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Posts Tagged ‘ratite’

Putting my morphologist hat back on today, I had an opportunity to dissect an Elegant-crested tinamou (Eudromia elegans) for the second time in my life. The last time was during my PhD work ~20 years ago. In today’s dissection I was struck by another reminder of how studying anatomy is a lifelong learning experience and sometimes it’s really fun and amazing even when it’s stinky.

Tinamou foot. I did know that tinamous don’t have a hallux; big “perching toe” (1st/”big toe” in us); true of ratites/palaeognaths more generally. Unlike a chicken or many other birds. Just the three main toes (2, 3 and 4) are here.

Stomach-Churning Rating: 7/10; you gotta have guts to learn about intestine-churning stuff.

Tinamous are neat little partridge-like ground birds but they are not close cousins of partridges or guineafowl at all. Their closest cousins are other ratites/palaeognaths such as ostriches and kiwis. And hence they are found in South America, especially Patagonia in Argentina. I’ve seen them there, much to my enjoyment.

Said tinamou.

What struck me today was that, as I delved into the digestive system of this bird, I saw features that were unfamiliar to me even after having dissected many species of birds from many lineages. The intestinal region was very lumpy, with little bud-like pockets full of dense droppings. Furthermore, on separating the tubes of the small and large intestines I realized that most of the intestinal volume itself was caecum (normally a modest side-pocket near the juncture of the small and large intestines). Indeed, that caecum was caeca (plural): it had two massive horns; it was a double-caecum, feeding back into the short rectum and cloaca. Birds have variable caeca and it is typical to see subdivision into two parts, but I’d never seen it to this degree.

Oh why not, here’s the gizzard/stomach showing its grinding pebbles and bits of food, plus the strong outer muscle layers (pink) for driving that grinding. Small intestine heads toward the bottom of the image. Yes, we do need a better dissection light…

I had to question my anatomical knowledge at this point, wondering if I was identifying things incorrectly—did I really screw up somehow and these were other organs, like giant ovaries? But no, they were clearly full of faecal matter; they were digestive organs. I finished the dissection, still puzzled, and hit the literature. Right away, Google-Scholaring for “tinamou caecum” I found the answer, here (free pdf link):

“at least one species (Elegant Crested Tinamou, [Eudromia elegans]), the ceca contain multiple sacculations, resulting in structures that look much like two bunches of fused grapes.”

The caeca in question.

OK buddy, those are the little lumpy buds I saw. Bunches of grapes—exactly.

And later:

“The paired ceca of the Elegant Crested Tinamou are extraordinary and probably unique within Aves (Fig. 3): long and wide (12.5-13.0 X 2.2- 2.5 cm; Wetmore 1926) and internally honeycombed by many small diverticula. These outpocketings gradually diminish in size and organization from the base to the tip of the organ, apically showing a more spiral form of internal ridges like ratite ceca. Externally, the basal diverticula protrude from the ceca as pointed lobes, gradually becoming flatter but still clearly apparent toward the organ’ s tip.”

Whoa! I never knew that! So I happened to be dissecting a bird, fairly common in its homeland, that has a really bizarre and singular form of caeca/ceca! That hit my morphologist sweet-spot so I was very pleased and decided to share with you. It is one of those many examples of times when you quickly go from confusion to illumination as a scientist, emerging with a neat fact about animal biology. And journal articles help you get there!

The bare “brood patch” on the back end of the tinamou’s belly; a nicely hotspot for keeping eggs warm. Perhaps for brooding bad puns, too.

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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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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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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.

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I have an impression that there is a large disparity between how the public views museums and how scientists who use museums view them. Presumably there are survey data on public attitudes, but surely the common impression is that museums mainly exist to exhibit cool stuff and educate/entertain the public. Yet, furthermore, I bet that many members of the public don’t really understand the nature of museum collections (how and why they are curated and studied) or what those collections even look like. As a researcher who tends to do heavily specimen-oriented and often museum-based research, I thought I’d take the opportunity to describe my experience at one museum collection recently. This visit was fairly representative of what it’s like, as a scientist, to visit a museum with the purpose of using its collection for research, rather than mingling with the public to oggle the exhibits — although I did a little of that at the end of the day…

Stomach-Churning Rating: 4/10; mostly bones except a jar of preserved critters, but also some funky bone pathologies! Darwin hurls once, totally blowing chunks, but only in text.

Early camel is sitting down on the job at the NHMLA.

Early camel is sitting down on the job at the NHMLA.

