• Tag Archives crocodylians
  • New study shows that gators are one-way breathers too.

    I would be remiss not to talk about this amazing discovery published last week in Science.

    Farmer,C.G. & Sanders,K. 2010. Unidirectional Airflow in the Lungs of Alligators. Science. vol.327:338-340

    The anatomical similarities of alligators and birds has been known for quite some time (at least 100 years), and this anatomical similarity extends down into the lungs. Though alligators lack the pneumatic carvings of the post-cranial skeleton (air sacs) that are seen in birds, saurischian dinosaurs and pterosaurs; their lungs and bronchi do share the same structural features.

    Birds have a unique lung design that allows air to pass through it in a single direction. Unlike mammals, there is no “dead end” to the avian lung. This provides the benefit of a constant supply of highly oxygenated air to the lung tissue; which allows for more efficient gas exchange. Up until last week, this lung design was thought to be a hallmark of birds, and possibly saurischian dinosaurs, and pterosaurs.

    Well it turns out that this unique avian synapomorphy is a heck of a lot older than we thought.

    Dr. Colleen Farmer, and Kent Sanders M.D. of the University of Utah, considered the uncanny anatomical similarities of the avian and crocodylian lung, and wondered if these similarities extended to the physiology too. In other words: If it looks like a unidirectional lung, does it also function like one?

    Farmer & Sanders set to work by removing the lungs of four dead alligators donated to her lab. They pumped air through them, and monitoring the direction in which it traveled (using flowmeters). They then surgically inserted flowmeters into anesthetized alligators, and measured the airflow direction in living animals. Lastly, to drive the point across completely, they filled up an excised lung with fluid that contained fluorescent beads, and proceeded to pump the water in and out. This last test was recorded, and three movies of it, were made available to the public. They can be viewed here. Three was probably overkill though, as once you’ve seen fluorescent beads move one way in a gator lung, you’ve seen them all. : )

    The results showed conclusively that alligator lungs pump air through them in one direction only. The repercussions of this find are actually pretty enormous. For starters, the similarity in anatomy and physiology of avian and crocodylian lungs, suggests that they are homologous. This would mean that both groups inherited these lungs from a common ancestor. This means that it was highly likely that all dinosaurs, pterosaurs, rauisuchians, aetosaurs, phytosaurs and the myriad of other archosaurs that graced this planet some 200 million years ago, housed this particular flow-through style lung.

    It also helps put to rest arguments about air sac functions. It has long been argued that the presence of a unidirectional lung, necessitates the presence of air sacs to “pump the air in.” (air sacs offer zero, or next to zero gas exchange potential, so there is no actual breathing going on in them). A lack of air sacs in ornithischian dinosaurs, has been used to suggest that their pulmonary physiology was more like mammals and lizards, than it was like birds (Ruben et al 1999). Data from previous research (O’Connor & Claessens 2005) has cautioned that the presence of air sacs does not guarantee the existence of a flow through system. These latest data now show us that a flow-through system can, and likely did, evolve without the “need” for an air sac pump.

    CT scan of alligator, with 3D reconstruction of lungs. For more details on what the colours mean, click the picture.

    Exactly how all of this works, is still not understood. The “hepatic piston” diaphragmatic pump of crocodylians is well known, and is likely the ultimate driver of respiration in these animals, but the nuts & bolts of how all this unidirectional flow takes place (the fluid dynamics of the lung) remains a mystery. One question that would be worthy of a follow up study (which the author’s have hinted at doing) is whether, or not a cross-current, or counter-current system (where deoxygenated blood flows perpendicular, or opposite the direction of highly oxygenated air) is present in crocodylians too. A cross-current system is found in birds. Is that unique to them, or was this also a phylogenetic “hand-me-down?” Hopefully now, with this new discovery, future research will be done on the crocodylian lung, to further understand how it actually works.

