Combining our past life with our present improves the foundation and deeper understanding of our evolutionary tree

Fossils improve phylogenetic analyses of morphological characters

Nicolás Mongiardino, Russel J Garwood, Luke A. Perry.                                                         

Summarized by Sadira Jenarine, a senior at The University of South Florida. She is a geology major and plans on attending graduate school following graduation in the summer. Once she earns her degree, she hopes to work along the lines of environmental conservation and preservation or become a professor. When she’s not looking at rocks, you can usually find her at the local Starbucks making a latte or in the town’s own “Lettuce Lake Conservation Park”.     

What data were used: The authors conducted a simulation of 250 evolutionary trees, also called phylogenies, which were used to determine the most accurate method of creating phylogenetic trees. Programs were designed to account for species’ traits, including strengths and weaknesses as well as their ability and likeliness to survive natural disaster, such as mass extinction events, and/or predation.     

Methods: This study was completed by testing different phylogenetic inference methods: maximum parsimony (MP), Bayesian inference (BI) and tip-dating. MP is essentially the path of least resistance in evolution; the fewer branches you must jump on “the tree of life”, the more closely related a species likely is. Bayesian inference, combined with tip-dating is a method of dating fossils by analysis that gives a numerical age of the specimen, and then tests whether it is statistically accurate using an equation called Bayes Theorem. These methods differ from a more common technique, ‘node dating’ which determines the age through age constraints that are formed by the first and last seen specimen in the fossil record. These new forms of analysis were tested based on the 250 trees as well as over 11,000 different traits that these organisms share. 

Results: This experiment was conducted by testing the results of the length of the simulated evolutionary trees. The graph (Figure 1) measures the accuracy of the placement of the species on the tree among all inference methods performed by testing different accuracy measures, which are measured by using the number of nodes (i.e., the branching point on an evolutionary tree). We see that even with accounting for missing data (i.e., when species don’t have the entire suite of characters used in a phylogenetic analysis), one type of accuracy, quartet-based accuracy, increases proportional to the fossil sample. In turn, bipartition-based accuracy shows a difference in accuracy when there is missing data. This effect is mostly seen when examining tip-dated inference which uses multiple morphological (body shape) and molecular (DNA) data from fossils themselves. Tip-dating is a newer method of inference and should therefore be used with caution, as it is sensitive to missing data, something very common when using fossils. 

Graph in top left measures the topological accuracy of bipartitions based on the proportion of missing fossils in maximum parsimony (MP), Bayesian inference (BI) and tip-dating (clock). No missing data concludes a higher accuracy in all 3 inferences with the most outstanding in clock dating. Even amongst high levels of missing data, the topological accuracy for clock dating is outstanding in comparison to other methods. The bottom left graph measures the same variables however with quartet-based analysis. This graph remains the same even with different levels of missing data. The graphs to the right measures the topological precision. In MP precision decreases as more levels of missing data are introduced, same with BI and clock, however not as outstanding. In quartet-based analysis all three inference methods maintain similar precision even amongst missing data.
Figure 1. The graph shows both topological accuracy (left) and topological precision (right) using both forms of measurement; bipartitions (top) and quartet (bottom). Colors indicated in the graph account for the levels of missing data. Amongst all methods, we see increased accuracy than that of parsimony. Issues arise with the tip-dating (clock) method when levels of missing data are high.

Why is this study important? Using complete morphological and/or molecular data of fossils, as well as data from living organisms, provides the most accurate evolutionary tree reconstruction. This shows us that tip-dating, which is the inclusion of fossils into the construction of the evolutionary tree, creates a more accurate and precise tree. This study compares its results to those from previous analyses and examines a new angle: accounting for missing data. This is beneficial, because this study helps us understand the limitations of a number of methods, which can help us create more realistic phylogenies. 

The big picture: Here, we are learning that using fossils along with modern species, when many studies use just modern species or just fossil species, really gives us a more accurate representation of how life on Earth has evolved through time. Because some of these methods of inference are newer, like tip-dating, there is much room for progress and development. By no means does it mean that new methods should be immediately widely accepted, but that it is our duty to continue to study this new form of inference dating. By understanding how what we have, what we had, and what we lost, we can get a better grasp of the evolutionary tree that we are working to perfect.   

Citation: Mongiardino Koch, Nicolás, et al. “Fossils Improve Phylogenetic Analyses of Morphological Characters.” Proceedings of the Royal Society B: Biological Sciences, vol. 288, no. 1950, 2021, https://doi.org/10.1098/rspb.2021.0044. 

