Feeds:
Posts
Comments

Posts Tagged ‘anatomy’

(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.

Read Full Post »

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.

Read Full Post »

Sorry about the title. It’s the best I could do. In case you missed it on our Anatomy to You blog, we unleashed a hefty database of CT (and some MRI) scans of our frozen crocodile cadavers last week, for free public usage. In total, it’s about 34 individuals from 5 species, in 53 databases constituting around 26,000 individual DICOM file format slices of data. This page has a table of what the data/specimens are. I am writing this post to share some more images and ensure that word gets out. We’re thrilled to be able to finally release this first dataset. We have plans to let loose a LOT more such data in the future, for various organisms that we study.

Stomach-Churning Rating: 2/10- be glad that these data don’t come with an olfactory component, especially the five rotten, maggot-ridden Morelet’s croc specimens, which are among the stinkiest things I’ve dealt with.

Crocodiles are no strangers to this blog, of course, as these past links testify. Indeed, most of the crocodile images I’ve blogged with come from specimens that are in this scan dataset. We even released a “celebrity crocodile, “WCROC” or FNC7 in our dataset, which is the 3.7m long Nile croc from “Inside Nature’s Giants”. It broke our CT scanner back in ~2009 but we got the data, except for the torso, and we also got some MRI scans from it, so we’re chuffed.

Above: The only spectacled caiman (Caiman crocodilus); and indeed the only alligatorid; in our dataset. To watch for: stomach contents/gastroliths, and all the damn osteoderms that I did/didn’t segment in this quickly processed file. This specimen had its limbs dissected for one of our studies, so only the right limbs are visible.

There are some more specimens to come- e.g. five baby Nile crocs‘ datasets (“GNC1-5”) are hiding somewhere in our drives and we just need to dig them up. You might also know that we published some scan data for crocodile vertebral columns (including fossils) in our recent paper with Julia Molnar et al. (and related biomechanical data discussed here), and we published all of our anatomical measurements for a huge set of crocodylian species in our papers by Vivian Allen et al. And then I had an enjoyable collaboration with Colleen Farmer and Emma Schachner on the lung anatomy of various crocodylian species, using these same specimens and related scan datasets.

 

Above: rotating Crocodylus moreletii (specimen FMC5 from our database) in a happy colour.

Sharing these kind of huge datasets isn’t so easy. Not only do few websites host them cheaply, and with reasonable file size limits, and limited headaches for what info you have to provide, and with some confidence that the websites/databases will still exist in 5-20 years, but also we were hesitant to release the dataset until we felt that it was nicely curated. Researchers can now visit my lab and study the skeletons (or in some cases, the still-frozen specimens) matched up with the scan data, and known body masses or other metadata. We’re not a museum with dedicated curatorial staff, so that was not trivial to reliably organize, and I still worry that somewhere in the dataset we mis-identified a specimen or something. But we’ve done our best, and I’m happy with that for now.

Above: rotating Osteolaemus tetraspis (specimen FDC2 from our database), which was obviously dissected a bit postmortem before we could scan it, but still shows some cool features like the extensive bony armour and the cute little doglike (to me, anyway) skull. I worked with these animals (live) a bit >10 years ago and came to love them. Compared to some other crocodiles we worked with, they had a pleasant demeanour. Like this guy:

Osteolaemus (resting) set up with motion capture markers for a yet-to-be-published study that we did in 2005 (ugh!). It wasn't harmed by this.

Osteolaemus (resting) set up with motion capture markers for a yet-to-be-published gait study that we did in 2005 (ugh!). It wasn’t harmed by this.

Anyway, as a person who likes to maintain quality in the science we do, I also was hesitant to “just” release the DICOM file data rather than beautiful segmented 3D skeletal (or other tissue) geometry that is ready for 3D printing or animation or other uses, or interactive online tools like Sketchfab. Other labs (e.g. Witmerlab) do these kind of things better than we do and they inspire us to raise our game in the future, but I am sure that we will be forgiven for releasing big datasets without gorgeous visuals and more practical, processed files — this time.🙂  We agree with many other scientists that sharing data is part of modern, responsible science– and it can be fun, too! Oddly enough, in this case we hadn’t used the CT/MRI data much for our own studies; most of the scans were never fully digitized. We just scan everything we get and figured it was time to share these scans.

