Signs of Injury and Disease in Jurassic Marine Reptiles

Palaeoepidemiology in extinct vertebrate populations: factors influencing skeletal health in Jurassic marine reptiles

Judith M. Pardo-Pérez, Benjamin Kear, and Erin E. Maxwell

Summarized by: Kailey McCain

What data were used? Researchers wanted to create a baseline for measuring overall health of large marine animals in the Jurassic period. Given the prevalence of Ichthyosauria, a large extinct marine reptile, researchers chose to survey five different species/taxa (i.e., biological classification of organisms) that lived at different ocean depths and varied in size: Hauffiopteryx, Stenopterygius, Suevoleviathan, Eurhinosaurus, and Temnodontosaurus.

A total 236 specimens were collected at a Lagerstätte deposit in Germany, which is a site with exceptional (in quantity or quality) fossil preservation.

Figure 1: This image represents four examples of the skeletal pathologies found by researchers. (a) shows stiffness in the femur and fibula (limb bones). (b) shows stiffness in the spinal column. (c) shows a fracture in the gastralium, which provided support in the abdomen. (d) shows a fracture in the rib cage.

Methods: The 236 specimens were classified by species, and then further classified by age range (i.e., juvenile, young adult, adult). Researchers began studying the fossils for signs of trauma that could have resulted from injury or skeletal diseases (pathologies). Due to the large availability of the Stenopterygius specimens, researchers dated and grouped them into three categories regarding the Toarcian Oceanic Anoxic Event (T-OAE). This was a time in the Jurassic Period when the oxygen levels were depleted and toxic greenhouse gases (e.g., carbon dioxide and hydrogen sulfide) became the major component of the atmosphere; the specimens were grouped as before T-OAE, during  T-OAE, and after T-OAE. The purpose behind comparing pathological data to the T-OAE is to determine if the depletion of oxygen had any significant effect on marine health.

All of the data was inputted into a statistical software, R, to determine any significant correlations and variables. 

Results: The data collected showed that trauma associated with healing was the most common pathology recorded; however, there was not a skeletal region significantly affected more than the others. These commonalities were shared by all five taxa of ichthyosaurs . Additionally, when comparing the overall size of the specimens and percentage of pathologies found, it was determined that the large species were approximately 2.4 times more likely to show signs of trauma and disease. This correlation was also found to be true when looking at the developmental data collected for Stenopteryguis; it was concluded that the adults were 4 times more likely to have signs of disease or trauma than the juvenile specimens.Regarding the data collected for the Toarcian Oceanic Anoxic Event , researchers could not find any significant data that could correlate an increase in pathologies due to the depletion of oxygen.

Figure 2: This image shows a fully preserved fossilized ichthyosaur, Stenopterygius .

Why is this study important? This study showed the differences in skeletal pathologies present in a diverse set of marine reptiles. By differing in size, age, time, and ocean depth, researchers were able to obtain an overall survey of health and easily compare the pathology data to other ecological conditions (e.g., climate change).

The big picture: The research collected in this study provided a baseline for variables that affected the skeletal health of Jurassic marine reptiles. The data supporting the correlations between size and age range of different taxa within the extinct Ichthyosauria can be compared to other extant (i.e., living) reptiles to provide an estimation and a possible explanation for the prevalence of skeletal pathologies.

Citation: Palaeoepidemiology in extinct vertebrate populations: factors influencing skeletal health in Jurassic marine reptiles. (2019). Royal Society Open Science, 6(7).

Understanding how Tectonic Activity affected Triassic Vegetation and Climate

Triassic vegetation and climate evolution on the northern margin of Gondwana: a palynological study from Tulong, southern Xizang (Tibet), China

by: Jungang Peng, Jianguo Li, Sam M. Slater, Qianqi Zhanga, Huaicheng Zhu, Vivi Vajda

Summarized by: Kailey McCain

What data were used? Researchers noticed that while there was extensive research in North American and European paleobotany (i.e., plant fossils) from the Triassic period, data was very limited for Southern Asia. To fill this gap in knowledge, 147 samples were collected across China and examined for pollen, dust, and other microscopic fossils (also known as palynomorphs). Additionally, rock samples that dated through the Early Triassic were collected and processed. 