About two weeks ago, I had the pleasure to spend a fast-paced day in the Ornithology collection of the Natural History Museum of Los Angeles County (NHMLA or LACM). I arranged the visit (you have to be a credible researcher to get access; luckily I seemed to be that!) via email, took an Uber car to the museum, and was quickly cut loose in the collection. I was hosted by the Collections Manager Kimball Garrett, who is an avid birder (adept at citizen science, too!) and a longtime LA native.

Amongst museum curators and collections managers (there can be a distinction between the two but here I’ll refer to them all as “curators”), there is a wide array of attitudes toward and practices with museum collections, regarding how the curators balance their varied duties of not only making the museum collection accessible to researchers (via behind-scenes studies) and the public (via exhibits and behind-scenes tours etc.), but also curation (maintaining a record of what they have in their collection, adding to it, and keeping the specimen in good condition), research, admin, teaching and other duties.

Most curators I’ve known, like Kimball, are passionate about all of these things, and very generous with their time to help scientists make the most of the collection during their visit, offering hospitality and cutting through the bureaucracy as much as possible to ensure that the science gets done. There are those few curators that aren’t great hosts because they’ve had a bad day or a bad attitude (e.g. obsession with paperwork and finding obstacles to accessing specimens for research; or just not responding to communication), but they are few and far between in my experience.

Regardless, the curator is the critical human being that keeps the wheels of specimen-based museum research rolling, and I am appreciative of how deeply dedicated and efficient most curators are. Indeed, I enjoy meeting and chatting with them because they tend not only to be fun people but also incredibly knowledgeable about their collection, museum, and area of expertise. Sadly, this trip was so time-constrained that I didn’t get much time at all for socializing. I had about five hours to get work done so I plunged on in!

Images, as always, can be clicked to emu-biggen them. Thanks to the NHMLA for access!

My initial look down the halls of the osteology storage. Rolling cabinets (on the right) are a typical sight.

My initial look down the halls of the osteology storage. Rolling cabinets (on the right) are a typical sight.

Freezers ahoy!

Freezers ahoy! With Batman watching over them.

A jar of bats? Why not? Batman approves.

A jar of bats? Why not? Batman approves.

The curator cleared a space on a table for me to set bones on. Then the anatomizing and photographing began!

The curator cleared a space on a table for me to set bones on. Then the anatomizing and photographing began!

On entering a museum collection, one quickly gets a sense of its “personality” and the culture of the museum itself, which emerges from the curator, the collection’s history, and the museum’s priorities. There are fun human touches like the ones in the photos below, interspersed between the stinking carcasses awaiting skeletonization, the crumbling bone specimens on tables that need repair or new ID tags, or the rows upon rows of coffee cups ready to fuel the staff’s labours.

Yet another reason why Darwin kicks ass.

Yet another reason why Darwin kicks ass. And fine curator-humour!

Ironic bird pic posted on the wall.

Ironic bird pic posted on the wall.

Below a typical wall-hanging of a bovid skull, an atypical display of a clutch of marshmallow peeps. Contest to see whether the mammalian or pseudo-avian specimens last longest?

Below a typical wall-hanging of a bovid skull, an atypical display of a clutch of marshmallow peeps. Contest to see whether the mammalian or pseudo-avian specimens last longest?

The NHMLA’s collection is a world-class one, which I why I chose it as the example for this post. When I entered the collection, I got that staggering sense of awe that I love feeling, to look down the halls of cabinets full of skeletonized specimens of birds and be overwhelmed by the vast scientific resource it represents, and the effort it has taken to create and maintain it. Imagine entering a library in which every book had the librarian’s hand in writing and printing it, and that those books’ contents were largely mysteries to humanity, only some of which you could investigate during your visit. Museum collections exist to fuel generations of scientific inquiry in this way. Their possibilities are endless. And that is why I love visiting them, because every trip is an adventure into the unknown– you do not know what you will find. Like these random encounters I had in the collection’s shelves:

Sectioned moa thigh bones, showing thick walls and spars of trabecular bone criss-crossing the marrow cavities.

Sectioned moa thigh bones, showing thick walls and spars of trabecular bone criss-crossing the marrow cavities.

My gut reaction was that this is a moa wishbone (furcula)- not often seen! It is definitely not a shoulder girdle (scapulocoracoid), which would be larger and more robust, and have a proper shoulder joint. It could, though, be a small odd rib, I suppose.