Enjoy. If you do something cool with the data that we’ve made accessible, please let us know so we can spread the joy!

And if you’re a researcher headed to ICVM next week, I hope to see you there!

Read Full Post »

Who needs “Ice Road Truckers” when you have the “John’s Freezer” team on the road with fossils, amphibians, felids and 3D phenotype fun? No one, that’s who. We’re rocking the Cheltenham Science Festival for our first time (as a group), and pulling out all the stops by presenting two events! Here’s the skinny on them, with updates as the week proceeds.

Stomach-Churning Rating: 2/10 for now (just bones), but it could change once the cheetah dissection is under way… 8/10 bloody cheetah bits but only at the end (updated)

Right now, Lauren Sumner-Rooney (of “Anatomy To You” and other fame) is on-site with a rotating team of others from our lab, in the “Free Activity Tents” area of the Imperial Gardens/Square, inside a marquee where we’ll be showing off our NERC-funded tetrapod research all week. This “First Steps” event features not only our past and present work with Jenny Clack, Stephanie Pierce, Julia Molnar and others on Ichthyostega & its “fishapod” mates, but also our “scampering salamanders” research in Spain, Germany and England. I’ve blogged a lot about all that, and won’t repeat it here, but you can see a 3D-printed Ichthyostega skeleton, view the skeleton in a virtual reality 3D environment, see related specimens and engage in kid-friendly activities, and talk to our team about this and other related research.

Ichthyostega 3D printed backbone is born!

Ichthyostega 3D printed backbone is born!

The central themes of that event are how bone structure relates to function and how we can use such information, along with experimental measurements and computer models of real salamanders, to reconstruct how extinct animals might have behaved as well as how swimming animals became walking ones. How did fins transform into limbs and what did that mean for how vertebrates made the evolutionary transition onto land? If you know my team’s work, that encapsulates our general approach to many other problems in evolutionary biomechanics (e.g. how did avian bipedalism evolve?). Added benefits are that you too can explore this theme in a hands-on way, and you can talk with us about it in person. That continues all week (i.e. until Saturday evening); I’ll be around from Thursday afternoon onwards, too. Kids of all ages are welcome!

Ichthyostega 3D print taking shape!

Ichthyostega 3D print taking shape!

Then, on Saturday for our second free event we join forces with Ben Garrod (master of primate evolution, the secrets of bones, and “Attenborough and the Giant Dinosaur”) and RVC’s forensic pathologist Alexander Stoll as well as Sophie Regnault (“sesamoid street” PhD student w/me). As the “Large Animal Dissection” title hints, it’s not the right kind of gig to bring small kids to. There will be blood and stuff— we’ll be dissecting a cheetah together from 10am-4pm. This will involve walking through all the major organ systems, giving evolutionary anecdotes, and plenty more, with an aim to understand how the magnificent adaptations of cheetahs evolved—but also to investigate what problem(s) this animal faced that led to its sad demise. By the day’s end, there will just be a skeleton left. Get a front row seat early for this event, which serendipitously ties into “Team Cat”’s Leverhulme Trust-funded research project (we wanted a big animal and it just happened to be a cheetah; I had hoped for a giant croc or a shark or something but can’t complain!).

Ichthyostega 3D print is ready!

Ichthyostega 3D print is ready!

If you miss these events, please do cry bitter tears of regret. But don’t despair, there will be another “big cat dissection” in the London area in ~November (watch here for details), and plenty more fossil tetrapod stuff to come, plus a LOT more dinosaurs on the horizon!

Guess the bones! (photo by Zoe Self)

Guess the bones! (photo by Zoe Self)

And please come back to this blog post for more pics and stories as the week carries on… For hashtag afficionados, you can follow the fun on Twitter etc. at #firststepsCSF16. What a world we live in!

Update 1: While you’re here, check out our Youtube playlists of tetrapod-related videos:

Lobe-finned fishes

Ichthyostega‘s awesome anatomy

Tetrapod evolution: Tiktaalik to salamanders!

