The morphologic variability of a fossil assemblage is of interest in many paleontological studies. However, many fossil assemblages are time-averaged; that is, many generations of non-contemporaneous organisms are mixed into the same fossil bed. Assemblages of robust mollusk shells deposited in nearshore marine environments are often time-averaged over 100's to 1000's of years. Mixing many generations of a taxon can increase measured morphologic variability over that of a single generation if morphology is changing during the interval of time-averaging. If morphology is changing, time-averaging can also alter observed correlations between morphologic variables, as well as allometric growth patterns. If morphology is static, then time-averaging will not increase variability or otherwise obscure patterns of morphologic variability. Testing the effects of time-averaging on morphology will help determine the reliability of information derived from the fossil record. In this study, morphologic variability was compared between 6 standing crop, living populations of Mercenaria campechiensis (Bivalvia) and two fossil assemblages of M. campechiensis and M. permagna. One fossil sample was collected as a series of superposed units that could be analyzed individually or in aggregate. The x,y coordinates of 13 landmarks and pseudolandmarks were recorded on over 600 valves, and variability was calculated using Least Squares Procrustes Analysis. Once corrections were made for allometry, the variabilities of the samples drawn from single time-averaged fossil beds were indistinguishable from the variabilities of the recent samples. For this data set, the variabilities of the fossil samples could be used without reservation to estimate the variability of the standing crop populations from which they formed. Morphology was quite stable over the 100's to 1000's of years that likely passed as the assemblages accumulated. A small amount of analytical time-averaging of the samples increases variability slightly, but additional analytical time-averaging causes no further increase. Very slight morphologic fluctuations are evident at time spans exceeding 100's to 1000's of years. Lumping geographically separated samples and samples of different species also increases variability. Morphologic stasis is evident in Mercenaria over 100's to 1000's of years, but previous studies have indicated that evolutionary rates over this time frame are typically high. These studies are based on colonization events, however, and are biased towards high rates. Data gathered here and in previous studies suggest that local populations may evolve rapidly at their founding, but that stasis follows this initial burst of change. This model describes a pattern similar to Punctuated Equilibrium at a lower level of the genealogical hierarchy, and is here termed "Punctuated Equilibrium, Jr." This model can be further tested in empirical studies and should aid in determining the causes of species-level evolutionary patterns. / Master of Science

At the macroscopic scale, vertebrate fossils are considered exceptional when non-biomineralized (soft) tissues are preserved. Histologically, high quality is defined by trueness to original shape of a bone, preservation of fine details (e.g. canaliculi), and presence or absence of matrix material in void spaces. Some fossils are hypothesized to preserve cells and durable organelles. Traditionally, cytological details and biomolecular remains have been sought in exceptional fossils. Durable cytological features such as melanosomes do appear to follow feather preservation, but traditionally exceptional fossils are not necessarily exceptional on a microscopic scale. Here, we analyze a feathered dinosaur specimen from the Jehol Lagerstätte to assess claims of blood cell preservation and the state of potential biomolecular preservation. Beipiaosaurus inexpectus is a fairly complete specimen with preserved feathers. Though crushed, fine details in thin section are prevalent. Using Raman spectroscopy, Energy Dispersive X-ray Spectrometry, and Time-of-Flight Secondary Ion Mass Spectroscopy we found no evidence of exceptional molecular preservation. Instead, we found evidence that the vasculature, once hypothesized to contain preserved red blood cells, is filled with clay minerals, with the purported cells chemically indistinguishable from materials of other shapes infilling the vessels. Despite yielding exceptional fossils, the preservational environment of the Jehol biota does not necessarily preserve exceptional details cytologically or biomolecularly. Consequently, we conclude that a systematic approach to biomolecular and cytological preservation studies should rely on traits other than classic exceptional preservation. / Master of Science / What makes a fossil particularly