    Ultimately that is the biggest piece of news to come out of this paper. For well over 100 years, the crocodylian lung was just assumed to be a “dead-end” space that worked in a manner similar to that of mammals. It wasn’t until someone actually thought “what do we really know about this structure” did we find something quite the opposite taking place. This is hardly the first time that this has happened either (for instance). As I have mentioned (ranted/harped on) before, reptiles tend to get the short end of the stick when it comes to a lot of biological and paleontological studies (especially if they involve comparison between broad animal groups [classes]). I’m always amazed (though rarely surprised) when a study that actually looks into commonly held assumptions about these critters, finds said assumptions to be quite off the mark. Here’s hoping that we continue to see future studies like this, go on.

    In the end, all of this brings us closer to the truth about how life really works; which is why we do all of this stuff in the first place.



    Farmer,C.G. & Sanders,K. 2010. Unidirectional Airflow in the Lungs of Alligators. Science. vol.327:338-340

    O’Connor, P.M.& Claessens, A.M. 2005. Basic Avian Pulmonary Design and flow-Through Ventilation in Non-Avian Theropod Dinosaurs. Nature. Vol. 436:253-256.

    Ruben, J.A., Dal Sasso, C., Geist, N.R., Hillenius, W.J., Jones, T.D. 1999. Pulmonary Function and Metabolic Physiology of Theropod Dinosaurs. Science. Vol.283(5401):514-516.

  • Mechanics of bipedalism suggest dinosaurs had to be warm-blooded. Or: Why the aerobic capacity model needs to be retired.

    The old "cold blooded or warm blooded" argument once again rears its ugly head.

    [Editor’s note: A response from the authors can be found here. It answers many of the questions I had about the paper, though I feel the biggest question remains open for debate. I appreciate the authors taking their time to answer my questions, and PLoS ONE for allowing this type of open communication.]

    This post has taken an inordinate amount of time to write up. Mostly because it required finding enough free time to sit down and just type it out. So I apologize ahead of time for bringing up what is obviously old news, but I felt this paper was an important one to talk about, as it relied on a old, erroneous, but very pervasive, popular and rarely questioned hypothesis for how automatic endothermy (mammal and bird-style “warm-bloodedness”) evolved.

    Back in November, a paper was published in the online journal: PLoS ONE. That paper was:

    Pontzer, H., Allen, V. & Hutchinson, J.R. 2009. Biomechanics of Running Indicates Endothermy in Bipedal Dinosaurs. PLoS ONE.Vol 4(11): e7783.

    Using muscle force data for the hindlimbs of theropods, and applying it to a model based on Pontzer (2005, 2007), the authors were able to ascertain the approximate aerobic requirements needed for large bipedal theropods to move around. Their conclusion was that all but the smallest taxa had to have been automatic endotherms (i.e. warm-blooded).

    Time to stop the ride and take a closer look at what is going on here.

    In 2004, John Hutchinson – of the Royal Veterinary College, London UK – performed a mathematical study of bipedal running in extant taxa. He used inverse dynamics methods to estimate the amount of muscle that would be required for an animal to run bipedally. He then tested his models on extant animals (Basiliscus, Iguana, Alligator, Homo, Macropus, Eudromia, Gallus, Dromaius, Meleagris, and Struthio). The predictive capacity of his model proved to be remarkably substantial and stable (Hutchinson 2004a). A follow up paper in the same issue (Hutchinson 2004b) used this model to predict bipedal running ability in extinct taxa (Compsognathus, Coelophysis, Velociraptor, Dilophosaurus, Allosaurus, Tyrannosaurus and Dinornis). Results from this study echoed previous studies on the running ability of Tyrannosaurus rex (Hutchinson & Garcia 2002), as well as provided data on the speed and agility of other theropod taxa.