Update 2: Photos of our main stand (about tetrapod evolution)

csf2016-display

Our poster/banner display looks nice.

20160609_143548

Our tent brings in some punters.

20160609_151508

Our bones excite people young and old, sighted and blind.

20160610_090009

Fun with stickers and lab t-shirts.

And…

Update 3: Cheetah meat & greet
Ben, Alex, Sophie and I tackled the cheetah dissection today and it went GREAT! Much better than I’d optimistically expected. Rain didn’t scare the crowds off and neither did the gore, which there was some of (gelatinous spinal cords, lumpy tumors and at least one flying tiny bit of cheetah flesh that landed on a good-natured audience member!). Photos will tell the tale:

20160611_091345

Peek-a-boo!

20160611_093828

Sophie and Alex help us get set up in our tent.

20160611_094554

Our initial rough schedule- although we ended up improvising more after lunch.

20160611_095500

Dissectors assemble!

20160611_105126

The beast revealed. It was skinned by the museum that loaned it to us.

20160611_110748

Alex showing his talent: removing the viscera in one piece from end to end, starting with the tongue.

20160611_153148

Impressive finding of a surgical fixture (plate and wires) on the tibia, which had been used to hold the shattered bone back together long enough for it to heal. Added to the kidney disease and liver-spleen-lung cancer, this cheetah was in the sorriest shape of any cadaver I’ve seen yet.

20160611_153213

Cheetah coming to pieces: (from bottom) lumbar/pelvic region, hindlimb, thorax, forelimb and other bits.

20160611_155452

Dr Adam Rutherford, an eye expert, did a nice dissection of the cheetah’s eye, here showing the tapetum lucidum (reflective membrane), which shows up as light blue colour. Its small size befits the not-very-nocturnal habits of cheetahs.

20160611_155459

The lens of the cheetah’s eye. Now cloudy because of dehydration and crystalization, but still fascinating to see.

Want to see more images and the enthusiastic responses from the audience (we got some great feedback)? Check out Twitter’s #cheltscifest feed, or more simply my Storify condensation of the cheetah-related tweets here.

Read Full Post »

Happy Darwin Day from the frozen tundra sunny but muddy, frosty lands of England! I bring you limb muscles as peace offerings on this auspicious day. Lots of limb muscles. And a new theme for future blog posts to follow up on: starting off my “Better Know A Muscle” (nod to Stephen Colbert; alternative link) series. My BKAM series intends to walk through the evolutionary history of the coolest (skeletal/striated) muscles. Chuck Darwin would not enjoy the inevitable blood in this photo-tour, but hopefully he’d like the evolution. Off we go, in search of better knowledge via an evolutionary perspective!

There is, inarguably, no cooler muscle than M. caudofemoralis longus, or CFL for short. It includes the largest limb muscles of any land animal, and it’s a strange muscle that confused anatomists for many years– was it a muscle of the body (an axial or “extrinsic” limb muscle, directly related to the segmented vertebral column) or of the limbs (an “abaxial” muscle, developing with the other limb muscles from specific regions of the paraxial mesoderm/myotome, not branching off from the axial muscles)? Developmental biologists and anatomists answered that conclusively over the past century: the CFL is a limb muscle, not some muscle that lost its way from the vertebral column and ended up stranded on the hindlimb.

The CFL is also a muscle that we know a fair amount about in terms of its fossil record and function, as you may know if you’re a dinosaur fan, and as I will quickly review later. We know enough about it that we can even dare to speculate if organisms on other planets would have it. Well, sort of…

Stomach-Churning Rating: 8/10. Lots of meaty, bloody, gooey goodness, on and on, for numerous species. This is an anatomy post for those with an appetite for raw morphology.

Let’s start from a strong (and non-gooey) vantage point, to which we shall return. The CFL in crocodiles and most other groups is (and long was) a large muscle extending from much of the front half or so of the tail to the back of the femur (thigh bone), as shown here:

Julia Molnar's fabulous illustration of Alligator's limb muscles, from our 2014 paper in Journal of Anatomy.