Methods: The samples were processed using hydrochloric acid (HCl is strong acid and has a low pH value ~1) and hydrofluoric acid (HF is a weak acid and has a higher pH value ~6) lab techniques. By using these acids, the microfossils were isolated from the sediment sample and placed on a microscope slide for further investigation. 

The palynology samples were tested for pollen and spores (cells that are capable of developing into a new individual without another reproductive cell). The abundance of specific species were then mapped to illustrate vegetation and climate during the Olenekian, a period of time during the Early Triassic. The identified microfossils can be seen in figure 1. 

Results: The data collected showed that there are roughly three vegetation stages throughout the Early Triassic. The first stage is dominated by pteridosperms (fern-like vegetation lacking spores), which indicated a warm and dry climate. The following stage exhibited a decrease in pteridosperms and an increase in conifers (woody plants). This change in vegetation indicates a decrease in temperature and an increase in humidity. The final stage exhibits a steady increase in conifers and a diverse range in ferns, thus indicating a stable and temperate climate.

Using these stages, researchers were then able to compare the shifts in vegetation and climate to the tectonic activity due to the rifting (splitting) of Gondwana, an ancient supercontinent that split from Pangea. Through the examination of the rifts and ocean levels, the researchers hypothesized that the separation of Gondwana was a driving factor in regional climate and vegetation shifts. 

Figure 1: This image shows some of the microscopic pollen and spore fossils identified. Additionally, the image shows a scale bar (located under F and G) that represents 20 micrometers (µm), which is 1,000,000 times smaller than a meter!

Why is this study important? This study provided insights into the ways tectonic activity affected the environment in an area that lacked prior research. It drew important correlations between climate and tectonic activity. Additionally, evaluating the specific abundance and lack of certain vegetation helps establish evolutionary patterns not only in the Triassic, but also in supercontinents. 

The big picture: Paleobotany and palynological data paint a great picture of what Earth was like during certain time periods. Specifically, the data collected in this study shows a correlation in Triassic vegetation and climate evolution during the rifting of Gondwana in Southern Asia.

Citation: Triassic vegetation and climate evolution on the northern margin of Gondwana: a palynological study from Tulong, southern Xizang (Tibet), China. (2019). Journal of Asian Earth Sciences, 175, 74–82.

Kailey McCain, Interdisciplinary Natural Sciences Undergraduate

Kailey hiking in the Nantahala National Forest in December, 2019.

Hello, my name is Kailey and I’m a Junior at the University of South Florida majoring in interdisciplinary natural sciences, with an emphasis on geology, chemistry, and biology. Most people are surprised by my degree, and I get a lot of questions about the interdisciplinary aspect. As a future scientist, I believe it is critical to have an interdisciplinary approach to solve problems. Sir Francis Bacon, developer of the scientific method, urged not only scientists, but all people, to remove the lens they look at problems through and take into consideration the myriad of perspectives. To me, my degree embodies that. 

Upon graduation I plan on pursuing a PhD in ecology and evolutionary biology and my research interests are centered around dissecting the effects anthropogenic factors, or human activity, have on disease prevalence and transmission. 

What is your favorite aspect about being a scientist?

Graphic explaining the difference between primary (original research) and secondary evidence (syntheses, summaries).

Growing up, I always had an insatiable curiosity about life and our world. That curiosity has ranged from why we have an atmosphere to how human activity has caused harm, not only to our climate, but to all of ecology. I found that studying natural sciences challenges me, but rewards me by answering those questions.

Another aspect of science I love is the community that being in the sciences gives you! As a young woman, it is incredibly motivating to see such a diverse set of individuals working towards one common goal: expanding the knowledge of humankind. Before I immersed myself into the community, it was hard to see myself as a scientist. This was due to a lack of representation of female scientists; however, now I know that I can be whoever I want and I hope to show other young girls that too.

