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.
Key:
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

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)

Origins of nocturnal habits in modern-day birds: how did modern birds become both diurnal and nocturnal creatures?

Evolutionary Origin of Nocturnality in Birds

by Yonghua Wu

Summarized by: Ana Jimenez Bustos is a geology undergraduate student at the University of South Florida. She plans to attend graduate school in a field related to volcanology, possibly planetary geology. Once she has her degree, she would like to teach and continue to do research in volcanology or planetary geology. Outside of school, she enjoys eclectic, noisy music, her dog Miranda, and loves reading and learning about birds and parrots. 

What data were used? This study compiled data from scientific literature that analyzed genomes, physical characteristics such as eye sizes, ear structure, and anatomy of fossils of ancient and modern birds. Molecular, genetic, morphologic, and evolutionary data was used to determine whether the origin of these nocturnal habits (or the habit of being active at night) was based on a common ancestor or if it evolved along the way. The active and inactive genes (genes that are ‘turned on’ or ‘turned off’ in creatures’ bodies) of eyes involved in light reception and transport were used to try to understand when birds began to live, hunt, and forage in the dark. The study analyzed the compilation of these articles’ conclusions to try to determine whether nocturnality in birds was a trait inherited from a common ancestor or if it evolved side by side in different bird species.

Methods: This study used an array of existing scientific literature to study the evolutionary origin of nocturnality in extant bird species. By analyzing existing scientific literature, the study drew conclusions regarding ancient and modern bird habits.  

Results: It is likely that the nocturnal habits of birds evolved from a common ancestor, representing some of the earliest birds. This hypothesis is supported by the morphology of existing birds, such as large eye to body ratio when compared to other vertebrates because larger eyes allow more light into the retina for clearer nocturnal vision. In addition, these birds have a relatively advanced hearing apparatus that could have evolved from the need to communicate in the dark. The lack of certain organs like the parietal eye in crocodilians and birds (today found only in lizards), which is a light sensitive organ connected to the part of the brain responsible for hormone regulation, suggests that birds had a nocturnal origin, as this organ would have been rendered useless in the dark; the ancestors of birds lost this organ millions of years ago. 

In addition, certain genes that are related to detecting movement (specifically, GRK1 and SLC24A1) are thought to have been present in the common ancestor of birds. These genes would have helped to avoid predation in low-light conditions and support the hypothesis that their ancestor was at the very least both diurnal and nocturnal. 

Activity of birds and phylogeny based on reviewed and published studies. Taxa in red present species with true nocturnality, while taxa in green contain species with occasional nocturnal habits.

Specific adaptations to nocturnal life present in modern birds likely evolved independently from each other. Owls’ asymmetric ears, for example, evolved to precisely locate prey in the dark. This trait was likely not preset in the owls’ ancestors. The deactivation of specific genes related to color vision in nocturnal birds was also likely an evolutionary adaptation to the lack of need for color vision in birds that hunt and forage in the dark. This mutation is present in owls, kiwis, and nocturnal parrots. Some modern birds such as nightjars (Caprimulgiformes) have also evolved a tapetum, which is an extra layer in the back of the eye that reflects light back into the retina. This structure often gives eyes a “shiny” look when flashed with bright lights and can help to give animal clearer vision at night. 

Genetic and morphological evidence suggests that it is possible that birds evolved nocturnal habits in parallel to each other, but it is still possible that the common ancestor of all modern birds was both diurnal and nocturnal. Since the activity patterns of modern birds’ ancestors are still mostly unknown more analysis is needed to understand the habits of ancestral birds. 

Why is the study important? Nocturnality of mammalian creatures is largely understood to have evolved to avoid competition and predation from creatures that lurked during the day, but the origin of nocturnality in birds is not so well understood. Did ancient avian (bird) ancestors also have diurnal and nocturnal habits or was it a trait that was picked up along the evolutionary road? Did this nocturnality evolve in several different species or was it inherited from a single ancestor? Studying extant nocturnal birds and birds that have a combination of diurnal and nocturnal habits may help shed light on the evolutionary history of these behaviors. Understanding these behaviors in birds (or avian dinosaurs) can also help understand the behavior of non-avian dinosaurs like other theropods such as Tyrannosaurus rex the distant past. 