Paleocene-Eocene thermal maximum (PETM): a potential foresight into the future of ocean life

Shallow marine ecosystem collapse and recovery during the Paleocene-Eocene Thermal Maximum

Skye Yunshu Tian, Moriaki Yasuhara, Huai-Hsuan M. Huang, Fabien L. Condamine, Marci Robinson

Summarized by Mathew Burgos, University of South Florida undergraduate geology student. Interested fields of study include solar radiation, hydrology, hydrogeology, hydroelectricity, geochemistry, and environmental sustainability.

What data were used? Rich fossil records of ostracod arthropods (the group that also includes spiders, trilobites, and insects), extracted from a Salisbury embayment (i.e., a recessed coastal body where there is a direct connection to a larger body of water) near the coast of Maryland, eastern United States. Ostracods inhabit nearly all aquatic environments on earth; their tiny shells make them look like “seed shrimp”, and they were among the only marine invertebrate fossils with a strong enough fossil record to reconstruct the group’s response to the PETM (Paleocene-Eocene thermal maximum), a time on Earth where the global temperatures skyrocketed for a geologically short period of time. A core sample was utilized to study the ostracods; a core is a cylindrical section of the Earth where the sediments, rocks, and organisms within are removed from the subsurface for analyzation. 

Methods: A sediment core was dug from the ground in the embayment, and the ostracod content within the core was analyzed for carbon-13 isotope values, to later determine the survival rate of the species during and post-PETM. Studying fossil records of creatures that existed during that time may lead to future impacts on marine life and our oceans future health. Carbon-13 isotopes can indicate periods or events of warmer temperatures when the values trend negatively, so the isotope values here helped identify the stages of the PETM alongside the fossils. The PETM (Paleocene-Eocene Thermal Maximum) is an event that occurred roughly 56 million years ago, and it was a climatic event similar to the current global warming crisis because of prolonged greenhouse climate conditions; however, the current crisis is happening at a much faster rate.

Four panel image with differences described in caption. Each panel represents a time slice to show the changes in environment that is tracked by marine species.
Top left, Pre-PETM setting: regular oceanic conditions for marine life above the oxygen minimum zone (OMZ).
Top right, During peak PETM: shallow marine migrating upslope for survival. Deep low oxygen species also moving upslope and separating from their fellow deep marine species that are adapted to low oxygen.
Bottom left, Recovery phase I: Species that survived the PETM returning to pre-event locale above OMZ.
Bottom Right, Recovery phase II: Mixing of potentially new warm adapted species and shallow marine species.

Results: Analysis of the ostracod abundance illustrated a substantial elimination of the shrimp just before the thermal maximum event, followed by a recovery and diversification of the species once the ocean temperature normalized a couple of million years later. Potential detriments of the thermal maximum are the irreversible impact that climate change had on the marine life, primarily due increased temperature and deoxygenation of the water. As deoxygenation spread (Figure 1), only species who were able to move into different areas of the water column were able to survive; those who could not went extinct. Some species nearly went extinct during the PETM but were able to recover and diversify after the event, even potentially returning to a healthy population. 

Why is this study important? This study made connections between the PETM and modern climate change that is human-driven, which is extremely harmful to marine life, as the PETM is likely the best analog to the current climate crisis. Effects of modern-day climate change are like the happenings of the Paleocene-Eocene Thermal Maximum. This is an indicator of the importance of the impact humans could possibly have on the ocean in a short period of time, relative to the Paleocene and Eocene Epochs.

The big picture: The recent global warming effects that humans have had on could prove to be detrimental to our existence. This study focuses on the PETM that occurred over a vastly longer time scale compared to the short duration of the current age of industrialization. Humans are essentially replicating an extreme thermal event, that would otherwise be relatively naturally occurring in Earth’s time, but at a rate which is exponentially smaller in timeframe. With the status of the Earth’s oceans warming, we could potentially see the ramifications of eliminated marine species within our time at an unprecedented rate.

Citation: S.Y. Tian, M. Yasuhara, H.-H.M. Huang, et al., Shallow marine ecosystem collapse and recovery during the Paleocene-Eocene Thermal Maximum, Global and Planetary Change (2018), https://doi.org/10.1016/j.gloplacha.2021.103649

An Important Look Back on the Unjust Past of Paleontology

Our past creates our present: a brief overview of racism and colonialism in Western paleontology

Summarized by Kaleb Smallwood, a junior undergraduate geology student at the University of South Florida who intends to use his degree to pursue a career in vertebrate paleontology. Outside of geology, his interests include video games, anime, and mythology.

Rather than a traditional scientific study using data and presenting results, here the authors attempt to unravel the racism, coverings, exclusion, and colonialism of paleontology’s past in order to better understand the racism present in the sciences today and how best to go about rooting this bias out. 

