Comparing Diatom Paleo-Assemblages to Determine How Different Environments Affect Diversity in the Geological Rock Record

Comparison of Diatom Paleo-Assemblages with Adjacent Limno-Terrestrial Communities on Vega Island, Antarctic Peninsula 

By: Marie Bulínová, Tyler J. Kohler, Jan Kavan, Bart Van de Vijver, Daniel Nývlt, Linda Nedbalová, Silvia H. Coria, Juan M. Lirio, and Kateřina Kopalová

Summarized by: Dani Storms, a senior undergraduate student at the University of South Florida seeking to earn a degree in Geology with a concentration in geophysics. Dani changed her major from English to Geology her sophomore year after taking an Introduction to Earth Science class taught by Dr. Sarah Sheffield. Dr. Sheffield played a significant role in helping her discover a love and curiosity of how geology shapes our everyday lives. She is interested in furthering her education by attending graduate school to earn a master degree in the field of natural hazards, preferably landslides or avalanche control. She hopes to eventually obtain a PhD as well. Dani has loved being in the outdoors her whole life. In her free time, she enjoys hiking, camping, biking, crocheting, and spending quality time with her pup, Zion. 

What data were used? Diatoms are extremely abundant microfossils that are composed of silicon dioxide (SiO2) and can be used to reconstruct different environments through the rock record (i.e., paleoenvironments). This study used statistical analysis to discover if there was a significant difference of diversity within diatom assemblages from core samples derived from two Antarctic lakes, both with varying habitats. Core samples contain sediment that was deposited in paleoenvironments and obtained by drilling into the earth, and these can give insight into how climate has changed over time. The lakes were on Vega Island, in Devil’s Bay (Lake Anónima) and Cape Lamb (Lake Esmeralda). 

The samples were viewed under 100x magnification in order to determine diatom species. The species were then categorized into sub-Antarctic, Maritime Antarctic, and Continental Antarctic groups to determine their biogeographic distribution. Samples were taken from ponds, streams, mosses, and steep habitats to compare the core samples to modern day environments. However, not enough data could be collected from the stream, mosses, and steep habitats for a fair comparison. Therefore, the comparison of habitat differences on different sides of the island was restricted to only ponds.

In order to determine if there was a significant difference between the distributions, the study considered relative abundance, species richness and evenness in relation to diatom counts. Relative abundance refers to the percentage of diatoms found in each sample, richness is the number of species found in the sample, and evenness is comparison of the relative abundance of each individual species. 

Results: Overall, diatom assemblages varied in composition significantly, most likely due to the differences in waterway connections between sites and due to some sites being isolated. Between the categories, Maritime Antarctic Region contained the greatest number of species. Nearly 43% of the taxa found on Vega Island were Antarctic in distribution, while only 6% were found within the Antarctic Continent. Sub-Antarctic accounted for 3% and less than 1% were contributed by the Antarctic Region. The study then addresses the most abundant genus and species within Lake Esmeralda and Lake Anónima. Between the 132 species observed, 100 were found within Lake Esmeralda and only 32 species were found in both lakes. This means that Lake Esmeralda has a greater richness since it contained more species. 

Lake Anónima was found to be most similar to modern environments with the most noteworthy similarities being derived from streams on Devil’s Bay. However, there were several species found only within the core sample containing the paleo-assemblage. The paleo-assemblage consisted primarily of pond and stream species. For Lake Esmeralda, many of the taxa were not found within the modern environment at all. The taxa not found in the modern environment contained both aquatic and terrestrial species of diatoms. 

The authors of the study hypothesize that the connectivity of waterways and habitat type contributed to the difference in diatom assemblage structures. Lake Esmeralda is hydrologically disconnected, meaning it does not have connections to other bodies of water. The disconnect would result in less carbon being funneled into the lake from an outside source, which could alter the chemical makeup of the lake, allowing only certain species to survive as pH levels change. There is also a possibility that Lake Esmeralda might have had a higher preservation rate that allowed for a clearer comparison of paleo-assemblages versus modern, which would explain the higher amounts of diversity between the two. 

However, Lake Anónima is the complete opposite. It is well-connected to a stream that allows for the transportation of diatoms. It also has underground drainage that connects it to other lake-systems and surface streams. The study notes that even if the transport of diatom valves were to not occur, the connection of waterways would result in similar hydrochemistry between the connected water and lakes. This could have led to less viable conditions for preservation that could result in the lower amounts of diversity found. 

