A call for unifying methods within taxonomy of Tardigrada (the water bears)

Systematics of Tardigrada: A reanalysis of tardigrade taxonomy with specific reference to Guil et al. (2019)

by: James F. Fleming and Kazuharu Arakawa

Summarized by Joshua Golub, a senior at the University of South Florida in the department of geosciences. His specific interests in geology are geophysics and the use of near surface geophysics to gain a better understanding the physical aspects of observing earth processes. While attending the University of South Florida, Joshua has worked full time in the geotechnical engineering industry. Working in the geotechnical engineering industry in soil analysis has given him a perspective on soil properties, as well as utilizing these skills for government projects.  

What data were used? The data that was used came from several sources including from the recently published paper Guil et al. (2019), which was partially criticized by the authors of this paper for having incomplete data to determine taxonomic orders within tardigrades (Figure 1). Authors used the data from all of these sources to re-analyze and understand tardigrade taxonomy. Authors used a type of analysis called BUSCO to uncover the genetic patterns of highly conserved genes (i.e., genes that don’t change for a long period of time) of the species used in this study; BUSCO is a type of analysis that helps determine the full completeness of genes within groups of tardigrades. 

Figure 1: A picture of a Tardigrade (water bear). These organisms are generally 1mm long. Image: Schokraie et al., 2012.

Methods: Evolutionary trees can be constructed with two types of data; morphological data and molecular data. Morphological data comes from the specific external shape of the organism, whereas the molecular data is collected using the DNA of the organism. Often, researchers do not have both the molecular and morphological data to construct these evolutionary trees, but when researchers do have both, it can lead to much more accurate results. This paper tries to determine if the evolutionary relationships of tardigrades are better uncovered by using both molecular and morphological data. Recent articles used primarily morphological means to determine tardigrade taxonomy, so this article set out to see how adding molecular data would change the results. Authors in this paper tested to see if using only morphological data could negatively affect the branch lengths of an evolutionary tree, which explains when certain species diverge and become independent of one another (Figure 2). One specific hypothesis that the authors tested was from a previous paper, which used morphological evidence to elevate a group within Tardigrada to Apotardigrada. This paper included an analysis of genes to determine if the findings in Guil et al. (2019), the previous paper in question, had merit to make these major changes to the taxonomy of Tardigrada. They went about this by including several additional methods to the study, including genome sequencing (uncovering the patterns of DNA in each species tested), BUSCO, and a topology analysis, which is used to determine the branch lengths and when the common ancestors of certain tardigrade groups diverged (i.e., became separate populations). 

Figure 2: This figure shows the taxonomic tree for the four tardigrade orders, the branch lengths are inserted with each branch showing the results from each particular part of the data. Each color represents a particular method of data collection that was used. These numbers determine branch length, which helps determine when specific groups of tardigrades split and became distinct species.

Results: The authors had some parts of their assessments that agreed with Guil et al., the paper that used only morphological data, but the authors determined that their analyses don’t support establishing Apotardigrada as a formal taxonomic grouping. The assessment of this paper is that a consensus has not been met when approaching the organization of Tardigrada. Among all the additional analyses that the authors introduced into the discussion of Tardigrada taxonomy, what they make abundantly clear is that there needs to be a reanalysis in how we classify and name subdivisions of Tardigrada and unite a consensus of nomenclature (the names and terms that we use to discuss the group) that can avoid leading to further confusion into the research of these organisms. 

Why is this study important? There is a vast lack of consensus on how to properly organize the taxon of Tardigrada. The proposals that the authors make is for a unification of terms and research to further advance the research of a fairly mysterious organism, but in a way that will be the most accurate. 

The big picture: This call for action, to standardize nomenclature and research methods, is one that can be utilized in all fields of science. Depending on the region of the world, research can get stuck in echo chambers, creating their own terms that are not properly shared with the rest of the scientific community so that anyone who wants to study a particular subject, like Tardigrades, can do so effectively. The authors of this paper state that these holes that sometimes lie within research creates a hindrance on the study of the subject and calling for a consensus in any field of science is always a better route than tackling a topic on your own and exempting others’ research. 

Citation: Fleming, James F., and Kazuharu Arakawa. “Systematics of tardigrada: A reanalysis of tardigrade taxonomy with specific reference to Guil et al.(2019).” Zoologica Scripta (2021).

Dogs, humans, and wolves, oh my! The evolution of prehistoric dogs

Origins and genetic legacy of prehistoric dogs: the evolution of prehistoric dogs

Summarized by Jon Belcher, a fourth-year geology major at the University of South Florida. He plans to become a hydrogeologist after graduation or become a sailor in the US Navy, whichever happens first. He is an avid backpacker and enjoys cooking.

What data were used?: Bergström and others compiled and analyzed genetic data to better understand the population history of dogs. To do so, Bergström and others sequenced 27 ancient dog genomes (i.e., the complete set of genes in an organism), and compared them against both ancient human genomes and modern-day wolf genomes. The data was obtained from using other studies, and the sequencing was performed by the researchers themselves.