Since the inception of the discipline, paleontologists have extracted fossils, minerals, and fossil fuels from other lands, often without regard to the Indigenous peoples or otherwise residing there. This results in environmental destruction and displacement, as the scars left by this extraction tear up land and plants, leaving holes where digs occurred. On the topic of environmental devastation, the history of paleontology is also inextricably linked to the oil, coal, and gas industries. Paleontologists have served these industries in the location and extraction of nonrenewable resources in exchange for funding, job security, and support since they began to better understand how and where oil forms, implicating them in climate change. Another form of extraction exercised by paleontologists is that of biological specimens, both living and dead. For example, the several species of the finches (Figure 1) Darwin studied and extracted on his voyage on the HMS Beagle, such as the saffron-cowled blackbird and vampire finch, were pulled from their habitat and sent to Europe. Paleontologists have also participated in grave robbing, removing the remains of Native Americans and Black slaves to examine their cranial structures in an effort to further their racist views that these peoples are more closely related to primates than white people. Many of these remains of people are still held in storage and studied. While the loss of biodiversity from an ecosystem is a grave consequence of extraction of animals, the removal of humans from their lands is also an egregious crime of paleontologists. It is a flagrant act of disrespect to the culture and lives of the people from which they are taken. 

There is also the issue of the Myanmar amber trade, from which paleontologists have gained amber for examination in exchange for money that has been used to fund a decades-long civil war resulting in numerous deaths. Measures to limit and prohibit the publication and procurement of such amber have been put in place, but not all are ubiquitously accepted. Scientists are strictly forbidden, however, from publishing on Myanmar amber obtained after the most recent coup in February 2021.

Depicted are three type specimens of birds from Darwin’s voyage on the HMS Beagle. They appear as mockingbirds with light brown feathers on their underside and darker brown and white feathers on the wings. They are ordered by increasing size, with the smallest at the top of the image and the largest at the bottom. The eyes of the birds are missing, and they have tags tied around their feet displaying their taxonomic names. From top to bottom they are labeled as Orpheus parvulus, Orpheus melanotis, and Orpheus trifasciatus.
Figure 1. Specimens of birds from Darwin’s voyage on the HMS Beagle. From top to bottom they are labeled as Orpheus parvulus, Orpheus melanotis, and Orpheus trifasciatus. Image Credit: “Voyage of HMS Beagle (1831-1836).” Natural History Museum, Natural History Museum.

Returning to the topic of museums, scientists often take materials from other countries and peoples for the purpose of education and exhibition without asking, and this colonial way of obtaining their exhibits is cited as a cause for concern. Museums often refuse to acknowledge the methods by which they procure their items, do not credit the places they got them from, refuse to compensate these countries or return their property, have disproportionate wealth and resources compared to other museums, lack diversity in their staff, and pay their staff little for their work. Accountability, inclusion of the voices of the people whose history they display, and a willingness to return items would go a long way in correcting these flaws.

There are also injustices present in the teaching of paleontology. As the authors point out, textbooks and courses in the Americas tend to omit the ways in which scientists in the field have previously trampled upon Black and Native American people. For example, the erasure of their history and the fact that the first known fossils in the Americas were discovered by slaves is rarely mentioned. As is apparent, science has never been the unbiased and apolitical field students are led to believe it is. Furthermore, these courses are often taught by white men, further excluding other racial groups. The power system this creates makes it difficult for those with concerns to voice them for fear of reproach.

Why is this important/The big picture: Underscoring each point in this article is the constant reminder that the challenging task of acknowledging and reflecting on the past and current racially discriminatory of paleontology, the geosciences, and science as a whole, is a crucial first step in resolving those same issues. The writers call on paleontologists to consider whether the specimens they use come from Indigenous lands and ask who truly owns their specimens; they ask paleontologists to consider the people that their research may impact and their role in it, as giving proper credit to the right people without bias or exclusion is a crucial practice in any field, not just the sciences.

Monarrez, P., Zimmt, J., Clement, A., Gearty, W., Jacisin, J., Jenkins, K., . . . Thompson, C. (2021). Our past creates our present: A brief overview of racism and colonialism in Western paleontology. Paleobiology, 1-13. doi:10.1017/pab.2021.28 

Antarctic foraminifera and their implications on paleoclimate

Holocene foraminiferal assemblages from Firth of Tay, Antarctic Peninsula: Paleoclimate implications

By: Wojciech Majewski & John B. Anderson

Summarized by: Baron Hoffmeister

What data were used?: This study analyzed 166 sediment samples taken from sediment cores in the Antarctic Peninsula. 

Methods: This study used a quantitative analysis of foraminifera assemblages found in sediment cores to determine past environmental factors relating to climate change.  