As to how I got interested in science, I originally went into college as planning on pursuing medicine,  but after taking a history of life course through the Geosciences department, my whole trajectory changed. I suddenly found myself so excited for the lecture and I started asking questions that didn’t have concrete answers, and that captivated me. I always wanted to help people and the world, and becoming a research scientist seemed to fit that more so than anything else.

How does your research and education contribute to the understanding of climate change and to the betterment of society?

By studying the ways in which human activity affects wildlife diseases, scientists are able to predict what our future world will look like, attempt to change the trajectory of diseases, and protect some of the world’s most amazing ecosystems. I also think it’s important to expand on this catch all term “human activity”. This can include, but is not limited to, deforestation, climate change, light pollutants, and habitat fragmentation. All of these actions are intertwined in how we look at protecting the world’s ecosystems, while still allowing for human development.

3D scan of Gyrodes abyssinus, which is Late Cretaceous in age (~100-66 million years ago).

What are your data, and how do you obtain them?

I am currently working on a systematic review of all the meta-analyses (I’ll explain what this means below) on Toxoplasma gondii, which is a type of parasite that is predominantly found in cats and humans. The data collected for this study is not found in the field or even the lab, but in other scientific publications, which is why we call it a meta-analysis! My job is to find all studies that are relevant and point out potential positive correlations between the data for other researchers to explore further.

I am also currently interning at a 3D visualization lab scanning paleontological collections (fig. 2)! The purpose of 3D scanning is to digitize collections that can be shared to people all over the world.The softwares utilized are Geomagic Wrap and Zbrush.

What advice do you have for aspiring scientists?

My advice to aspiring scientists is to not give up! As an undergrad, is it incredibly difficult to remove this level of perfection we place on ourselves, but it is necessary. Everyone has messed up, everyone has failed a test, and no one is perfect. Your well being and mental health is more important than any grade. 

Another piece of advice is to always try. There have been countless opportunities that I could have had, but I was too scared of rejection. At the end of the day, rejection is a part of life (especially the academic life).


3D Visualization Undergraduate Internship

Hey everyone! It’s Kailey, an undergraduate student at the sunny University of South Florida.

The image shows a specimen, Gyrodes abyssinus, sitting on a mesh block with a scan via geomagic wrap on the screen in the background.

I wanted to take some time and share with you guys an amazing opportunity I was given earlier this year. As any ambitious college student will tell you, internships are extremely important when it comes to choosing a career path. Not only do they grant students hands-on experience in a particular field, but also general time and knowledge in the workforce. Good internships are hard to come by, which is why I was elated when I got the opportunity to intern at the 3D visualization lab at USF! 

And yes, the lab is as cool as it sounds.

For a place where complex research happens daily, the mission of the lab is rather simple: to harness 3D scanning equipment and data processing softwares. These technological tools have been a wonderful addition to the arts, the humanities, and STEM everywhere, as it has not only supported, but completely transformed, the research in these worlds. This dynamic lab embodies the philosophy of open access research and data sharing, meaning that scientists and researchers from all over the world are able to use its different collections and visit historical sites from the comfort of their homes and offices.

This image shows the Faros arm scanner extended.

My job at the lab was to scan and process some specimens from the department of geosciences’ paleontological collection. The first step in this process is to use a laser scanner and scan my object in various positions (figure 1) using the FaroArm scanner (figure 2). This bad boy has three different joints, making the scanner move around any object seamlessly. The FaroArm also has a probe with a laser, which is essentially taking a bunch of pictures of the object and overlays them. An important note is that these “various positions” need to be easily and manually connected in a software called Geomagic Wrap; therefore, every scan must seamlessly match up like a puzzle! This was probably the most difficult thing to learn, as you not only must think more spatially, but pay close attention to the small, yet distinguable,details, like contour lines and topography (figure 3). In some cases, these small details mean the most to research scientists by showing things like predation scarring and growth lines.

This image shows a close-up shot of the contour lines and topography on the 3D model.