My gut reaction was that this is a moa wishbone (furcula)- not often seen! It is definitely not a shoulder girdle (scapulocoracoid), which would be larger and more robust, and have a proper shoulder joint. It could, though, be a small odd rib, I suppose. EDIT: Think again, John! See 1st comment below, and follow-ups. I seem to be totally wrong and the ID of scapulocoracoid is right.

A cigar box makes an excellent improvised container for moa toe bones- why not?

A cigar box makes an excellent improvised container for moa toe bones- why not?

Moa feet: all the moa to love!

Moa feet: all the moa to love!

May the skull of the magpie goose (Anseranas semipalmata) haunt your nightmares.

May the skull of the magpie goose (Anseranas semipalmata) haunt your nightmares.

Double-owie: headed shank (tibiotarsus) bone of a magpie goose (Anseranas semipalmata). No mystery why this guy died: vet staff at the zoo tried to fix a major bone fracture, and it had time to heal (frothy bone formation) but presumably succumbed to these injuries/infection.

Healed shank (tibiotarsus) bone of the same magpie goose as above. It had its own nightmares! No mystery why this guy died: vet staff at the zoo tried to fix a major bone fracture (bracing it with tubes and metal spars), and it had time to heal (see the frothy bone formation) but presumably succumbed to these injuries/infection.

Kiwi (Apteryx australis mantelli) hand, showing feather attachments and remnant of finger(s).

Kiwi (Apteryx australis mantelli) hand, showing feather attachments and remnant of finger(s).

Now that I’m in the collection shelves area, it brings me to this trip and my purpose for it! I wanted to look at some “basal birds” for our ongoing patella (kneecap) evolution project, to check which species (or individuals, such as juveniles/adults) have patellae. Every museum visit as a scientist is fundamentally about testing whether what you think you know about nature is correct or not. We’d published on how the patella evolved in birds, but mysteries remain about which species definitely had a patella or how it develops. Museum collections often have the depth and breath of individual variation and taxonomic coverage to be able to address such mysteries, and every museum collection has different strengths that can test those ideas in different, often surprising, ways. So I ventured off to see what the NHMLA would teach me.

Shelves full of boxes, begging to be opened- but unlike Pandora's box, they release joyous science!

Shelves full of boxes, begging to be opened- but unlike Pandora’s box, they release joyous science!

Boxes of kiwis, oh frabjous day! A nice sample size like this for a "rare" (to Northern hemispherites) bird is a pleasure to see.

Boxes of kiwis, oh frabjous day! A nice sample size like this for a “rare” (to Northern hemispherites) bird is a pleasure to see.

Well, in my blitz through this museum collection I didn’t see a single damn patella!

As that kneecap bone is infamously seldom preserved in nice clean museum specimens, this did not surprise me. So I took serendipity by the horns to check some of my ideas about how the limb joints in birds in general develop and evolve. One thing I’ve been educating myself about with my freezer specimens and with museum visits (plus the scientific literature) is how the ends (epiphyses) of the limb bones form in different species of land vertebrates (tetrapods). There are complex patterns linked with evolution, biomechanics and development that still need to be understood.

Left side view of the pelvis of a very mature, HUGE Casuarius casuarius (cassowary). The space between the ilium (upper flat bone) and ischium (elongate bone on middle right side) has begun to be closed by a mineralization of the membrane that spanned those bones in life. A side effect of maturity, most likely. But cool- I've never seen this in a ratite bird before, that I can recall.

Left side view of the pelvis of a very mature, HUGE Casuarius casuarius (cassowary). The space between the ilium (upper flat bone) and ischium (elongate bone on middle right side) has begun to be closed by a mineralization of the membrane that spanned those bones in life. A side effect of maturity, most likely. But cool- I’ve never seen this in a ratite bird before, that I can recall.

Hatchling ostrich thigh bones (femora), showing the un-ossified ends that in life would be occupied by thick cartilage.

Hatchling ostrich thigh bones (femora), showing the pitted, un-ossified ends that in life would be occupied by thick cartilage.

A more adult ostrich's femora, with more ossified ends and thinner cartilages.

A more adult ostrich’s femora, with more ossified ends and thinner cartilages.

Rhea pennata (Darwin's rhea) femora (thigh bones), left (top) one with major pathology on the knee end; overgrown bone. Owie!

Rhea pennata (Darwin’s rhea) femora; right (top) one with a major pathology on the knee end; overgrown bone (osteoarthritis?). Owie!

Also very-unfused knee joints of a Darwin's rhea. Cool Y-shape!

Also very-unfused knee joints of a Darwin’s rhea hatchling. Cool Y-shape!