Methods: The ancient dog genomes were matched to the ancient human genomes in both time and space, providing a map for how and when dogs and humans spread across the globe. To compare dogs and wolves, the aforementioned prehistoric dog genomes and modern-day wolf genomes were both sequenced, and the similarities analyzed. 

Results: It was found that the population history of dogs mirrored human lineages, suggesting that when humans expanded their ranges and moved into new areas, they took their dogs with them. Dogs largely moved with humans and evolved alongside them. However, there are some instances where the pattern of humans and dogs moving together doesn’t appear to be the case; it is believed that dogs were occasionally traded or otherwise moved between groups of humans, or that humans moved without dogs. One example given in the article is that there were clear genetic similarities between human and dog populations in East Asia and Europe. Humans and dogs in East Asia and Europe were both more closely related to each other than other populations groups that were geographically closer, such as those in the Near East (which is synonymous with the Middle East).

The distribution of domesticated dog breeds and their genetic legacies. The chart on the left side of the figure color codes the ancestry sources of these various breeds and can be used to determine the relative genetic legacy of each breed.

The researchers found that the genomic data, both ancient and modern, were consistent with the idea that there was a single point in the evolutionary transition of wolves from dogs. Furthermore, gene flow between these two species has been mainly unidirectional since that point. The concept of gene flow can best be summarized as the mixing and mingling of genes between two populations through individuals from both populations interbreeding. It was found that the wolves studied were equally related to all dog breeds analyzed, as shown in Figure 2 in the paper. The researchers used this information to further support the idea that the gene flow was unidirectional.

Modern breeds, as seen in the figure below, are mainly composites of the ancient groups studied. There are not many modern breeds that are descended only from one dog lineage. Dogs such as the Alaskan Malamute descend from the Baikal, America, and Modern European lineages. This information is useful in trying to decipher the origin of dog breeds and tracking how different lineages have interacted over time. 

Why is this study important?: This information helped to reveal how dogs have changed over time, including how they have spread over the globe and how modern breeds formed. This relationship between the movement of humans and dogs is a complex one and can have varying outcomes on the actual genetic makeup of populations. 

The geographic origin of dogs remains unclear, as the researchers could not narrow down a singular location from the data. To further their research, the authors of this paper suggest collecting data from even older populations of wolves and dogs, and utilizing other disciplines such as archaeology, anthropology and ethology (i.e., the science of animal behavior) to help pinpoint that precise moment where the first modern dogs originated. 

The big picture: While earlier studies have suggested bidirectional flow of genes between dogs and wolves, this study found that gene flow was mainly from dogs to wolves. Thus, the study helped to overturn incorrect thinking.

The study also raised multiple new questions. One from the article is “how did dogs spread across Eurasia and the Americas by the Holocene”? This question is raised because there is no currently known major human movements that are concordant with this proliferation of dogs. Another question is why, if gene flow can be bidirectional between dogs and wolves, is it only observed as unidirectional. Do dogs that have a higher amount of wolf genes tend to become wilder and thus are either killed or set free and do not survive? Or do wolves generally not have the chance to spread genes to dogs? The data presented in the article mostly talks about no gene flow for “some wolves”, so does this mean that there are other wolf populations that do receive dog gene flow? Further studies may shed light on these questions. 

Citation: Bergström, A., Frantz, L., Schmidt, R., Ersmark, E., Lebrasseur, O., Girdland-Flink, L., Lin, A.T., Storå, J., Sjögren, K.G., Anthony, D. and Antipina, E., 2020. Origins and genetic legacy of prehistoric dogs. Science370(6516), pp.557-564.

Growth patterns or models of early Cambrian trilobites

Absolute axial growth and trunk segmentation in the early Cambrian trilobite Oryctocarella duyunensis

By: Dai, T., Hughes, N., Zhang, X., & Fusco, G.

Summarized by Jared Duncan. Jared Duncan is a senior at University of South Florida working to be a geologist. He plans to work as a hydrogeologist after graduation. 

What data were used? The data used in this research came from approximately 1700 specimen of the trilobite species Oryctocarella duyunensis. From this collection, usable specimens were sorted out, as some were were too damaged or too incomplete to be able to recognize the key features of the fossils. The most important key feature the researchers were looking at in this analysis was measurements of a feature called the trunk (Figure 1). Along the trunks are numerous small ridges; the researchers recorded the distances between each ridge. 

Methods: The method for recording the sizes of these specific parts of the trilobites was through the use of calipers, a kind of ruler that gives precise measurements. Researchers also used high quality photographs of the specimens that were then measured using computer programs for precise measurements. 

Figure 1 The specimen looks like this and the trunks are the ridges with the pink squares located down the center of the fossil.

