, or RoM).

 

Our methods: get fossil, scan fossil, make virtual fossil and play with it.

Our methods: get fossil (NHMUK), scan fossil, make virtual fossil and play with it.

Above: Video of a single virtual inter-vertebral joint from the trunk of Pelagosaurus typus (NHMUK) showing maximum osteological range of motion in the lateral direction (video). Note the very un-modern-croc-like flat surfaces of the vertebral bodies! (modern crocs have a ball-and-socket spinal joint with the socket on the front end)

While this was a lot of fun, what we really wanted to find out was whether, as crocodylomorphs became specialized for different types of locomotion, the shapes of their vertebrae changed similarly to those of mammalian lineages. For example, many terrestrial mammals have a lumbar region that is very flexible dorsoventrally to allow up-and-down movements during bounding and galloping. Did fast-running crocodylomorphs have similar dorsoventral flexibility? And did fast-swimming aquatic crocodylomorphs evolve a stiffer vertebral column like that of whales and dolphins?

Above: Video of how we modelled and took measurements from the early crocodylomorph Terrestrisuchus gracilis (NHMUK).

Our first results were puzzling. The Nile croc had greater RoM in side-to-side motions, which makes sense because crocodiles mostly use more sprawling postures and are semi-aquatic, using quite a bit of side-to-side motions in life. The part that didn’t make sense was that we found pretty much the same thing in all of the fossil crocodylomorphs, including the presumably very terrestrial Terrestrisuchus and Protosuchus. With their long limbs and hinge-like joints, these two are unlikely to have been sprawlers or swimmers!

So we started looking for other parts of the croc that might affect RoM. The obvious candidate was osteoderms, the bony scales that cover the back. We went back to John’s Freezer and got out a nice frozen crocodile to measure the stiffness of its trunk and found that, sure enough, it was a lot stiffer and less mobile without the osteoderms. If the fairly flexible arrangement of osteoderms in crocodiles had this effect on stiffness, it seemed likely that (as previous authors have suggested; Eberhard Frey and Steve Salisbury being foremost amongst them) the rigid, interlocking osteoderms running from head to tail in early crocodylomorphs would really have put the brakes on their ability to move their trunk in certain ways.

Testing stiffness of crocodile trunks to learn the effects of osteoderms, skin, muscles, and ribs. We hung metric weights from the middle of the trunk and measured how much it flexed (Ɵ), then removed bits and repeated.

Testing the stiffness of (Nile) crocodile trunks to learn the effects of osteoderms, skin, muscles, and ribs. We hung metric weights from the middle of the trunk and measured how much it flexed (Ɵ), then removed bits and repeated. Click to em-croccen.

Another cool thing we found was new evidence of convergent evolution to aquatic lifestyles in the spines of thalattosuchians. The more basal thalattosuchians, thought to have been near-shore predators, had stiffness and RoM patterns similar to Crocodylus. But Metriorhynchus, which probably was very good at chasing down fast fish in the open ocean, seems to have had greater stiffness. (The stiffness estimates come from morphometrics and are based on modern crocodiles; see here again, or just read the paper already!) A stiff vertebral column can be useful for a swimmer because it increases the body’s natural frequency of oscillation, and faster oscillation means faster swimming (think tuna, not eel). The same thing seems to have happened in other secondarily aquatic vertebrate lineages such as whales, ichthyosaurs, and mosasaurs.

So, our results were a mixed bag of adaptations particular to crocs and ones that seem like general vertebrate swimming specializations. Crocodylomorphs are important because they are the only group of large vertebrates other than mammals that has secondarily aquatic members and has living members with a reasonably similar body plan, allowing us to test hypotheses in ways that would arguably be impossible for, say, non-avian dinosaurs and birds. The take-home message: crocodylomorphs A) are awesome, and B) can teach us a lot about how vertebrates adapt to different modes of life.

Another take on this story is on our lab website here.

