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Posts Tagged ‘evolution’

I had a spare hour in Cambridge this weekend so I dared the crowds in the revamped UMZC’s upper floor. In my prior visit and post I’d experienced and described the lower floor, which is almost exclusively mammals. This “new” floor has everything else that is zoological (animal/Metazoa) and again is organized in an evolutionary context. And here is my photo tour as promised!

Inviting, soft lighting perfuses the exhibits from the entryway onwards.

All images can be clicked to mu-zoom in on them.

Stomach-Churning Rating: 5/10 for spirit animals, by which I mean dissected/ghostly pale whole specimens of animals in preservative fluids.

The exhibits are on a square balcony overlooking the lower floor, so you can get some nice views. It does make the balcony crowded when the museum is busy, so take that in mind if visiting. Strollers on this upper floor could be really difficult. But the ceiling is very tall so it is not cramped in a 3D sense. The lower floor is more spacious.

Like phylogenies? You got em! Tucked away at the beginning of each major group; not occupying huge valuable space or glaringly obvious like AMNH in NYC but still noticeable and useful. To me, it strikes a good balance; gives the necessary evolutionary context for the displayed specimens/taxa.

Introductory panels explain how names are given to specimens, how specimens are preserved and more.

The exhibits give due focus to research that the UMZC is doing or has been famous for. Hey I recognize that 3D tetrapod image in the lower left! 🙂

There is ample coverage of diversity throughout Metazoa but my camera tended to be drawn to the Vertebrata. Except in some instances like these.

Some larger chelicerates.

Some smaller, shadowy sea scorpion (eurypterid) fossils.

Watch here for more about ophiuroids (brittlestars) in not too long!

A BIG fish brain! Interesting!
Before I go through specimens in evolutionary “sequence”, I will feature another thing i really liked: lots of dissected spirit-specimens that show off cool anatomy/evolution/adaptation (and technical skills in anatomical preparation). Mostly heads; mostly fish.

Salps and other tunicates! Our closest non-vertebrate relatives- and some insight into how our head and gut came to be.

Salp-reflection.

Lamprey head: not hard to spot the commonalities with the salps; but now into Vertebrata.

Hagfish head: as a fellow cyclostome/agnathan, much like a lamprey but never forget the slime glands!

Shark head. Big fat jaws; all the better to bite prey with!

Lungfish (Protopterus) head showing the big crushing tooth plates (above).

Sturgeon vertebrae: tweak some agnathan/shark bits and here you are.

Worm (annelid) anatomy model, displaying some differences from/similarities to Vertebrata. (e.g. ventral vs. dorsal nerve cord; segmentation)

Dissected flipper from a small whale/other cetacean. Still five fingers, but other specializations make it work underwater.

Wonderful diversity of tooth and jaw forms in sharks, rays and relatives. I like this display a lot.

More of the above, but disparate fossil forms!

On with the evolutionary context! Woven throughout the displays of modern animals are numerous fossils, like these lovely placoderms (lineage interposed between agnathans, sharks and other jawed fish).

Goblin shark head.

I seem to always forget what ray-finned fish this is (I want to say wolffish? Quick Googling suggests maybe I am right), but see it often and like its impressive bitey-ness.

Bichir and snakefish; early ray-finned fish radiations.

Armoured and similar fish today.

Armoured fish of the past; some convergent evolution within ray-fins.

Convergence- and homology- of amphibious nature in fish is another evolutionary pattern exemplified here.

Gorgeous fossils of ray-finned fish lineages that arose after the Permian extinctions, then went extinct later in the Triassic.

Note the loooooong snout on this cornetfish but the actual jaws are just at the tip.

Flying fish– those ray-fins are versatile.

Diversity of unusual ray-finned fish, including deep-water and bottom-dwelling forms.

Can you find the low-slung jaws of a dory?

Recent and fossil perch lineage fish.