Results: From the data, they were able to find potential growth stages of the trunks. What this means is that as the trilobite grew, it kept growing more ridges to the trunk until a specific age was reached, where it stopped adding them. They found ample amounts of information regarding the actual growth patterns of the trunks. The growth between stages was not constant, but researchers were able to identify some patterns. The first 4 stages showed increasing growth rate, then there was a significant stall in growth for the fifth stage. From there, the growth was relatively constant, but slower than the initial growth stages. Last, the growth slowed down through the final stages. Usually, crustaceans and other organisms like the one studied here (trilobites belong to Arthropoda, the same group crustaceans belong to) experience indeterminate growth. This means that the creature grows until it dies. Arthropods in particular grow by molting (i.e., shedding their exoskeleton) as well, so trilobites usually grow using both of these methods. Indeterminate growth was not found in the species they researched. That lead them to conclude that it is plausible that the species had a single holaspid stage, meaning the time after the thorax (the middle section) was fully grown. It was found that, instead, they experienced determinate growth, which means the species had a molt at a specific time then stopped molting and growing larger from that point. 

Why is this important? This research is important because it came with some new discoveries on the growth of Oryctocarella duyunensis. They were able to figure out that the species showed determinant growth pattern, alongside with getting extensive data on the specific stage growths of the trunks. 

The Big Picture: Having access to this big of a collection of a type of fossil is important. Having loads of data helps make conclusions about the biology and the growth of fossil species more concrete. It further expands our knowledge on not only this extinct creature, but also gives a way for us to make comparisons with other closely related creatures. By knowing how this one kind of trilobite grows, we can make connections to other trilobites and expand on that knowledge. 

Citation: Dai, T., Hughes, N., Zhang, X., & Fusco, G. (2021). Absolute axial growth and trunk segmentation in the early Cambrian trilobite Oryctocarella duyunensis. Paleobiology, 1-16. doi:10.1017/pab.2020.63

Examining fossils of an ancient worm-like creature uncovers new features and evolutionary history

A Tube-Dwelling Early Cambrian Lobopodian

Written by: Richard J. Howard, Xianguang Hou, Gregory D. Edgecombe, Tobias Salge, Xiaomei Shi, Xiaoya Ma

Summarized by: Jace Chastain is a 3rd year student studying geology at the University of South Florida. He is looking to work in the oil or natural gas industry after graduating. Aside from geology, he enjoys writing and watching movies.

What data were used? Researchers found nine new fossils of a worm-shaped animal called Facivermis from the evolutionary group Lobopodia. These organisms lived in the Cambrian Period and were found in the Yunnan Province of China. Previously found fossils similar to these were also re-examined. All specimens were housed at the Yunnan Key Laboratory for Paleontology. 

Methods: The Facivermis fossils were examined using a microscope with both polarized and non-polarized light. Polarized light is created when light is passed through a thin slit to limit it to a certain orientation. When polarized light is used in a microscope, it can allow the user to see details that would otherwise not be seen. To detect fine details on the specimens, an electron microscope was used. One fossil was investigated using X-ray spectroscopy, which measures the way X-rays interact with different chemical elements to determine what the fossil is composed of. Phylogenetics (determining the evolutionary history) of Facivermis was done using Bayesian inference (a statistical technique in which the probability is updated as more information becomes available), parsimony (the assumption that the simplest path of evolution is most likely correct), and maximum likelihood estimation (a technique in which under a statistical model, the observed data is considered the most probable). Read more about phylogenetic methods on this  Time Scavengers blog post. Finally, drawings were created by tracing the outlines in the fossils. These drawings can be seen in Figure 1. 

Figure 1. Anatomy diagrams were created by tracing over the Facivermis fossils. D illustrates fossil A, E illustrates fossil B, F illustrates fossil C. Labels with arrows in D, E, and F point to notable features.
an, annuli (ring, similar to earthworms); g, gut; l1–5 and r1–5, left/right lobopods (limbs) 1–5; ph, posterior hooks; ps, posterior swelling; t, tube; ta, terminal anus. The alimentary canal (route where food passes through the body) is highlighted in orange where visible, with the surrounding body cavity in dashed lines. Scale bars, (A and B) 5mm; (C) 3mm.

Results: Facivermis was a worm-like animal living during the Cambrian Period from the phylum Lobopodia. As can be seen in Figure 1, it has a long worm-shaped body with a bulb at the end, and a small head at the front with feathery limbs branching off of the body. Additionally, this study discovered preserved tubes in some of the fossils that the researchers believe formed around the body for protection, like feather-duster worms today. In the past, paleontologists believed Facivermis was a stationary predator that used its long appendages to catch food. However, thanks to this study, it was discovered that Facivermis did not do this. Using the hooks on its bulb-like end, it attached itself to the sea floor, but the arms were used for filter-feeding (pulling floating food particles from the water) rather than predation. Due to the phylogenetic analysis described in the methods section, the researchers determined that Facivermis was part of the family Luolishaniidae (Figure 2). They also determined that the worm-shaped body was unique to Facivermis and considered that the lack of armor compared to its ancestors supported the idea that it lived in tubes to hide.

Figure 2. Phylogenetic tree showing the evolutionary relationships of organisms closely related Facivermis and its place in the family Luolishaniidae. Facivermis has a soft, unarmored body similar to the hallucigeniids to which it is closely related.

