The molecular components of life (i.e., biomolecules such as DNA, proteins, lipids) have the potential to preserve in animals that have been extinct for millions of years, offering a scale of analysis previously inaccessible from the fossil record. As new technology (e.g., high resolution mass spectrometry) has been incorporated into fossil analyses, researchers have begun to detect biomolecules in terrestrial vertebrates dating back to the Triassic Period (~230 Ma). However, these biomolecules have not been demonstrated to be the biological remains of these ancient animals and may instead be exogenous organic contaminants. Here, I developed a series of analytical techniques to detect and interpret the preservation of the degraded remains of the most common protein in bone, collagen, in terrestrial vertebrates from two time slices that represent the two ends of the preservation spectrum: a "shallow time" study of fossils <150,000 years old from different burial environments (i.e., permafrost, fluvial and hot springs) and a deep time study of dinosaurs (~212 - 66 Ma) from the same burial environment (i.e., fluvial), representing the current limit of the reported protein preservation in the fossil record. Unlike previous studies that have focused on organic extractions to detect biomolecules, I studied intact fossil bones and the rocks they were found in, to understand more about the effect of burial conditions on preservation and potential alternative sources of organic compounds. I found endogenous amino acids (the degradation products of proteins) and lipids in the mammoth bones, although they were already heavily degraded in fluvial environments, even on such short timescales. I also found that there were amino acids and lipids preserved in the dinosaur bones, however tests on the age of the amino acids and the types of lipids present, demonstrate that they are not original to the animals in this study. Therefore, fluvial environments, one of the most common depositional environments preserved in the geologic record, are not conducive to the preservation of proteins on long timescales and researchers should be cautious when using these biomolecules to make interpretations about the biology of ancient animals. / Doctor of Philosophy / An outstanding challenge in the geosciences is understanding how living tissues are altered and preserved when an organism enters the fossil record. Studying the information encapsulated in fossils holds the key to an organism’s journey from death to discovery. Over the last few decades, studies of the taphonomy (i.e, how an organism decays and fossilizes) of extinct organisms have shifted their focus from how animals are preserved to what of the original tissues remain. The preservation of organic molecules (e.g., nucleic acids) over long time scales has raised a number of interesting questions (e.g., the preservation potential of DNA) and has been met with equal shares of optimism and apprehension. But ultimately, the preservation of molecular information has the potential to expand what is currently known about the biology of ancient animals and lead to a better understanding of the processes of fossilization, goals that require an understanding of how organic molecules (biomolecules) are altered over short-term and long-term scales and what organic compounds have persisted over the organism’s journey from death to discovery. Considering burial context is critical in determining if the biomolecules (i.e., DNA, proteins and lipids) being detected in fossils are the biological remains of ancient animals or organic contaminants from other sources. Therefore, I studied terrestrial vertebrates from two different periods of time: the “shallow time” dataset consists of mammoth bones from different burial environments (i.e., permafrost, fluvial, hot springs) that are all less than 150,000 years old and the deep time dataset consists of dinosaur bones from the same burial environments (i.e., fluvial) and range from ~212 to 66 million years old. Focusing on the influence of fluvial environments, where the majority of terrestrial vertebrate fossils are found, is key to understanding the long term preservation potential of the most common organic biomolecule in bone, collagen. Researchers have detected biomolecules like amino acids (as far back as the Triassic Period, ~230 million years), that they have linked to collagen preservation, however, no definitive evidence has been found to determine that the biomolecules detected belong to the animal preserved. I studied intact fossil bone to determine what biomolecules are present and if they can be definitively linked to the animal in which they were found. Mammoth bones are preserved on a timeline that is conducive to collagen preservation (<150,000 years) and preserve original amino acids (the degradation products of collagen) and lipids. However, degradation of these biomolecules is already apparent in the bones found in fluvial environments. The dinosaur bones have both amino acids and lipids (as well as other organics, like lignin, which is found in plants) present in the bones that are not present in the rocks where the bones were found. However, tests on the ages of the amino acids indicate that the amino acids are not old enough to be original. Therefore, I have found no evidence of original biomolecules in the dinosaur bones and suggest researchers proceed with caution when attempting to make biological interpretations about ancient animals from biomolecules discovered in fluvial environments, particularly on long (i.e., millions of years) timescales.

The extinct oyster Exogyra (Ostreoida: Gryphaeidae) thrived during the Cretaceous Period. The Genus was especially abundant in the southern parts of the United States, as these areas were once covered under a shallow sea. Left (lower) valves of the species Exogyra costata (Say, 1820), show different variations of the shells including differences in size and scarring of the scar remaining from the point of substrate attachment. The scars are often created by attaching to another organism, leaving an impression of it via a process called bioimmuration. This research analyses specimens from three sites within two different geological formations (Owl Creek Formation, Prairie Bluff Formation). Statistical analysis of attachment frequencies of collected specimens, as well as the analysis of the overall substrate availability reveals certain patterns of attachment, in addition to variations in lithologies of the study areas.

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Paleontological documentation of hybridization events has the potential to address a multitude of evolutionary and paleobiological issues unanswerable by purely biological means. However, previous studies of modern hybrids suggest that their morphology is often insufficient for their reliable discrimination. This study analyzes the morphology of an extant, genetically-identified <i>Mercenaria</i> spp. (Bivalvia: Veneridae) hybrid zone using Bookstein coordinates and multivariate methods to answer two questions: (1) can hybrid <i>Mercenaria</i> spp. individuals be identified based on morphology alone, and (2) would a <i>Mercenaria</i> spp. hybrid zone be recognizable in the fossil record? Multivariate statistical procedures (principal components analysis, canonical variate analysis, etc.) using Bookstein coordinates demonstrate that, within the hybrid zone, hybrid individuals cannot be identified due to extreme overlap with the parental taxa. The hybrid zone as a whole, however, can be identified by comparison with pure-species populations sampled from outside the hybrid zone. Hybrid zones occupy parental species morphospace plus intermediate morphospace. The technique of using multiple pure-species populations to establish species morphospace is introduced to control for processes that may also result in morphological intermediates at ecological time scales (dimorphism, ecophenotypy, and geographic variation). Four alternative causal explanations of morphological intermediates through geological time (primary intergradation, uncoupled genetic and morphological divergence, time-averaged evolving populations, and developmentally instable populations) are evaluated. A literature survey strongly suggests that neither time-averaging nor developmental instability is occurring at the beginning of a lineage's evolutionary history, and that hybridization may be much more extensive than paleontological data suggest. / Master of Science

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