    The difference between effective limb length and total limb length in the leg of Tyrannosaurus rex

    Meanwhile in 2005, Herman Pontzer – of Washington University in St. Louis, Missouri – did a series of experiments to determine what was ultimately responsible for the cost of transport in animals. To put it another way: Pontzer was searching for the most expensive thing animals have to pay for in order to move around. One might intuitively assume that mass is the ultimate cost of transport. The bigger one gets, the more energy it requires to move a given unit of mass, a certain distance. However experiments on animals found the opposite to be the case. It actually turns out that being bigger makes one “cheaper” to move. So then what is going on here?

    Pontzer tested a variety of options for what could be happening; from extra mass, to longer strides. In the end Pontzer found that the effective limb length of animals, was ultimately the limiting factor in their locomotion. Effective limb length differs from the entirety of the limb. Humans are unique in that our graviportal stance has us using almost our entire hindlimbs. Most animals, however, use a more crouched posture that shrinks the overall excursion distance of the hindlimb (or the forelimb). By taking this into account Pontzer was able to find the one trait that seemed to track the best with cost of transport in animals over a wide taxonomic range (essentially: arthropods – birds).

    This latest study combines these two technique in order to ascertain the minimum (or approx minimum) oxygen requirements bipedal dinosaurs would need in order to walk, or run.

    As with the previous papers, the biomechanical modeling and mathematics are elegant and robust. However, this paper is not without its flaws. For instance in the paper the authors mention:

    We focused on bipedal species, because issues of weight distribution between fore and hindlimbs make biomechanical analysis of extinct quadrupeds more difficult and speculative.

    Yet this did not stop the authors from applying their work on bipeds, to predicting the maximum oxygen consumption of quadrupedal iguanas and alligators. No justification is ever really given for why the authors chose to do this. Making things even more confusing, just a few sentences later, it is mentioned (ref #s removed to avoid confusion):

    Additionally, predicting total muscle volumes solely from hindlimb data for the extant quadrupeds simply assumes that the fore and hindlimbs are acting with similar mechanical advantage, activating similar volumes of muscle to produce one Newton of GRF. This assumption is supported by force-plate studies in other quadrupeds (dogs and quadrupedal chimpanzees)

    The force plate work cited is for quadrupedal mammals. However, mammals are not reptiles. As Nicholas Hotton III once mentioned (1994), what works for mammals, does not necessarily work for reptiles. This is especially so for locomotion.

    In many reptiles (including the taxa used in this study) the fore and hindlimbs are subequal in length; with the hindlimbs being noticeably longer and larger. Most of the propulsive power in these reptiles comes from the hindlimbs (which have the advantage of having a large tail with which to lay their powerful leg retractor on). The result is that – unlike mammals – many reptiles are “rear wheel drive.”

    The last problem is by far the largest, and ultimately proves fatal to the overall conclusions of the paper. The authors operated under the assumptions of the aerobic capacity model for the evolution of automatic endothermy.

    It is here that we come to the crux of the problem, and the main subject of this post.

    Continue reading  Post ID 548

  • Two new paleo-herps illustrate the problems of a persistent reptile myth.


    Titanoboa picture by the paper’s co-author: Jason Bourque

    I was trying to wait until I could nab the papers for these guys, but since Geology does not feel like updating their site, I’m going to have to move without them.

    Reported on 1st February, John Tarduno of the University of Rochester, and his team have discovered an alleged freshwater turtle fossil in the Canadian Arctic. The animal – given the gorgeous name of Aurorachelys (“Dawn turtle” or “Arctic turtle” as the case may be) – was found in strata dating back to the late Cretaceous. According to the press release (which is all I have to go on at the moment), the presence of the turtle has lead Tarduno and his colleagues to suggest the presence of an immense halocline in the paleo-arctic ocean.? According to Tarduno:

    …the Arctic Ocean was more separated from the rest of the world’s oceans at that time, reducing circulation. Numerous rivers from the adjacent continents would have poured fresh water into the sea. Since fresh water is lighter than saltwater, Tarduno thinks it may have rested on top, allowing a freshwater animal such as the aurora turtle to migrate with relative ease.