Why is this study important? Understanding where Facivermis lies on the evolutionary tree of life allows us to get a clearer picture of how life evolved, especially lobopodians. It also gives us a rare example in the Cambrian of a filter-feeding role being filled. The worm-like shape of Facivermis is important because it is autapomorphic (i.e., unique to this species), and the authors’ interpretation is that feeding off of food particles suspended in the water column was not the origin of paired appendages, as was previously thought.

The big picture: This study shows that Facivermis had a tube similar to the feather-duster worms of today, which it used as protection in a similar way. It also was a filter-feeder, like feather-duster worms, which is a more uncommon ecological niche and gives us insight into how the Cambrian ecosystem worked. The Cambrian was one of the earliest periods in complex life’s history on Earth and contained creatures so different from what is alive today that our knowledge is very limited. A discovery like this gives us a lot of insight into those ancient animals. Overall, this clarified Facivermis’ place in evolutionary history, and disproved a previous hypothesis as to the origin of paired appendages.

Citation: Howard, R. J., Hou, X., Edgecombe, G. D., Salge, T., Shi, X., & Ma, X. (2020). A tube-dwelling early Cambrian lobopodian. Current Biology30(8), 1529-1536.

How can the ear bones of fish help scientists determine the change of a coral reef’s fish community over time?

Reconstructing reef fish communities using fish otoliths in coral reef sediments.

By:  Chien-Hsiang Lin, Brigida De Gracia, Michele E. R. Pierotti, Allen H. Andrews, Katie Griswold, Aaron O’Dea

Summarized by Erica Fancher, a geology major at the University of South Florida. Currently, she is a senior. Although she is undecided about what field she wants to enter, she plans to attend graduate school later when the time is appropriate. When she is not studying geology, she enjoys spending time outside, reading, and being with her family. 

What data were used? In this study, the authors wanted to determine if fish otoliths (ear bones) found in coral reef sediments were an effective way of recreating the diversity of ancient fish communities. The authors stated that little is known about how the fish communities among coral reefs has changed over time, and there has not been a viable way of conducting the research. Fish otoliths were thought to be too rare to provide any significant data to research like this, until the authors sorted through coral reef sediment and found a significant number of otoliths. Juvenile otoliths were found to be indistinguishable between each other, so the authors were unable to use them in their study.

Methods: Before the authors could conduct a study, they first had to see if otoliths were a viable option for collecting data. Their hypothesis was: are scientists able to use the ear bones of fish to effectively see a change over time in ancient fish communities? To do this, the authors collected coral reef sediment from the two regions of Caribbean Panama and the Dominican Republic. Both regions had coral reefs from the mid-Holocene (the last 11,700 years) and sub-recent periods that were used in the sampling; this gave the scientists a total of four sediment samples. After the sediment was dried and weighed, they used mesh screens of varying sizes to find otoliths, the ear bones of fish. Using specific references and other guides, they sorted over 4,000 otoliths into their respective families and sometimes were able to identify the genus. After the otoliths were sorted, the authors compared the diversity and species richness among the sample reef regions and time periods.

Results: The authors concluded that using fish otoliths was an effective way of seeing a change in diversity among fish communities in coral reefs. Due to the high amount of predation in fish communities, there was an abundance (over 5,000) of otoliths found, 4,000 of which were able to be properly sorted and used to identify change in communities over time. 

The number of otoliths identified from each sediment sample. (Note that otolith counts are log-transformed.)

Why is this study important?  This study will help scientists have a clear understanding of not only coral reefs, but of the diversity that surrounds them. This research can now be replicated and applied to further investigations. Although the data of juvenile otoliths cannot be used due to indistinguishable similarities, there is still a significant number of otoliths available for study due to the natural predation among fish. Research of this nature is important in paleontology because it forged a new way of gathering information on a topic that was not well known beforehand. In this field, scientists often have limited material to work with with and the fossil record is biased because of how difficult it is for organisms of the past to become fossilized. Because of this study, the authors made available information that scientists will now be able to use in further research on similar topics. 

The big picture: Because of the outcome of this study, scientists are now able to use the information gained to apply more knowledge of paleoecology, climate change, and patterns of diversity to not only coral reefs, but the fish community around them. Coral reefs and the fish communities that inhabit them have a mutually beneficial relationship that allow each to survive and flourish. If scientists wish to continually study coral reefs and their importance to Earth’s oceans, understanding how the fish are affected through time is a vital piece of knowledge as well. As sorting guides and references improve, our taxonomic resolution will become better. This study, and all science studies in general, are a vital process in the science community because without new hypotheses and new methods of testing those hypotheses, science would not progress. This process allows new ideas to reach countless amounts of people and can spread data and methods that could further another’s research creating a ripple effect of knowledge.

Citation: Lin, C. H., De Gracia, B., Pierotti, M. E., Andrews, A. H., Griswold, K., & O’Dea, A. (2019). Reconstructing reef fish communities using fish otoliths in coral reef sediments. PloS one14(6), e0218413.

