Thesis (M.A.)--Texas State University--San Marcos, 2010. / Vita. Appendices: leaves 59-98. Includes bibliographical references (leaves 99-104).

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Disarticulated, commingled, and fragmented assemblages occur over a range of geographic and temporal contexts, yet the relationship between the representation and weathering of bone in these collections is unclear. Previous studies have produced inconsistent results and there is little elaboration discussing why the representation of large bones differ from small bones in archaeological collections containing commingled remains. The purpose of this research was to determine which bones were better represented, and if the representation correlated to the weathering of bone in the collection of human remains from the Battle of Stoney Creek, a War of 1812 site. The soldiers from the battle were likely buried in a mass grave; however, almost 200 years of extensive taphonomic disturbances created an assemblage that was disarticulated, commingled, and fragmented. A database of the collection was used to gather information on bone fragment completeness recorded using the zonation method (Knüsel and Outram 2004), and weathering scores recorded using the scale by McKinley (2004). Results from the Z-statistic and Wilcoxon Rank-Sum statistic indicated that small bones (metacarpals, metatarsals, tali and calcanei) were better represented and less weathered than long upper and lower limb bones (femora, tibiae, fibulae, humeri, ulnae and radii) (p=0.05). The binomial distribution also determined that the crania were underrepresented in comparison to two cemetery sites; the West Tenter Street and Cross Bones burial ground (p=0.1). There are a number of possible reasons for this expression of representation and weathering including the size, morphology, and density of bones, taphonomic disturbances, the burial environment (e.g., soil characteristics, the feather edge effect), and clothing. This study highlights the importance of preservation analyses in commingled, disarticulated, and fragmented collections. The findings from this research suggest that small bones may be better represented than the larger limb bones at sites with extensive taphonomic disturbances. / Thesis / Master of Arts (MA)

Pre-Pleistocene freshwater fish assemblages in the eastern United States are exceedingly rare, limited to only a handful of localities. The Gray Fossil Site, an early Pliocene sinkhole fill in northeast Tennessee, has yielded an abundance of vertebrate remains, including fish. Comparison with extant and fossil fish taxa reveals a depauperate ichthyofauna consisting of only two centrarchid genera: Micropterus cf. M. salmoides (black bass) and Lepomis sp. (sunfish). This material includes hundreds of specimens and represents the oldest centrarchid material from the eastern United States; it has potential to inform our understanding of centrarchid evolution and diversification. Fishes of the genus Micropterus are opportunistic predators that feed increasingly on fish and even terrestrial vertebrates as they increase in size. Lepomis, smaller Micropterus, and terrestrial vertebrates such as frogs and salamanders likely formed a major food source for Gray Fossil Site Micropterus. Extant fishes in the genus Lepomis are generally predators of aquatic insect larvae, small crustaceans, zooplankton, and other aquatic invertebrates and prey occasionally on small fish. Lepomis from the Gray Fossil Site were likely non-specialized predators of aquatic invertebrates – they are “short-jawed,” indicating low levels of piscivory and lack the robust pharyngeal jaws associated with extensive feeding on mollusks. Extant species of Micropterus and Lepomis occupy a wide variety of freshwater habitats but typically only spawn in shallow, open water with soft substrate overlying gravels. This suggests these conditions were present in the sinkhole pond. The absence of other fish species that are ubiquitous in streams and rivers in the southeastern United States today suggests that the sinkhole pond was not connected to surrounding waterways by surface hydrology. In addition to large numbers of isolated bones, several articulated and partially articulated fish specimens have also been recovered and show minimal evidence of postmortem disarticulation or scavenging. This suggests a cold and/or anoxic hypolimnion within the sinkhole pond as well as an absence of scavengers such as crayfish, which have not been documented from the site. Osteological thin sectioning of fish atlantes suggests slow growth rates in Gray Fossil Site fishes and small overall size for their age, possibly due to high competition or limited surface area of the pond they inhabited.

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.

