Palaeontology is a Real Science Part 2: Using CT Scans

This week, we'll continue on with our theme of "palaeontology is a real science" by talking about how palaeontologists use computed tomography (CT) to view and analyse fossils. Many of you have probably heard of CT scans in terms of medicine. The basis of this technique is that it uses x-rays to produce cross-sectional tomographic images ('slices') of the area of the body in question. These slices can then be studied for abnormalities such as tumours, as it can show some soft tissue as well. If several x-rays are taken around an axis of rotation, the slices can be put together to form a 3-dimensional model of the structure in question, showing the internal and external structure. 

Example of CT slices from the base of the skull (top left) to the top of the head (top right)

In palaeontology, CT scans can be very useful. First of all, they allow analysis of a bone if it is still in the rock. In some cases, a bone cannot be completely removed from the rock because of preservation, or in cases where the original geometry of the rock needs to be retained like an egg or several specimens in a single section that show interesting behaviour. In these cases, CT can be very useful to see the full structure of the bone, and what else is in the rock. 

Example of a dinosaur egg as a whole, and showing the internal structure after CT scanning (Balanoff et al. 2008)

In addition to allowing you to see the full external structure, it also allows visualisation of the internal structure of the bone. One especially cool aspect of CT scans is that it allows for the reconstruction of soft tissue, such as the brain. Because brains are incased in a braincase of bone, CT scans of the braincase can show the shape and structure of brains from extinct animals. This has been done in a number of fossils, including dinosaurs (e.g. Spinophorosaurus) and pterosaurs (e.g. Anhanguera). There is a palaeontology lab in the USA run by Dr. Larry Witmer that does many of these studies, and has produced endocasts (the casts made from the braincase) for several extinct animals. 

Example of a braincase from the sauropod dinosaur Spinophorosaurus  from Knoll et al. 2012. To see a 3D animation, go here

Related to reconstructing brain cases, CT scans can allow us to see structures within the bones like replacement teeth, or the roots of teeth. This can help to determine things like tooth replacement patterns in extinct animals. 

Example of the teeth and bone from the right dentary (lower jaw) of the small dinosaur Fruitadens from Butler et al. 2012

The third main way that CT scans are used in palaeontology is to create a 3D model of the skull or bones, often using a relatively new strategy of analysing fossils called Finite Element Analysis (FEA). Now for any engineers out there, you will know that FEA has been around for a long time. It's used by engineers to determine areas of high stress and strain in things like bridges and buildings. This method can also be used in fossils to see where the areas of high stress and strain in a dinosaur's skull might be. This method was used by Arbour and Currie (2012) to determine different taphonomic (what happens to an animal after it dies and becomes fossilised) pressures necessary to cause the deformation seen in an anylosaur dinosaur. The models created from CT scans can also be used to determine muscle attachment points and therefore aid in muscle reconstruction (see our previous post on muscle reconstruction in fossils). 

Finite Element Analysis on the skull of the ankylosaur dinosaur Minotaurasaurus showing areas of low (blue) and high (red/white) stress (Arbour and Currie 2012).

Hopefully you now understand a very useful piece of technology for palaeontologists, and how we can better understand fossils using CT scans. 

Links:
If you're interested in learning more about CT scans and palaeontology, check out the University of Bristol page on CT in palaeontology.
For more cool stuff from the Witmer Lab, check out their website, especially looking at projects and 3D visualization.

Open Access (freely accessible) References:
Arbour, V. M., and Currie, P. J. (2012) Analyzing taphonomic deformation of ankylosaur skulls using retrodeformation and Finite Element Analysis. PloS One e39323.
Butler, R. J. et al. (2012) Anatomy and cranial functional morphology of the small-bodied dinosaur Fruitadens haagarorum from the Upper Jurassic of the USA. PloS One e31556.
Knoll, F., et al. (2012) The braincase of the basal sauropod dinosaur Spinophorosaurus and 3D reconstructions of the cranial endocast and inner ear. PloS One e30060.

References (not Open Access):
Balanoff A. M., et al. (2008) Digital preparation of a probable neoceratopsian preserved within an egg, with comments on microstructural anatomy of ornithischian eggshells. Naturwissenschaften 95: 493-500.