It’s hard to get far into talking about evolution without bringing up the adaptive radiation of east African cichlid fish, and UMZC researchers are keen on this topic too.

Lobe-fins! Everybody dance!

Rhizodonts & kin: reasons to get out of Devonian-Carboniferous waters.

A Cretaceous fossil coelacanth (skull); not extremely different from living ones’.

Let’s admire some fossil and modern lungfish skulls, shall we? Big platey things  (here, mainly looking at the palate) with lots of fusions of tiny bones on the skull roof.

Eusthenopteron fossils aren’t that uncommon but they are still great to see; and very important, because…

OK let’s stop messing around. The UMZC has one of the best displays of fossil stem-tetrapods in the world! And it should.

Another look at the pretty Acanthostega models.

Acanthostega vs. primate forelimb: so like us.

Ichthyostega parts keep Acanthostega company.

A closer look at the “Mr. Magic” Ichthyostega specimen, which takes some unpacking but is incredibly informative and was a mainstay of our 2012 model. Back of skull, left forelimb, and thorax (from left to right here).

Eucritta, another stem-tetrapod.

Closer look at Eucritta‘s skull.

Weird stem-tetrapod Crassigyrinus, which we’re still trying to figure out. It’s a fabulous specimen in terms of completeness, but messy “roadkill” with too many damn bones.

The large skull of Crassigyrinus, in right side view.

Early temnospondyl (true amphibian-line) skulls and neck.

Nectrideans or the boomerangs of the Palaeozoic.

Cool fossil frogs.

Giant Japanese salamander!

Fire salamanders: not as colourful as the real thing, but here revealing their reproductive cycle in beautiful detail.

Closeup of oviduct in above.

Sexual dimorphism in Leptodactylus frogs: the males have bulging upper arms to (I am assuming) help them hold onto females during amplexus (grasping in mating competitions).

Did I forget that Leptodactylus has big flanges on the humerus in males, to support those muscles? Seems so.

An early stem-amniote, Limnoscelis (close to mammals/reptiles divergence); cast.

Grand sea turtle skeleton.

One of my faves on display: a real pareiasaurian reptile skeleton, and you can get a good 3D look around it.

Details on above pareiasaurian.

Mammals are downstairs, but we’re reminded that they fit into tetrapod/amniote evolution nonetheless.

Let there be reptiles! And it was good.

Herps so good.  (slow worm, Gila monster, glass lizard)

A curator is Dr Jason Head so you bet Titanoboa is featured!

Crocodylia: impressive specimens chosen here.

It ain’t a museum without a statuesque ratite skeleton. (There are ~no non-avian dinosaurs here– for those, go to the Sedgwick Museum across the street, which has no shortage!)

Avian diversity takes off.

Glad to see a tinamou make an appearance. They get neglected too often in museums- uncommon and often seemingly unimpressive, but I’m a fan.

I still do not understand hoatzins; the “cuckoo” gone cuckoo.

Dodo parts (and Great Auk) near the entrance.

Wow. What an oilbird taxidermy display! :-O

There we have it. Phew! That’s a lot! And I left out a lot of inverts. This upper floor is stuffed with specimens; easier there because the specimens are smaller on average than on the lower floor. Little text-heavy signage is around. I give a thumbs-up to that– let people revel in the natural glory of what their eyes show them, and give them nuggets of info to leave them wanting more so they go find out.

Now it’s in your hands– go find out yourself how lovely this museum is! I’ve just given a taste.

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One of my favourite museums in the world, and certainly one of the best natural history museums in the UK, is Cambridge’s Museum of Zoology, AKA “University Museum of Zoology at Cambridge” (UMZC). It is now nearing a lengthy completion of renovations; the old museum exhibits and collections were excellent but needed some big changes along with the re-fabbed “David Attenborough Building” that houses them. As a longtime fan of the exhibits and user of the collection (and microCT scanner), I hurried to see the new museum once it officially opened.