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If you’ve been working in science for long enough, perhaps not very long at all, you’ve heard about (or witnessed) scientists in your field who get listed as co-authors on papers for political reasons alone. They may be an uninvolved but domineering professor or a fellow co-worker, a friend, a political ally, an overly protective museum curator, or just a jerk of any stripe. I read this article recently and felt it was symptomatic of the harm that bad supervisors (or other collaborators) do to science, including damage to the general reputation of professors and other mentors. There are cultural differences not only between countries (e.g. more authoritative, hierarchical cultures probably tolerate behaviour like this more) but also within institutions because of individual variation and local culture, tradition or other precedent. But this kind of honorary co-authorship turns my stomach—it is co-authorship bloat and a blight upon science. Honorary co-authorship should offend any reasonable scientist who actually works, at any level of the scientific hierarchy. So here’s my rant about it. Marshmallows and popcorn are welcomed if you want to watch my raving, but I hope this post stimulates discussion. A brief version of this did do that on my personal Facebook account, which motivated me to finish this public post.

Stomach-Churning Rating: 0/10 but it may provoke indigestion if you’ve been a victim of co-author bloat.

At its root, honorary co-authorship (HONCO) shows disdain for others’ efforts in research. “I get something for nothing, unlike others.” It persists because of deference to pressures from politics (I need to add this co-author or they’ll cause me trouble), other social dynamics (this person is my buddy; here’s a freebie for them), careerism (oneself/ally/student needs to be on this paper to boost their CV and move up in their career; or else), or even laziness (a minimal publishable unit mentality- e.g. any minor excuse for being a co-author is enough). All of these reasons for tolerating it, and apathy about the status quo, keep the fires of HONCO burning. My feeling from my past 20 years of experience in academia is that, as science is getting increasingly complex and requiring more collaborators and co-authors, the fire is raging to a point where it is visibly charring the integrity of science too often to just keep quiet about it and hope it doesn’t cause much damage.

There’s a flip side to HONCO, too– it’s not that, as some might take the article above to imply, we all need to boot senior authors off of papers. Senior authors, like other collaborators, have a reason for existing that encompasses — but is not limited to — boosting the careers of those they mentor. We scientists all want the satisfaction of doing science, even if the nature of our involvement in research evolves (and varies widely). Part of that satisfaction comes from publishing papers as the coup de grace to each project, and it’s a privilege that should be open to being earned by anyone qualified. Indeed, if adding HONCOs to papers is fraud, then removing worthy contributors from papers can be seen as a similar kind of fraud (unless a result of mutually agreed I’ll-help-you-for-nothing generosity). The broader point is, authors should deserve to be authors, and non-authors should not deserve to be authors.

On that latter issue, I think back to my grad school days and how my mentors Kevin Padian, Rodger Kram, Bob Full and others often gave me valuable input on my early papers (~1998-2002) but never earned co-authorship on them (exception: mentor Steve Gatesy’s vital role in our 2000 “abductors, adductors” paper). And frankly I feel a little bad now about that. Some of those mentors might have deserved co-authorship, but even when asked they declined, and just appeared in the Acknowledgements. It was the culture in my department at Berkeley, like many other USA grad schools at the time and perhaps now, that PhD students often did not put their supervisors on their papers and thus published single-author work. I see that less often today — but still varying among fields; e.g. in biomechanics, less single-authorship globally; in palaeontology and morphology, more single-authored work, but perhaps reducing overall. That is my off-the-cuff impression from the past >10 years.

I was shocked to see less (or often no) single-authored papers by lab colleagues once I moved to the UK to take up my present post– the prevalence of supervisors as senior authors on papers was starkly evident. On reflection, I now think that many of those multi-authored papers deserved to be such. It was not solo work and involved some significant steering, with key ideas originating from supervisors and thus constituting valid intellectual input. Yet I wondered then if it was a good thing or not, especially after hearing student complaints like waiting six months for comments from their supervisor on a manuscript. But this gets into a grey area that is best considered on a paper-by-paper basis, following clear criteria for authorship and contributions, and it involves difficulties inherent to some supervisor-supervisee relationships that I will not cover here. Much as supervisors need to manage their team, their team needs to manage them. ‘Nuff said.