excellent? Traditionally, fossils from animals with skeletons were considered high quality when many or most of the bones from an animal are preserved. If these bones line up with one another like they would in the animal when it was alive (i.e. are articulated) the fossil is even better. To be exceptional, though, soft tissues, or parts of the animal that were not hardened with minerals while the animal lived (e.g. feathers, skin) need to be preserved. All of these traits can be observed with the naked eye. With the use of a microscope, we can see how much a skeleton has been crushed and whether the spaces in the bone for blood vessels and cells have been well preserved. Additionally, we may be able to observe preserved cells, which would be exceptional. On an even smaller scale, the molecules present in a bone might be well or poorly preserved. How much the minerals that make up the bone have changed chemically from when the animal was alive is one indicator of quality. Another might be preservation of molecules that come from the animal such as DNA and the proteins present in bone. In this study, we chose an exceptional fossil based on the traits visible to the naked eye (many of the bones are present and it has feathers) and looked for evidence of cell and unique molecule preservation. On the microscope, we saw beautiful details of the structures in the bone that held bone cells and blood vessels. We also observed red spheres which have been described by other researchers as possible blood cells in the spaces for blood vessels. Using three types of machine which can identify minerals, elements, and molecules in the bone and vessels, we did not find any evidence that the spheres represent preserved blood cells. Nor did we find any evidence of exceptional molecules. However, we did find evidence that the bone itself is not highly changed from when the animal lived, though we see elements and molecules in the vessels that probably did not come from the animal. We started this study knowing that the fossil we chose is exceptional in some ways, but what we found shows that it has a mix of excellent and poor traits visible on the microscope and it does not have any excellent traits in terms of its molecules besides the minerals in the bone itself. We conclude that fossils that are exceptional in the traditional sense are not necessarily exceptional in other ways. / What makes a fossil particularly excellent? Traditionally, fossils from animals with skeletons were considered high quality when many or most of the bones from an animal are preserved. If these bones line up with one another like they would in the animal when it was alive (i.e. are articulated) the fossil is even better. To be exceptional, though, soft tissues, or parts of the animal that were not hardened with minerals while the animal lived (e.g. feathers, skin) need to be preserved. All of these traits can be observed with the naked eye. With the use of a microscope, we can see how much a skeleton has been crushed and whether the spaces in the bone for blood vessels and cells have been well preserved. Additionally, we may be able to observe preserved cells, which would be exceptional. On an even smaller scale, the molecules present in a bone might be well or poorly preserved. How much the minerals that make up the bone have changed chemically from when the animal was alive is one indicator of quality. Another might be preservation of molecules that come from the animal such as DNA and the proteins present in bone. In this study, we chose an exceptional fossil based on the traits visible to the naked eye (many of the bones are present and it has feathers) and looked for evidence of cell and unique molecule preservation. On the microscope, we saw beautiful details of the structures in the bone that held bone cells and blood vessels. We also observed red spheres which have been described by other researchers as possible blood cells in the spaces for blood vessels. Using three types of machine which can identify minerals, elements, and molecules in the bone and vessels, we did not find any evidence that the spheres represent preserved blood cells. Nor did we find any evidence of exceptional molecules. However, we did find evidence that the bone itself is not highly changed from when the animal lived, though we see elements and molecules in the vessels that probably did not come from the animal. We started this study knowing that the fossil we chose is exceptional in some ways, but what we found shows that it has a mix of excellent and poor traits visible on the microscope and it does not have any excellent traits in terms of its molecules besides the minerals in the bone itself. We conclude that fossils that are exceptional in the traditional sense are not necessarily exceptional in other ways.