The big picture: This study addresses the origins of nocturnal behavior in birds. It suggests that these habits were present in extremely distant relationships going all the way back to the time of the non-avian dinosaurs. Understanding the habits of modern-day bird ancestors can help understand how ancient birds, and even dinosaurs like Tyrannosaurus or Velociraptor, lived in the past. Previous studies have been absolutist in their approach by classifying ancient birds and their ancestors as either nocturnal or fully diurnal, but the complete story may be significantly more complex and requires more studies to fully understand. Analyzing molecular, morphological, and phylogenetic relationships together can provide a better picture of the origin of these behaviors.  

Citation: Wu, Y. (2020). Evolutionary origin of nocturnality in birds. ELS, 483-489. doi:10.1002/9780470015902.a0029073

Oldest preserved DNA gives new insight on mammoth evolution and speciation

Million-year-old DNA sheds light on the genomic history of mammoths.

By: Tom van der Valk, Patrícia Pečnerová, David Díez-del-Molino

Summarized by: Amanda Gaskins, a senior at the University of South Florida studying geology and astronomy. After she graduates, she plans on continuing her education and obtaining her master’s degree in Geological Oceanography, where she hopes to find ways to combat the effect of global warming on coral reefs. In her free time, she loves to spend time in nature and read mystery novels.

What data were used? A team of scientists made paleogenetic (i.e., studying the DNA preserved in fossils) history by extracting what turned out to be the oldest genome data from the molar teeth belonging to three different mammoth species. 

Methods: To reveal the age and makeup of the mammoth’s genetic data, the authors isolated the DNA from molars found in the Siberian permafrost. Fortunately, the cold temperatures of Siberia reduced the effects of DNA break down throughout time. From there, they used methods that maximized the restoration of short fragments of DNA. The authors utilized biostratigraphy, a branch of stratigraphy that involves correlating and assigning the relative ages of rock strata by using the fossil fauna captured within them, in order to gain an idea of when the mammoths lived. They did this by correlating the fossil remains found at the Siberian site with fossils at locations where absolute dates are available. Moreover, in order to observe how these species of mammoths adapted to their cold environment in Siberia, the authors compared the genomes of the woolly mammoth descendants with those of the ancient specimens. 

Results: Through their experiments, the authors were able obtain ages for each of the three mammoths under speculation; each mammoth specimen is discussed here using a nickname given to them by researchers. The youngest of the mammoth group, nicknamed Chukochya, lived approximately 680,000 years ago. By examining the nuclear DNA that is contained within every cell nucleus of a eukaryotic organism, the team was able to construct a phylogenetic (evolutionary) tree (Figure 1) and discovered that Chukochya actually shares a common ancestor with the wooly mammoth. This confirms the hypothesis that Chukochya was a representative of an early form of the woolly mammoth. Adycha is the second-oldest mammoth of the group, whose life span aged back 1.34 million years ago amidst the early Pleistocene. It lived before Chukochya but is an ancestor to the woolly mammoths. The oldest mammoth of the bunch was dubbed Krestovka, with mitochondrial genome (DNA found only in the mitochondria in the cell) dating confirming that it roamed the earth 1.65 Mya in the early Pleistocene.

Figure 1. This figure is a visual of mammoth evolution throughout time. The three points on the timeline represent the three species of mammoths (represented here by their nicknames) that the authors have sequenced the DNA from.

Why is this study important?: This study provides an excellent example of the potential that ancient paleogenomics have to help uncover the mysteries of evolutionary processes like speciation, in which populations evolve and develop into distinct species. Not much research has been done on deep-time paleogenomics with respect to speciation, as it would require a sample with a long range of genome time sequences, ranging at least a million years old, which the vast majority of fossils do not preserve. The previous oldest genomic data on record was recovered from a horse specimen dating back only 780-560 thousand years ago. The experiment also gives insight on the potential of utilizing DNA as a component of biostratigraphy to help correlate the ages of the rocks and fossils contained within them.

The big picture: Overall, this study shed light on the evolution of mammoths while breaking records in paleogenomic history by uncovering the most ancient DNA sample ever analyzed, pushing our knowledge of genomics all the way back into the Ice Age. The ideas and methods displayed in this experiment will be beneficial in future studies regarding temporal data.