Many institutions and journals have clear criteria for co-authorship, and publications have “author contributions” sections that are intended to make it clear who did what for a given paper – and thus whose responsibility any problems might be, too. HONCOs take credit without responsibility or merit, and are blatant fraud. I say it’s time we stand up to this disease. The criteria and contributions aspects of paper are part of the immune system of science that is there to help defend against academic misconduct. We need to work together to give that system a fighting chance.

There are huge grey areas in what criteria are enough for co-authorship. I have to wrestle with this for almost every paper I’m involved in– I am always thinking about whether I truly deserve to be listed on a paper, or whether others do. I’ve been training myself to think, and talk, about co-authorship criteria early in the process of research— that’s essential in avoiding bad blood later on down the line when it’s time to write up the work, when it’s possibly too late for others to earn co-authorship. This is a critical process that is best handled explicitly and in writing, especially in larger collaborations. What will the topic of any future paper(s) be and who will be involved as co-authors, or not? It’s a good agenda item for research meetings.

There are also grey areas in author contributions. How much editing of a paper is enough for co-authorship justification? Certainly not just spellchecking or adding comments saying “Great point!”, although both can be a bit helpful. Is funding a study a criterion? Sometimes– how much and how directly/indirectly did the funding help? Is providing data enough? Sometimes. In these days of open data, it seems like the data-provision criterion, part of the very hull that science floats upon, is weakening as a justification for co-authorship. It is becoming increasingly common to cite others’ papers for data, provide little new data oneself, and churn out papers without those data-papers’ authors involved. And that’s a good thing, to a degree. It’s nicer to invite published-data-providers on board a paper as collaborators, and they can often provide insight into the nature (and limitations or faults!) of the data. But adding co-authors can easily slide down the slippery slope of hooray-everyone’s-a-co-author (e.g. genetics papers with 1000+ co-authors, anyone?). I wrote up explicit co-authorship criteria here (Figshare login needed; 2nd pdf in the list) and here (Academia.edu login needed) if you’re curious how I handle it, but standards vary. Dr. William Pérez recently shared a good example of criteria with me; linked here.

In palaeontology and other specimen-based sciences, we get into some rough terrain — who collected the fossil (i.e. was on that field season and truly helped), identified it, prepared and curated it, published on it, or otherwise has “authority” over it, and which of them if any deserve co-authorship? I go to palaeontology conferences every year and listen over coffee/beers to colleagues complain about how their latest paper had such-and-such (and their students, pals, etc.) added onto the paper as HONCOs. Some museums or other institutions even have policies like this, requiring external users to add internal co-authors as a strong-arm tactic. An egregious past example: a CT-scanning facility I used once, and never again, even had the guff to call their mandatory joint-authorship policy for usage “non-collaborative access”… luckily we signed no such policy, and so we got our data, paid a reasonable fee for it, and had no HONCOs. Every time I hear about HONCOs, I wonder “How long can this kind of injustice last?” Yet there’s also the reality that finding and digging up a good field site or specimen(s); or analogous processes in science; takes a lot of time and effort and you don’t want others prematurely jumping your claim, which can be intellectual property theft, a different kind of misconduct. And there is good cause for sensitivity about non-Western countries that might not have the resources and training of staff to earn co-authorship as easily; flexibility might be necessary to avoid imperialist pillaging of their science with minimal benefit to their home country.

Yet there’s hope for minimizing HONCO infections. A wise person once said (slightly altered) “I’d rather light a candle than curse the darkness.” Problems can have solutions, even though cultural change tends to be agonizingly slow. But it can be slower still, or retrograde, if met with apathy. What can we do about HONCOs? Can we beat the bloat? What have I done myself before and what would I do differently now? I’ll take an inward look here.