Results: This study found that different foraminifera and their physical attributes correlate with several different environmental conditions during the Holocene epoch, the geologic time unit that spans from nearly 11,000 years ago to present time ( figure 1). A time span between 9400 years and 7750 years before present time was correlated with having coarse (large) sediment and coarse foraminifera. This indicates a high influence from warming sea currents that melted glaciers and deposited coarse sediments. This was a period of glacial retreat and warming temperatures. From 7750 to 6000 years before the present, the elevated appearance of foraminifera species M. arenacea represents open water and conditions in which glaciers were spread out from each other. The foraminifera species M. arenacea is also known for its tolerance to cold corrosive bottom waters and high salinity fluctuations. The assemblage dominated by M. arenacea indicates that the bottom waters at this time dissolved other species of foraminifera, and M. arenacea was the dominant foraminifera species at this time. Foraminifera tests, (i.e., their shells) are made of calcium carbonate, and it dissolves in acidic conditions. Around 3500 years before the present time, it was found that due to an increase in abundance of foraminifera species P. bartramiP. antarctica is when the cooling trend of the mid-Holocene occurred. There weren’t any corresponding foraminifera assemblages found that correlate with warming over the last century. 

Image contains many examples of foraminifera at different angles to showcase the variation and how it can be employed as a tool to assess climate.
Different species of foraminifera can be used to identify different ecological conditions in which they existed. The physical properties of foraminifera, like roundness or angularity of their tests, can also determine transport history, depositional environments, and likely effects from environmental influences. This is a microscopic image of several different foraminifera species found in the core samples used for this study. The different shapes of this foraminifera and the textures observed were used to determine environmental conditions in the Antarctic peninsula.

Why is this study important?: The results of this study allow us to better understand how foraminifera can relate to changing environmental conditions. This study provides a more cohesive understanding of climate change and how glacier and ocean currents around the south pole respond to changes in climate. The data used in this study can be used in future studies regarding foraminifera assemblages and their implication on climate change. 

The big picture: Foraminifera are some of the most abundant shelled organisms in marine environments and can be used to reconstruct past climatic conditions. The importance of understanding how these organisms correlate to climate change can help link current-day climate trends to prehistoric climate events. This can be used to make predictions on how climate change is occurring currently, and what the effects of it might be worldwide. 

Citation: Majewski, W., & Anderson, J. B. (2009). Holocene foraminiferal assemblages from Firth of Tay, Antarctic Peninsula: Paleoclimate implications. Marine Micropaleontology, 73(3-4), 135-147. doi:10.1016/j.marmicro.2009.08.003

Paleoclimate implications from a sediment core taken in a frozen Antarctic lake

Limnological Investigation of Antarctic Lakes and their Paleoclimate Implications

By: Pawan Govil

Summarized by: Baron Hoffmeister 

What data were used?: A 78 cm sediment core from a freshwater lake in Larsemann Hills, East Antarctica was used to interpret historic climate patterns from the late Quaternary period. 

Methods: The sediment core was analyzed using grain size distribution, as well as biological productivity indicators such as organic carbon and biogenic silica. Biogenic silica makes up diatom cell walls and is commonly called opal. This study used radiocarbon dating to measure total organic carbon present, and the biogenic silica was also evaluated using a wet alkaline extraction. A wet alkaline extraction is a method that isolates plasmid DNA or RNA from bacteria. This was used to determine the biogeochemical attributes of this lake.

Results: Using radiocarbon dating, this study found that this core is from the Holocene Epoch, a time that began around 11,700 years ago. This core was dated to be 8,300 years old. Most of the material in the core was sand, and clay and silt were rarer (sand, clay, and silt are defined by grain size in geology- sand is the coarsest grain size in this example; figure 1)The silica content within this was very low, indicating a very low abundance of silicate microfossils. The total carbon was low or negligible in the lower part of the core, likely due to the high sedimentation rates of sand during this time. The area of the core that had the most organic carbon was the top of the core that contained the small amounts of clay and silt. This study showed that this was due to a build of algae. The particles of clay and silt prevented oxygen from  decomposing the organic matter. This indicates that during this time, approximately 4,000 years ago, there were low sedimentation rates and low oxygen levels in this lake. This algal mat at the top of the core indicates warming temperatures during this time, and that the lake had little interference with glacial ice. The fine grained sediments were deposited due to ice meltwater (as water slows down, fine grained sediments drop out of water suspension) and can be seen in the upper core. The lower portion of the core contains high sand content, which implies glacial river input (i.e.,fluvioglacial) before 6,000 ago. The overall paleoproductivity implications of the core are as follows.  From 8,300 ago to around 6,000 years ago there was a period of warming. Around 4,000 ago, the warm temperatures allowed the lake to be free of ice and exposed to sunlight, and therefore this was the highest level of productivity and can be reflected in the upper core’s higher total carbon content. 