And that makes a great excuse to present a photo-shoot from my visit. This focuses on the “mammal floor” below the entrance- the upper floor(s?) are still being completed and will have the birds, non-avian tetrapods, fish, etc. But the UMZC is strong in mammals and so it is natural for them to feature them in this chock-full-o-specimens display. Less talk, more images. Here we go!

All images can be clicked to mu-zoom in on them.

Stomach-Churning Rating: 3/10; bones and taxidermy and innocuous jars.

The building. The whale skeleton that hung outside for years is now cleaned up and housed right inside; you walk under it as you enter.

Entrance.

First view past the entryway: lots of cool specimens.

View from the walkway down into the ground/basement level from the entry. As specimens-per-unit-volume goes, the UMZC still scores highly and that is GOOD!

Explanation of frog dissection image below.

Gorgeous old frog dissection illustration; such care taken here.

Leeuwenhoek’s flea woodcut; I think from Arcana Naturae Detecta (1695). There is an impressive display of classic natural history books near the entryway.

Dürer/other rhino art image and info.

Darwin was famed for collecting beetles when he should have been studying theology at Cambridge as a youth, and here is some of his collection. Dang.

Darwin’s finches!

Darwin kicked off some of his meticulous work with volumes on barnacles; specimens included here; which helped fuel insights into evolution (e.g. they are “retrograde” crustaceans, not mollusks).

Darwin’s voyage: fish & other preserved specimens.

I think this is a solitaire weka (flightless island bird; see Comment below). I’ve never seen them displayed w/skeleton + taxidermy; it’s effective here.

Eryops cast. More early tetrapods will surely be featured on the upper floor; this one was on the timeline-of-life-on-Earth display.

I LOVE dioramas and this seabird nesting ground display is very evocative, especially now that I’ve visited quite a few such islands.

Mammal introduction; phylogenetic context.

Monotreme glory.

UMZC is well endowed with thylacines and this one is lovely.

“TAZ FEEL NAKED!”

Narwhal above!

Rhinocerotoidea past, present, and fading glory. 😦

Ceratotherium white rhino. The horn is not real; sadly museums (and even zoos) across the world have to worry about theft of such things, given that some people think these horns are magic.

Ceratotherium staring match. You lose.

Ceratotherium stance.

Foot of a Sumatran rhino juxtaposed with a horse’s for Perissodactyla didaction.

A tapir. As a kid, I used to wander around the house pretending to be a tapir but I did not know what noise they’d make so I’d say “tape tape tape!”.

Big Southern Elephant Seal.

Squat little fur seal.

Hippopotamus for the lot of us. (baby included)

Hippo facedown.

Skull of a dwarf Madagascar hippo.

Cave bear and sabretooth cat make an impressive Ice Age demo.

It’s a wombat.

Ain’t no don like a Diprotodon! (also note its modern miniature cousin the wombat, below)

Diprotodon facial.

Diprotodon shoulder: big clavicles bracing that joint region.

Diprotodon knee: even in big marsupials, the “parafibula”/lateral sesamoid of the knee is still generally present. And why it is there/what it does deserves much more study.

Diprotodon hip. I just find this animal’s anatomy fascinating head-to-tail.

Diprotodon front foot. Absolutely freakish.

Diprotodon hind foot. Even weirder.

Your view after having been trampled in a supine position by a Diprotodon. Not a good way to go.

Diprotodon got back.

Elephant seal’s butt continues my series of photos of big animals’ bottoms.

Asian elephant’s butt view.

African elephant butt.

Sectioned elephant skull to show pneumatic resonating chambers.

Paenungulates: hyraxes, Sirenia, elephants & kin (evolutionary demo).

AND MY HYRAX!
Sorry. Had to.

Megatherium side view.

Megatherium. Yeah!

Megatherium hindlegs fascinate me. Well-heeled.

Tamandua duo.

Silky anteater; wonderful.

Armadillos.