Silurian trilobites: a breakdown of gregarious behavior as it relates to predation

Summarized by David Elias (he/him). David Elias is an undergraduate student at USF expecting graduation in Summer 2021. An avid rock climber, it was only a matter of time before David found he would have a passion for studying the very rocks he climbed on. After taking a gap year, David will attend graduate school for either geophysics or structural geology. Upon graduation, David will have completed a B.Sc. in Geology with a minor in Geographical Information Systems, with undergraduate research in geophysics having contributed to the NASA TubeX project. Beyond academics, David enjoys the outdoors and stewarding it for others that are interested in getting outside. Other interests of his include spending time loved ones, coffee, and most furry animals (sorry, spiders).

What data were used? A cluster of 18 Arctinurus boltoni trilobites were extracted from the famous Caleb Quarry of Orleans County, New York. Notable for its astounding preservation potential, the locality sits within the Silurian-age Rochester Shale, placing the specimens’ age at approximately 425 million years old. Many of these trilobite fossils had evidence of injuries on their bodies. Injuries were defined by location and description. Twelve measurements were made on each specimen’s body for analysis of how similar morphology was within the collected cluster.

Methods: After collection from the Caleb Quarry in 2006, this cluster of trilobite specimens underwent preparation by minor reconstruction to fuse pieces of the specimens collected, without reducing fossil quality in visible light. After preparation, this slab of trilobites called the American Museum of Natural History (New York City, USA) home. Areas that underwent reconstruction were visible under UV light (Fig. 1) but weren’t easy to pick out under the fluorescent lights of a lab. Injury sites of each specimen were assessed under both visible and UV light in order to differentiate between injuries and reconstruction sites. The authors ran analyses to determine if there were any tangible differences in body shape between injured and uninjured trilobite specimens by employing morphometrics. Morphometrics, simply put, is analysis of body proportions of an individual specimen to other specimens. Twelve defined measurements, or landmarks, were made and compared to one another for each specimen to aid in morphometrics analysis. One specimen was left out since it had another fossilized organism covering the body. A Principle Component Analysis (PCA) was employed for morphometric analysis. A PCA essentially boils down all the different measurements made in an analysis into two variables plotted against one another to more easily understand how similar the specimens measured are. Scientists then used a statistical test, called Procrustes ANOVA, to determine significant differences in body shapes of the 18 Arctinurus boltoni trilobites. 

Results: Of the 18 Arctinurus boltoni specimens, 44% of them have injuries. Injuries to the right side comprise 87.5% of the injured specimens. All injuries found were located primarily on the pygidium (the rear end) of the trilobites, but none on the cephalon (the head). Types of injuries described were W-shaped, U-shaped, and V-shaped, as well as single spinal injuries (SSIs). It is unclear exactly which ancient predators were responsible for these injuries, though ancient mollusks or arthropods were likely suspects for the time period. It should be noted that injuries to the specimens were likely not a result of transport, as there is evidence for rapid burial in place. The depositional environment of the Rochester Shale bed was periodically tumbled by storm events, which would have suddenly buried these organisms alive. Each specimen in the cluster was also lying in similar, outstretched position, a sign that they likely aggregated during life.

An example of injuries sustained to specimen AMNH-FI-101520. Figure A points to injuries to the thorax (middle) and pygidium (end towards the left of the photo) under plain light. Figure B shows the same area under UV light. It is easy to see areas of reconstruction under UV light that might otherwise look like an injury. Scale = 1 mm.

Why is this study important?: A big question paleontologists ask is “How did critters interact with one another in the past?”. This may be a harder question to answer than you might think. Preservation of predator-prey interactions are rare in the fossil record, leaving large holes in the understanding of past ecosystems, also known as paleoecology. In order to try and fill in the blanks in this area, this cluster of 18 Arctinurus boltoni trilobites were put under the microscope, so to speak. One technique to better our understanding of paleoecology has been to use extant species as analogues for the past, and that’s just what Bicknell et al. did. Animal behavior today gave researchers a window into the past, gaining better understanding of how these trilobites received their injuries. Documenting this cluster of Arctinurus boltoni shed light on whether the cluster shows signs of predation, and if so, did the predator or prey have a strategy against one another? Were the specimens clustered together before or after death? Findings by the authors suggest the cluster had been predated on, predator-prey strategies were indeed at play, and that these individuals had aggregated before death. 

The big picture: Bicknell et al. determined that there may have been multiple predator groups that caused a range of injuries in the cluster of trilobites. Based on the preference for injuries to be on the posterior right side of the injured trilobites, either the trilobites had a lateralized defense or predators had a lateralized attack strategy. These deductions painted a picture where these trilobites were likely gathered in a group to provide protection from predators on a more open sea floor when they were buried by a storm event. This behavior has been observed in animals alive today. A dilution effect is created, making it harder for one individual to be picked off from the group. Knowing these extinct organisms engaged in gregarious behaviors as a defense mechanism from multiple predator groups gives future paleontologists a better idea of overall paleoecology in times that may otherwise seem otherworldly and perplexing.

