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Inside fossils

The increasingly widespread use of computed tomography permits detailed analysis of bones of extinct animals

Euparkeria capensis, shown above in an artist’s rendering, was the size of a cat

Desenho Taenadoman, Wikimedia Commons Euparkeria capensis, shown above in an artist’s rendering, was the size of a catDesenho Taenadoman, Wikimedia Commons

Seeing inside an egg was a matter of great concern for paleontologist Sérgio Alex Azevedo, a researcher at the National Museum of the Federal University of Rio de Janeiro (UFRJ) in the early 1990s. At that time he was studying a presumably intact egg from the museum’s collection, laid by an ancestral species of turtle more than 65 million years ago, transformed into solid rock and found in inland Sāo Paulo State. Sawing through the extremely rare artifact to study it was unthinkable. He took an X-ray, but the misshapen blotch on the photographic plate didn’t provide much help. With the help of colleagues, he obtained access to a computed tomography machine, which combines X-ray images of several sections of a body and generates a three-dimensional map of its parts and interior cavities, at the São Lucas Hospital at the Pontifical Catholic University of Rio Grande do Sul (PUC/RS) in Porto Alegre. In the tomography images, it was possible to distinguish the general outlines of the head, back and vertebrae of the embryo, which measured less than five centimeters in length. “I wasn’t convinced of what I was seeing until I showed the images to a radiologist,” Azevedo says. His paper, published in 2000 in Anais da Academia Brasileira de Ciências, was one of the first in Brazil to apply computed tomography to paleontology.

While this technique was still a novelty 20 years ago, even among paleontologists in other countries, today it is more accessible, mainly due to the development of microtomography and the higher resolution of the machines. The images are now generated by X-rays that have greater penetration capability than that of medical X-ray machines, and computers combine hundreds of images. Researchers are able to identify micrometric details inside fossil bones without needing to break them or completely extract them from the block of rock in which they were found. In addition to preserving the fossils, scanning the material generates data that can be used to create three-dimensional models and computer animations, which help researchers to better understand the structure and movements of extinct animals. In Brazil, the machines of this type for use in paleontology number fewer than 10, so researchers must resort to using the ones at institutions in the fields of medicine, engineering, geosciences or physics, since it is very difficult to leave the country with fossils. Brazilian museums and universities are increasingly investing in their own computed microtomography machines despite the cost. The computer software license for the equipment alone can cost about R$50,000.

“Microtomography is still costly, but it has become standard practice in the field,” says paleontologist Gabriela Sobral of the Federal University of Santa Catarina (UFSC). In 2012, while working on her PhD, she used the microtomography machine at the Berlin Museum of Natural History to reconstruct the history of the evolution of the inner ear of archosaurs, a group of animals that includes crocodiles, dinosaurs and the direct descendants of birds—the only non-extinct subgroup of dinosaurs (see Pesquisa FAPESP Issue nº 202). “Before tomography, it was only possible to access internal structures of the skull, such as those of the inner ear, if the fossil was broken,” she says.

The X-ray of the skull shows details of the inner ear cavities and reinforces the hypothesis about its agility

Gabriela Sobral The X-ray of the skull shows details of the inner ear cavities and reinforces the hypothesis about its agilityGabriela Sobral

In an article published in July 2016 in the journal Royal Society Open Science, Sobral and other specialists from Germany, the United Kingdom, the United States and South Africa presented the tomograms of the inner ear of Euparkeria capensis, a cat-sized reptile that became extinct 245 million years ago. The images revealed the shape of the bone cavities that housed the three semi-circular canals of the inner ear—structures related to the animal’s ability to maintain balance while the body is moving.”The results confirmed the hypothesis that Euparkeria was a more active and agile animal than most reptiles of the era.” The researchers suggest that this species, discovered in South Africa in 1913, most closely approximates the common ancestor of all archosaurs. Understanding the anatomy of Euparkeria, however, helps explain how archosaurs were identified as an evolutionarily unique group among the other groups of reptiles.

Sobral explains that operating a microtomography machine is not a trivial process; the researchers at the museum in Berlin spent three years learning to use the machine correctly. “The scanner’s X-ray adjustments have parameters similar to those of a professional camera, such as time of exposure and flash intensity,” she says. Each fossil requires a different analysis,” Azevedo of UFRJ notes. Since 2002, his group has been using the X-ray machines of a private medical clinic and the hospital of Rio de Janeiro State University and microtomography machines from UFRJ and PUC/Rio de Janeiro to study fossil and archeological materials, such as Egyptian mummies (see Pesquisa FAPESP Issue nº 215).

