• Tag Archives crocodilian
  • The 3D alligator

    Model organisms are a staple of biology. They are taxa that are used to answer larger questions about that group as a whole, or some general biological problem. Model organisms are chosen for their ease of handling, cheap acquisition, generally “generic” structures, or all of the above. Every major class has a model organism to represent it. Just among vertebrates we have:


    A stillborn hatchling rests inside the left nostril of a large 3.7m (12ft) adult which is some 5000 times larger!
    A stillborn hatchling rests inside the left nostril of a large 3.7m (12ft) adult which is some 5000 times larger!

    Mammals with mice (Mus musculus), dogs (Canis familiaris [or Canis lupus familiaris if you lean that way]), cats (Felis catus [or Felis sylvestris catus for the same reason as dogs]), guinea pigs (Cavia porcellus) and rhesus monkeys (Macaca mulatta).

    Birds with chickens (Gallus gallus), pigeons (Columba livia), and zebrafinch (Taeniopygia guttata).

    Ray finned fish with zebrafish (Danio rerio), swordtails (Xiphophorous) and cichlids (Cichlidae).

    Amphibians with the African clawed frog (Xenopus laevis), and axolotol (Ambystoma mexicanum).

    Reptiles with anoles (Anolis), fence lizards (Sceloporous), painted turtles (Chrysemys picta) and finally, the American Alligator (Alligator mississippiensis).

    Alligators are relatively new to the model organism realm, but they have proven to be extremely informative. They seem to the be most even tempered of extant crocodylians, making them “more safe” for researchers to work with. Hatchlings start off as miniscule 68 gram (0.15 lbs) animals that later can grow to 363 kg (800 lbs) adults, passing through an enormous size range throughout ontogeny. This growth rate is very food dependent, making it possible to raise alligators almost as bonsai trees. Also, with their unique position on the organismal family tree, alligators are one of the closest living relatives to dinosaurs. Along with birds, they have the potential to help constrain our assumptions about dinosaurs; thus making them very popular subjects for paleontological research as well.

    Today, alligators get to make one more stamp on human knowledge with the release of the 3D alligator project from the Holliday and Witmer labs.

    Researchers from both labs went through the painstaking process of digitizing the skulls of an adult and a hatchling American alligator, and then digitally separated each bone. The result is a 3D model that can have each bone turned on and off at will. The neat thing is that both labs have made these data freely available for anyone to look at, and download as 3D pdfs, wirefusion models, and multiple movies.

    So if one every wanted to know just how many bones make up a crocodylian skull, or how each bone aligns to each other, I highly recommend downloading the 3D pdfs of the adult and hatchling. Not only will one learn all the different bones that compose the skull, but by comparing hatchling to adult, one can see just how radically these bones change throughout ontogeny.

    It’s neat, free, informative and reptilian. What more can one ask for. 🙂


  • Alligators can shift their lungs and lizard ecology determines movement.

    There were two new papers released today in the Journal of Experimental Biology.

    The first one is the biggest, as it received a news story.

    Uriona, T.J., and Farmer, C.G. 2008. Recruitment of the diaphragmaticus, ischiopubis and other respiratory muscles to control pitch and roll in the American alligator (Alligator mississippiensis). J. Exp. Biol. Vol. 211: 1141-1147 doi: 10.1242/jeb.015339


    We used electromyography on juvenile American alligators to test the hypothesis that the following muscles, which are known to play a role in respiration, are recruited for aquatic locomotion: M. diaphragmaticus, M. ischiopubis, M. rectus abdominis, M. intercostalis internus, and the M. transversus abdominis. We found no activity with locomotion in the transversus. The diaphragmaticus, ischiopubis, rectus abdominis and internal intercostals were active when the animals executed a head-down dive from a horizontal posture. Weights attached to the base of the tail resulted in greater electrical activity of diaphragmaticus, ischiopubis and rectus muscles than when weights were attached to the head, supporting a role of this musculature in locomotion. The diaphragmaticus and rectus abdominis were active unilaterally with rolling maneuvers. Although the function of these muscles in locomotion has previously been unrecognized, these data raise the possibility that the locomotor function arose when Crocodylomorpha assumed a semi-aquatic existence and that the musculoskeletal complex was secondarily recruited to supplement ventilation.

    Scientists at the University of Utah have discovered the unique internal subtleties that allow crocodylians to sink, rise, pitch and roll; all without disturbing the water (much). It turns out that the main muscles used for breathing, are also used to actually shift the lungs within the body!