In birds, most of the bones don’t have anything that truly could be called an epiphysis– the bone ends are capped with thick cartilage that only gradually becomes bone as the birds get older, and even old-ish birds can still have a lot of cartilage (see photos above)– no “secondary centre” (true epiphysis) of bone mineralization ever forms inside that cartilage. However, there are two curious apparent exceptions to this absence of true epiphyses in avian limbs:

(1) in the knee joint, something like an epiphysis forms on the upper end of the tibia (shank bone) and fuses during growth (shown below). Sometimes that unfused epiphysis is confused with a patella, as our recent paper discussed; in any case, where that “epiphysis” came from in avian evolution is unclear. But also:

(2) in the ankle joint, several bones on both sides (shank and foot) of the joint fuse to the long-bones of the limbs, acting like epiphyses. It is well documented by the fossil record of non-avian and avian dinosaurs that these were the tarsals: at least five different bones (astragalus, calcaneum and distal tarsals) were individual bones for millions of years in various dinosaurs, then these all fused to form the “epiphyses” of the shank and foot, eventually completing this gradual fusion within the bird lineage. Modern birds obliterate the boundaries between these five or more bones as they grow.

These are worthwhile questions to pursue because they show us (1) how odd, little-explored features of the avian skeleton came to be; and (2) potentially more generally why limb bones develop the many ways they do in vertebrates, and how they might develop incorrectly — or heal if damaged.

Images below from the NHMLA collections show how this is the case. Fortunately(?) for me, they supported how I thought the “epiphyses” of avian limbs develop/evolved; there were no big surprises. But I still learned neat details about how this happens in individual species or lineages, especially for the knee joint.

Juvenile kiwi's shank (tibiotarsus) bones viewed from the top (proximal) ends, showing the bubbly nubbins of bone (very bottom of each bone image) that are the "cranial tibial epiphyses" often mistaken for patellae.

Juvenile kiwi’s shank (tibiotarsus) bones viewed from the top (proximal) ends, showing the bubbly nubbins of bone (very bottom of each bone image; lighter region) that are the “cranial tibial epiphyses” often mistaken for patellae.

Subadult kiwi's tibiotarsi in same view as above, showing the epiphyses fusing onto the tibiae.

Subadult kiwi’s tibiotarsi in same view as above, showing the smooth triangular epiphyses fusing onto the tibiae.

Adult kiwi's tibiotarsi (sorry, blurry photo) in which all fusion is complete.

Adult kiwi’s tibiotarsi (sorry, blurry photo) in which all fusion is complete.

Looking down at the top/ankle end of the tarsometatarsal (sole) bones in a hatchling ostrich: the three bones are separate and hollow, where "cartilage cones" would have filled them in.

Looking down at the top/ankle end of the tarsometatarsal (sole) bones in a hatchling ostrich: the three bones are separate and hollow, where “cartilage cones” would have filled them in. The left and right bones have different amounts of ossification; not unusual in such a young bird.

Ossified tendons (little spurs of long, thin bone) on the soles of the feet (tarsometatarsal bones) of a brush-turkey (Alectura lathami)- seldom described in this unusual galliform bird or its close relatives, and thus nice to see. These would be parts of the toe-flexor tendons.

Ossified tendons (little spurs of long, thin bone) on the soles of the feet (tarsometatarsal bones) of a brush-turkey (Alectura lathami)- seldom described in this unusual galliform bird or its close relatives, and thus nice to see. These would be parts of the toe-flexor tendons. Another nice thing about these two tarsometatarsus specimens is that their fusion is basically complete- each is one single bone unit, as in normal adult birds, rather than five or more.

My visit to the NHMLA bird bone collection was a lot of fun, because I got to do what I love: opening box after box of bone specimens, with bated breath wondering what would be inside. In this case, familiarity was inside, but my knowledge of avian bone development and evolution still improved. I got to look at a lot of ostriches, rheas, cassowaries and kiwis, more than I’d seen in one museum before, and that broadened my sample of young, juvenile and adult animals that I’d seen for these species. Their knees and ankles all grew in grossly similar ways, supporting this assumption in my prior work and building my confidence in published ideas. It’s always good to check such things. Each box opened takes some careful observation and cross-checking against all the facts and ideas swirling around in your head. You take notes, scale photos, measurements, do comparisons between specimens, and just explore; letting your curiosity run unleashed as you assemble knowledge, Tetris-like, in your mind.