    The other major discovery came out today in Nature.? Researcher John Jason Head, and colleagues have discovered the world’s largest snake. The new snake has been dubbed: Titanoboa cerrejonensis, and it has been estimated to grow to a whopping 13 meters in length (43ft) and could have weighed as much as 1,135kg (2,500lbs).? The fact that this immense animal even existed, is amazing enough, but the researchers took their find a little further.

    Since snakes are poikilotherms that, unlike humans, need heat from their environment to power their metabolism, the researchers suggest that at the time the region would have had to be 30 to 34 degrees Celsius for the snake to have survived. Most large snakes alive today live in the South American and southeast Asian tropics, where the high temperatures allow them to grow to impressive sizes.

    This is where I have my problems. First for Aurorachelys; how are the researchers determining that this animal was a freshwater turtle? As I mentioned prior, I have not had a chance to read either of these papers yet, but just off the top of my head, I can’t think of any specific osteological trait that can be used to determine whether an animal is capable of salt-excretion (i.e. marine). Edit: See Nick’s comment for a list of papers on osteological correlates to salt excretion. This is what I get for posting something right before bed. 🙂? Are the researchers, instead, using the extant phylogenetic bracketing method (EPB), and figuring that Aurorachelys was a freshwater inhabitant, based of critters it was most closely related to?

    If it’s the latter, then I have reason to pause. Uniformitarianism, or the assumption that present day processes are likely the same now as they were in the past, is a very useful tool.? It’s especially useful in the realm of geology, where rock cycles are unlikely to have changed.? In biology, too, uniformitarianism can be helpful for studying processes like evolution and ecological partitioning. However a uniformitarian view of life is much less sturdy when dealing with more labile things like behaviour, or the evolution of a specific trait. If the researchers are assuming that Aurorachelys was a freshwater animal based off of EPB, then I would have to assume that salt excreting glands must be a hard thing to evolve. But are they? I’m not sure we have an answer there.

    Another issue this raises is, if Aurorachelys was a freshwater turtle that was cast adrift, then what are the chances that it would have been fossilized in the first place. Fossilization is a one in a million process as it is. In general, parsimony tells us that unique individuals / behaviours, are unlikely to be preserved. When we find a giant representative of a species, it probably was not unique, but rather a high end average animal. So too, it would seem, with Aurorachelys.? It is highly unlikely that this turtle was caught out of its element.? This may mean that this large halocline was present and that freshwater turtles were undertaking this migration rather often, or it means that the ability to remove excess salt from the body, was present in this species. Interestingly, a similar situation exists for the giant alligatoroid Deinosuchus. Salt excreting glands appear to be a unique adaptation of crocodyloids,? and not their alligatorish kin. Yet Deinosuchus founds some way to cross the saltwater filled Western Interior Seaway. Again, how hard is it to evolve salt removing glands?

    The case of Titanoboa cerrejonensis is much the same. In this case, it appears to be a clear case of the erroneous belief that reptiles make good ecological thermometers; despite the presence of leatherbacks (Dermochelys coriacea) in the freezing Northern Atlantic, or the small Chinese alligator (Alligator sinensis) living in a part of China that readily freeze, or even the relatively tiny Andean lizards ((Liolaemus multiformis), who live in parts of the Andes mountain range that experience an average daytime temperature of 10?C (50?F) , all while maintaining body temperatures of 35?C (95?F).? Both the Aurorachelys and Titanoboa cerrejonensis papers appear to make assumptions that seem questionable given the evidence.? However I will reserve final judgement until I’ve had a chance to read the respective papers. Hopefully there is some hard evidence to back up the assertions that have been proposed.

    Photo by Ray Carson

    Photo by Ray Carson

    Until then, check out the comparison on the vertebrae of a large Eunectes murinus (green anaconda) and Titanoboa cerrejonensis. This beast was huge.