Anteaters round out a fab display on Xenarthra.

The UMZC has everything from aardvarks to zebus. Here, conceptualized with other Afrotheria.

Golden moles: the more I read about them, the more they fascinate me.

We can all use some more solenodons in our lives!

Example of the phylogenetic context used throughout exhibits.

If you’ve got a good Okapi taxidermy, you’d better use it.

It’s a giraffe. Did you guess right?

Gerenuk showing off its bipedal capacity.

Warthogs have an inner beauty.

Pangolin. Glad to see it back on exhibit.

Nice little brown bear.

Double-barrelled shot of hyenas.

Colugo!

Nice to see some Scandentia featured.

My brain says this is a springhare (Pedetes) so I am going with what my brain says and anyway I really like this display.

When I saw this I thought, “That’s a nice… rodent thingy.” And so “rodent thing” it shall be labelled here. Enjoy the rodent thingy. Some serious taxidermy-fu in action.

Moonrats– now there’s something you seldom see a full display of. Well done!

That’s part I of this sneak peek at the evolving exhibits- I will put up a part II once the upper floor exhibits open. I highly encourage a visit!

For Mike: gimlet

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A personal story here for Darwin Day 2018. I knew about as much about Charles Robert Darwin as any typical science-interested student when I was growing up. But eventually I had the good fortune of taking a history of science class at the University of Wisconsin as an undergrad, and it inspired me with the story of Darwin as a human being, not just some clever scientist with a long argument that changed the world.

Stomach-Churning Rating: 0/10 unless you have Darwin’s gut-wrenching problems.

I devoured Desmond & Moore’s amazing biography of Darwin “the tormented evolutionist”, which was the transformative event for me. At the time I was experiencing the beginnings of some health problems that didn’t seem that far from problems Darwin suffered for much of his life, and then, as I read more about his life, I saw more features of this man that brought him vividly to life. I still think about those traits and how some parallel my life in certain ways (not that I am in any way a giant of science like him!!). And so this blog post was born, thusly:

I’m writing this post early on Darwin Day and entirely from memory, rather than doing my usual research into the post while I go; to keep the post more personal and less academic (e.g. just quick Wikipedia links below). I feel connected to Darwin’s life experience because, like him, I wandered about as a student, unsure about my direction in life and causing my parents some consternation early on. He tried medical school (Edinburgh; too bloody) and theology (Cambridge; faith just was not his thing) but found hunting for beetles on the heaths more exciting. In high school I played with ideas such as Hollywood screen-writing (too risky), radio DJ (I had no skills) and truant or criminal (I hung out with some shady characters even though I still had some morals; despite transgressions and convictions).

I then took a standardized “what is your best career fit?” test in biology class which conclusively told me that biology was best for me as a career; and that rang true. I’d always loved nature and so that was the idea I had when I went to undergrad. I signed up for the wrong college (Agriculture & Life Sciences, not Letters & Science; confusing divisions!) at the UW. I got some early research experience in that first college: I tried my hand at raising colonies of Indian mealmoths (Plodia interpunctella; I can still identify them!) and their parasitoid wasps. At that same agricultural lab I got to do my own experiments in a basement wind tunnel over my summer holiday, in which I released those pesky moths to fly down the tunnel toward various kinds of pheromone-based lures, finding that one kind seemed to work best. But I didn’t like that and frankly found agricultural science boring, for me. We didn’t connect, nor did some other lab experiences I had. But I grew from them and still value them (and respect the science and people involved) very much.