Tolerating HONCOs isn’t a solution. I looked back on my experiences with >70 co-authored papers and technical book chapters since 1998. Luckily there are few instances where I’d even need to contemplate if a co-author was a HONCO. Most scientists I’ve worked with have clearly pulled their weight on papers or understood why they’re not co-authors on a given paper. More about that below. In those few instances of possible HONCOs, about five papers from several years ago, some colleagues provided research material/data but never commented on the manuscripts or other aspects of the work. I was disgruntled but tolerated it. It was a borderline grey area and I was a young academic who needed allies, and the data/specimens were important. Since then, I’ve curtailed collaborations with those people. To be fair, there were some papers where I didn’t do a ton (but did satisfy basic criteria for co-authorship, especially commenting on manuscripts) and I got buried in Middle-Authorland, and that’s fine with me; it wasn’t HONCO hell I was in. There were a few papers where I played a minor role and it wasn’t clear what other co-authors were contributing, but I was comfortable giving them the benefit of the doubt.

One anti-HONCO solution was on a more recent paper that involved a person who I had heard was a vector of HONCO infection. I stated early on in an email that only one person from their group could be a co-author on the resulting paper, and they could choose who it was and that person would be expected to contribute something beyond basic data. They wrote back agreeing to it and (magnanimously) putting a junior student forward for it, who did help, although they never substantially commented on the manuscript so I was a little disappointed. But in the grand scheme of things, this strategy worked in beating the HONCO bloat. I may have cost myself some political points that may stifle future collaborations with that senior person, but I feel satisfied that I did the right thing under the constraints, and damn the consequences. Containment of HONCO has its attendant risks of course. HONCO-rejects might get honked off. Maybe one has to pick their battles and concede ground sometimes, but how much do the ethics of such concessions weigh?

Another solution I used recently involved my own input on a paper. I was asked to join a “meta-analysis” paper as a co-author but the main work had already been done for it, and conclusions largely reached. I read the draft and saw places where I could help in a meaningful way, so with trepidation I agreed to help and did. But during the review process it became clear that (1) there was too much overlap between this paper and others by the same lead author, which made me uncomfortable; and (2) sections that I had contributed to didn’t really meld well with the main thrust of the paper and so were removed. As a consequence, I felt like a reluctant HONCO and asked to be removed from the paper as a co-author, even though I’d helped write sections of the main text that remained in the paper (but this was more stylistic in my view than deeply intellectual). I ended up in the Acknowledgements and relieved about it. I am comfortable removing myself from papers in which I don’t get a sense of satisfaction that I did something meriting co-author status. But it’s easier for more senior researchers like me to do that, compared to the quandary that sink-or-swim early-career researchers may face.

More broadly in academia, a key matter at stake is the CVs of researchers, especially junior ones, which these days require more and more papers (even minimal publishable units) to be competitive for jobs, awards and funding. Adding HONCOs to papers does strengthen individuals’ CVs, but in a parasitic way from the dilution of co-author contributions. And it’s just unethical, full stop. One solution: It’s thus up to senior people to lead from the front, showing that they don’t accept HONCOs themselves and encouraging more junior researchers to do the same when they can—or even questioning the contributions that potential new staff/students made to past papers, if their CV seems bloated (but such questions probe dangerous territory!). Junior people, however, still need to make a judgement call on how they’ll handle HONCOs with themselves or others. There is the issue of reputation to think about; complicity in the HONCO pandemic at any career level might be looked upon unfavourably by others, and scientists can be as gossipy as any humans, so bad ethics can bite you back.