Palaeontology is Real Science Part 1: Muscle reconstruction

This week's Mesozoic Mondays post is going to be a bit different from usual. Since working at Jurassic Forest, I've been amazed by how many people don't consider palaeontology to be a real science, and how surprised they are to see a speaker talk about their research. In particular, I remember one set of parents who were engineers, that came to watch a particularly technical talk on theropod tail muscles. After the talk, the father said "I had no idea so much science was involved in palaeontology"! In response to this, I'm going to do a few posts based on this, showing some of the different scientific techniques palaeontologists use in their research. It's not all digging and assembling skeletons you know! 

To continue with the topic mentioned above, I'm going to talk a bit about muscular reconstruction first. It may sound trivial, but reconstructing fossil muscles is extremely important to understand how an extinct animal was able to move, and it's also very difficult to do correctly. There are two important pieces of information needed to reconstruct fossil muscles. The first, is something called the extant phylogenetic bracket (Witmer 1995). To first understand this, you must understand phylogenies. A phylogeny is something like an evolutionary family tree that shows how different groups of animals are related to each other, based on different features that the animals share, or new derived features. By using living animals (extant) that 'bracket' the extinct form in question on either side, an idea of how the muscle may have appeared in the bracketed animal may be possible. This is by assuming the theory of parsimony, that it is more likely that if something is present before and after, it is most likely also present in the evolutionary middle, rather than losing the feature and re-evolving it. I know, it's a bit complicated! For a good explanation of phylogenetic bracketing, check out the Wikipedia page, which is quite good and full of examples. One example is that theropod dinosaurs are bracketed between crocodiles, their closest living relatives that evolved before dinosaurs, and birds, which of course evolved from dinosaurs. Anything present in both crocodiles and birds was likely present in theropods, whereas something that is not present in either probably wasn't in theropods.

Example of a cladogram showing the phylogenetic relationships of modern reptiles (including birds).  An example of extant phylogenetic bracketing is also seen. The four-chambered heart is present in both crocodilians and birds, and therefore most likely present in dinosaurs. Image from Palaeos.com

Now, once you know what the animals look like that evolved before and after the animal in question, the next key is to look at muscle scars. For this, I'm going to use a paper by Persons and Currie (2011a) from the University of Alberta as an example, as it is open access, so anyone can download it if they would like. By looking at the caudal (tail) vertebrae of the theropod dinosaurs Carnotaurus and Aucosaurus, muscle attachment sites can be viewed. By combining muscle attachment sites with the phylogenetic bracket, it's possible to determine what muscles attach where, and possibly how big they were. Persons and Currie (2011b) used a combination of both methods by dissecting modern caimans to understand their musculature in order to reconstruct the tail musculature of Tyrannosaurus. Although still controversial, this new muscle reconstruction suggested that Tyrannosaurus was a pretty fast guy, using large muscles that ran from its tail to its leg to run. Pretty cool stuff coming out of the University of Alberta! You may have guessed by now that it was actually a talk by Scott Persons that spurned the "paleontology is a real science" discussion. 

Caudal vertebra of Aucosaurus showing a sequence of muscle scars from the ischiocaudalis and caudofemoralis muscles. (Persons and Currie 2011a)

That was an introduction into how palaeontologists can reconstruct muscles from bones, and hopefully it taught you something you didn't know! Muscle reconstruction is really quite important in order to understand some aspects of behaviour and locomotion, as seen in the study of Tyrannosaurus. If it was really as fast as suggested, he was definitely an active hunter rather than a scavenger like some people suggest. Of course, this isn't an easy thing to do since most fossils are incomplete, and it can be difficult to see things like muscle scars. It can also be difficult to determine the phylogenetic position of an extinct animal, and changing the position can greatly change the reconstruction. That being said, this is a very common method used in palaeontology, and it's very important to understand the anatomy and muscular systems of living animals in order to better understand extinct animals!

References:
a Persons, W.S., and Currie, P.J. 2011. Dinosaur speed demon: the caudal musculature of Carnotaurus sastrei and implications for the evolution of South American abelisaurids. PlosOne 6: e25763. --> Freely available online, so take a look if you're interested!
b Persons, W.S., and Currie, P.J. 2011. The tail of Tyrannosaurus: reassessing the size and locomotive importance of the M. caudofemoralis in non-avian theropods. The Anatomical Record 294: 1442-1461. --> unfortunately not open access.
Witmer, L.M. 1995. The extant phylogenetic bracket and the importance of reconstructing soft tissues in fossils. In: Thomason, J (ed.) Functional Morphology in Vertebrate Paleontology. pp. 19-33. Cambridge University Press.