Once the scan is connected and we have a 3D model, the file is switched to a different software called Zbrush. This is where the fun and creative aspects come in! Zbrush allows users to fill in any holes that appear in the scan and clean up any overlapping scan data. This happens when the scans aren’t matched up properly in Geomagic. Next, we paint texture onto the model using different pictures of the fossil. Then, voila, you have a bonafide 3D model (figure 4). The model shown in figure 4 is of Gyrodes abyssinus Morton, a mollusc from the Late Cretaceous. 

I completed a total of three data scans and processes, but was cut short due to the coronavirus pandemic. While my time at the lab was short, I learned so much in terms of technical skills and problem solving. However, the most notable thing I learned was just how interdisciplinary science and research operates at the university level. Networking with archeologists, geologists, anthropologists, and so many more opened my eyes to the different fields contributing to the research world. The experiences I gained at the 3D visualization lab will follow me through my entire academic career.

This is an image of the final 3D model of Gyrodes abyssinus with coloration and texture.

You can visit for information on the 3D lab and visit to view the rest of my collection.

How Climate Change Impacts the Mortality Rate of Latin American Frogs

An Interaction Between Climate Change and Infectious Disease Drove Widespread Amphibian Declines

by: Jeremy M. Cohen, David J. Civitello, Matthew D. Venesky, Taegan A. McMahon, Jason R. Rohr

Summarized by: Kailey McCain

What data were used? 

This study combined laboratory experiments, field data, and climate records together to support their hypothesis that amphibians have a higher mortality (death) rate when exposed to warmer temperatures, this is known as the “thermal mismatch hypothesis”


Atelopus zeteki or the Panamanian Golden Frog in their natural habitat.

The laboratory experiments consisted of a temperature gradient and a temperature shift experiment. Both experiments exposed an endangered captive frog, Atelopus zeteki or the Panamanian Golden Frog, to a disease causing fungus, Batrachochytrium dendrobatidis, and measured the rate of death. The temperature gradient gradient slowly increased the temperature, while the temperature shift experiment exposed the frog to the fungus at specific temperature units: 14°C, 17°C, 23°C, or 26°C.  

The data was then compared to field data collected from the International Union for Conservation of Nature red list database to observe a real time decline in a total of 66 species of frog. The geographical range for the field data was limited to Latin America and the rate of decline was compared to historic monthly climate data.


The results of the temperature gradient and temperature shift experiments show that mortality increased when the infected frog was exposed to higher temperatures. However, it also shows that temperature did not affect the mortality rate of the control group, the non infected frogs. As for the field data collected, the results showed that the frogs’ decline could not be correlated to precipitation nor altitude, but climate change, the thermal mismatch hypothesis clearly  predicted an increased decline of the species.

Figure A represents the data collected for the temperature gradient experiment and shows a linear decline in survival time with an increase in temperature. Figure B represents the data collected for the temperature shift experiment and shows the different temperature units plotted by the proportion alive versus time. The graph indicates that the warmest temperature has the lowest survival rate.

Why is this study important? 

This study tackles two of the largest challenges facing the modern world: climate change and disease prevalence. Some believe these issues are falsely linked, but the evidence collected in this study shows a positive correlation between disease induced death and increased temperature, both in a laboratory environment and the outside world. 

The big picture: 

While this study was isolated in geographical terms, the data collected gives researchers a look into what the future might hold for the spread of diseases in a warming world. Alone, the rising temperatures were not found to increase the rate of mortality; however, when mixed with a pathogen, a deadly combination was created and increased the rate of mortality greatly.

Citation: full citation of paper 

Cohen, J. M., Civitello, D. J., Venesky, M. D., McMahon, T. A., & Rohr, J. R. (2019). An interaction between climate change and infectious disease drove widespread amphibian declines. Global Change Biology, 3, 927.

Black Lives Matter & STEM

As I write this post, the date is May 30, 2020, approximately five days since the senseless murder of George Floyd by members of the Minneapolis Police Department. Protests have erupted in many cities across the country, and my city, Tampa, is no different. I am faced with the reality of our justice system, racism, and my own privilege as a white American. With this intense (and necessary) magnifying glass set on our country, I can not help but reflect on my surroundings and university. 