Julia Molnar’s fabulous illustration of Alligator‘s limb muscles, from our 2014 paper in Journal of Anatomy. Note the CFL in blue at the bottom right.

As the drawing shows, the CFL has a friend: the CFB. The CFB is a shorter, stumpier version of the CFL restricted to the tail’s base, near the hip. The “B” in its name means “brevis”, or runty. It gets much less respect than its friend the CFL. Pity the poor CFB.

But look closer at the CFL in the drawing above and you’ll see a thin blue tendon extending past the knee to the outer side of the lower leg. This is the famed(?) “tendon of Sutton“, or secondary tendon of the CFL. So the CFL has two insertions, one on the femur and one (indirectly) onto the shank. More about that later.

Together, we can talk about these two muscles (CFL and CFB) as the caudofemoralis (CF) group, and the name is nice because it describes how they run from the tail (“caudo”) to the femur (“femoralis”). Mammal anatomists were late to this party and gave mammal muscles stupidly unhelpful names like “gluteus” or “vastus” or “babalooey”. Thanks.

But enough abstract drawings, even if they rock, and enough nomenclature. Here is the whopping big CFL muscle of a real crocodile:

Huge Nile crocodile, but a relatively small CFL.

Huge Nile crocodile, but a relatively small CFL.

Bigger crocs have smaller legs and muscles.

Bigger crocs have smaller legs and thus smaller leg muscles, relatively speaking. CFL at the top, curving to the left.

The giant Nile croc's CFL muscle removed for measurements.

The giant Nile croc’s CFL muscle removed for measurements. 2.35 kg of muscle! Not shabby for a 278 kg animal.

However, maybe crocodile and other archosaur CFL muscles are not “average” for leggy vertebrates? We can’t tell unless we take an evolutionary tack to the question.

Where did the CFL come from, you may ask? Ahh, that is shrouded in the fin-limb transition‘s mysteries. Living amphibians such as salamanders have at least one CF muscle, so a clear predecessor to the CFL (and maybe CFB) was present before reptiles scampered onto the scene.

But going further back through the CF muscles’ history, into lobe-finned fish, becomes very hard because those fish (today) have so few fin muscles that, in our distant fishy ancestors, would have given rise eventually to the CF and other muscle groups. With many land animals having 30+ hindlimb muscles, and fish having 2-8 or so, there obviously was an increase in the number of muscles as limbs evolved from fins. And because a limb has to do lots of difficult three-dimensional things on land while coping with gravity, more muscles to enable that complex control surely were needed.

OK, so there were CF muscles early in tetrapod history, presumably, anchored on that big, round fleshy tail that they evolved from their thin, finned fishy one — but what happened next? Lizards give us some clues, and their CFL muscles aren’t all that different from crocodiles, so the CFL’s massive size and secondary “tendon of Sutton” seems to be a reptile thing, at least.

Courtesy of Emma Schachner, a large varanid lizard's very freshly preserved CFL and other hindlimb muscles.

Courtesy of Emma Schachner, a large varanid lizard’s very freshly preserved CFL and other hindlimb muscles.

Courtesy of Emma Schachner, zoomed in on the tendons and insertions of the CFL muscle and others.

Courtesy of Emma Schachner, zoomed in on the tendons and insertions of the CFL muscle and others. Beautiful anatomy there!

Looking up at the belly of a basilisk lizard and its dissected right leg, with the end of the CFL labelled.

Looking up at the belly of a basilisk lizard and its dissected right leg, with the end of the CFL labelled. It’s not ideally dissected here, but it is present.

An unspecified iguanid(?) lizard, probably a juvenile Iguana iguana, dissected and showing its CFL muscle at its end. The muscle would extemd about halfway down the tail, though.

An unspecified iguanid(?) lizard, probably a juvenile Iguana iguana, dissected to reveal its CFL muscle near its attachment to the femur. The muscle would extend further, about halfway down the tail, though.

Let’s return to crocodiles, for one because they are so flippin’ cool, and for another because they give a segue into archosaurs, especially dinosaurs, and thence birds:

A moderate-sized (45kg) Nile crocodile with its CFL muscle proudly displayed.