I took Evolution and also Functional Morphology courses, didn’t do great (I was young for the classes), and then finally took that history class—boom! Aha, scientists can be human! Not just hypothesis-robots! Darwin was a man of great privilege, having his estate and wealth handed down from his funky grandpa Erasmus and stern father Robert. But, in addition to his meanderings that eventually forced him (via his father’s impatient urgings) to become the Beagle’s naturalist for a five year voyage, he suffered in quite human ways throughout much of his life. The greater trials commenced during that voyage, with still-mysterious health problems and the fractious relationship with eccentric Captain Fitzroy. They continued with his marriage to cousin Emma Wedgwood (yes, of that pottery-famed lineage) in which they lost four of ten children at young ages (most critically, beloved Annie at 10 years old) and in which they struggled with Darwin’s diminishing faith and Emma’s stalwart beliefs.

Finally, Darwin struggled famously with his “big book” for >20 years, afraid of its impact and its reception, and of its need to have a watertight, evidence-based argument from many perspectives, with his hand forced by Alfred Russel Wallace’s converging ideas. Along the way, with his health and family problems, he had to contend with his mentors’ and peers’ reactions to his ideas—although one could call the acceptance of much of his main arguments to be a “happy ending” (the post-mortem eclipse of Darwinism, and its eventual resurrection + syntheses, aside). These trials that Darwin faced as a human are all relatable, and the more one learns about him the more complex, flawed, emotional and yes, tormented he becomes. He can be both a hero and a tragic figure or a cautionary tale.

When I get the chance, I like to teach students about this human side of Darwin. It is a way into the heart of the science, to show a person’s journey along with the wonder of discovery, and how such a journey is not necessarily a simple or even joyful one. I can feel the many facets of Darwin in my own life—the intensely curious, peripatetic, enthusiastic young man who loved experiencing nature in all its raw forms, the chronically suffering disabled person who sometimes could not enjoy the work or other aspects of life that he treasured, the family man who loved time at home, the explorer who treasured roaming the local heath or far-flung foreign terrain, the meticulous scientist who exhaustively gathered tiny bits of data in isolated studies to slowly build toward grander ideas, and much more.

But Darwin is a different human, too. We live in such different times, when there the world of science is far larger but the world feels far smaller, more interconnected. Naturalists today are not simply landed noblemen who can play with science in their luxurious spare time, nor do they work alone at their pursuits. Anyone can be a scientist, and a career scientist can, if they are fortunate and skilled enough, assemble their own laboratory in which they lead a team to tackle their big questions that captivate them. The individual questions in science tend to be smaller (more incremental and specialized) today, yet can overall (across career(s)) be bigger because we can tackle -and have tackled- some of the bigger ones; Darwin’s big questions being among the giant ideas we are now poised upon.

It’s not all about science, though. Darwin’s story, which I think about so often, reminds me of how we all struggle in our lives and amidst the joy of discovery in everyday life there can be considerable suffering and regret. It is a bittersweet story; an ever-so-human story. And today is a good day to reflect on that, and to celebrate life while we lament what has been lost.

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An epiphysean Sispyhean task today: solve this mystery that has been bothering me for >15 years. It’s about bird knees. Read on.

Stomach-Churning Rating: 1/10- bones and brief words. Nothing to worry about.

Here is an ostrich. I was interviewing undergrads the other day and looked up to see it, then thought something like: “Oh yeah, that little bit of bone really bothers me. I cannot figure it out.” What little bit of bone?

Right leg, side view, ostrich…

This little bit of bone. Zooming in on that ostrich’s knee:

Who am I? (femur above; tibiotarsus below; “PTE” is the crest of bone with the white arrow on it)

The little bit of bone is not talked about much in the scientific literature on bird knees. But we know it’s there and it is part of the composite bone called the tibiotarsus (ancestral tibia, this bit of bone, and the proximal tarsal [ankle] bones on the other end; the astragalus and calcaneum of earlier dinosaurs).

What is it? We call it something like the proximal tibial epiphysis (PTE for short, here). An epiphysis is an end of a bone that fuses up with the shaft during growth, around the time of skeletal maturity; ultimately ending longitudinal (length-wise) growth of that bone. Mammals almost ubiquitously have them. So do lizards and tuataras. And some fossil relatives. Not much else– except birds, in this particular region (the two ends of the tibiotarsus; also in the foot region; the tarsometatarsus; which also has its share of mysteries such as the hypotarsus; I won’t go there today). You can see the PTE in mostly cartilaginous form if you take apart a chicken drumstick.