“Students increasingly want to use this technique,” observes Alexander Keller, a paleontologist at the National Museum. Although the apparatus isn’t from the museum itself, one of his master’s students, Arther Blum, used an X-ray machine from the Petrobras Research Center to analyze bone fragments of an abelisaur, a type of dinosaur found in inland São Paulo State that resembles a tyrannosaurus, measuring just three meters in length. The images, published in May 2016 in Cretaceous Research, confirmed that abelisaurs had porous bones, similar to those of birds.

Paleontologia_Info_246237-million-year-old teethmarks
In collaboration with Kellner, biologist Voltaire Paes Neto of the Federal University of Rio Grande do Sul (UFRGS) identified the oldest teethmarks ever recorded. They were left by jawed insects on the bone of an animal from the dicynodont group—herbivores the size of a rhinoceros—237 million years ago. Paes Neto used a tomography apparatus from the Hospital das Clínicas in Porto Alegre.

It took Paes Neto four years to characterize the marks on the fossils, since he found perforations that no one could explain on the bone of an archosaur that he received for cleaning when he arrived at the paleontology laboratory headed by Marina Bento Soares at UFRGS in 2011. Since the 4-millimeter-diameter orifices were perfect, he discarded the possibility that they resulted from some type of bone disease, which would probably not leave such regular marks. He finally concluded that the channels and jaw marks must have been made by insects similar to present-day beetles and termites, which today still feed on bones and decomposing animal remains.

One of the marks, a track left by jaws, has so far been recorded only on bones of cynodonts—animals that gave rise to mammals—in present-day southern Brazil, earning it the name Osteocallis infestans. Insect marks on bones have a scientific name giving the genus and species, which indicate the behavior of the extinct animals that made them. In the geological period known as the Triassic, between 252 million and 201 million years ago, beetles had only begun to diversify, conquer new environments and form a group that numbers over 350,000 species. “I think it’s possible to find similar marks on fossils even older than these,” Kellner says.

“Since three-dimensional images require computers with a large processing capacity, tomography has transformed paleontology—which used to be relatively inexpensive—into an expensive science,” observes Felipe Montefeltro, a paleontologist at São Paulo State University (Unesp) in Ilha Solteira who studies the evolution of the inner ear of crocodiles and has used microtomography machines at research institutions in Canada and the United Kingdom. Similarly, biologist Tiana Kohlsdorf of the Riberão Preto School of Philosophy, Science and Languages and Literature (FCLRP) of the University of São Paulo (USP) analyzes species of present-day reptiles and amphibians using the microtomography machine belonging to the Biosciences Institute (IB) at USP, working with zoologist Gabriel Marroig, also of the IB (see Pesquisa FAPESP Issue nº 230).

Much more than dust
Gabriela Sobral is preparing to begin a postdoctoral project in September 2016, using the microtomography machine at the USP Zoology Museum (MZ-USP), acquired in 2015, which is identical to the one she used in Berlin. She plans to record the stages of development of yacare caiman embryos in collaboration with animal scientist Willer Girardi, using special dyes that make it possible to distinguish muscles and viscera in tomography images. “Microtomography is also being used quite a lot in comparative biology,” says Hussam Zaher, a zoologist specializing in snakes who heads the project to purchase and install the new machine at the MZ. Now, he points out, a researcher interested in learning about the internal structure of a species does not necessarily need to dissect the intact body of an animal preserved in alcohol at the museum. “The technique helps preserve the collections.” Kellner, from UFRJ, underscores that point: “Forget the image of the paleontologist just blowing dust off of fossils. Paleontology is becoming more and more sophisticated as technology enables us to investigate increasingly complex questions about animals that lived millions of years ago.”

Scientific articles
AZEVEDO, S. A. et al. A possible chelonian egg from the Brazilian Late Cretaceous. Anais da Academia Brasileira de Ciências. V. 72, No. 2, p. 187-93. 2000.
SOBRAL, G. et al. New information on the braincase and inner ear of Euparkeria capensis Broom: implications for diapsid and archosaur evolution. Royal Society Open Science. July 13, 2016.
BRUM, A.S. et al. Morphology and internal structure of two new abelisaurid remains (Theropoda, Dinosauria) from the Adamantina Formation (Turonian – Maastrichtian), Bauru Group, Paraná Basin, Brazil. Cretaceous Research. V. 60, p. 287-96. 2016.
PAES NETO, V. D. et al. Oldest evidence of osteophagic behavior by insects from the Triassic of Brazil. Palaeogeography, Palaeoclimatology, Palaeoecology. V. 453, p. 30-41. 2016.