Carbonaceous Compressions are a widespread preservational style for fossils, yet their taphonomy remains poorly understood. Previous studies focusing on the taphonomy of carbonaceous compressions have primarily looked at exceptionally preserved faunas in plane view. The precious nature of these fossils leaves destructive techniques of analysis out of the question, but these techniques are necessary if the taphonomy of carbonaceous compressions is to be deciphered. This study analyzes Neoproterozoic carbonaceous compressions from the Yangtze Gorges area in order to address this issue. Chuaria fossils from the Jiulongwan, Sixi, and Sifangtan sections of the Doushantuo Formation and Vendotaenia fossils from the Wuhe and Miaohe sections of the Denying Formation are microchemically analyzed in both plane view and cross section in order to gain a greater understanding of the makeup of carbonaceous compressions. Results confirm and elaborate on previous studies. Likely clay coats are detected on some Chuaria specimens, while they are absent on less thermally mature specimens. Evidence for sulfate reduction in association with carbonaceous compressions is found. Sulfur enrichment, rather than clay coats, is found in association with Vendotaenia fossils. These observations lead to the hypothesis that while organic remains require a very precise set of taphonomic conditions in order to be preserved as carbonaceous compressions, there may be more than one set of conditions that allow for preservation. More studies of a greater taxonomic and taphonomic range of carbonaceous compressions are needed, however, if the mechanisms which control this preservational pathway are to be fully understood. / Master of Science

The Ediacaran, particularly the late Ediacaran-Cambrian (E-") boundary (551-541 Ma), has been noted as a major time of biological and biochemical transition, including: the rise of predators, the emergence of skeletons, the radiation of bioturbators, and large fluctuations in oceanic chemical conditions (e.g. anoxia/euxinia/ferruginia) with emerging data  suggesting that it is not until the late Ediacaran Period (551-542 Ma) when pervasive oxidation of the deep oceans occurred. In addition, the study of Ediacaran paleobiology involves numerous factors, including but not limited to, restricted amount of outcrops, taphonomic biases, metamorphism, enigmatic phylogenetic affinities, non-actualistic atmospheric and oceanic conditions, and unusual taphonomic windows, making it difficult to assign order to the myriad types of fossils (both body and trace) found during this time . It is with these problems in mind that my dissertation focuses on taphonomic questions in the late Ediacaran. We observe fossil through the taphonomic window and thereby colors all aspects of the study of that organism. By understanding how an organism was preserved we can learn about other factors affecting it, such as their taxonomic affinities, paleoecology, and morphology. All of these factors were examined through taphonomic investigations and this can be seen in the analytical path through my chapters. In chapter two I examined the preservation of trace fossils in the late Ediacaran. In chapter three I analyzed the taphonomy of an exceptionally preserved Ediacaran fossil to solve its affinity, tubular trace or tubular soft-bodied fossil. In chapter four, understanding the nature of exceptional preservation, I investigated the taphonomy of an Ediacara fossil in coarse grained sediments. In chapter five, I combined the findings of the previous chapters and applied that knowledge to analyze the in situ three dimensional morphology of an Ediacara fossil. Each of the projects presented pairs new technologic methodologies (SEM, BSE-Z, EDS, Raman, microCT) with traditional paleontological and petrologic investigations (field work, hand sample, and petrographic thin-section analysis). The result of this union of Old and New are findings that expand our understanding of these earliest multicellular organisms, their modes of life, and their biological affinities. / Ph. D.

No / An increased number of police enquiries involving human remains buried with lime have demonstrated the need for more research into the effect of different types of lime on cadaver decomposition and its micro-environment. This study follows previous studies by the authors who have investigated the effects of lime on the decay of human remains in laboratory conditions and 6 months of field experiments. Six pig carcasses (Sus scrofa), used as human body analogues, were buried without lime with hydrated lime (Ca(OH)2) and quicklime (CaO) in shallow graves in sandy-loam soil in Belgium and recovered after 17 and 42 months of burial. Analysis of the soil, lime and carcasses included entomology, pH, moisture content, microbial activity, histology and lime carbonation. The results of this study demonstrate that despite conflicting evidence in the literature, the extent of decomposition is slowed down by burial with both hydrated lime and quicklime. The more advanced the decay process, the more similar the degree of liquefaction between the limed and unlimed remains. The end result for each mode of burial will ultimately result in skeletonisation. This study has implications for the investigation of clandestine burials, for a better understanding of archaeological plaster burials and potentially for the interpretation of mass graves and management of mass disasters by humanitarian organisation and DVI teams.