    That’s just crazy awesome. Uriona & Farmer’s work raises the question of how prevalent this ability is in other semi-aquatic animals (e.g. seals, terrapins, manatees). By shifting the lungs further back in the body, crocodylians are able to change their local density. This allows the front, or back of the animal to rise and sink separately from the rest of the body. So too does moving the lungs from side to side allow for rolling in the water. All of this can occur without the need to move any external body parts. This means no extra turbulence gets created in the water, thus allowing crocodylians to better sneak up on their fishy, or fleshy prey.

    Baby crocodiles exhibiting their unique pulmonary powers.

    If anything, it sure speaks to why crocodyliformes have held dominion over the semi-aquatic niche for over 200 million years. Uriona and Farmer do suggest that the ability of these respiratory muscles to do this might not be an exaptation. Rather, this might have been the initial impetus behind the evolution of these muscles. Only later would they have been exapted to help with breathing on land. Though the authours provide some good parsimonious reasons for why this may be (basically it would take less evolutionary steps to accomplish than the other way around), it doesn’t really jive with the fossil evidence. Part of the reason why the crocodylian diaphragm works, is because the pubis (the forepart of the hip bone in most animals, and the part that juts out so prominently in theropod dinosaurs), is mobile. This mobility occurred early on in crocodyliforme evolution, with the crocodylomorph Protosuchus having a pubis that was almost mobile. The problem arises when one looks at this early crocodylomorph. Protosuchus was obviously terrestrial. If Protosuchus was evolving a mobile pubis already, then it was doubtful that it was being used to allow lung shifting in the body (an ability that is helpful when underwater, but pretty pointless on land). Furthermore, Crocodylia proper is the umpteenth time that crocodyliformes have returned to a semi-aquatic existence. It is doubtful that all the numerous land outings that occurred during crocodyliforme evolution, would have retained the ability to move the lungs to and fro. It seems far more likely that this was an ability that evolved in Crocodylia, or somewhere close by on the evolutionary tree, in some taxa that was still semi-aquatic.


    Protosuchus richardsoni. An example of an early crocodylomorph.

    Of course it is also possible that crocodyliforme phylogeny is just all f-ed up. With the amount of convergence rampant in that lot, this remains a distinct possibility.

    Either way this is a cool discovery, and one worthy of adding to the crocodylian pages.

    The second paper also comes from the Journal of Experimental Biology. This one involves lizards.

    McElroy, E.J., Hickey, K.L., Reilly, S.M. 2008. The correlated evolution of biomechanics, gait and foraging mode in lizards. J. Exp. Biol. Vol. 211: 1029-1040. doi: 10.1242/jeb.015503


    Foraging mode has molded the evolution of many aspects of lizard biology. From a basic sit-and-wait sprinting feeding strategy, several lizard groups have evolved a wide foraging strategy, slowly moving through the environment using their highly developed chemosensory systems to locate prey. We studied locomotor performance, whole-body mechanics and gaits in a phylogenetic array of lizards that use sit-and-wait and wide-foraging strategies to contrast the functional differences associated with the need for speed vs slow continuous movement during foraging. Using multivariate and phylogenetic comparative analyses we tested for patterns of covariation in gaits and locomotor mechanics in relation to foraging mode. Sit-and-wait species used only fast speeds and trotting gaits coupled with running (bouncing) mechanics. Different wide-foraging species independently evolved slower locomotion with walking (vaulting) mechanics coupled with several different walking gaits, some of which have evolved several times. Most wide foragers retain the running mechanics with trotting gaits observed in sit-and-wait lizards, but some wide foragers have evolved very slow (high duty factor) running mechanics. In addition, three evolutionary reversals back to sit-and-wait foraging are coupled with the loss of walking mechanics. These findings provide strong evidence that foraging mode drives the evolution of biomechanics and gaits in lizards and that there are several ways to evolve slower locomotion. In addition, the different gaits used to walk slowly appear to match the ecological and behavioral challenges of the species that use them. Trotting appears to be a functionally stable strategy in lizards not necessarily related to whole-body mechanics or speed.

    I haven’t had a chance to read much more than what was written already. I do take a bit of offense to the authours referring to scleroglossan foraging technique as “slow,” but what are you going to do?

    I do find it interesting that lizards seem to have lost the ability to “walk” numerous times. That almost seems bizarre. The study points out that ecology produces heavy pressures on lizards in terms of their locomotion type. This is extremely pertinent given how often one hears the old (and wrong!) adage about “reptiles” being incapable of intense aerobic activity.

    According to the above study (among others), it all depends on the animals being tested.

    There we go. Two really cool papers on reptiles, being released in one day.


    Yes, I know. I used jive. I’m sorry.