I try to revisit co-authorship and the criteria involved throughout a project, especially as we begin the writing-up stage, to reduce risks of HONCOs or other maladies. An important aspect of collaboration is to ensure that people that might deserve co-authorship get an early chance to earn it, or else are told that they won’t be on board and why. Then they are not asked for further input unless it is needed, which might shift the balance and put them back on the co-author list. Critically, co-authorship is negotiable and should be a negotiation. One should not take it personally if not on a paper, but should treat others fairly and stay open-minded about co-authorship whenever possible. This has to be balanced against the risk of co-authorship bloat. Sure, so-and-so might add a little to a paper, but each co-author added complicates the project, probably slows it down, and diminishes the credit given to each other co-author. So a line must be drawn at some point. Maybe some co-authors and their contributions are best saved for a future paper, for example. This is a decision that the first, corresponding and senior author(s) should agree on, in consultation with others. But I also feel that undergraduate students and technicians often are the first to get the heave-ho from co-author considerations, which I’ve been trying to avoid lately when I can, as they deserve as much as anyone to have their co-author criteria scrutinized.

The Acknowledgements section of a paper is there for a reason, and it’s nice to show up there when you’ve truly helped a paper out whether as quasi-collaborative colleague, friendly draft-commenter, editor, reviewer or in other capacities. It is a far cry from being a co-author but it also typically implies that those people acknowledged are not to blame if something is wrong with the paper. I see Acknowledgements as “free space” that should be packed with thank-you’s to everyone one can think of that clearly assisted in some way. No one lists Acknowledged status on their CVs or gets other concrete benefits from them normally, but it is good social graces to use it generously. HONCOs’ proper home, at best, is there in the Acknowledgements, safely quarantined.

The Author Contributions section of a paper is something to take very seriously these days. I used to fill it out without much thought, but I’ve now gotten in the habit of scrutinizing it (where feasible) with every paper I’m involved in. Did author X really contribute to data analysis or writing the paper? Did all authors truly check and approve the final manuscript? “No” answers there are worrying. It is good research practice nowadays to put careful detail into this section of every paper, and even to openly discuss it among all authors so everyone agrees. Editors and reviewers should also pay heed to it, and readers of papers might find it increasingly interesting to peruse that section. Why should we care about author contribution lists in papers? Well, sure, it’s interesting to know who did what, that’s the main reason! It can reveal what skills an individual has or lacks, or their true input on the project vs. what the co-author order implies.

But there’s a deeper value to Author Contributions lists that is part of the academic immune system against HONCOs and other fraud. Anyone contributing to a particular part of a paper should be able to prove their contribution if challenged. For example, if a problem was suspected in a section of a paper, any authors listed as contributing to that section would be the first points of contact to check with about that possible problem. In a formal academic misconduct investigation, those contributing authors would need to walk through their contributions and defend (or correct) their work. It would be unpleasant to be asked how one contributed to such work if one didn’t do it, or to find out that someone listed you as contributing when you didn’t, and wouldn’t have accepted it if you had known. Attention to detail can pay off in any part of a research publication.

Ultimately, beating the blight of HONCO bloat will need teamwork from real co-authors, at every career level. Too often these academic dilemmas are broken down into “junior vs. senior” researcher false dichotomies. Yes, there’s a power structure and status quo that we need to be mindful of. Co-authorships, however, require collaboration and thus communication and co-operation.

It’s a long haul before we might see real progress; the fight against HONCOs must proceed paper-by-paper. There are worse problems that science faces, too, but my feeling is that HONCOs have gone far enough and it’s time to push back, and to earn the credit we claim as scientific authors. Honorary co-authorship is a dishonourable practice that is very different from other “honorary” kudos like honorary professorships or awards. Complex and collaborative science can mean longer co-author lists, absolutely, but it doesn’t mean handing out freebies to chums, students needing a boost, or erstwhile allies. It means more care is needed in designing and writing up research. And it also means that science is progressing; a progress we should all feel proud of in the end.

Do you have abhorrent HONCO chronicles of your own (anonymized please; no lynch mobs here!) or from public record? Or ideas for handling HONCO hazards? Please share and discuss.