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Forensic taphonomy is concerned with investigation of graves and grave sites. The primary aim of forensic taphonomy is development of accurate estimations of postmortem interval (PMI) and/or postburial interval (PBI). Soil has previously been largely ignored, therefore this thesis is designed to investigate changes in decomposition as imparted by the soil. Furthermore the impact of cadaver interment on the surrounding soil may offer prospects for identification of clandestine graves. A series of laboratory controlled decomposition experiments using cadavers (Mus musculus) and cadaver analogues (skeletal muscle tissue (SMT); Sus scrofa, Homo sapiens, Ovis aries and Bos Taurus) were designed to investigate decomposition in burial environments. Sequential destructive harvests were carried out to monitor temporal changes during decomposition. Analyses conducted included; mass loss, microbial activity (CO2 respiration) and soil chemistry (pH, EC and extractable NH4 +, NO3 -, PO4 3- and K+). Several experimental variables were tested; frozen-thawed versus refrigerated SMT, different mammalian sources of SMT, different soil type and contribution of soil versus enteric microbial communities. Mass loss measurements for SMT experiments demonstrated a sigmoidal pattern of mass loss, however, larger cadavers (Mus musculus, 5 weeks) did not. The inhumation of SMT (frozen, unfrozen, different mammalian sources) or cadavers leads to an increase in microbial activity (CO2 respiration) within 24 hours of burial. A peak of microbial activity is attained within a week, followed by a decrease and eventual plateau. The rapid influx in microbial activity is matched by corresponding increases in pH and NH4 + concentration. pH and NH4 + are strongly correlated in soils with acidic basal pH, by comparison highly alkaline soil demonstrated no relationship. NH4 + concentration also appeared to be related directly to NO3 - concentration and cadaver or SMT mass. A decrease in NH4 + corresponds with an increase in NO3 -, however, nitrification was unpredictable. Rapid nitrification was observed in sand systems when SMT was interred, but was not noted when cadavers were interred. By comparison both sandy clay loam and loamy sand soils demonstrated rapid nitrification after inhumation of a cadaver. When cadaver or cadaver analogue mass was larger, so were NH4 + and NO3 - concentrations in systems that experienced nitrification.

[Truncated abstract] One of the standard ways of assessing time since death is from the stages of decomposition of the body. It is well known that the rate of decomposition is affected by environmental factors such as temperature and humidity. Another factor that can affect decompositional rates is the presence of breaches in the protective barrier of the skin, whether arising from antemortem injury or postmortem damage, including that occurring from animal necrophagy. Scavengers have the potential to affect decomposition by breaching the skin allowing access to associated insect material, feeding on the maggot masses, or by consumption of the carcass itself. Each locality will have its own set of features determining the rate of decomposition of the body, and variation may occur within localities based on the seasons. Such variation implies the need for local calibration of time since death against degree of decomposition and to establish the magnitude of interseasonal variation. When the localities are outdoors, the influence of potential scavengers, and the factors affecting their activity need also to be taken into account. This study investigates the interaction of environmental factors and animal scavenging on the rate of decomposition of pig (Sus scrofa) carcasses at four south-west Western Australia sites; Jandakot, Shenton Park, Perup Forest, and Watheroo National Park. Jandakot and Shenton Park are both close to the Perth metropolitan area and the western coast while Perup Forest is southern and inland and Watheroo is northern and inland. ... The most common insectivore feeding in relation to the carcasses was the Willie Wagtail (Rhipidura leucophrys) which was associated with the carcasses in all seasons and all locations except for Perup Forest. The breeding cycle appeared to have a marked influence on the intensity of scavenging by several species. The effect of season on decompositional rates was greatly reduced in carcasses that were exposed to scavenging. It took no additional time for carcasses to achieve skeletonization in winter than in the other seasons in the presence of scavenging. Scavenging had no significant impact on the rate of breakdown of carcasses in summer, when decompositional rates were greatest and scavenging at a minimum. v In Western Australia, it is not uncommon for bodies to remain undiscovered in bush environments for lengthy periods of time due to the low human population density. This study shows conclusively that it is not sufficient simply to consider the accumulated degree day (ADD) when estimating time since death by the degree of decomposition of the body. Attention must also be given to local wildlife assemblages and variations in their activities with the seasons. The implications of this research are in the determination of time of death. If the effects of scavengers accelerate decomposition this must be taken into account when any calculation since time of death is determined. The marked variations between sites in the rates of decomposition of carcasses exposed to natural animal scavenging in this study highlights the need for local calibration of time since death to decompositional stages for all locales. The techniques devised in this study are straight forward and easily conducted yet are informative and essential in determining time since death for bodies which have been exposed to animal scavenging.