Citation: Russell D.C. BicknellJohn R. Paterson, and Melanie J. Hopkins “A Trilobite Cluster from the Silurian Rochester Shale of New York: Predation Patterns and Possible Defensive Behavior,” American Museum Novitates 2019(3937), 1-16, (9 September 2019). https://doi.org/10.1206/3937.1

Understanding the origins of primates with new fossil evidence

Earliest Palaeocene purgatoriids and the initial radiation of stem primates

Gregory P. Wilson Mantilla, Stephen G. B. Chester, William A. Clemens, Jason R. Moore, Courtney J. Sprain, Brody T. Hovatter, William S. Mitchell, Wade W. Mans, Roland Mundil, and Paul R. Renne

Summarized by Conlan Hale, who is currently a senior at USF planning to graduate in summer 2021 with a B.S. in Geology and B.A. in Mathematics. He plans on becoming a math or science teacher after graduation, and enjoys watching Rays baseball, listening to music, and playing video games when he isn’t finding something new to learn about.

What data were used? Teeth of a new species of purgatoriid mammal (early ancestors of primates) were found in Montana, USA, as well as teeth from other purgatoriid species. The new species signals an earlier date for the spread of the ancestors of primates than originally thought.

Methods: Authors collected tooth and jaw fragments from quarries and the surrounding areas, then analyzed the shapes of the teeth based on 3D model scans.

Results: The researchers discovered several new dental and jaw fragments of Paleocene age (~66 – 56 million years old) leading them to name a new species: Purgatorius mckeeveri (after Frank McKeever, one of the first to sponsor field work in the area where the fossils were found). Based on tooth shape of other specimens from the early Paleocene, researchers were able to classify this new species within the larger family, called the Purgatoriidae. Tooth shape can also be studied to learn about an animal’s diet, and the tooth shape of P. mckeeveri is different from all other purgatoriids in having lower molars with more inflated cusps and rounded crests, as well as having slightly larger molar dimensions than other known species (among other differences). This indicates that this species’ diet was more varied and omnivorous, closer to the early ungulates (ancestors of hoofed mammals) that Purgatorius lived alongside and further from later ancestors of primates, whose diets were primarily fruit, similar to modern lemurs. 

Graph comparing the shapes of molars of Late Cretaceous to Early Paleogene mammals, with P. mckeeveri included. Notice how the Purgatorius species (yellow stars) are closer in diet to the early ungulates (green plus signs) than later plesiadapiforms (other stars).

Why is this study important? This new species pushes back the date of evolution for the ancestors of primates, and they appear from as little as 105 to 139 thousand years after the Cretaceous-Paleogene extinction (~66 million years ago). This means that Purgatorius (and, in turn, other proto-primates) began to thrive across the globe sooner than originally thought. This study also shows how helpful looking at teeth can be as a tool for understanding how and when prehistoric animals lived.

The big picture: These findings show how the ancestors of modern-day primates (and in turn, us humans) adapted and thrived the early Paleogene environment after the loss of the non-avian dinosaurs and many other species. This helps us to further understand both our origins as a species and how speciation as a process works through small changes over time, like the shape of some teeth changing to allow an animal to take advantage of a new food source.

Citation: Wilson Mantilla, Gregory P. et al, 2021, Earliest Palaeocene purgatoriids and the initial radiation of stem primates: Royal Society Open Science 8: 210050. https://doi.org/10.1098/rsos.210050

Late Cretaceous Aged Sharks Teeth in Iron Age (8th-9th century BCE) Stratigraphic Layers

Strontium and Oxygen Isotope Analysis Reveal Late Cretaceous Sharks Teeth in Iron Age Strata in Southern Levant

Thomas Tütken, Michael Weber, Irit Zohar, Hassan Helmy, Nicolas Bourgon, Omri Lernau, Klaus Peter Jochum and Guy Sisma-Ventura

Summarized by Colton Carrier, who is a senior at University of South Florida studying for his Bachelor of Science in geology.

What data were used: Fossil teeth were found in the City of David, Jerusalem (Figure 1) from two different categories of oceanic fish: bony fish and cartilaginous fish (sharks). The bony fish included Conger conger, a fish residing in deep water at approximately 1000 feet, and Sparus aurata, a coastal water fish. Both fish are extant and currently live in the Mediterranean. What researchers found in another site in Gilead and from City of David, Jerusalem was six Sparus aurata teeth. Researchers also found 10 shark teeth in City of David: teeth of Centrophorus granulosis, a deep-sea shark from the Mediterranean, and Carcharhinus plumbeus, a neustonic (living at the water surface) shark from Red Sea. Because teeth preserve different isotope levels, the extant fish and shark teeth were sampled to construct a database of the strontium and oxygen isotope levels. This data was collected because the shark teeth and other teeth in sediments from the Southern Levant (which is an area of Palestine/Israel) are of different ages and the isotopes preserved can inform us of their true ages. To complement their dataset, they also used a dataset of strontium and oxygen isotope values derived from modern fish: Centophorus granulosis, a deep-sea filter feeding shark, and modern Conger conger, to use as a reference to the shark teeth found.