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Deck the ‘Nets With PeerJ Papers— please sing along!

♬Deck the ‘nets with PeerJ papers,
Fa la la la la, la la la la.
‘Tis the day to show our labours,
Fa la la la la, la la la la.

Downloads free; CC-BY license,
Fa la la, la la la, la la la.
Read the extant ratite science,
Fa la la la la, la la la la.

See the emu legs before you
Fa la la la la, la la la la.
Muscles allometric’ly grew.
Fa la la la la, la la la la.

Follow the evolvin’ kneecaps
Fa la la la la, la la la la.
While we dish out ratite recaps 
Fa la la la la, la la la la.

Soon ostrich patellar printing
Fa la la la la, la la la la.
Hail anat’my, don’t be squinting
Fa la la la la, la la la la.

Dissections done all together
Fa la la la la, la la la la.
Heedless of the flying feathers,
Fa la la la la, la la la la♪

(alternate rockin’ instrumental version)

Stomach-Churning Rating: 5/10: cheesy songs vs. fatty chunks of tissue; there are no better Crimbo treats!

Today is a special day for palaeognath publications, principally pertaining to the plethora of published PeerJ papers (well, three of them anyway) released today, featuring my team’s research! An early Crimbo comes this year in the form of three related studies of hind limb anatomy, development, evolution and biomechanics in those flightless feathered freaks of evolutionary whimsy, the ratites! And since the papers are all published online in PeerJ (gold open access), they are free for anyone with internet access to download and use with due credit. These papers include some stunning images of morphology and histology, evolutionary diagrams, and a special treat to be revealed below. Here I’ll summarize the papers we have written together (with thanks to Leverhulme Trust funding!):

1) Lamas, L., Main, R.P., Hutchinson, J.R. 2014. Ontogenetic scaling patterns and functional anatomy of the pelvic limb musculature in emus (Dromaius novaehollandiae). PeerJ 2:e716 http://dx.doi.org/10.7717/peerj.716 

My final year PhD student and “emu whisperer” Luis Lamas has published his first paper with co-supervisor Russ Main and I. Our paper beautifully illustrates the gross anatomy of the leg muscles of emus, and then uses exhaustive measurements (about 6524 of them, all done manually!) of muscle architecture (masses, lengths, etc.) to show how each of the 34 muscles and their tendons grew across a more than tenfold range of body mass (from 6 weeks to 18 months of age). We learned that these muscles get relatively, not just absolutely, larger as emus grow, and their force-generating ability increases almost as strongly, whereas their tendons tend to grow less quickly. As a result, baby emus have only about 22% of their body mass as leg muscles, vs. about 30% in adults. However, baby emus still are extremely athletic, more so than adults and perhaps even “overbuilt” in some ways.

This pattern of rapidly growing, enlarged leg muscles seems to be a general, ancestral pattern for living bird species, reflecting the precocial (more independent, less nest-bound), cursorial (long-legged, running-adapted) natural history and anatomy, considering other studies of ostriches, rheas, chickens and other species close to the root of the avian family tree. But because emus, like other ratites, invest more of their body mass into leg muscles, they can carry out this precocial growth strategy to a greater extreme than flying birds, trading flight prowess away for enhanced running ability. This paper adds another important dataset to the oft-neglected area of “ontogenetic scaling” of the musculoskeletal system, or how the locomotor apparatus adapts to size-/age-related functional/developmental demands as it grows. Luis did a huge amount of work for this paper, leading arduous dissections and analysis of a complex dataset.

Superficial layer of leg muscles in an emu, in right side view.

Superficial layer of leg muscles in an emu, in right side view. Click any image here to emu-biggen. The ILPO and IC are like human rectus femoris (“quads”); ILFB like our biceps femoris (“hams”); FL, GM and GL much like our fibularis longus and gastrocnemius (calf) muscles, but much much bigger! Or, perhaps FL stands for fa la la la la?