Graph depicting age dating of a sediment core.
This is a chronological interpretation of the sediment core taken from this study. Sand dominated the core with low percentages of silt and clay. This graph shows records dating back to 8.22 thousand years ago (right) working its way to around 1 thousand years ago (left).

Why is this study important?: Antarctica and its surrounding oceans influence climate across the entire planet. Antarctica holds around 90% of the world’s ice and about 70% of the world’s freshwater trapped in ice. The ability to be able to interpret past climate conditions that influenced climate patterns in Antarctica can allow scientists to better predict current day climatic changes in Antarctica and its effects globally.  More information about Antarctica and its ice sheets can be found here

The big picture: Today, the ice sheets are melting at a rate that has never been seen before. The effects of this could be catastrophic to life on Earth. Studies like these can allow scientists to better understand current-day climate patterns that could potentially help reduce the impact of widespread climate change. 

Citation: Govil, P. (2019). Limnological Investigation of Antarctic Lakes and their Paleoclimatic Implications. Ministry of Earth Sciences, (24), 289-303. Retrieved May 24, 2020.

New Late Cretaceous Shark found in North America

A new large Late Cretaceous lamniform shark from North America, with comments on the taxonomy, paleoecology, and evolution of the genus Cretodus

by: Kenshu Shimada, Micheal J. Everhart

Summarized by: Baron Hoffmeister

What data were used? : This study examined a partial skeleton of the Late Cretaceous shark, Cretodus, collected from the Blue Hill Shale in north-central Kansas, U.S.A. It had unique teeth not present in any other species of Cretodus

Methods: This study used a taxonomic analysis of the fossilized remains found and compared them to other members of the Cretodus genus. 

Results: The study found that the species of the fossilized partial shark skeleton found does not share enough similar features with any of the other four known species within the genus Cretodus. Therefore it has been listed as a new species, C. houghtonorum. Researchers found that it had a unique tooth size and pattern that didn’t match any previously discovered species (figure 1). Its calcified cartilage scales along with the inference that this shark had a large girth due to its bone structure that was preserved, indicated that this organism was likely a sluggish shark that lived in a nearshore environment. This study examined growth bands in its vertebral column and found that this shark had a lifespan of around 51 years. 

Image of many shark teeth from various angles to showcase how many different types of teeth exist for sharks
These are the 115 well-preserved teeth of C. houghtonorum. Sharks shed their teeth over their lifespan, and have several rows of teeth in both their upper and lower jaws. As one tooth falls out, it is replaced by the one in the row behind it. Each species of shark has unique teeth and jaw structures.

Why is this study important? Aside from discovering a new species, this study recognizes the fact that the evolutionary relationships of several shark families is still relatively unknown. However, this new finding provides data linking it with other members at the genus level. Without understanding these relationships, it’s difficult to understand the distribution of these organisms, how they changed over time, and why they went extinct. 

The big picture: Overall, this study is useful in determining possible links between extant and extinct shark species. This study provides data that can rework our understanding of evolutionary traits between extinct and modern-day sharks as well. The skeletal and dental data found in this study can be useful for other studies incorporating evolutionary trends, prehistoric ecology, and the taxonomic differences within the genus Cretodus.

Citation:  Shimada, K., & Everhart, M. J. (2019). A new large Late Cretaceous lamniform shark from North America, with comments on the taxonomy, paleoecology, and evolution of the genus Cretodus. Journal of Vertebrate Paleontology, 39(4). doi: 10.1080/02724634.2019.1673399

How genetic research can help to explain carnivoran (dog and cat) evolution

FGF gene family characterization provides insights into its adaptive evolution in Carnivora

Qinquo Wei, Yuehuan Dong, Guolei Sun, Xibao Wang, Xiaoyang Wu, Xiaodong Gao, Weilai Sha, Guang Yang, Honghai Zhang

Summarized by Kale Headings,  a senior at the University of South Florida. They are getting a dual degree in geology and environmental science and policy. They intend to study planetary geology or glaciology in graduate school next, and then work as a researcher or professor after they finish graduate school. In their free time they like to draw, play video games, and hang out with friends!

What data were used? The researchers looked at FGF genes, or fibroblast growth factors, from humans, domestic dogs and cats, mice, and other Carnivora genes from GenBank. FGFs affect a variety of biological functions including metabolism and development.

Methods: The researchers searched for Carnivora genetic sequences in GenBank, which is a database of genetic information of various species and confirmed that the genetic sequences they found were FGF genes. They did a phylogenetic analysis on the Carnivora species to determine their evolutionary relationships and the relationships of their FGF genes, using the FGF genes of mice and humans as an outgroup (outgroups ‘root’ the tree). In other words, comparing carnivoran FGF genes to human and mice FGF genes could help researchers determine which FGF genes are unique to carnivorans, and which are present across many groups and species, including mice and humans. Much of this analysis utilized various advanced computer programs and techniques. The researchers referenced preexisting phylogenetic trees for Carnivora and used Bayesian inference methods to create phylogenetic trees that included FGF genes alongside the Carnivora tree. Bayesian inference methods use Bayes theorem, an equation, to help infer which evolutionary relationships between species are most supported by the data. 