Methods: First, the researchers identified the teeth and then did isotope analysis on the dental tissue, where they measured the amount of strontium and oxygen isotopes. They then did a screening for diagenetic alteration, or how the teeth were changed through the fossilization process, which consisted of X-ray diffraction, total organic carbon content determination, and LA-ICP-MS which is spectrometry (or shooting lasers at an object and seeing what rebounds back). Using LA-ICP-MS, they were able to perform the isotope analyses. Following this, they did a linear discriminant analysis to match the found fossil teeth to the teeth in the dataset in order to effectively determine the ages of the teeth. 

(A) Potential fish habitats and main bodies of water. (B) Location of Rock Cut Pool, where the fossil teeth were uncovered. (C) Location of fossils discovered in Rock Cut Pool.


Results: The results determined the age of the shark teeth found in the City of David to be of Late Cretaceous (100mya-65mya). They found the bony fish (Sparus aurata) had a lower apatite crystallinity than the shark teeth samples, meaning they were younger. Fluorapatite was the primary phase of mineral, this indicates diagenetic uptake into tooth tissue, which means the shark teeth had a longer burial time/older age. Total Organic Carbon (TOC) content of the shark teeth is 40 times lower than other pelagic sharks like the Great White Shark, and 8 times lower than the bony fish teeth found, meaning the shark teeth have been decaying longer, also lending evidence for the age of the fossil teeth. Trace elements found using spectrometry analysis were uranium and neodymium, which are typical of fossilized shark teeth. With all of the data, the shark teeth were estimated to be approximately 86.5 to 76.3 million years in age. The S. aurata teeth were similar to modern fish.

Why is this study important: Late Cretaceous shark teeth were found in Iron Age layer, 8th-9th century BCE. There is no clear answer as to how the shark teeth got there, so this raises interesting questions as to how humans may have interacted from fossils during this time. 

The big picture: Other animals can interwork fossils into new sediments, just as the authors scientifically assume that humans did to these teeth in the Iron Age. This should be a bias that should be considered in future investigations. This study is also an important interdisciplinary analysis of archaeology and paleontology that may help us begin to learn more about how humans viewed fossils and if they were moved or collected frequently in the past. 

Citation: Tütken, T., Weber, M., Zohar, I., Helmy, H., Bourgon, N., Lernau, O., Jochum, K.P., and Sisma-Ventura, G., 2020, Strontium and Oxygen Isotope Analyses Reveal Late Cretaceous Shark Teeth in Iron Age Strata in the Southern Levant: Frontiers, https://www.frontiersin.org/articles/10.3389/fevo.2020.570032/full 

Using Female Antlers to Understand Caribou Landscape Use

Historical Landscape Use of Migratory Caribou: New Insights From Old Antlers

Joshua H. Miller, Brooke E. Crowley, Clément P. Bataille, Eric J. Wald, Abigail Kelly, Madison Gaetano, Volker Bahn, and Patrick Druckenmille

Summarized by Claudia Johnson, who is a geology major at the University of South Florida. She is currently a senior who will be graduating in Fall 2021. She is interested in environmental geology and may like to work in the National Park Service after graduation. In her free time, she enjoys biking and reading.

What data were used? Caribou are a type of deer where both the males and females shed their antlers, contrary to most other deer where only males exhibit this behavior. The female caribou typically shed their antlers after they calve (i.e., give birth). Due to this timing, these antlers can give insight about the seasonal travels of the caribou. These herds have been living on this land for over 700 years but have only recently started being studied. By analyzing past antlers shed, a fuller picture of their history can be put together. This study looked at two herds in the Arctic National Wildlife Refuge of Alaska: the Central Arctic Herd on the Western Coastal Plain, and the Porcupine Caribou Herd on the Central and Eastern Coastal Plains. Their seasonal ranges are shown in Figure 1.

Methods: These antlers were collected from Alaska and analyzed for a number of variables. First, each antler was categorized based on degree of physical weathering by observing how much of the original bone texture was preserved. The antlers were separated into either recent (post-1980) or historical (pre-1980). Next, rubidium–strontium dating, a type of radiometric dating was performed. When a particular isotope of rubidium decays, it slowly decays into stable (i.e., non-decaying) strontium at an extremely consistent rate. So, by measuring the amount of strontium (⁸⁷Sr/⁸⁶Sr) in the bone, they will be able to determine the age of the antler. This analysis was also used to try to determine differences in herds and location by comparing it to available ⁸⁷Sr/⁸⁶Sr in the environment.