My name is Kailey and I am a student at the University of South Florida. A focal point of our university is the Martin Luther King Jr. plaza: here, you will notice a large bust of Dr. King overlooking a reflection pond, as well as his famous “I Have a Dream” speech immortalized in stone. While this part of campus serves as a rallying point for peaceful protests and events, the true meaning and impact of Dr. King’s message is lost in nearly every aspect of society, and higher education is no different.

A National Science Foundation study in 2019 reported that out of all bachelor’s degrees earned in biological sciences in 2014, 4.23% of those were by Black women. 2.83% of all physical science degrees were earned by Black women, and 0.99% of engineering degrees were earned by Black women. While these statistics specifically quantify the degrees earned by  Black women, all marginalized populations face significant barriers to STEM education. Scientific culture and broader society have built these barriers, causing incredible talent and perspective to leave science, or not enter into STEM fields in the first place due, in part, to a lack of representation. 

A lack of diverse and inclusive representation permeated my education growing up, and very likely the majority of my peers. For many people, myself included, the idea of a scientist was dictated by the scientists we learned about and heard from in class: white men. This concept has shifted the dreams of many young people to aspire to enter these fields because they never saw themselves represented as scientists and weren’t encouraged or provided opportunities by the education system to explore this path further. This is oppressive because it paints a completely inaccurate history of science that ignores the achievements of Black scientists, further entrenching science history in white supremacy. Further, lack of representation and over-representation of white men in science cements for white students the idea of “who” is allowed to participate in science- when you only see white scientists, your mind forms that stereotyped image. This negative cycle continues and the problem is exacerbated when marginalized people, and specifically Black people, are made to feel unsafe in public spaces and in outdoor environments. This means that white scientists often make assumptions about Black scientists, paving the way for microaggressions and harassment at scientific institutions. 

As scientists, we cannot remain silent. We need to take action to not only raise awareness of the obstacles Black scientists face, but also actively work towards making the science community anti-racist. Science is not apolitical and it never has been. White scientists, for hundreds of years, have been performing racist experiments, claiming that Black people are “less evolved” or “less intelligent”; scientists have experimented horribly on Black bodies causing unspeakable pain, and developing methods and medications we still use in modern science (e.g., Henrietta Lacks, Tuskegee Syphilis Experiment, etc.)

Science has been shaped by white supremacy, just as every other system in the United States has been. The history of racism in science continues to shape how we, meaning white people, treat our Black colleagues and students and this is unacceptable. We cannot remain silent and we must stand with our Black colleagues and neighbors. Finally, we must take action. 

Educate yourself. Read books and articles written by Black writers. Listen and learn from Black activists, professors, community members. Understand that as much as we can try, we will never understand what it is like to live as a Black person in a racist society. Speak out. If you see or hear racism from non-Black people, step in and correct them. If you’re non-Black, you will mess up sometimes. Apologize, listen, and make sure to do better next time. Support initiatives to create programs for Black students at your university, and initiatives to increase support programs for Black students and faculty. I encourage you to contact your local government, make your opinions known, stand up for what you know to be right, and vote! 

These protests all over the country are providing something stronger than a “like” or a “comment” on a social media post can. With the ear-pounding sounds of mourning, and the bravery of those protesting, those that demand peace, equality, and justice for every Black person, they are working towards creating a better world for all. 

I challenge every person with a platform to use that platform for good. Silence is no longer an option. We have to be better and be active allies to causes for racial equality, as well as to our fellow neighbors who have been continually victimized and oppressed by police, the “impartial” criminal justice system, and individual prejudices/biases.

I would like to also recognize and thank Dr. Sarah Sheffield, a geosciences professor at the University of South Florida (USF), Mckenna Dyjak, a recent graduate from USF, and Lisette Melendez, an undergraduate at USF, for editing this post and ensuring our message is heard.

Note from the Editors: If you are interested in more actionable items, ways to become anti-racist, and a list of organizations to financially support please see our statement on Black Lives Matter.