Results: The researchers found 660 new FGF genes in 30 different carnivora genomes. The phylogenetic trees created both with and without the FGF data were similar, and the FGF genes were able to be classified into 10 subfamilies (Figure 1) based on their locations on the phylogenetic tree. There were positive selection sites for two FGF genes that control metabolism and muscle development in Carnivora, which is significant because these features are important to these animals’ predatory habits. There was also a positive selection gene for FGF19 in the group of carnivora that was semiaquatic, and this is notable because it may indicate that FGF19 helps semiaquatic animals to regulate their body temperature and keep their balance in water. 

Alt text: Image of two concentric color-coded wheels, with the outer wheel containing text to label FGF subfamilies 19, 22, 5, 3, 7, 8, 1, 9, 4, and 11. The inner wheel shows individual FGF genes that are a part of each subfamily. Inside the space in the center of the two wheels is a tree-like diagram representing the phylogenetic families of Carnivora, with each section of the tree lined up with and color-coded to match the FGF gene and subfamily that it corresponds to.
Figure 1. The phylogenetic tree of Carnivora with the corresponding FGF subfamilies and specific genes, as determined by the researchers using Bayesian inference methods.

Why is this study important? The researchers concluded that the FGF gene family of Carnivora should be divided into 10 subfamilies. The researchers also found positive selection for several individual FGF genes that may be related to the diet and predator status of Carnivora animals, as these genes help to metabolize fats and develop muscles. They also found that habitat plays a role in what FGF genes are selected for, as notably FGF19 was selected for in semiaquatic carnivorans, and several other FGF genes also showed a strong relationship with the animals’ habitat types. These conclusions show how FGF genes can be used to further understand the evolutionary relationships and significance of specific evolutionary traits across a variety of species of mammals, since other groups of mammals besides Carnivora also have FGF genes. 

The big picture:  This study may help researchers better understand the evolutionary pathways taken by earlier carnivorans in the fossil record. In the specific case of FGF genes, these genes contain key physiological processes, just a few of which are metabolism and muscle development. Therefore, better understanding of the FGF genes and how they function across groups of mammals and how they vary due to evolutionary relationships may also help us to better understand our own FGF genes and how they work in our own human bodies.  

Citation: Wei, Q., Dong, Y., Sun, G., Wang, X., Wu, X., Gao, X., Sha, W., Yang, G., & Zhang, H. (2021). FGF gene family characterization provides insights into its adaptive evolution in Carnivora. Ecology and Evolution, 11, 9837– 9847. https://doi.org/10.1002/ece3.7814

Updating the Fossil Record of Whales

THE AWKWARD RECORD OF FOSSIL WHALES

Publication Date: 29 November, 2019

Stefano Dominici, Silvia Daniseb, Simone Cauc, Alessandro Freschic

Summarized by Jacob T. Booe. Jacob is in his senior year at the University of South Florida pursuing a B.S. degree in Geology. Growing up on the east coast of Florida near Kennedy Space Center, science and engineering has surrounded him for much of his educational career. While Jacob’s current trajectory is geared towards Earth Sciences, at the time of high school graduation, Jacob had no clue what his future career path was. Therefore, he enrolled in his local community college, Eastern Florida State College, where he graduated with his A.A. degree. However before obtaining an A.A. degree, Jacob found himself as an avid musician, pursuing the idea of acoustics and audio engineering. It wasn’t until his last year before receiving his A.A. degree that Jacob decided to take an intro to geology elective. After that course Jacob found himself committed to a career in geology transferring to USF in Spring 2020.

What data were used: The research team began with the analysis of 719 records of fossil whales, whose first origins are in the Cenozoic Era, across the Miocene, Pliocene, and Pleistocene epochs, approximately 11,000 to 23 million years ago (Figure 1). Researchers also used fossil whale occurrences to supplement their dataset from the Paleobiology Database (PBDB), which is a public database of global fossil occurrences that researchers update with new fossil finds. Along with the fossil occurrences, researchers collected information about the characteristics of rocks (i.e., their lithology). in which the fossils were found, where in the world they were found, and the time at which they lived. 

Methods: Researchers created six categories of lithology based on composition and grain with carbonate (like limestone) and siliciclastic rocks (like sandstone); these can be considered to represent the environments they likely have lived in. The skeletal system of the whales was categorized into four parts: skull, teeth, limbs, and spinal column. In addition, each fossil was graded on its quality of preservation. These data were analyzed to determine what relationships these variables shared. Other data, like measurements of the whale bones, were used to determine growth patterns of the organisms.  