This PTE, like other well-behaving epiphyses, fuses with the tibiotarsus in mature birds, forming one bone. But the young ostrich’s knee above shows the PTE nicely; and other living birds show more or less the same thing.

It begs for explanations. I’ve talked about it in a few of my papers. But I’ve always punted on what it really means– does it have anything to do with the patella (they appear at similar times in evolution; we know that much, roughly)? Where does it come from, developmentally? (we sort of know that but more work is needed in different species and in high resolution) When did it evolve? What does it tell us? Why is it there in living birds and almost no other extinct birds/other dinosaurs? Does it have anything to do with why birds, during their evolution, seem to gradually increase the fusion of skeletal elements or ossify new ones (tendons, kneecaps, etc)? Why here and not in the femur or several other long bones of birds? How much do these PTEs vary between (or within) bird species?

This is the challenge in the post’s title. I present to you: solve this puzzle. Developmentally, biomechanically, evolutionarily, genetically, whatever– why does this PTE happen? There are hints– e.g. this paper proposes why growth rates of long bones favour the formation of “secondary centres of ossification” like this. But I’m unable to satisfy myself with any solutions I can find. Maybe you can complete The Bird Knee Challenge?

Have a go at it in the Comments below! There are plenty of papers or even a grant or something involved in sorting out this single mystery; one of the many basic mysteries about animal anatomy.

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As 2017 approaches its end, there have been a few papers I’ve been involved in that I thought I’d point out here while I have time. Our DAWNDINOS project has been taking up much of that time and you’ll see much more of that project’s work in 2018, but we just published our first paper from it! And since the other two recent papers involve a similar theme of muscles, appendages and computer models of biomechanics, they’ll feature here too.

Stomach-Churning Rating: 0/10; computer models and other abstractions.

Mussaurus patagonicus was an early sauropodomorph dinosaur from Argentina, and is now widely accepted to be a very close relative of the true (giant, quadrupedal) sauropods. Here is John Conway’s great reconstruction of it:

We have been working with Alejandro Otero and Diego Pol on Mussaurus for many years now, starting with Royal Society International Exchange funds and now supported by my ERC grant “DAWNDINOS”. It features in our grant because it is a decent example of a large sauropodomorph that was probably still bipedal and lived near the Triassic-Jurassic transition (~215mya).

In our new study, we applied one of my team’s typical methods, 3D musculoskeletal modelling, to an adult Mussaurus’s forelimbs. This is a change of topic from the hindlimbs that I’ve myopically focused on before with Tyrannosaurus and Velociraptor [in an obscure paper that I should never have published in a book! pdf link], among other critters my team has tackled (mouse, elephant [still to be finished…], ostrich, horse, Ichthyostega… dozens more to come!). But we also modelled the forelimbs of Crocodylus johnstoni (Australian “freshie”) for a key comparison with a living animal whose anatomy we actually knew, rather than reconstructed.

Mussaurus above; Crocodylus below; forelimb models in various views; muscles are red lines.

The methods for this biomechanical modelling are now standard (I learned them from their creator Prof. Scott Delp during my 2001-2003 postdoc at Stanford): scan bones, connect them with joints, add muscle paths around them, and then use the models to estimate joint ranges of motion and muscle moment arms (leverage) around joints. I have some mixed feelings about developing this approach in our 2005 paper that is now widely used by the few teams that study appendicular function in extinct animals. As a recent review paper noted and I’ve always cautioned, it has a lot of assumptions and problems and one must exercise extreme caution in its design and interpretation. Our new Mussaurus paper continues those ruminations, but I think we made some progress, too.