And I had a lot of fun because a museum collection visit is like swimming in anatomy. You’re surrounded by more specimens than you could ever fully comprehend. Sometimes you run across an odd specimen whose anatomy tells you something about its life, like pathologies such as the terrible fractured magpie goose leg shown above. Or you see some curatorial touch that makes you chuckle at an apparent inside joke or mutter respect for their careful organization in tending their charges. That feeling of pulling open a museum drawer or box lid and peering inside is like few others in science — there might be disappointment inside (e.g. “Crap, that specimen sucks!”), boredom (“Oh. Another one of these!?”) or the joy of discovery (“Holy *@$£, I’ve never seen that before!”). My first scientific publication (in 1998) came from rummaging through the UCMP museum collections as a grad student and spotting an obscure pelvic bone that turned out to be highly diagnostic for the equally obscure clade of bird-like dinosaurs called alvarezsaurids. I happened to open that drawer with the alvarezsaurid specimen at the right time, shortly after the first ever specimen of that dinosaur had been described in the literature (~1994). Before then, no one could have identified what that bone was!

There is time for hours of quiet introspection during museum collection studies, immersed in this wealth of anatomical resources and isolated in a silent, climate-controlled tomb-like hall. It is relaxing and overwhelming at the same time. Especially in my case with just five hours to survey numerous species, you have to budget your time and think efficiently. It’s a unique challenge to explore a museum collection as a researcher. If you don’t learn something — especially in a good museum collection — you’re doing it wrong. In this time of tight finances and trends to close museums or stow away precious collections, it is important to vocally celebrate what a vast treasure museum collections are, and how the people that maintain them are vital stewards of those treasures.

I set the cat amongst the pigeons by also visiting the Page Museum at the La Brea Tar Pits in LA, to study fossil cats-- like this American lion (Panthera atrox) code-named "Fluffy", that we CT scanned during my LA visit-- more about that later!

I set the cat amongst the pigeons by also visiting the Page Museum at the La Brea Tar Pits in LA, to study fossil cats– like this American lion (Panthera atrox), code-named “Fluffy”, that we CT scanned during my LA visit– more about that later!

EDIT: I hurried this post off during my free time today, and still feel I didn’t fully capture the deep, complex feelings I have regarding museum collections and the delight I get from studying them. Other freezerinos, please add your thoughts in the Comments below!

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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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Construction of the Phyletisches Museum in Jena, Germany began on Goethe’s birthday on August 28, 1907. The Art Nouveau-styled museum was devised by the great evolutionary biologist, embryologist and artist/howthefuckdoyousummarizehowcoolhewas Ernst Haeckel, who by that time had earned fame in many areas of research (and art), including coining the terms ontogeny (the pattern of development of an organism during its lifetime) and phylogeny (the pattern of evolution of lineages of organisms through time) which feature prominently in the building’s design and exhibits (notice them intertwined in the tree motif below, on the front of the museum). Ontogeny and phylogeny, and the flamboyant artistic sensibility that Haeckel’s work exuded, persist as themes in the museum exhibits themselves. Haeckel also came up with other popular words such as Darwinism and ecology, stem cell, and so on… yeah the dude kept busy.

Cavorting frogs from Haeckel's masterpiece Kunstformen der Natur (1904).

Cavorting frogs from Haeckel’s masterpiece Kunstformen der Natur (1904).

I first visited the Phyletisches Museum about 10 years ago, then again this August. Here are the sights from my latest visit: a whirlwind ~20 minute tour of the museum before we had to drive off to far-flung Wetzlar. All images are click-tastic for embiggenness.

Stomach-Churning Rating: 3/10 for some preserved specimens. And art nouveau.

Willkommen!

Willkommen!

Frog ontogeny, illustrated with gorgeous handmade ?resin? models.

Frog ontogeny, illustrated with gorgeous handmade ?resin? models.

Fish phylogeny, illustrated with lovely artistry.

Phylogeny of Deuterostomia (various wormy things, echinoderms, fish and us), illustrated with lovely artistry.

Phylogeny of fish and tetrapods.

Phylogeny of fish and tetrapods.

Slice of fossil fish diversity.

Slice of fossil fish diversity.

Plenty of chondryichthyan jaws and bodies.

Plenty of chondrichthyan jaws/chondrocrania, teeth and bodies.

Awesome model of a Gulper eel (Saccopharyngiformes).

Awesome model of a Gulper Eel — or, evocatively, “Sackmaul” auf Deutsch (Saccopharyngiformes).

Lobe-finned fishes (Sarcopterygii)- great assortment.