Figure 3: These boxplots visualize the comparison of species richness (S), Shannon Diversity (H’), and evenness (J’) between Esmeralda Lake and Anónima Lake core samples. The thicker black lines display median values.

Why is this study important? Looking at the conditions in which modern diatoms are found compared to that of paleo-assemblages can help construct a model, or standard, that can be applied to diatoms in the fossil record. This would allow us to reconstruct paleoclimates and trends associated with how they are affected by waterway connectivity. The differences in diatom-assemblages and species could be used as indicators of climate change. The different modern species that were found to be specific to ponds, mosses, and streams could give insight to what type of habitat fossilized diatoms would have been found in. 

The big picture: As the climate begins to warm and ice melts away, the connection between waterways will more than likely increase, this would cause a more uniform distribution of diatom assemblages and loss of diversity due to the similar chemical compositions of the water. The concept of creating a model that can be applied to the differences of diatom assemblages in modern and paleo-environments could essentially allow for paleoclimate and hydrological connectivity reconstruction. For instance, if we found a more uniform distribution in a general area, we might be able to determine if there was more connectivity between body of waters at some point in the geological record. Another example would be how on average, modern-day dry mosses contain fewer species of diatoms than wet mosses. Knowing this, we could analyze fossilized mosses to give insight into whether they would have been dry or wet. We could also use the findings of this study to determine what bioregion ancient diatoms would have been in based off species type and the diversity of the assemblage. 

Bulínová M, Kohler TJ, Kavan J, Van de Vijver B, Nývlt D, Nedbalová L, Coria SH, Lirio JM, Kopalová K. Comparison of Diatom Paleo-Assemblages with Adjacent Limno-Terrestrial Communities on Vega Island, Antarctic Peninsula. Water. 2020; 12(5):1340.

A Model of Sea Star Locomotion Using Tube Feet

Sea star inspired crawling and bouncing

by: Sina Heydari, Amy Johnson, Olaf Ellers, Matthew J. McHenry, and Eva Kanso

Summarized by Max Botwin, a geology major at the University of South Florida. He is currently a senior and will be graduating in Summer 2021. He is planning to move to Texas in May and looks forward to learning more about the world of geology as he works in the field. In Max’s free time, he enjoys playing with his dog Nilla and exploring the local trails around USF’s campus.

What data were used? The model was created by the researchers using parameters that were observed and measured from Asterias rubens sea stars, such as tube foot length during extension or contraction, density of water, buoyancy, and others.

Methods: To effectively model the locomotion of sea stars, the researchers adhered to what they called “hierarchical control laws”, which was the idea that the sea star controls the direction of movement for all of its tube feet, but the power and the recovery from a contraction is determined by each tube foot at an individual level. The researchers observed sea star movement and created a mathematical model to encompass as many parameters involved with tube foot locomotion as possible, including buoyancy of the feet, density of water, extension of tube feet, etc. Researchers were also able to quantify the pull of tube feet from extending and push from contracting using length of tube feet. Researchers were able to use their model and the data they collected to run many simulations with varying numbers of tube feet over different terrain to test the speed, stability, coordination, and overall effectiveness of tube feet locomotion. Examples of the simulations run by the researchers can be found in the link here.

Results: From this study, researchers have found that sea stars give a general command to the tube feet to move in a certain direction, but the power and the recovery from a contraction of the tube feet is controlled by the individual tube feet. This allows for a crawling movement from the sea star which allows it to travel across most terrain underwater and even swim. Tube feet are only effective underwater, since they work through jet propulsion where the tube foot will extend and fill a vacuole with water, then contract and squeeze out that water to propel themselves. The tube feet on sea stars are only related to one another by their attachment to the sea star and nothing else; there is no communication between the tube feet. Despite this, tube feet seem to fall into coordinated movements, where some tube feet are angled backwards and push forwards and some are angled forwards to “pull” the sea star forward. This pseudo coordination of movement is not limited to tube feet that are adjacent to one another, which means that tube feet can fall into the same locomotion “group”, even though they are not located near one another. When this occurs, the sea star goes from crawling to a bouncing gait which is much faster, but also requires more energy and was therefore found to only be useful under certain circumstances. Researchers saw that sea stars preferred to “pull” when moving vertically and pushing when moving horizontally.

Figure 2 from Heydari et al. (2020). (a) Common sea star used in the study called Asterias rubens. (b) Image of tube feet on Asterias rubens. (c) Image showing the bouncing gait of Asterias rubens. (d) Cross section of Asterias rubens to show the parts of its nervous system. (e) The anatomy of tube feet for mature sea stars. (f) The different actions that tube feet can undertake to perform locomotion. (g) This is a schematic of the mechanical rendition of a sea star including tube feet to help model sea star movement. (h) A flow chart to describe the hierarchical motor control used to command the tube feet in the mechanical sea star.