Data for an extra set of emus studied by coauthor Russ Main in the USA, which grew their muscles similarly to our UK group. The exponents (y-axis) show how much more strongly the muscles grown than isometry (maintaining the same relative size), which is the dotted line at 1.0.

Data for an extra set of emus studied by coauthor Russ Main in the USA, which grew their muscles similarly to our UK group. The exponents (y-axis) show how much more strongly the muscles grew than isometry (maintaining the same relative size), which is the dotted line at 1. The numbers above each data point are the # of individuals measured. Muscle names are partly above; the rest are in the paper. If you want to know them, we might have been separated at birth!

2) Regnault, S., Pitsillides, A.A., Hutchinson, J.R. 2014. Structure, ontogeny and evolution of the patellar tendon in emus (Dromaius novaehollandiae) and other palaeognath birds. PeerJ 2:e711 http://dx.doi.org/10.7717/peerj.711

My second year PhD student Sophie Regnault (guest-blogger here before with her rhino feet post) has released her first PhD paper, on the evolution of kneecaps (patellae) in birds, with a focus on the strangeness of the region that should contain the patella in emus. This is a great new collaboration combining her expertise in all aspects of the research with coauthor Prof. Andy Pitsillides‘s on tissue histology and mine on evolution and morphology. This work stems from my own research fellowship on the evolution of the patella in birds, but Sophie has taken it in a bold new direction. First, we realized that emus don’t have a patella– they just keep that region of the knee extensor (~human quadriceps muscle) tendon as a fatty, fibrous tissue throughout growth, showing no signs of forming a bony patella like other birds do. This still blows my mind! Why they do this, we can only speculate meekly about so far. Then, we surveyed other ratites and related birds to see just how unusual the condition in emus was. We discovered, by mapping the form of the patella across an avian family tree, that this fatty tendon seems to be a thing that some ratites (emus, cassowaries and probably the extinct giant moas) do, whereas ostriches go the opposite direction and develop a giant double-boned kneecap in each knee (see below), whereas some other relatives like tinamous and kiwis develop a more “normal”, simple flake-like bit of bone, which is likely the state that the most recent common ancestor of all living birds had.

There’s a lot in this paper for anatomists, biomechanists, palaeontologists, ornithologists, evo-devo folks and more… plenty of food for thought. The paper hearkens back to my 2002 study of the evolution of leg tendons in tetrapods on the lineage that led to birds. In that study I sort of punted on the question of how a patella evolved in birds, because I didn’t quite understand that wonderful little sesamoid bone. And now, 12 years later, we do understand it, at least within the deepest branches of living birds. What happened further up the tree, in later branches, remains a big open subject. It’s clear there were some remarkable changes, such as enormous patellae in diving birds (which the Cretaceous Hesperornis did to an extreme) or losses in other birds (e.g., by some accounts, puffins… I am skeptical)– but curiously, patellae that are not lost in some other birds that you might expect (e.g., the very non-leggy hummingbirds).

Fatty knee extensor tendon of emus, lacking a patella. The fatty tissue is split into superficial (Sup) and deep regions, with a pad corresponding to the fat pad in other birds continuous with it and the knee joint meniscus (cushioning pad). The triceps femoris (knee extensor) muscle group inserts right into the fatty tendon, continuing over it. A is a schematic; B is a dissection.

Fatty knee extensor tendon of an emu, showing the absence of a patella. The fatty tissue is split into superficial (Sup) and deep regions, with a pad corresponding to the fat pad in other birds continuous with it and the knee joint meniscus (cushioning pad). The triceps femoris (knee extensor) muscle group inserts right into the fatty tendon, continuing on over it. A is a schematic; B is a dissection.

Sectioning of a Southern Cassowary's knee extensor tendon, showing: A Similar section  as in the emu image above. revealing similar regions and fibrous tissue (arrow), with no patella, just fat; and B, with collagen fibre bundles (col), fat cells (a), and cartilage-like tissue (open arrows) labelled.