Results: The majority of whale fossils that have currently been described originated in the Northern hemisphere. The team compared their findings to that of the existing PBDB and found that the PBDB had a more global sampling, with more even coverage between the north and south hemispheres. Researchers note that more exploration for fossils in the southern hemisphere must continue; other areas for further research include West Africa and Antarctica. In regard to lithological findings, results show that whale fossils are mainly found in fine-grained siliciclastic rocks while carbonates contribute considerably fewer occurrences. This differs from the PBDB, where carbonate lithologies had more occurrences than fine-grained siliciclastic. In terms of the growth of an organism, the team compared the fossil whales against the growth of a modern whale, the river dolphin. The results showed that in ancestral whales, skull size increases while the tympanic bulla (an ear bone) decreases; however, modern whales show skulls that increase concurrently with the tympanic bulla, with a special type of growth called “isometric growth”. 

The figure shows a global map projection denoting whale fossil finding by colored dots. Each dot is assigned a color based on its region locality. Regions are classified into nine groups as follows: 1) Western coast of Central and North America, 2) Western Coast of Southern America, 3) Eastern Coast of North America, 4) Eastern Coast of South America, 5) Western Coast of Europe and North Africa, 6) Mediterranean, Central and Eastern Europe, and Asian Near East, 7) Eastern Coast of Asia, 8) Oceania, 9) Indian Ocean and Austral Africa. The figure visually identifies that most samples are present in regions of North America (regions one and three), Europe (regions five and six) and Japan/Eastern Asia (region seven); or simply put the Northern Hemisphere.
Figure: The figure above displays the various distributions of whale fossil findings. The team grouped together nine regions showcasing which areas have been sampled. This also shows which areas are under sampled and could provide excellent locations for future studies.

Why is this study important: The current information used to study whales and their evolution is incomplete and biased towards known fossil localities in the northern hemisphere. In order to fill in the gap of whale fossils, this study shows some trends towards what environments is more likely to hold preserved whale fossils. 

The big picture: In this study, the authors tried to determine the quality and quantity of fossil data of whales. Identifying the gaps in our knowledge, and discovering why those gaps currently exist, can have an impact on how scientists approach whale paleontology moving forward. As the authors point out, places like West Africa are under-sampled, which leads to biases in our dataset. It is critical to determine whether under sampled areas of the world are due to a lack of fossil record or if scientists are not approaching the search for fossils globally. 

Citation: Dominici, S., Danise, S., Cau, S., & Freschi, A. (2020). The awkward record of fossil whales. Earth-Science Reviews, 205, 103057.https://doi.org/10.1016/j.earscirev.2019.103057

A comprehensive report on the morphology of the scales adorning the iconic horned theropod dinosaur, Carnoturus sastrei

The scaly skin of the abelisaurid Carnotaurus sastrei (Theropoda: Ceratosauria) from the Upper Cretaceous of Argentina.

By: Christophe Hendrickx and Phil R. Bell

Summarized by: Israel J. Rivera-Molina, a senior Geology major at the University of South Florida. He plans to attend graduate school in paleontology in order to start a career within the field of dinosaur morphology and evolution. 

What data were used? The holotype (i.e., the fossil specimen that ‘defines’ a species) of Carnotaurus, which was recovered from La Colonia Formation in Argentina; scientists also looked  at skin casts and 3D models of various other dinosaur taxa.

Methods: In this study, fossilized skin impressions of Carnotaurus were studied and a 3D model was generated using a camera and various imaging softwares. The skin was examined and then compared to various other taxa of dinosaurs from repositories, museums and other places where researchers keep fossils, from around the world.

Results: The scales covering the Carnotaurus (Figure 1) were found to be different in shape, size, orientation, and distribution. It was previously thought that the scales of the Carnotaurus were the same throughout the animal’s body, but it turns out that that is not the case. On the contrary, the scales were diverse: coming in six different shapes from elliptical to diamond-shaped scales. The scales also differed in textures ,ranging from smooth to granular, and were oriented in more than one way depending on which part of the body being observed. The tail especially displayed scales of a wide array of shapes that were arranged in various directions, while also ranging in size. 

A slab of preserved Carnotaurus skin containing grooved skin and circular scales; important scaled features circled to show which parts were measured by the researchers. There are 17 marked features, but none are discussed in depth in this summary here.
Figure 1: Portion of the skin located on the tail of Carnotaurus; outlined are the areas containing scale structures whose areas were measured by Hendrickx and Belll this was done to categorize the size and shape of the scales, compared to scales on other regions of the body.