The fossil population structure of the gastropod Neptunea angulata from the late Pliocene and Early Pleistocene was investigated in this project in order to contribute to a wider study on the influence of predation on populations and the evolutionary history of organisms. Over time, predator-prey relationships can drive evolution in a way similar to the Red Queen Hypothesis. However, before the effects of predation can be understood one must determine how the population dynamics functioned without the influence of predation. There are a number of problems that arise when determining population dynamics for fossil assemblages. These are usually caused by missing fossil data and the uncertain nature of their absence. Bias is rife within fossils at various stages from post-portem processes to when they are present in museum collections. One way to estimate these biases is to investigate the population structures of the fossils both directly from the fossil record and from museum collections. The variation in oxygen istopes found in N. angulata shells corresponded to yearly cycles which then were counted to determine the age of the specimen at time of death. Measuring the length of the spiral at yearly intervals provided the growth rate for the organism while it was alive. The growth rates were then used to determine the ages of specimens based on their size. The resulting ages were organized into an age distribution graph which was used to determine any museum bias. Bias in the preservation was also investigated by measuring the taphonomic damage of organisms of different size and then determine the distributions of size vs taphonomy. The ages of three specimens were found to differ even though the organisms had similar whorl lengths. As a result the growth equations differed and so different age distributions were calculated from each growth equation. All the age distributions demonstrated that the museum collections did show some bias against the smaller sized and thus younger specimens. There also appeared to be a size bias towards small N. angulata within the fossil record, with the extremely small individuals missing. The majority of the smallest specimens found in the field collections were not actually N. angulata specimens. A major problem with the results was a lack of data and a small sample size and it is highly recommended that an extensive collection and review of material be undertaken to fully determine the population structure present in the fossil assemblages. Other parts of the study, for example, the growth rates also require larger data sets in order for the confidence of the data to be improved. / I detta projekt studerades snäckpopulationer (Neptunea angulata) från Pliocen och Pleistocen för att besvara bredare frågeställningar om predation och dess inflytande på populationer och evolution. Innan man kan fastställa effekten av predation så behöver man förstå hur populationen betedde sig utan predationstryck. Flertalet problem uppstår när man studerar fossila populationer: tillgången på data kan vara begränsad och det kan vara svårt att se vad som saknas och varför. Information från fossil förloras från tiden som organismen dör fram till att de återfinns i museisamlingar. Ett sätt att uppskatta informationsförlusten är att studera fossil såväl i fossilbäddar som i museisamlingar. Genom att använda sig av den observerade cykliska skillnaden i stabila syreisotoper mellan olika tillväxtzoner i skalen av Neptunea angulata var det möjligt att uppskatta åldern på en organism vid en viss längd. Hastigheten med vilken snäckan växte beräknades genom att mäta förändringen i längd mellan olika åldrar. Genom att beräkna hur snabbt en snäcka växte så var det möjligt att använda storleken på fossilerna för att uppskatta dess ålder då den dog. Fossilen organiserades efter ålder för att visa populationsstrukturer. Förluster av fossil efter deposition uppskattades undersöktes genom att bestämma om mindre storleksgrupper var mer skadad än större storleksgrupper . Den varierade tillväxten hos olika snäckor användes för att beräkna dess åldrar. Det upptäcktes att museisamlingar tenderade att inneha större och äldre individer. Det tycktes också finnas färre små fossil av Neptunea angulata inom opartisk samling. Några av de extrement små individerna saknades helt och majoriteten av de minsta fossilen var inte ens Neptunea angulata. Skador på fossilen var större ju mindre individerna var. Mängden data inverkade negativt på denna studie och därför rekommenderas en omfattande genomgång av de tillgängliga samlingarna för att bättre kunna besvara frågor kring denna population i framtiden.