Sectioning of a Southern Cassowary’s knee extensor tendon, showing: A, Similar section as in the emu image above. revealing similar regions and fibrous tissue (arrow), with no patella, just fat; and B, With collagen fibre bundles (col), fat cells (a), and cartilage-like tissue (open arrows) labelled.

Evolution of patellar form in birds. White branches indicate no patella, blue is a small flake of bone for a patella, green is something bigger, yellow is a double-patella in ostriches, and grey is uncertain. Note the uncertainty and convergent evolution of the patella in ratite birds, which is remarkable but fits well with their likely convergent evolution of flightlessness and running adaptations.

Evolution of patellar form in birds. White branches indicate no patella, blue is a small flake of bone for a patella, green is something bigger, yellow is a double-patella in ostriches, black is a gigantic spar of bone in extinct Hesperornis and relatives, and grey is uncertain. Note the uncertainty and convergent evolution of the patella in ratite birds (Struthio down to Apteryx), which is remarkable but fits well with their likely convergent evolution of flightlessness and running adaptations.

3) Chadwick, K.P., Regnault, S., Allen, V., Hutchinson, J.R. 2014. Three-dimensional anatomy of the ostrich (Struthio camelus) knee joint. PeerJ 2:e706 http://dx.doi.org/10.7717/peerj.706

Finally, Kyle Chadwick came from the USA to do a technician post and also part-time Masters degree with me on our sesamoid grant, and proved himself so apt at research that he published a paper just ~3 months into that work! Vivian Allen (now a postdoc on our sesamoid bone grant) joined us in this work, along with Sophie Regnault. We conceived of this paper as fulfilling a need to explain how the major tissues of the knee joint in ostriches, which surround the double-patella noted above, all relate to each other and especially to the patellae. We CT and MRI scanned several ostrich knees and Kyle made a 3D model of a representative subject’s anatomy, which agrees well with the scattered reports of ostrich knee/patellar morphology in the literature but clarifies the complex relationships of all the key organs for the first time.

This ostrich knee model also takes Kyle on an important first step in his Masters research, which is analyzing how this morphology would interact with the potential loads on the patellae. Sesamoid bones like the patella are famously responsive to mechanical loads, so by studying this interaction in ostrich knees, along with other studies of various species with and without patellae, we hope to use to understand why some species evolved patellae (some birds, mammals and lizards; multiple times) and why some never did (most other species, including amphibians, turtles, crocodiles and dinosaurs). And, excitingly for those of you paying attention, this paper includes links to STL format 3D graphics so you can print your own ostrich knees, and a 3D pdf so you can interactively inspect the anatomy yourself!

(A) X-ray of an ostrich knee in side view, and (B) labelled schematic of the same.

Ostrich knee in side view: A, X-ray, and (B) labelled schematic.

3D model of an ostrich knee, showing: A, view looking down onto the top of the tibia (shank), with the major collateral ligaments (CL), and B, view looking straight at the front of the knee joint, with major organs of interest near the patella, sans muscles.

3D model of an ostrich knee, showing: A, View looking down onto the top of the tibia (shank), with the major collateral ligaments (CL), and B, View looking straight at the front of the knee joint, with major organs of interest near the patella, sans muscles.

You can view all the peer review history of the papers if you want, and that prompts me to comment that, as usual at PeerJ (full disclosure: I’m an associate editor but that brings me £0 conflict of interest), the peer review quality was as rigorous at a typical specialist journal, and faster reviewing+editing+production than any other journal I’ve experienced. Publishing there truly is fun!

Merry Christmas and Happy Holidays — and good Ratite-tidings to all!

And stay tuned- the New Year will bring at least three more papers from us on this subject of ratite locomotion and musculoskeletal anatomy!

♬Should auld palaeognathans be forgot, 
And never brought for scans? 
Should publications be soon sought, 
For auld ratite fans!♪

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