Yes

This study utilized freshwater mussel shells to assess the role of mercury contamination in the North Fork Holston River, an aquatic habitat affected by extensive extirpations of mussel populations starting in the early 1970's. Mussel shells (n=366) collected from 5 sites, upstream and downstream of Saltville (where mercury was used from 1950-1972) were analyzed to test if: (1) geochemical signatures of shells record variation in mercury levels relative to the contamination source; and (2) shell taphonomy could be used to differentiated affected and unaffected sites. Analysis of 40 shells for geochemical signatures using atomic absorption spectroscopy indicated a strong longitudinal pattern. Mercury content was as follows: upstream sites had low Hg concentrations (<5 to 31ppb), shells directly below Saltville had high concentrations (23-4,637ppb), shells 18km downstream of Saltville displayed intermediate values (7-115ppb), and those 38.4km downstream were comparable to upstream sites (<10ppb). Two pre-industrial shells collected from Saltville in 1917 also yielded Hg estimates (5-6ppb) comparable with upstream estimates. The Hg content was not correlated with shell length (r=-0.3; p=0.2) or degree of taphonomic alteration (r=0.18; p=0.28). Analysis of 366 shells for taphonomic signatures indicated that shells are most heavily altered and fragmented directly downstream of Saltville. In contrast, upstream sites, inhabited by reproducing mussel populations, contain many fresh-dead shells. Taphonomic signatures can thus be used to differentiate sites with different extirpation histories. Relic mussel shells can provide useful spatial and temporal data on Hg concentrations in polluted ecosystems and offer a tool for delineating areas with unknown extirpation histories. / Master of Science

Carbonaceous fossil preservation is an important taphonomic window that provides critical perspectives on the evolutionary history of life. However, phylogenetic interpretation of carbonaceous fossils is not straightforward. This is largely because critical biological information is usually lost during fossilization and three-dimensional morphologies are flattened into two-dimensional compressions. Hence, innovative techniques and methods are required in order to better understand the evolutionary significance of these fossils. To achieve this goal, this dissertation is focused on using an array of innovative research techniques to investigate the paleobiology, biostratigraphy, and taphonomy of carbonaceous fossils in critical times of early life evolution, including Neoproterozoic and Cambrian. Chapters 2 to 5 in this dissertation present original research that helps to decipher hidden biological structures of various carbonaceous fossils using a series of research methods. An improved understanding of these carbonaceous remains will ultimately advance our knowledge regarding the early evolutionary history of life on Earth. Chapter two describes new cellular structures of the carbonaceous compression macrofossil Chuaria using backscattered electron scanning electron microscopy. The data show that Chuaria, which is one of the most common fossils in Neoproterozoic and whose phylogenetic interpretation has been uncertain, is likely a multicellular eukaryote. Chapter three is aimed to resolve a long debate on the depositional age of the Gouhou Formation in the Huaibei region of North China and to constrain the Precambrian-Cambrian (P-C) boundary in this area. Using a low manipulation maceration technique, this study reveals a diverse assemblage of organic-walled microfossils from the lower Gouhou Formation, suggesting that the lower Gouhou Formation is Tonian in age and the P-C boundary may be located within the Gouhou Formation. Chapter four reports a group of problematic carbonaceous compression macrofossils from the Hetang Formation in South China. Taphonomic analysis using optical and electron microscopy tentatively suggests that these carbonaceous macrofossils are probably carapaces of bivalved arthropods. The last chapter describes a group of sponge fossils with carbonaceous preservation from the early Cambrian Hetang Formation in South China. Using an array of electron microscopy techniques, this study reveals that siliceous spicules of the Hetang sponges have large axial filaments and large proportions of organic material, suggesting early sponge in the Precambrian and Cambrian may have had weakly mineralized or entirely organic skeletons. Results from this study helps to reconcile the apparently conflicting molecular clocks, biomarker fossils, and spicular fossils of early sponges. / PHD / Carbonaceous fossils can provide important information about the life on Earth in deep time. However, biological interpretation of carbonaceous fossils is not always straightforward, largely because critical biological information is usually lost during fossilization. To address this matter, this dissertation presents original research that helps to decipher hidden biological structures of various carbonaceous fossils using a series of innovative research techniques and methods. Specifically, Chapter two describes new cellular structures of the carbonaceous compression macrofossil Chuaria using backscattered electron scanning electron microscopy. The data show that Chuaria, which is one of the most common fossils in Neoproterozoic and whose biological interpretation has been uncertain, is likely a multicellular eukaryote. Chapter three is aimed to resolve a long debate on the depositional age of the Gouhou Formation in the Huaibei region of North China and to constrain the Precambrian-Cambrian (P-C) boundary in this area. Using a low manipulation maceration technique, this study reveals diverse organic-walled microfossils from the lower Gouhou Formation, suggesting that the lower Gouhou Formation is Tonian in age and the P-C boundary may be located within the Gouhou Formation. Chapter four reports a group of problematic carbonaceous compression macrofossils from the Hetang Formation in South China. This study, using optical and electron microscopy, suggests that these carbonaceous macrofossils are probably carapaces of bivalved arthropods. The last chapter describes a group of sponge fossils with carbonaceous preservation from the early Cambrian Hetang Formation in South China. Using an array of electron microscopy techniques, this study reveals that the Hetang sponges developed spicules with large proportions of organic material, suggesting early sponge in the Precambrian and Cambrian may have had weakly mineralized or entirely organic skeletons. Therefore, an improved understanding of these carbonaceous remains presented in this dissertation will ultimately advance our knowledge regarding how the early life on Earth evolved through time.