Citation: van der Valk, T., Pečnerová, P., Díez-del-Molino, D. et al. Million-year-old DNA sheds light on the genomic history of mammoths. Nature 591, 265–269 (2021). https://doi-org.ezproxy.lib.usf.edu/10.1038/s41586-021-03224-9

Was it possible for trilobites to live in brackish water?

Were all trilobites fully marine? Trilobite expansion into brackish water during the early Palaeozoic

By: M. Gabriela Mángano , Luis A. Buatois, Beatriz G. Waisfeld, Diego F. Muñoz, N. Emilio Vaccari and Ricardo A. Astini

Summarized by: Abby McAleer, a senior at the University of South Florida.  She is majoring in geology with a minor in geographic informational systems. After graduation she plans to get a job in conservation or become an elementary school science teacher. In her free time, Abby loves to hike and travel with her friends. 

What data were used? Trilobite trace fossils (meaning, the marks left behind by an organism, separate from a body fossil) from the early Paleozoic were used along with stratigraphic sections from four ancient estuary (an area where fresh and sea water mix) sites. The specimens were found in sediment structures located in Northwest Argentina.  

Methods: The methods used in this study were a combination of ancient estuary outcrop identification, analysis of the different sediment types from these outcrops, and an analysis of the tracks, burrows, and trace fossils of the trilobites to compare fully marine trilobite fossils to fossils of trilobites found in brackish waters. The ancient estuary sediments were identified by dividing the valley systems of the Paleozoic Northwest Argentina Basin into 3 estuary zones; inner fluvio-estuarine (closer to the river), middle estuarine, and outer estuarine (closer to the ocean). The ancient estuary sediments were examined in a stratigraphic log, which describes the vertical changes of sediments from bottom to top in a particular area. Additionally, an analysis of how the fossil record of trilobites was altered by sedimentary processes was preformed to create a connection between paleobiology and the stratigraphic layers of the outcrops. Lastly, body fossil analysis was preformed on the trilobites to compare characteristics of offshore and onshore assemblages (deeper and shallower water, respectively). 

Results: The presence of trilobite fossils in ancient estuary environments supports the hypothesis that trilobites could handle a change of salinity and still survive. Although the presence of these fossils in the ancient estuary fossil record does not mean that the trilobites permanently inhabited these regions, it leads us to believe that trilobites migrated to these areas for food and possibly a safe place to nest and spawn. It is likely that the realization that tidal influenced estuaries were not fully marine environments helped us come to this conclusion. Figure 1 illustrates the 4 stratigraphic logs that were taken from the ancient estuaries. In this figure, we can see the expansion of the trilobites from marine to brackish water. 

Figure 1. This diagram represents the four stratigraphic logs of the ancient estuaries. In this figure, we can see the expansion of the trilobites from marine to brackish water through the column.

Why is this study important? This study helps us understand that trilobites made evolutionary changes to be able to handle the salinity change to survive, unlike other strictly marine invertebrates, like echinoderms. We can use the findings of this study to better understand the lifestyles of other marine organisms that lived during this time. 

The big picture: Previously, it was believed that trilobites could not handle salinity changes.  After this study, it has been indicated that trilobites were able to migrate to areas with fluctuating salinity for evolutionary advantages. This has helped scientist understand that assumptions of an organism’s tolerance for salinity may need to be reevaluated to limit future biases in paleontological studies.  

Citation: Mángano MG, Buatois LA, Waisfeld BG, Muñoz DF, Vaccari NE, Astini RA. 2021 Were all trilobites fully marine? Trilobite expansion into brackish water during the early Palaeozoic. Proc. R. Soc. B 288: 20202263. https://doi.org/10.1098/rspb.2020.2263

Molecular phylogeny of an elephant-like species

A molecular phylogeny of the extinct South American gomphothere through collagen sequence analysis

By: Michael Buckley, Omar P. Recabarren, Craig Lawless, Nuria Garcia, Mario Pino

Summarized by: Stormie Gosdoski a student at the University of South Florida. She will be receiving her Bachelor of Science in Geology this December, 2020. After school she plans to join the scientific community and put her degree to good use. 