A moderate-sized (45kg) Nile crocodile with its CFL muscle proudly displayed. Note the healthy sheath of fat (cut here) around the CFL.

American alligator's CFL dominates the photo. Photo by Vivian Allen.

American alligator’s CFL dominates the photo [by Vivian Allen].

Black caiman, Melanosuchus, showing off its CFL muscle (pink "steak" in the middle of the tail near the leg).

Black caiman, Melanosuchus, showing off its CFL muscle (pink “steak” in the middle of the tail near the leg), underneath all that dark armour and fatty superficial musculature.

A closer look at the black caiman's thigh and CFL muscle.

A closer look at the black caiman’s thigh and CFL muscle.

Like I hinted above, crocodiles (and the anatomy of the CFL they share with lizards and some other tetrapods) open a window into the evolution of unusual tail-to-thigh muscles and locomotor behaviours in tetrapod vertebrates.

Thanks in large part to Steve Gatesy’s groundbreaking work in the 1990s on the CFL muscle, we understand now how it works in living reptiles like crocodiles. It mainly serves to retract the femur (extend the hip joint), drawing the leg backwards. This also helps support the weight of the animal while the foot is on the ground, and power the animal forwards. So we call the CFL a “stance phase muscle”, referring to how it mainly plays a role during ground contact and resisting gravity, rather than swinging the leg forwards (protracting the limb; i.e. as a “swing phase muscle”).

The “tendon of Sutton” probably helps to begin retracting the shank once the thigh has moved forward enough, facilitating the switch from stance to swing phase, but someone really needs to study that question more someday.

And thanks again to that same body of work by Gatesy (and some others too), we also understand how the CFL’s anatomy relates to the underlying anatomy of the skeleton. There is a large space for the CFL to originate from on the bottom of the tail vertebrae, and a honking big crest (the fourth trochanter) on the femur in most reptiles that serves as the major attachment point, from which the thin “tendon of Sutton” extends down past the knee.

Femur bones (left side) from an adult ostrich (Left) and Nile crocodile (Right).

Femur bones (left side; rear view) from an adult ostrich (left) and Nile crocodile (right). Appropriate scale bar is appropriate. The fourth trochanter for the CFL is visible in the crocodile almost midway down the femur. Little is left of it in the ostrich but there is a bumpy little muscle scar in almost the same region as the fourth trochanter, and this is where the same muscle (often called the CFC; but it is basically just a small CFL) attaches.

That relationship of the CFL’s muscular anatomy and the underlying skeleton’s anatomy helps us a lot! Now we can begin to look at extinct relatives of crocodiles; members of the archosaur group that includes dinosaurs (which today we consider to include birds, too), and things get even more interesting! The “tendon of Sutton”, hinted at by a “pendant” part of the fourth trochanter that points down toward the knee, seems to go away multiple times within dinosaurs. Bye bye! Then plenty more happens:

A large duckbill dinosaur's left leg, with a red line drawn in showing roughly where the CFL would be running, to end up at the fourth trochanter. Many Mesozoic dinosaurs have skeletal anatomy that indicates a similar CFL muscle.

A large duckbill dinosaur’s left leg, with a red line drawn in showing roughly where the CFL would be running, to end up at the fourth trochanter. Many Mesozoic dinosaurs have skeletal anatomy that indicates a similar CFL muscle.

We can even go so far as to reconstruct the 3D anatomy of the CFL in a dinosaur such as T. rex ("Sue" specimen here; from Julia Molnar's awesome illustration in our 2011 paper), with a fair degree of confidence.

We can even go so far as to reconstruct the 3D anatomy of the CFL in a dinosaur such as T. rex (“Sue” specimen here; from Julia Molnar’s awesome illustration as part of our 2011 paper), with a fair degree of confidence. >180kg steak, anyone?

As we approach birds along the dinosaur lineage, the tail gets smaller and so does the fourth trochanter and thus so must the CFL muscle, until we’re left with just a little flap of muscle, at best. In concert, the hindlimbs get more crouched, the forelimbs get larger, flight evolves and voila! An explosion of modern bird species!