On to the nuts and bolts of the science (it’s a 60 page paper so this summary will omit a lot!): first, we wanted to know how the forelimb joint ranges of motion in Mussaurus compared with those in Crocodylus and whether our model of Mussaurus might be able to be placed in a quadrupedal pose, with the palms at least somewhat flat (“pronated”) on the ground. Even considering missing joint cartilage, this didn’t seem very plausible in Mussaurus unless one allowed the whole forearm to rotate around its long axis from the elbow joint, which is very speculative—but not impossible in Crocodylus, either. Furthermore, the model didn’t seem to have forelimbs fully adapted yet for a more graviportal, columnar posture. Here’s what the model’s mobility was like:

So Mussaurus, like other early sauropodomorphs such as Plateosaurus, probably wasn’t quadrupedal, and thus quadrupedalism must have evolved very close to in the Sauropoda common ancestor.

Second, we compared the muscle moment arms (individual 3D “muscle actions” for short) in different poses for all of the main forelimb muscles that extend (in various ways and extents) from the pectoral girdle to the thumb, for both animals, to see how muscle actions might differ in Crocodylus (which would be closer to the ancestral state) and Mussaurus. Did muscles transform their actions in relation to bipedalism (or reversal to quadrupedalism) in the latter? Well, it’s complicated but there are a lot of similarities and differences in how the muscles might have functioned; probably reflecting evolutionary ancestry and specialization. What I found most surprising about our results was that the forelimbs didn’t have muscles well-positioned to pronate the forearm/hand, and thus musculoskeletal modelling of those muscles reinforced the conclusions from the joints that quadrupedal locomotion was unlikely. I think that result is fairly robust to the uncertainties, but we’ll see in future work.

You like moment arms? We got moment arms! 15 figures of them, like this! And tables and explanatory text and comparisons with human data and, well, lots!

If you’re really a myology geek, you might find our other conclusions about individual muscle actions to be interesting—e.g. the scapulohumeralis seems to have been a shoulder pronator in Crocodylus vs. supinator in Mussaurus, owing to differences in humeral shape (specialization present in Mussaurus; which maybe originated in early dinosaurs?). Contrastingly, the deltoid muscles acted in the same basic way in both species; presumed to reflect evolutionary conservation. And muuuuuuch more!

Do you want to know more? You can play with our models (it takes some work in OpenSim free software but it’s do-able) by downloading them (Crocodylus; Mussaurus; also available: Tyrannosaurus, Velociraptor!). And there will be MUCH more about Mussaurus coming soon. What is awesome about this dinosaur is that we have essentially complete skeletons from tiny hatchlings (the “mouse lizard” etymology) to ~1 year old juveniles to >1000kg adults. So we can do more than arm-wave about forelimbs!

But that’s not all. Last week we published our third paper on mouse hindlimb biomechanics, using musculoskeletal modelling as well. This one was a collaboration that arose from past PhD student James Charles’s thesis: his model has been in much demand from mouse researchers, and in this case we were invited by University of Virginia biomechanical engineers to join them in using this model to test how muscle fibres (the truly muscle-y, contractile parts of “muscle-tendon units”) change length in walking mice vs. humans. It was a pleasure to re-unite in coauthorship with Prof. Silvia Blemker, who was a coauthor on that 2005 T. rex hindlimb modelling paper which set me on my current dark path.

Mouse and human legs in right side view, going through walking cycles in simulations. Too small? Click to embiggen.

We found that, because mice move their hindlimb joints through smaller arcs than humans do during walking and because human muscles have large moment arms, the hindlimb muscles of humans change length more—mouse muscles change length only about 48% of the amount that typical leg muscles do in humans! This is cool not only from an evolutionary (mouse muscles are probably closer to the ancestral mammalian state) and scaling (smaller animals may use less muscle excursions, to a point, in comparable gaits?) perspective, but it also has clinical relevance.