Data: Phylogenetic trees are created to determine the closest possible relationships between species, like a family tree. The phylogenetic tree containing gomphotheres, a group related to modern elephants, was created by analyzing molecular differences across species and determine the relationships between gomphotheres and true elephants and mammoths. One of the most informative ancient biomolecules that scientists can use for this type of study is collagen, which is the most abundant protein in bones and teeth. 

The scientists sampled four different gomphothere fossils belonging to a genus called Notiomastodon from South America. To reduce extraneous variables that could be present in the dataset, all the fossils were taken from the same location: the Pilauco Site in Osorno, Chile. They were also taken from the same layer of sediment. The layers of sediment on Earth can be read like a book, if no other geologic event has altered their positions. The ability to read each layer like a book gives scientists the ability to date the specimens; 13,650 ± 70 years ago to 12,372 ± 42 years ago. The fossils collected from this site included two root molars, a piece of rib, and a skull fragment.

Methods: The bones had fragments removed from them using a diamond-tip Dremel drill. They were then demineralized in hydrochloric acid (meaning, the scientists removed the minerals from the bones). The collagen was extracted from the solution. It was analyzed by a machine called a Matrix Assisted Laser Desorption Ionization Mass Spectrometry Time-of-Flight Mass Spectrometry (MALDI-ToF-MS). This type of equipment is used specifically to find the protein fingerprint of cells (which, just like our fingerprints, are unique to specific groups). The data collected from these methods were compared and searched for on the Swiss-Prot database for any potential matches to the primary protein sequences that are present in the collected data. This database is a protein sequence database. A potential match in the database would mean the species are more closely related. Once the analysis was complete, the scientists then performed a phylogenetic analysis of the data collected. Meaning, they compiled this information and ran the phylogenetic analysis using these new specimens and animals belonging to the closely related proboscideans, the group including elephants and mammoths, in the database as well, to determine relationships of the organisms in question.

Results: The protein fingerprint spectra of the four specimens collected in this study compared to the spectra of woolly mammoth and American mastodon was determined to differ from one another. The collagen fingerprints were similar, but there were three variations observed in the data (figure 1). At this point, using parsimony, Bayesian analysis, and maximum likelihood (the three methods of determining evolutionary relationships) a range of phylogenies was generated. This range compared three extinct proboscideans (Mammuthus, Mammut (the American mastodon), and Notiomastodon) and other closely related mammals. The results of these comparisons showed a closer relationship between Notiomastodon and Mammut. Meaning, the South American gomphothere has a close relationship to the American mastodon (figure 2).

Figure 1 This figure is the mass spectrometry of the three species. (Top to bottom) gomphothere (green), mastodon (blue), and woolly mammoth (red). This shows observed peak difference in the spectra between the three species.

Importance: This determination of the relationship between gomphotheres and mastodons can change how scientists interpret the relationships of other species in phylogenetic studies. Are there other relationships that need to be changed? How accurate can the scientific community get with the relationships of species? How does this affect our relationship to other species? How can we use this type of analysis to track our own evolution through time? This relationship is but one small portion of a larger question and we can use this to refine what we already know about ancient and present species.

The Big Picture: As scientists, we cannot rely on what our eyes are seeing to determine the relationships between species. Using molecular analyses can give a better idea of how closely related species are to one another. This type of analysis can also show how elephants have evolved and changed through history. This can give scientists a better understanding of the biology of elephants. Who knows- maybe it could lead to predictions of how the species will evolve in the future?

Figure 2 This is the phylogenetic tree that was generated from the analysis with ancient ancestor Paenungulata at the bottom (yellow) and the branch containing the common ancestor at the focus of the study, Proboscidea (pink). The South American gomphothere (green) is the sister taxon to the American mastodon (blue). It further shows the relationships of the other species. On the left is the geologic time scale, which shows when each species was alive.

Citation: Buckley, M., Recabarren, O. P., Lawless, C., García, N., & Pino, M. (2019). A molecular phylogeny of the extinct South American gomphothere through collagen sequence analysis. Quaternary Science Reviews, 224, 105882.