    Head, J.J.,Bloch, J.I., Hastings, A.K., Bourque, J.R., Cadena, E.A., Herrera, F.A., Polly, D.P., Jaramillo, C.A. 2009.
         Giant Boid Snake from the Palaeocene Neotropics Reveals Hotter Past Equatorial Temperatures. Nature. Vol 457 :715-717
    Vandermark, D., Tarduno, J.A., Brinkman, D.B., Cottrell, R.D., Mason, S. 2009. New Late Cretaceous Macrobaenid Turtle with Asian
        ?Affinities from the High Canadian Arctic: Dispersal via Ice-Free Polar Routes.Stephanie Mason. Geology, Vol 37.

  • The return of fruit eating crocodylians.

    Back in 2002, a short paper came out that commented on the observation that captive caimans would eat fruit left in their cage. When I initially read the paper, I found it interesting. In the end, though, I assumed this to just be a fairly anomalous incident.

    Now Darren Naish of Tet Zoo has followed up on this story with further evidence of frugivory in crocodylians.

    As one can see, this observation has been filmed at least once.

    So does this mean that crocodylians are not as completely carnivorous as once thought? It’s hard to say. All observations made so far have been from alligatorids (alligators and caimans). This might be an apomorphic trait to this group. Only more observations will say for sure.

    Another option that Darren pointed out, is that this was a learned trait of these captive animals. In each case, observed animals were found to be sharing their enclosures with herbivorous animals (usually tortoises). This type of operant learning is rather rare, and would be amazing if found to be true.

    However, as evidenced by the comments of St. Augustine Alligator Farm park director, John Brueggen, fruit eating has been observed in wild animals too; so this is not simply a case of bored captives.

    Whatever the case, these observations do illustrate just how adaptaptable crocodylians are as a group.


  • Study shows shunting in crocs is all about the acid

    Baby _C.palustris_ says:

    Yesterday a new study was released in the journal of Physiological and Biochemical Zoology. Researchers from the University of Utah, studied the effects of the well documented right-to-left shunt in crocodylians.Okay, let’s get the exposition out of the way first.

    Mammals and birds are both characterized by a 4 chambered heart. This heart allows the complete separation of oxygenated and deoxygenated blood streams. Less publicized, but equally as important, this separation also allows for a pressure differential to exist between the two ventricular chambers. That way the right – pulmonary side – of the heart can pump deoxygenated blood at low pressure to the delicate walls of the alveoli in the lungs, while the left – systemic side – of the heart, can pump oxygenated blood at much higher pressure (~7 times higher) to the entire body.

    Reptiles and amphibians differ from mammals and birds, in that they have a heart divided into 3 chambers (two atria, one ventricle). This allows for mixing of oxygenated and deoxygenated blood, which reduces aerobic efficiency.

    Please note the qualifier: aerobic.

    Now, as is often the case with herps, this is a rather broad generalization. The hearts of all reptiles, show various degrees of ventricular separation. Also, for all extant reptiles, there are physiological/haemodynamic mechanisms in place that reduce the amount of blood mixing. Meanwhile, some lizards (e.g. varanids), and snakes (e.g. pythons) have such a large muscular septum near the middle of their ventricle, that it actually completely separates the ventricle during the contractile phase (ventricular systole). Thus making varanids and various snakes, functionally four chambered. These reptiles are capable of producing pressures on their systemic side, that are 7 times higher than the pressures in their pulmonary side. In other words, their functional four chambered hearts allow for pressure differentials that are on par with mammals.

    Then there are the crocodylians. Crocs have the most complicated heart of any vertebrate. They are the only reptiles that have evolved a complete seperation of their ventricles. They are anatomically four chambered. Yet, they also retain the ability to mix their oxygenated and deoxygenated blood supplies. This is accomplished through a small connection between the right and left aortic arches (which come out of each respective ventricle). This connection is referred to as the foramen of Panizza. Making things more interesting still, croc hearts also feature a cog toothed valve that can completely block the flow of blood to the lungs, thus turning their hearts into a double pump systemic circuit.