Dimetrodon

Dimetrodon is always in books on dinosaurs, often alongside dinosaurs and pterosaurs, as a big-scaly sail-backed reptile. Unfortunately, these books usually leave out an important fact: that Dimetrodon, along with pterosaurs, is not a dinosaur. If you've been out to Jurassic Forest and seen Dimetrodon, you likely already knew this. However, many of you were probably quite surprised to hear it. 

In order to first explain why our favourite sail-backed reptile is not a dinosaur, let's bring us back to one of the very first Mesozoic Mondays post on What is a dinosaur? Fortunately, this explanation is shorter than why pterosaurs were not dinosaurs. Remember back in the beginning when I was talking about holes in the back of the skull? The temporal fenestrae as we call them? Well if you remember, dinosaurs belonged to the group called the diapsids, which have two holes, one above and one below. Dimetrodon, on the other hand,belongs to the group called the synapsids, which have only one hole in the back of their skull. This is a very fundamental difference, and something that developed quite early in the evolution of tetrapods. 

Skull of Dimetrodon. The first hole on the left is the temporal fenestra, which distinguishes it as a synapsid.

Another problem with the books showing Dimetrodon walking alongside dinosaurs, is that they didn't actually live at the same time. Dimetrodon lived during the Permian Period, approximately 299-270 million years ago. It went extinct long before the first dinosaurs ever appeared, about 40 million years later. In fact, Dimetrodon is what some people would call a "mammal-like reptile", as mammals evolved from reptiles similar to it. This means that Dimetrodon is actually more closely related to us than it is to dinosaurs. Who would have thought??

Dinosaurs definitely weren't the only formidable predators around in the past. Long before the dinosaurs, Dimetrodon was terrorising the small animals with its long caniniform (canine-like) front teeth, and remarkably strong bite force. At up to 5 and half metres long and 250 kg, he could pack a punch. The sail-like structure on it's back also helped it be a faster predator. As Dimetrodon was an ectotherm, meaning its body temperature depended on its surroundings and could not be controlled internally, a way of helping to warm it up and cool it down is very handy. The sail on its back was actually formed by a highly vascularised (so it had lots of blood running through it) membrane stretched between elongated spines of its vertebrae. This membrane acted as a thermoregulator, increasing its temperature quickly when it went into the sun, and decreasing quickly in the shade. This allowed some control over its body temperature, which means it could be more active when it wanted to be. Reptiles are very slow and sluggish when it gets too cold, and this is a way of adapting to that. 

Dimetrodon. Image from Wikimedia Commons user DiBgd 

Dimetrodon fossils are most often found in the USA, but have also been found in Germany. These fossils come from areas that were wetlands during the Permian, suggesting it lived in something very much like Jurassic Forest, with lots of standing water and vegetation (albeit different vegetation). Those of you that have been to Jurassic Forest will know that our Dimetrodon hangs out by our small pond, surveying the water, much like he would have in the Permian, while hunting for fish! 

Palaeontology in Alberta

As most of you will already know, Alberta is a hotspot for palaeontology and fossils. This week, I'll be outlying a few of the places in Alberta that fossils can be found, as well as the kinds of fossils. Some of these I'm sure you will already be aware of, while some of them will come as quite a surprise! 

Dinosaurs

Of course, one of the most common group of fossils found in Alberta are dinosaurs. There are several localities in Alberta that have dinosaur fossils, and many different kinds of dinosaurs too. 

Dinosaur Provincial Park 

This is likely the most obvious place in Alberta to find dinosaur fossils. Dinosaur Provincial Park is located southwest of Drumheller, meaning that the Royal Tyrrell Museum of Palaeontology is not actually located within the park. Dinosaur Prov. Park is where palaeontologists like Dr. Phil Currie go each summer to find new bones. Individual bones are found, as well as nearly complete skeletons, and even large bonebeds. For example, there is a large Styracosaurus bonebed found here that provides evidence that these large herbivores moved in herds, like modern herbivores. 