Ozburt (72)

Left femur of an ostrich in side view (hip is toward the right side) showing many muscles that attach around the knee (on the left), then the thin strap of CF muscle (barely visible; 2nd from the right) clinging near the midshaft of the femur.

Another adult ostrich's CF muscle complex, removed for study.

Another adult ostrich’s CF muscle complex, removed for study. Not enough ostrich myology for you yet? Plenty more in this old post! Or this one! Or this one… hey maybe I need to write less about ostriches? The CF muscle complex looks beefy but it’s no bigger than any other of the main hindlimb muscles, unlike the CFL in a crocodile or lizard, which puts everything else to shame!

STILL not enough ostrich for you yet? Take a tour of the major hindlimb muscles in this video:

And check out the limited mobility of the hip joint/femur here. No need for much femur motion when you’re not using your hip muscles as much to drive you forwards:

But I must move on… to the remainder of avian diversity! In just a few photos… Although the CF muscles are lost in numerous bird species, they tend to hang around and just remain a long, thin, unprepossessing muscle:

Chicken's right leg in side view. CFC (equivalent of CFL) muscle outlined and labelled.

Chicken’s right leg in side view. CFC muscle (equivalent of CFL; the ancestral CFB is confusingly called the CFP in birds, as it entirely resides on the pelvis) outlined and labelled.

A jay (species?) dissected to show some of the major leg muscles, including the CF. Photo by Vivian Allen.

A jay (species? I forget) dissected to show some of the major leg muscles, including the CFL-equivalent muscle; again, smallish. [Photo by Vivian Allen]

Finally, what’s up with mammals‘ tail-to-thigh CF-y muscles? Not much. Again, as in birds: smaller tail and/or femur, smaller CF muscles. Mammals instead depend more on their hamstring and gluteal muscles to support and propel themselves forward.

But many mammals do still have something that is either called the M. caudofemoralis or is likely the same thing, albeit almost always fairly modest in size. This evolutionary reduction of the CF muscle along the mammal (synapsid) lineage hasn’t gotten nearly as much attention as that given to the dinosaur/bird lineage’s CFL. Somebody should give it a thoroughly modern phylogenetic what-for! Science the shit outta that caudofemoralis…

Yet, oddly, to give one apparent counter-example, cats (felids) have, probably secondarily, beefed up their CF muscle a bit:

Cats have a pretty large CF muscle in general, and this jaguar is no exception! But mammals still tend to have fairly wimpy tails and thus CF muscles, or they even lose them (e.g. us?).

Cats have a pretty large CF muscle in general, and this jaguar is no exception! But mammals still tend to have fairly wimpy tails and thus CF muscles, or they even lose them (e.g. us?). [photo by Andrew Cuff, I think]

In summary, here’s what happened (click to embeefen):

Better Know A Muscle: The Evolution of M. caudofemoralis (longus)

Better Know A Muscle: the evolution of M. caudofemoralis (longus).

I hope you enjoyed the first BKAM episode!
I am willing to hear requests for future ones… M. pectoralis (major/profundus) is a serious contender.

P.S. It was Freezermas this week! I forgot to mention that. But this post counts as my Freezermas post for 2016; it’s all I can manage. Old Freezermas posts are here.

Read Full Post »

Tonight is the debut of the ballyhooed BBC1 programme “Attenborough and the Giant Dinosaur“, featuring Sir David and The Titanosaur-With-No-Name, at 6:30pm. Furthermore, this week I presided over a showing of “T. rex Autopsy” to our RVC undergrad Zoological Society, with a very enjoyable Q&A afterwards. So it seemed timely for me to do a post about a theme that links these two documentaries that I helped with, my own research, and science communication and palaeontological research more generally. But first let’s get this out of the way:

It was great.

It was great. I could gush more but that’s not what this post is about.

Stomach-Churning Rating: ~7/10; mainly the elephant leg dissection that’s not far below, which is a bit messy.