Results: A question posed by the researchers was whether the ⁸⁷Sr/⁸⁶Sr of the antlers would be enough to differentiate the two herds from each other in both recent and historical times. This study was able to do so. Comparing the recent and historic female antlers, no difference was found in the ⁸⁷Sr/⁸⁶Sr of the Porcupine Caribou Herd. However, the Central Arctic Herd had many differences, including an increase in variation and ⁸⁷Sr/⁸⁶Sr from historical to recent antlers. These differences in ⁸⁷Sr/⁸⁶Sr are used to understand landscape use, and these findings coincide with existing biomonitoring records, meaning that this is an accurate way to realize historic landscape use. 

Why is this study important? This study was able to provide data on caribou patterns further into history than had been done before in this area. By being able to analyze antlers hundreds of years old, as well as present-day age, the caribou’s response to environmental changes is clear. This study was able to occur because the Arctic provides excellent conditions for the preservation of antlers. The Arctic also provides a valuable setting to study the effects of climate change due to the acute effects of it that occur there. Only the Central Arctic Herd changed landscape use during the interval of change studied here, which researchers concluded was likely due to development for oil exploration, including roads and pipelines that became intrusive to the herd’s ranges in the 1970s.

The big picture: The Central Arctic Herd’s landscape use was shown to be affected by human influence. This solidifies the knowledge that human alteration of land does indeed affect organisms living in the area. In the ranges of this herd specifically, development for oil exploration has been occurring since the 1960s. It was around this time that the pregnant females had to change their old routes to avoid this infrastructure. These principals can be applied to animals elsewhere to better recognize how infrastructural development is affecting the way they live and could be harming them because they must seek out new places to live. 

Citation: Miller, Joshua H., et al. “Historical Landscape Use of Migratory Caribou: New Insights From Old Antlers.” Frontiers in Ecology and Evolution, vol. 8, 22 Jan. 2021, doi:10.3389/fevo.2020.590837.

Macroparasites and their megamammal hosts: Pleistocene-Holocene sloths

Macroparasites of megamammals: The case of a Pleistocene-Holocene extinct ground sloth from northwestern Patagonia, Argentina

by: María Ornela Beltrame, Victoria Cañal, Carina Llano, Ramiro Barberena

Summarized by Ariel Telesford, a geology major with a minor in G.I.S at the University of South Florida and is currently a senior. He plans to work within the structural geology field, whether it be in mining, construction or the oil and gas industry. He plans to complete his master’s degree in London, England in the near future. Outside of academics, he is an avid gym-goer and plays multiple sports, mainly soccer and volleyball. 

What data were used? Feces extracted from a cave in Patagonia, Argentina was examined for parasites and other variables to determine environmental factors and diet of these sloths. The samples of feces used for this study were a part of a stratigraphic unit that dated between 16,600 and 13,600 calendar years before present (B.P.). This falls within the Pleistocene Epoch that spans from 2.58 million years ago to 11,700 years ago. 

Methods: Optical microscopy at 100x and 400x was utilized to identify and study the parasites found in the feces, as well as the diet of the sloth. Pollen analysis of the feces was conducted to determine environmental factors during that time, as the types of pollen present can inform researchers about a number of environmental factors, like temperature or moisture in the area. Pollen found within these species were compared to the known pollen record.

Results: The pollen analysis revealed that the climate was generally colder than what it is today and were found to belong to a specific shrub steppe. This supports what we already know concerning a cooler climate during the Pleistocene. The microscopic work done revealed that the sloths’ diet consisted mainly of shrub and grass, due to woody fragments and herbaceous matter found. This was consistent with the type of parasites (Nematoda family, also known as roundworms) that were found within the feces, since these worms usually inhabit grassy environments. These parasites also had researchers considering the various health impacts that parasites could have had on these sloths. The species of parasites found in the feces were also found in modern-day herbivores, indicating that co-extinction did not occur along with the extinction of these sloths during the mega-mammal extinction event of the Pleistocene. These results led researchers to hypothesize that host-switching (i.e., finding a new host) likely occurred for these parasites to survive.

Figure showing the parasitic eggs found in 8 out of the 21 samples of feces. Most of these eggs belong to the nematode (roundworm) family, specifically Strongylida species.

Why is this study important? When looking at extinction events throughout geological time, a lot of focus is placed on the organisms that are directly impacted by the event. However, we know that nature is super connected and intertwined and thus we must consider the effects these extinction events have on the organisms that are extremely dependent on those that were wiped out. 

The big picture:  The research done here shows the importance of considering even the smallest organisms when we try to understand the ecology of prehistoric times. This study should improve our understanding of the relationship that organisms have with each other (parasite-host in this case). Further work in paleoparasitological studies will help us understand host-switching, co-extinction, and the domino effect of extinction events on dependent species, especially when trying to recreate prehistoric environments. 

Citation: María Ornela Beltrame, Victoria Cañal, Carina Llano, Ramiro Barberena. Macroparasites of megamammals: The case of a Pleistocene-Holocene extinct ground sloth from northwestern Patagonia, Argentina, Quaternary International, Volume 568, 2020. Pages 36-42. ISSN 1040-6182. Retrieved from https://doi.org/10.1016/j.quaint.2020.09.030. (https://www.sciencedirect.com/science/article/pii/S1040618220305796)