Styracosaurus, a common ceratopsian found in Dinosaur Provincial Park

The fossils in Dinosaur Provincial Park are from the Late Cretaceous, approximately 77-74 million years ago. There are three terrestrial rock formations within the park, with the Foremost Formation being the oldest, then the Oldman Formation, and finally the Dinosaur Park Formation, while the youngest formation is the Bearpaw Formation, which is marine, and therefore does not have dinosaurs. Now bear with me, because there are a lot of examples from these formations. Found in all three terrestrial formations are animals like mammals (Pediomys), turtles (Adocus, Aspideretes), and crocodile relatives (Champsosaurus, Leidyosuchus). Dinosaurs commonly found in both the Dinosaur Park Formation and Oldman include Centrosaurus, Corythosaurus, Gryposaurus, Stegoceras, Gorgosaurus, Dromaeosaurus, Saurornitholestes, and Troodon. Many dinosaurs are found solely in the Dinosaur Park Formation, like Styracosaurus, Lambeosaurus, Edmontonia, Daspletosaurus, and Ornithomimus. There are also amphibians, birds, marine reptiles, the only pterosaur remains in Alberta (Quetzalcoatlus) and many more found here. Also interesting is that dinosaur egg shells have been within these formations. The list goes on and on... this is truly one of the best places in the world for dinosaur fossils and fossils of this age. The Bearpaw formation will be discussed later, with respect to non-dinosaur sites. 

The badlands of Dinosaur Provincial Park, showing the high amounts of erosion that make it such a good place to find fossils. Photo from Wikimedia Commons user Scorpion0422).

Horseshoe Canyon Formation

The Horseshoe Canyon Formation has outcrops in many areas of the province, including many outcrops in and near Drumheller, along the Red Deer River valley, and even within the city of Edmonton. Dinosaurs found in this formation include Daspletosaurus, Ornithomimus, Saurornitholestes, Troodon, Ankylosaurus, Euoplocephalus, Saurolophus, Pachyrhinosaurus, and at more than one location within the city of Edmonton, Edmontosaurus and Albertosaurus. There are also amphibians, mammals, and crocodile relatives found here. 

Some visible bones from the Edmontosaurus bonebed in Edmonton. Photograph by the author.

Grande Prairie Region

Although the area of Grande Prairie is not as productive for fossils as southern Alberta, there are two Pachyrhinosaurus bonebeds that have produced many fossils, as well as fossils from Saurornitholestes, Troodon, and some hadrosaurs. More finds in recent years have lead to the Pipestone Creek Dinosaur Initiative, and more recently, the Philip J. Currie Dinosaur Museum, which will hopefully lead to a new dinosaur museum in northern Alberta. You may have heard about these areas in the news lately, because unfortunately, someone has been vandalising fossil sites in this region and destroying fossils destined for the new museum. 

Other Sites

Other areas in Alberta that have provided dinosaur fossils include Lundebreck Falls, where the famous T. rex skeleton 'Black Beauty' is from; Dry Island Buffalo Jump Provincial Park, where an Albertosaurus bonebed was found; and Warner, Alberta, where 10 dinosaur eggs (possibly from Hypacrosaurus) were found. Another very interesting dinosaur found came from the Suncor Mine near Fort McMurray a few years ago, when a 3D preserved skeleton of an ankylosaur was found. This is especially interesting because these sediments are marine, suggesting the animal died, then was swept out to sea, where it was buried and preserved. 

Cast of 'Black Beauty' at the Royal Tyrrell Museum of Palaeontology. Photo from Flickr user subarcticmike.

Non-Dinosaur Sites

Although I've mainly focused on places were dinosaurs have been found, Alberta is also home to many non-dinosaur fossils. For example, marine reptiles are often found in Alberta, such as Albertonectes, which was found near Lethbridge. Ammolite, which is the shiny remains of fossilised ammonites, is mined near Lethbridge as well. Although ammolite in itself is a fossil, marine reptiles can also be found here, and a mosasaur was found in the mine earlier this year. Marine reptiles can also be found in the oil sands and regions in northern Alberta. There are also isolated cases of mammals, amphibians, reptiles, insects and more throughout the provinces, but it would take me forever to list them! 

Albertonectes fossil from Kubo et al. (2012). The neck is to the right (you can see it is broken), while the tail is to the left. 

References and links:

Kubo et al. (2012) Albertonectes vanderveldei, a new elasmosaur (Reptilia, Sauropterygia) from the Upper Cretaceous of Alberta. Journal of Vertebrate Paleontology 32: 557-572.

The Paleobiology Database

Deep Alberta - A great book by John Acorn for anyone interested in dinosaurs in Alberta!