Thesis (MS )--Montana State University--Bozeman, 2008. / Typescript. Chairperson, Graduate Committee: David Varricchio. Includes bibliographical references (leaves 48-53).

Thesis (Ph. D.)--Ohio University, 2006. / Title from PDF title page (viewed on Jan. 27, 2007). Includes bibliographical references (p. 209-236).

No description available.

Paleontology is based on fossils but what is the link between fossil specimens and our reconstruction of life history seems to be ambiguous. The majority of paleontological studies focus on fossil morphology to infer their phylogenetic status, but recently increasing number of studies emphasize the role of paleontological data rather than particular specimens. Datasets construction and data processing are still basic in many paleontological studies, thus hampering the transition towards data-driven paleontology. More importantly, there has been a lack of understanding of the difference between data and information embedded inside. In this thesis, I present examples of three kinds of paleontological studies driven by fossil, data, and information, respectively, which shows the reconstruction of evolutionary history via different level of features from fossils. Chapter 1 shows the evolution and development of ceratopsian dinosaurs with emphasis on the fossil materials from the Gobi Desert, Mongolia. Chpater 1.1 reports Beg tse, a neoceratopsian dinosaur that is sister to all other know neoceratopsians, and morphologically and temporally between neoceratopsians and more basal ceratopsians. In chapter 1.2, to further explore the development of Protoceratops as well as other ornithischian dinosaurs, two embryonic Protoceratops skulls are CT-scanned and compared with more mature Protoceratops and other ornithischian dinosaurs. The results show strong peramorphosis in ceratopsian dinosaurs and conservative cranial development in stem ornithischians. Chapter 1.3 reports a new species of Protoceratops, P. tengri, which bears a regular wavy pattern along its neck frill that is absent in almost all previously reported Protoceratops. Such structure may function as display as it seems to be the ancestral form of other patterned cranial structures in more derived ceratopsids. Chapter 2 focus on data-driven paleontological studies, especially the applications of artificial intelligence (AI). Chapter 2.1 is based on the data comprised from chapter 1.2, deep neural networks (DNNs) are used to segment CT slices of embryonic Protoceratops fossils and have reached human comparable performance, but the generalization ability of such models remains questionable. Chapter 2.2 shows DNNs-based localization and segmentation of osteons in histological thin sections from Alvarezsaurian dinosaurs. The results indicate a truncated development pathway rather than compressed development during the miniaturization of this group. Chapter 2.3 is a short review about previous AI applications in paleontology, in which a large portion is based on data from foraminifera, insects, and other microfossils while only few are working with vertebrate fossils. There are approximate 10-year gap in algorithms and datasets between paleontology and mainstream AI studies. Chapter 3 explores the even basic level of data-driven paleontology, the information. Under the framework of information theory and communication system engineering, chapter 3.1 introduces the basic concepts of information theory and how they are represented in paleontological studies. Chapter 3.2 quantify the information entropy, mutual information, and channel capacity in morphological character matrices of various groups of vertebrates. The results suggest alternative weighting strategy in phylogenetic analysis and question current construction strategy of morphological character matrices. Chapter 3.3 makes further perspective about the application of information theory in paleontological study by treating it as a communication system. During the last two decades, the increase of data and appearance of novel methods have led many research fields transiting towards data driven. However, the construction of datasets, harnessing of novel data processing methods, and establishment of a general theory all indicate significant lags between paleontology and many other research fields. This thesis provides the very initial examples towards data-driven paleontological studies.

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.

No description available.

A dissertation submitted to the Faculty of Science, University of the Witwatersrand, in partial fulfilment of the requirements for the degree of Doctor of Philosophy. Johannesburg, 2016. / The Palaeontological record of South Africa is remarkable in that it preserves the two major temporal transitions of the Mesozoic: The Triassic–Jurassic boundary (the Elliot Formation) and the earliest depositional stages of the Cretaceous (the Kirkwood Formation). Work within the Elliot Formation has reiterated the importance of this horizon for our understanding of the early evolution and subsequent radiation/diversification of basal sauropodomorph dinosaurs. Moreover, inextricably contained within this radiation is the early evolution of the columnar-limbed, long necked sauropods, the largest terrestrial animals to have ever evolved. The Elliot Formation therefore imparts vital information on the genesis of the group that would become the dominant dinosaurian herbivores throughout most of the Mesozoic. However, several outstanding issues obscure a full understanding of this important radiation. Of primary concern is the complicated taxonomy of the sauropodomorphs of the Upper Triassic lower Elliot Formation and a lack of current consensus as to what precisely constitutes a true sauropod. The latter issue is further complicated by a lack of well-preserved sauropod material prior to the Toarcian. The discovery of new, associated material from both the lower and upper Elliot Formation has direct relevance to both of these concerns. Specifically, although the genus Eucnemesaurus is supported in the current analysis, the bauplan diversity of lower Elliot Sauropodomorpha remains relatively conservative save for the stocky pedal architecture of Blikanasaurus and the autapomorphically robust morphology of a newly rediscovered ilium that is potentially referable to it. Within the upper Elliot Formation, a recently discovered highly apomorphic bone-bed is diagnosed as a new species of sauropod that, in addition to placing the earliest unequivocal sauropods within the basal rocks of the Jurassic, suggests the underlying ecological factors driving the divergence of the derived sauropodan bauplan. In addition to new information provided by the Elliot Formation, two decades’ worth of collecting from the Early Cretaceous Kirkwood Formation affords a long overdue insight into the sauropod fauna occupying southern Gondwana at the outset of the Cretaceous. The surprising diversity of forms recognized from the Kirkwood suggests that the taxonomic decline of Sauropoda previously inferred for the earliest Cretaceous is a product of sampling bias compounded by a generally poor fossil record. However, a lack of absolute dates for the Kirkwood Formation means that the plethora of “Jurassic-type” specimens is potentially explicable via their being contemporaneous with similar Late Jurassic faunas of eastern Africa and North America. / LG2017

Thesis (MS)--Montana State University--Bozeman, 2008. / Typescript. Chairperson, Graduate Committee: David Varricchio. Includes bibliographical references (leaves 92-104).

Thesis (M.Sc.) - Carleton University, 2006. / Includes bibliographical references (p. 94-98). Also available in electronic format on the Internet.

Thesis (Ph. D.)--University of Chicago, Dept. of Organismal Biology and Anatomy. / Includes bibliographical references. Also available on the Internet.