For the titanosaur documentary with Sir David, and the incomparable Ben Garrod as well, we had an old elephant “friend” of mine (subject of many biomechanics studies we’d done) walk across a pressure pad to demonstrate how the elephant locomotion works and some of the basic similarities with how a giant sauropod dinosaur might walk:

A broader feature of that documentary, which elephants are linked into, is how we can use the skeleton to reconstruct some general aspects of the soft tissue anatomy, and thereby the physiology or even behaviour, of a giant titanosaur. Which brings me to this post’s subject: We dig up dinosaurs all the time, but what about digging into dinosaurs and using what’s preserved to reconstruct what isn’t? 

The "G-suit" compressive stocking that the fascia wrapped around elephant, and other large mammals, creates, and the underlying, interwoven muscles and tendons (hindlimb of a young Asian elephant).

Some of the “G-suit” compressive stocking that the fascia wrapped around elephant, and other large mammals, creates, and the underlying, interwoven muscles and tendons (hindlimb of a young Asian elephant that sadly died in captivity). Did some larger dinosaurs have something like this? I’d expect so.

Another view, more superficially, of that G-suit/stocking under the thick, tight skin of an elephant's leg.

Another view, more superficially, of that G-suit/stocking under the thick, tight skin of an elephant’s leg. You’ll hear more about this in the Attenborough show…

Once the documentary airs, I may be able to share some more images from it showing what they did for the titanosaur, but this BBC photo gives a good idea.

Once the documentary airs, I may be able to share some more images from it showing what they did for the titanosaur, but this BBC photo gives a good idea. Here, blood vessels and other tissues surrounding the skeleton. How would a titanosaur pump blood around its body? A good question.

I’ve covered the science behind these reconstructions before, along with the art (in numerous posts, actually). Here I want to inspect how it’s communicated through the media: what are good (and not so good?) ways to cover it, especially now that displaying raw anatomy is more tolerable on TV and other media? I’m not writing about Thanksgiving dinner dinosaur dissections; not really; or in technical terms how we build a dinosaur to dissect/depict internally (digitally or physically).

I wanted to focus more on the end product; the imagery or even physical object; and how it conveys what we think we know about dinosaur anatomy. I’ll do that via examples, using photos of dinosaur anatomy that I’ve collected over the years from museums or other media. There won’t be any profound points or long musings; it’s mainly a photo blog:

What your (inner?) child most needs is a dinosaur to dissect yourself! Why not a T. rex toy like this?

What your (inner?) child most needs is a dinosaur to dissect yourself! Why not a T. rex toy like this?

I could quibble, but for the price they did a good job.

For the price (~$30 in USA), the 4D Vision dinosaurs deliver a pretty good bargain, and the anatomy is satisfactory. I’ve been collecting this series. I could quibble, but hey: it’s a dinosaur you get to build/dissect yourself, and with many major organs in reasonable positions! Not so easy to put/keep together, but it’s fine. I would not pay a ton for it, though.

Poster of Velociraptor's anatomy I've had since grad school, adorning my office. For ~1996, it's damn good, mostly... (placeholder photos until I get to the office tomorrow and take better ones!)

Poster of Velociraptor’s anatomy I’ve had since grad school, adorning my office. For ~1996 (no feathers; “zombie hands“), it’s damn good, mostly… Closer views below (sorry, photo quality is crap– taking photos of wall poster turned out to be harder than I expected! Bad lighting.) :

Closeup of the leg muscles- hey, not bad!

Closeup of the leg muscles- hey, not bad! Pretty much the right muscles in the right places more or less, and plausible proportions. No air sacs in the torso, but again, this is mid-1990’s science shown. BUT…

I was happy with this poster until I got it home and read this final bit of text... Oh, America! You silly place.

I was happy with this poster until I got it home from the western-USA museum I bought it at and read this final bit of text… Oh, America! You silly place. (And unfortunately, these dinosaurs are not from the very end of the Cretaceous anyway, so “global catastrophe” is not implicated.)

Ornithomimid in Barcelona natural history museum. This was unexpected and got me excited when I first saw it.

Ornithomimid in Barcelona natural history museum. This was unexpected and got me excited when I first saw it.

Looking down onto the opened torso of the Barcelona ornithomimid. Strikingly realistic!