Why is this study important? This study is important because of the versatility that sea stars have in their movement across most surfaces underwater. If this locomotion can be accurately modeled, it can be recreated for robots, vehicles, or other such applications. The ability to traverse underwater terrain can have impactful applications in many industries that need to do work on the bottom of a body of water. Imagine a vehicle that is able to remain submerged and move along the ground while underwater to repair a bridge or to clean the bottom of a lake- the possibilities are endless!

The Big Picture: This study has shed light on unknown factors involved in how tube feet are controlled by the sea star and researchers were able to study and simulate sea star locomotion but were not able to match the complexity of real sea star locomotion. Answers beget more questions and that rings true here as well; the researchers were able to answer some of the “how” for sea star locomotion but were unable to explain the “why” behind it. This study can be used as a base for future models of the same type and can go further in detail using new parameters and improve their models to better depict the movement of tube feet on sea stars.

Citation: Heydari S, Johnson A, Ellers O, McHenry MJ, Kanso E. Sea star inspired crawling and bouncing. J R Soc Interface. 2020;17(162):20190700. doi:10.1098/rsif.2019.0700

Comparing humans and dogs: how two species in close communities relate

Trabecular bone in domestic dogs and wolves: Implications for understanding human self-domestication

by: Habiba Chirchir

Summarized by Maraley Santos. Maraley is an undergrad geology major at the University of South Florida. After graduating high school at the turn of the century, Maraley did what any student with an aptitude in science does when listening to others’ advice. She went to business school! After discovering a dislike of markets and business she put her college career on pause and reassessed life. Understanding her distaste of business but a love for data and science she decided to go back to school and major in her passion, earth science. Maraley believes it is never too late to learn, and this is the mantra she repeats to herself during all those restless nights of studying. She is supported by her wonderful partner in life Jeremy, their awesome daughter Leia, and her loyal pup Charlie. In her free time, she is an aquarist, hiker, rock collector, bassist, and is learning to build things that will work.

What data were usedSamples of the adult femoral head, highest point of the thigh bone, and distal bones, the ankles, of Canis lupus (gray wolf) and the largest Canis familiaris (domestic dog) breeds were acquired from the American Museum of Natural History (AMNH) in New York City, the Field Museum of Natural History (FMNH) in Chicago, and the National Museum of Natural History (NMNH) Smithsonian Institute in Washington D.C.. The 3D image results obtained from CT scans of these samples were analyzed and the qualitative results were summarized using numerous statistical methods. 

Methods: The robustness of bone, or trabecular bone fraction (TBF), was examined in this study to test the difference, if any, between grey wolves and their relatives, the domestic dog. The femora of both species were scanned using an X-ray CT at two separate facilities at the University of Texas (UT) and the University of Chicago (UC) while the distal tibiae (lower leg bone) were scanned using another type of CT scanner. The researchers hypothesized that domestic dogs have a more gracile, or delicate, bone structure their grey wolf relatives and they  scans hypothesized that the scans would show this. 

Results: TBF analyzation in the proximal (top part) femora and the distal tibiae of the domestic dog (C. familiaris)and the wolf  (C. lupus) revealed that the average TBF of these bones in wolves is greater than in domesticated dogs. Statistical analysis showed minimal error and boxplots helped visually assess the significant differences between the robustness of the bones in wolves and dogs, with wolves showing significantly thicker bones. Wilcoxon rank-sum tests (which essentially show if two populations show differences between them or not) showed the proximal femora (figure 1) and the distal tibia (figure 2) of the wolves showed greater TBF than of those in domesticated dogs. 

Figure 1 – proximal femora trabecular bone fraction

Why is this important? The analysis done in this study was used to test the hypothesis that domestic dogs have lower TBF (a more gracile or delicate bone structure) than their wolf ancestors due to self-domestication. In other studies, we see this pattern of gracility in human bodies when comparing it to our ancestors- our bones have also seen a trend of lower TBF through time. The ability of a dog to self-domesticate was due to their propensity of pro-sociality, or friendliness, with humans. This pro-sociality was reciprocated by humans, and the close relationship we see today between these two species is evident. As two species that domesticated alongside each other and live in close communities, we can study the effects of domestication in both species and make comparisons that can help us understand that process in humans. Unlike dogs, humans do not have such close living ancestors, so using relevant examples can help build that understanding.