This thesis presents the results of geoarchaeological investigations of several archaeological sites along the Elm Fork of the Trinity River in north central Texas. Archaeological data recorded from mitigation excavations in Denton and Cooke counties were analyzed to understand the geologic impacts on faunal preservation resulting from site formation processes. The faunal assemblages are highly fragmented, even in settings known for good preservation. A combined approach using geoarchaeological and taphonomic techniques was implemented to examine how fragmentation, evidence of soil weathering, and differential preservation were impacted by differing geologic conditions throughout the river basin. Intrasite and intersite results of the sites show that a great deal of variability of faunal preservation is present at difference scales of analysis.

A Dissertation submitted to the Faculty of Science, University of the Witwatersrand, Johannesburg, in fulfilment of the requirements for the degree of Master of Science. April, 2013 / Recognising the mechanisms that led to the deposition of the Plio-Pleistocene caves of South Africa provide an irreplaceable window into the environment at the time. Differentiating between various accumulating agents based on the markings and accumulation variances has become an integral part of palaeontological research. Large birds of prey have been investigated for their connection to the Australopithecus africanus type specimen, commonly, the Taung Child. The verreaux’s eagle, Aquila verreauxii, was investigated in this study to establish whether it produced a taphonomic signature that would be distinguishable from other similarly sized raptors and small mammalian carnivores. Prey remains were collected from 11 nesting-sites in the Gauteng and Northwest Provinces as well as nesting-sites from across the Northern and Western Cape Provinces. The objective was to illustrate how prey selection was directly influenced by the immediate environmental stresses. Prey was analysed in terms of prey choice, skeletal part representation and the markings that the skeletal elements bore. Of the total of 886 specimens that were collected, rock hyrax (Procavia capensis), hares (Lepus sp.), Smith’s red rock rabbit (Pronolagus rupestris) and helmeted guineafowl (Numida meleagris) were the most common. The skeletal part representation directly mirrors the feeding behaviour of Verreaux’s eagles: body parts with larger muscle attachments and skeletal elements covering choice meat options were most often targeted and damaged. Finally, ten damage types were recorded as well as the combinations thereof, of which chewed and crenulated edges, V-nicks, removal of bone and punctures featured prominently. The results showed that verreaux’s eagles do leave a characteristic taphonomic signature in terms of the assemblage composition as well as the markings on bone surfaces.