Lobe-finned fishes (Sarcopterygii)- great assortment including a fossil coelacanth.

Lungfish body/model and skeleton.

Lungfish body and skeleton.

Coelacanth!

Coelacanth!

Coelacanth staredown!

Coelacanth staredown!

Fire salamander! We love em, and the museum had several on display- given that we were studying them with x-rays, seeing the skeleton and body together here in this nice display was a pleasant surprise.

On into tetrapods– a Fire Salamander (Salamandra salamandra)! We love ’em, and the museum had several on display- given that we were studying them with x-rays, seeing the skeleton and body together here in this nice display was a pleasant surprise.

A tortoise shell and skeleton, with a goofball inspecting it.

A tortoise shell and skeleton, with a goofball inspecting it.

In a subtle nod to recurrent themes in evolution, the streamlined bodies of an ichthyosaur and cetacean shown in the main stairwell of the museum, illustrating convergent evolution to swimming locomotor adaptations.

In a subtle nod to recurrent themes in evolution, the streamlined bodies of an ichthyosaur and cetacean shown in the main stairwell of the museum, illustrating convergent evolution to swimming adaptations.

Phylogeny of reptiles, including archosaurs (crocs+birds).

Phylogeny of reptiles, including archosaurs (crocs+birds).

Gnarly model of an Archaeopteryx looks over a cast of the Berlin specimen, and a fellow archosaur (crocodile).

Gnarly model of an Archaeopteryx looks over a cast of the Berlin specimen, and a fellow archosaur (crocodile). The only extinct dinosaur on exhibit!

Kiwi considers the differences in modern bird palates: palaeognathous like it and fellow ratites/tinamous (left), and neognathous like most living birds.

Kiwi considers the differences in modern bird palates: palaeognathous like it and fellow ratites/tinamous (left), and neognathous like most living birds.

Echidna skeleton. I can't get enough of these!

Echidna skeleton. I can’t get enough of these!

Skulls of dugong (above) and manatee (below).

Skulls of dugong (above) and manatee (below), Sirenia (seacows) closely related to elephants.

Fetal manatee. Awww.

Fetal manatee. Awww.

Adult Caribbean manatee, showing thoracic dissection.

Adult Caribbean manatee, showing thoracic dissection.

Hyraxes, which Prof. Martin Fischer, longtime curator of the Phyletisches Museum, has studied for many years.  Rodent-like elephant relatives.

Hyraxes, which Prof. Martin Fischer, longtime curator of the Phyletisches Museum, has studied for many years. Rodent-like elephant cousins.

Old exhibit at the Phyletisches Museum, now gone: Forelimbs of an elephant posed in the same postures actually measured in African elephants, for the instant of foot touchdown (left pic) and liftoff (right pic). Involving data that we published in 2008!

Old exhibit at the Phyletisches Museum, now gone: Forelimbs of an elephant posed in the same postures actually measured in African elephants, for the instant of foot touchdown (left pic) and liftoff (right pic). Involving data that we published in 2008!

Gorilla see, gorilla do. Notice "bent hip, bent knee" vs. "upright modern human" hindlimb postures in the two non-skeletal hominids.

Eek, primates! Gorilla see, gorilla do. Notice the primitive “bent hip, bent knee” vs. the advanced “upright modern human” hindlimb postures in the two non-skeletal hominids.

Phylogeny of select mammals, including the hippo-whale clade.

Phylogeny of artiodactyl (even-toed) mammals, including the hippo-whale clade.

Hand (manus) of the early stem-whale Ambulocetus.

Hand (manus) of the early stem-whale Ambulocetus.

Carved shoulderblade (scapula) of a bowhead whale (Balaena mysticetus), which apparently Goethe owned. Quite a relic!

Carved shoulderblade (scapula) of a bowhead whale (Balaena mysticetus), which apparently Goethe owned (click to emwhalen and read the fine print). Quite a relic!

One of Haeckel's residences. There is also a well-preserved house of his that one can visit, but I didn't make it there.

One of Haeckel’s residences, across the street from the museum. There is also a well-preserved house of his that one can visit, but I didn’t make it there. I heard it’s pretty cool.

Jena is tucked away in a valley in former East Germany, with no local airport for easy access- but get to Leipzig and take a 1.25 hour train ride and you’re there. Worth a trip! This is where not just ontogeny and phylogeny were “born”, but also morphology as a modern, rigorous discipline. Huge respect is due to Jena, and to Haeckel, whose quotable quotes and influential research still resonate today, in science as well as in art.

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