Figure 2 – distal tibia trabecular bone fraction

The big picture: This study adds to the literature understanding self-domestication, a process that is not only behavioral, but also biological. Research has shown that self-domestication among most species lends to smaller body sizes, decrease in skeletal robusticity and possibly a decrease in bone density. Another hypothesis that is being studied is the effect domestication has on sedentism, the reduction of the need for a species to move long distances for survival (hunting for food and water resources), staying in one place. Studying domestication and understanding humans as being domesticated animals will help identify the long-term effects of sedentary lifestyle on our bodies, diseases that may arise of a lifestyle that isn’t compatible to our biology, and help expose the effects of extreme selection pressures among our best friend, the dog.

Citation: Chirchir, H. (2021). Trabecular bone in domestic dogs and wolves: Implications for understanding human self‐domestication. The Anatomical Record304(1), 31-41.

First signs of bird extinction from 40,000-1,700 years ago on Timor-Leste

First record of avian extinctions from the Late Pleistocene and Holocene of Timor Leste 

Summarized by Julie Sanchez, a senior at the University of South Florida who is majoring in Geology. She plans to graduate with her Bachelors of Science in summer of 2021 and wishes to continue her studies in graduate school, focused in petroleum geology. Outside of her academics, she loves to embrace her crafting side by painting or designing ceramic pieces. She also loves to walk trails and observe the beautiful rocks around her. 

What data were used? The researchers collected fossil birds from excavated sites in Timor Leste and then used collections of bird skeletons from the Smithsonian Institution’s National Museum of Natural History in Washington D.C. and Bergen University Museum in Norway to identify the newly found fossils. Here, the researchers were able to obtain information on what kinds of bird skeletons were resided in Timor, as well as bird skeletons that may have migrated to Timor. Research from a previous study of these skeletons provided useful information on the taphonomy of birds in Timor that added to the understanding of the results in this article.  

Methods: Researchers set up two locations of excavation in Timor: one in Jerimalaj and the second in Matja Kuru, both of which are located on the northeast part of Timor Leste (Figure 1).  Using mesh screens, the researchers were able to wet the screens and expose the bone/fragments found. As the fossils began to appear, they were measured with a digital caliper. The texture and porosity levels of the fossilized skeletons were also noted, to  help differentiate and categorize the juvenile bird bones from the mature bird bones. Radiocarbon dating was used to determine the ages of the bones/fragments found. 

This image shows the location of Matja Kuru and Jerimalai in Timor-Leste, where the fossils were excavated.

Results: The researchers recovered 416 bird bones from Jerimalai and Mataja Kuru. Throughout the excavation, there were more species found in Jerimalai than in Matia Kuru. Unfortunately, 65% of the fossils were not distinguishable. The reason for this was because most of bones were fragments, which only allowed them to narrow it down to being just a bird fossil. With the residual 147 identifiable fossilized specimens, it was determined that there were 29 bird species across 16 families. It was found that quails and buttonquail birds were more prominent at Maja Kuru, though they are considered rare in the city of Jerimalai today. There was also a crane species found that is extinct today. This represents the first known extinction event of birds in Timor. Their research also determined that although quails and buttonquails are morphologically similar, 29 different specimens were distinguished because of differences in bone structure. The results featured only a single fragment of Blue-breasted quail, S. chinensis, which was found in Jerimalai. Six specimens found in Jerimalai were determined as Metallic Pigeons. All of this information helps researchers better understand the modern day bird populations in this area/ 

Why is this study important? For about two hundred years, researchers have been studying the birds in this area. In spite of their research, the is still a big gap in regard to what kind of birds lived in Timor. This study allows the public to observe another perspective that was once “not there.” With the addition newly discovered bird species, it allows researchers to use this information in future studies of bird biodiversity, as well as understand what bird species coexisted during the Late Pleistocene and Holocene. 

The big picture: Knowing what types of birds existed on Timor can gives us insight about the environments the birds lived in, as well as climate change, and the relationships these animals could have had with other organisms. By understanding what bird species were once there, we can better understand what Timor was like during the Late Pleistocene and Holocene. We can also use this information to better understand global sampling, as many areas of southeast Asia are still underexplored for fossils. 

Citation: Meijer, Hanneke J. M., et al. “First Record of Avian Extinctions from the Late Pleistocene and Holocene of Timor Leste.” Quaternary Science Reviews, vol. 203, Jan. 2019, pp. 170–184. EBSCOhost, doi:10.1016/j.quascirev.2018.11.005.

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).