Simulated stride for mouse and human; with muscles either almost inactive (Act=0.05) or fully active (Act=1). Red curve goes through much bigger excursions (along y-axis) than blue curve), so humans should use bigger % of their muscle fibre lengths in walking. Too small? Click to embiggen.

My coauthors study muscular dystrophy and similar diseases that can involve muscle stiffness and similar biomechanical or neural control problems. Mice are often used as “models” (both in the sense of analogues/study systems for animal trials in developing treatments, and in the sense of computational abstractions) for human diseases. But because mouse muscles don’t work the same as human muscles, especially in regards to length changes in walking, there are concerns that overreliance on mice as human models might cause erroneous conclusions about what treatments work best to reduce muscle stiffness (or response to muscle stretching that causes progressive damage), for example. Thus either mouse model studies need some rethinking sometimes, or other models such as canines might be more effective. Regardless, it was exciting to be involved in a study that seems to deliver the goods on translating basic science to clinical relevance.

Muscle-by-muscle data; most mouse muscles go through smaller excursions; a few go through greater; some are the same as humans’.

Finally, a third recent paper of ours was led by Julia Molnar and Stephanie Pierce (of prior RVC “Team Tetrapod” affiliation), with myself and Rui Diogo. This study tied together a bunch of disparate research strands of our different teams, including musculature and its homologies, the early tetrapod fossil record, muscle reconstruction in fossils, and biomechanics. And again the focus was on forelimbs, or front-appendages anyway; but turning back the clock to the very early history of fishes, especially lobe-finned forms, and trying to piece together how the few pectoral fin muscles of those fish evolved into the many forelimb muscles of true tetrapods from >400mya to much more recent times.

Humerus in ventral view, showing muscle attachments. Extent (green) is unknown in the fossil but the muscle position is clear (arrow).

We considered the homologies for those muscles in extant forms, hypothesized by Diogo, Molnar et al., in light of the fossil record that reveals where those muscles attach(ed), using that reciprocal illumination to reconstruct how forelimb musculature evolved. This parallels almost-as-ancient (well, year 2000) work that I’d done in my PhD on reconstructing hindlimb muscle evolution in early reptiles/archosaurs/dinosaurs/birds. Along the way, we could reconstruct estimates of pectoral muscles in various representative extinct tetrapod(omorph)s.

Disparity of skeletal pectoral appendages to work with from lobe-fins to tetrapods.

Again, it’s a lengthy, detailed study (31 pages) but designed as a review and meta-analysis that introduces readers to the data and ideas and then builds on them in new ways. I feel that this was a synthesis that was badly needed to tie together disparate observations and speculations on what the many, many obvious bumps, squiggles, crests and tuberosities on fossil tetrapods/cousins “mean” in terms of soft tissues. The figures here tell the basic story; Julia, as usual, rocked it with some lovely scientific illustration! Short message: the large number of pectoral limb muscles in living tetrapods probably didn’t evolve until limbs with digits evolved, but that number might go back to the common ancestor of all tetrapods, rather than more recently. BUT there are strong hints that earlier tetrapodomorph “fishapods” had some of those novel muscles already, so it was a more stepwise/gradual pattern of evolution than a simple punctuated event or two.

Colour maps of reconstructed right fin/limb muscles in tetrapodomorph sarcopterygian (~”fishapod”) and tetrapod most recent common ancestors. Some are less ambiguous than others.

That study opens the way to do proper biomechanical studies (like the Mussaurus study) of muscle actions, functions… even locomotor dynamics (like the mouse study)– and ooh, I’ve now tied all three studies together, tidily wrapped up with a scientific bow! There you have it. I’m looking forward to sharing more new science in 2018. We have some big, big plans!

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

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

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

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

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

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

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

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

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

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

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

Early whale Ambulocetus, showing hefty kneecaps.

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

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

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

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

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

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

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

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

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

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

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

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

cheetah-verts

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

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

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

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

pta-cats

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

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

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

References used here:

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

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

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

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

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

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

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