    So now we know the how it works, the question we want answered next is: why did it evolve in the first place? The classic “orthodox” explanation has been that all of these traits evolved to allow formerly land dwelling crocodyliformes stay underwater for long periods of time. A four chambered heart is great for aerobic endurance, but pretty darn useless for an animal that spends most of its time holding its breath. In that arena, a three chambered heart is a more efficient system. By mixing oxygenated and deoxygenated blood together, crocodylians and other reptiles are able to siphon as much oxygen as possible from their blood, and thus stay underwater longer.

    As I said, that was the old explanation. Now there is a new one:

    Farmer, C.G., Uriona, T.J., Olsen, D.B., Steenblick, M., Sanders, K. The Right-to-left Shunt of Crocodilians Serves Digestion. Physiological and Biochemical Zoology. Vol. 81(2): 125-137. doi: 10.1086/524150

    Farmer et al studied several groups of juvenile American alligators (Alligator mississippiensis). Each group underwent surgeries of various sorts to measure, and/or block the right to left shunt. The working hypothesis was that crocodylians use their right to left shunt, to serve digestion, by providing a greater reservoir of hydrogen ions (left over from the retention of CO2) for stomach acid secretion. It was suspected that if this was true, then one should see a greater degree of right to left shunting in animals that have just eaten.

    So what did they find?

    Well, for one, they found that juvenile alligators have a preferred postprandial body temperature of ~30?C, and will maintain that temperature to within .03?C. That’s a degree of temperature control worthy of any mammal, or bird.

    Another thing they learned was that alligators that were allowed to stay at that temperature, were a real bugger to keep under control. So they had to drop the temp down 3 degrees, to 27?C instead.

    Farmer et al learned that gastric acid secretion is temperature sensitive. Alligators produced greater quantities of gastric acid at 27?C, than at 19?C.

    Oh yeah, they also learned that crocodylians produced a tonne of acid. At maximum secretion, acid production was an order of magnitude greater than that measured in any mammal, or bird. For those keeping tally at home; that’s 10 times greater.

    The authours final observations warrant some thoughts.

    That the left aorta, which arises from the right – pulmonary – ventricle, is the main blood delivery route for the digestive system. During right to left shunting, oxygenated blood from the left ventricle, gets shoved to the left aorta, and down to the digestive system. That this coincides with increased gastric acid secretion is telling, and strongly suggestive as to the role of the R-L shunt.

    Yet R-L shunting also occurs during dives, and this is still the best explanation for the cog toothed valve. If the crocodylian heart really was specifically developed to increase digestion, then why block the path to the lungs at all? This study shows that the gastrointestinal system benefits from increased oxygen to these tissues. So why block the lungs, if one is trying to keep them oxygenated. Unfortunately the paper doesn’t really mention whether, or not the cog toothed valve was activated during this process. Personally, I don’t remember reading any case of the R-L shunt being used in crocs, without incorporating the cog tooth valve, so…

    I felt that the authours put too much emphasis on endothermy vs. ectothermy. Their final observations involved a blanket statement regarding the R-L shunt in all reptiles. As I mentioned above, crocodylians are unique in their cardiovascular anatomy and physiology. They are also renowned for their very acidic stomach acid. It would seem more parsimonious to say that the R-L shunt in crocodylians, plays a large role in gastric acid secretion for these animals only; and wait for subsequent studies in other reptiles before saying this is true for the whole class.

    Okay, so maybe their acid isn’t quite this strong, but you get the point.

    Lastly (I know, I know, this just keeps going), I found it interesting that they studied the effects of gastric acid secretion on the vertebra of a cow. This vert took over 2 weeks to digest! While I can accept that this was partly due to the size of the object, and it’s material (bone is tough, after all.), but 2 weeks! Even at the lower temperature that the experimental group was kept at, it seems hard to believe. The authours gave no mention of gizzard usage in these animals, which suggests that the animals were never given access to gastroliths, which should have sped up the digestive process considerably.

    Either way, the study was interesting. I just think that the authours took their final results a little too far.

    ~ Jura