Why is the study important? This study is important because it calls to attention the lack of emphasis placed on the research done on the skin of the Carnotaurus. Carnotaurus has some of most well-preserved scales amongst the theropods (the bipedal, carnivorous dinosaurs), yet past articles made little to no mention of the skin of the dinosaur. The authors also suggested that regarding the function of scales, scientists should think outside the box when comparing dinosaurs to extant lifeforms. They encourage researchers to not be afraid to venture away from reptilian analogues to attempt to discern what use(s) the scales served.

Big picture: This research provided a more in-depth look into the architecture of the scales covering the Carnotaurus. This body of work encourages scientists to look at and think more critically about the scales of dinosaurs, not only to reconstruct their appearance, but also to possibly discern some of their behaviors. Whether the scales served as a means of thermoregulation or as sexual display structures, further studies done on scales can lead to a greater understanding of how extinct dinosaurs lived.

Citation: Hendrickx, C., Bell, P. B., 2021, The scaly skin of the abelisaurid Carnotaurus sastrei (Theropoda: Ceratosauria) from the Upper Cretaceous of Patagonia. Cretaceous Research, p. 1-18. https://doi.org/10.1016/j.cretres.2021.104994

How Much Bias Exists in Fossil Research?

Phylogenetic Signal and Bias in Paleontology

By Robert J. Asher and Martin R. Smith

Summarized by: Alyssa Anderson, a senior geology major at the University of South Florida. Her dream is to work with environmental sciences and geology in water-related fields, such as oceanography or hydrology. In her spare time, she enjoys writing or sketching.

What data were used? Six sets of morphological data (i.e., data about the physical characteristics of organisms) from previously published fossil studies were gathered and the genetic data (i.e., the DNA) from living examples of those organisms were matched with the fossils. This was used to create rudimentary evolutionary trees of mammals and birds, the primary subjects of the studies. The trees retained all of the character codes from previous studies, even if there had been critiques.  

Methods: This study only used taxa that had at least 50% of the molecular and morphological characters present. Researchers tested how missing data would affect the outcomes of the phylogenetic trees. To do this, researched used artificial extinction and artificial fossilization techniques. This means, the researchers used various computer programming packages to artificially remove all molecular data from fossil taxa (as most fossils do not have any molecular data preserved) and some of the morphological data was also removed, as is also common with fossils. 

Results: The researchers worked to test three hypotheses. The first hypothesis studied the reconstruction of evolutionary trees based on the missing fossil data and molecular data. The results found that the experiment created fairly accurate evolutionary trees from this. The second hypothesis tested how accurate morphological studies are without molecular data in creating evolutionary trees. This was also found to uncover accurate results. Finally, the third hypothesis tested if poorly fossilized data leads to misinformed conclusions. Results demonstrated that including poor fossil data with missing information created better trees than trees that had no fossil data. In summary, any data helps make the trees more accurate, and it generally does not result in inaccurate evolutionary relationships. The most accurate evolutionary trees are made when molecular data and morphology data are combined.

A picture of six different evolutionary trees of bird and mammal genera, each from previously published data. The trees are well resolved; broader clades (e.g., marsupials) are highlighted in each of the trees
Figure: Six trees gathered from the five studies investigated in this research paper. The animal groups focused on here are birds and mammals. The tips of the tree are the genera used in this study.

Why is this study important? Determining how important including fossil data is, even in cases of the fossils’ inevitable missing data, was important in this study. An additional question that researchers wanted to know was if fossil breakdown creates situations where unrelated fossils appear more similar to each other than they actually are. Many morphological features can look similar across species, even if they are not closely related, so the process of fossil decay can make it even more difficult to piece out how similar or different certain features are. However, it doesn’t seem that this bias of fossil decay affects the dataset very much. Their placement on the evolutionary tree were usually quite similar to the known trees the researchers used. 

The big picture: Identifying bias or limitations in scientific studies is one of the most important things scientist can do. Bias can never be fully removed, and limitations won’t ever be either, but investigating sources of bias and the ranges of our limitations can help reduce it in future studies. Studying fossils is a vital science as it shows the history of the world and how species have evolved over time. If the information gained from the fossils is misleading in evolutionary analyses, due to the fossils inability to provide DNA or or do not retain clear features that mean it can’t be properly identified, then that could mess up our study of history and evolution. Through this study, it was discovered that using multiple sources of data (i.e., morphology and molecular data) create far more accurate evolutionary trees than trees that don’t use both. The study of paleontology and other sciences can benefit from this knowledge to improve other experiments in the future and broaden our understanding of the world.

Citation: Asher, J. R. and Smith, R. M. 2021. Phylogenetic Signal and Bias in Paleontology. Syst. Biol. 0(0):1–23. DOI:10.1093/sysbio/syab072