Looking down onto the opened torso of the Barcelona ornithomimid. Strikingly realistic! Breastbone, heart, liver, intestines; not unreasonable positions and sizes. No feathers, but again hey– this was made in the earlier days.

Skinned Albertosaurus from the Drexel Academy of Sciences. I forget where I got this pic but I like the display.

Albertosaurus from the Drexel Academy of Sciences. I forget where I got this pic but I like the display– this is an impressive full-scale physical model. The transition from skeleton-only on the left to skinned in the middle to fully-fleshed and popping out atcha on the right is clever.

?T. rex? leg, photo that I took ages ago as a PhD student, if memory serves. Can anyone remind me where this was? California Academy of Sciences?

?T. rex? leg, photo that I took ages ago as a PhD student, if memory serves. Can anyone remind me where this was? California Academy of Sciences? I am embarrassed that I cannot recall. I remember geeking out about it. It has a toy-ish look, but I reckon they had to build this to withstand kids touching it.

Perhaps the best example I've seen in a museum: the AMNH's sauropod with internal organs and their functions projected onto it. Bravo!

Perhaps the best dino-dissection example I’ve seen in a museum: the AMNH’s sauropod Mamenchisaurus with internal organs and their functions projected onto it, in the “World’s Largest Dinosaurs” exhibit. Bravo! I stood and watched it for quite a while.

This is far from comprehensive– just several kinds of imagery that I mostly like. There’s the tension between showing too much realism, which science simply can’t back up, and being too cartoonish, losing the viewer’s immersion in the time-travelling fantasy. I do, however, like other kinds of more abstract, schematic depictions of dinosaur anatomy that simplify the details to focus on the basics of what organs should have been where and how they may have worked, such as this depiction from T. rex Autopsy, which also took the other extreme favouring ultra-realism (but with physical models, not so much with the CGI):

AIr flow through a T. rex: simplified but clear.

Air flow through a T. rex: simplified but clear. CGI used to explain, not abused. The real air sac anatomy would be too complex to show. You may see something similar with the titanosaur show.

That’s enough for now. I’ve stuck with relatively recent examples; of course in my particular field I also think back to Romer’s wonderful 1920’s drawings, which I covered in this post.

So, blog readers, help me out here: what examples of dinosaur internal, squishy anatomy from museums, documentaries or other not-entirely-done-by-nitpicky-scientists venues do you like, or not like so much? What works for you, or at least is memorable in some way?

Read Full Post »

Greetings Freezerinos, and Happy New Year! I have been quiet on this blog for health and other reasons but those will pass and there will be new posts in 2016. However, behind the scenes there have been super-cool things afoot. I am very happy to bring one of them to you now:

(but first: Stomach-Churning Rating: 6/10; video below shows a dissected sea turtle foot in motion)

We have just debuted our new social media “presence” (for lack of a better word) that is a sister blog to this one. It is called Anatomy To You (http://anatomytoyou.com/), as its intent is to bring a wide array of science about animal anatomy to “you”, the general public. This John’s Freezer blog will continue with it’s style of rambling longer posts targeted at a fairly geeky scientifically literate audience and focusing on my team’s research and my own disparate thoughts about science and related issues. Anatomy To You will bring you shorter posts, even just images, completely focused on celebrating the structure of organisms, and not just presenting my team’s research but also a wide array of anatomical science from around the globe. It will also be much more regular and frequent in its posts. We’ll welcome guest posts and I encourage you to get in touch with us if you want to jump on the bandwagon early, or have us feature your research for you!

More about the ATY blog is here, but there is also a Twitter feed and Facebook account. Our first major posts are on what skeletons are, and on a dissection of some sea turtles. Please follow us and join in the celebration of anatomy! My team’s scientific communicator/technician Dr. Lauren Sumner-Rooney is spearheading this ATY effort with me, so please follow her too!

Anatomy To You will continue to evolve over this coming year, so please stay with us and give us feedback; join in the morphological conversations with us. I am SUPER excited to see where this goes– it is an experiment that has a lot of potential, we think.

Sea turtle from our ATY dissection, foot muscles in action (found dead in the wild; don’t be ridiculous, we don’t kill sea turtles for our research)

Read Full Post »

Older Posts »