Dissertations / Theses on the topic 'Fossil records'

Fossil fuel combustion produces fly-ash particles that are released into the atmosphere and deposited in the environment. A particularly characteristic kind of fly-ash is spheroidal carbonaceous particles. They are composed of an amorphous carbon matrix in which other elements are dispersed. The elemental carbon content makes them very resistant to chemical degradation and these particles can be relatively easily extracted from sediment and soil samples using a method described in this thesis. The distribution of spheroidal carbonaceous particles in lake sediment profiles, surface sediments and forest soils has been studied. Cores from several Swedish lakes have been analysed and, although the lakes are from different parts of the country, consistent trends in the deposition of the carbonaceous particles have been found. The analyses of dated cores show that the carbonaceous particle deposition in the sediments follows the same general pattern as statistics for Swedish coal and oil combustion over the last two centuries. This indicates that the sediment records reflect the history of the atmospheric deposition of particulate pollutants from fossil fuel combustion. Analysis of surface sediment samples provides an integrated picture of the deposition over the preceding few years and can be used to indicate the contemporary geographical pattern of deposition from the atmosphere. Two sets of surface sediment samples (0-1 cm) were analysed. One comprised samples from 66 lakes around Sweden's second largest city, Gothenburg, and showed very high carbonaceous particle concentrations within a distance of 50 to 100 km from the city. The second set comprised surface sediment samples from 114 lakes distributed all over Sweden. This survey of Sweden demonstrated a geographical north-south gradient with more than a hundred times higher particle concentrations in the south than in the north. This distribution is similar to the distribution of other air pollutants (data obtained from a moss survey and an air monitoring program) and suggests that carbonaceous particles in palaeolimnological investigations of air pollution, can be used as tracers for pollutants that are otherwise difficult to determine in lake sediments. Spheroidal carbonaceous particles also accumulate in soils, and forest soil samples can be used for geographical surveys of particle deposition. In Swedish podzol soils the particles mainly accumulate in the thin organic horizon and concentrations in this layer reflect the total deposition since industrialisation, although most will have been deposited during the last few decades. Since the spheroidal carbonaceous particle record in Swedish lake sediments has a characteristic temporal pattern, carbonaceous particle profiles can be used for indirect dating of recent sediment cores. Analyses of multiple sediment cores from three lakes demonstrate that carbonaceous particles can also be used for studies of sediment distribution in lake basins. Results from Gårdsjön indicate that the acidification of the lake changed sediment distribution processes from a normal sediment focusing regime to a more even distribution of sediments over the lake bottom. Liming of the lake seems to have restored normal sedimentation processes.

Diss. (sammanfattning) Umeå : Umeå universitet, 1992, Härtill 8 uppsatser

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The Gray Fossil Site is a rich Hemphillian (North American Land Mammal Age) locality located in northeastern Tennessee which has produced tens-of-thousands of fossils of multiple taxa including hundreds of individual snake skeletal remains. Analyzed here are cranial and vertebral fossils identified as belonging to various colubrid taxa including Carphophis sp., Gyalopion sp., Heterodon sp., Natricinae indeterminate, Thamnophis sp., and a new, undescribed genus and species. In addition, multiple new features of snake vertebrae are described, some of which question the validity of the genus Neonatrix. Finally, the distribution and paleoecology of the listed genera allows an interpretation of how snake biogeography have transformed in the southern Appalachians since the Hemphillian.

Water management that alters riverine ecosystem processes has strongly influenced deltas and the people who depend on them, but a full accounting of the trade-offs is still emerging. Using palaeoecological data, we document a surprising biogeochemical consequence of water management in the Colorado River basin. Complete allocation and consumptive use of the river's flow has altered the downstream estuarine ecosystem, including the abundance and composition of the mollusc community, an important component in estuarine carbon cycling. In particular, population declines in the endemic Colorado delta clam, Mulinia coloradoensis, from 50-125 individuals m(-2) in the pre-dam era to three individualsm-2 today, have likely resulted in a reduction, on the order of 5900-15 000 tCyr(-1) (4.1-10.6 mol Cm-2 yr(-1)), in the net carbon emissions associated with molluscs. Although this reduction is large within the estuarine system, it is small in comparison with annual global carbon emissions. Nonetheless, this finding highlights the need for further research into the effects of dams, diversions and reservoirs on the biogeochemistry of deltas and estuaries worldwide, underscoring a present need for integrated water and carbon planning.

In this thesis the Weichselian history of northern Sweden is investigated, with emphasis on vegetation and climate during ice-free intervals. The main method used has been pollen analysis of sediments from pre-Late Weichselian landforms. To interpret fossil pollen assemblages, comparisons with modern pollen spectra were made. Modern pollen data were retrieved through monitoring of annual pollen deposition at seven sites in northern Sweden, from the boreal forest to above the present forest-line of birch. Eight years of pollen monitoring is described and put in a larger context through comparison with monitoring data from Iceland, Svalbard, Norway and Finland. A study of sediment cores from the Riipiharju esker shows evidence of two ice free phases during the Weichselian glacial; Tärendö I and Tärendö II. The Tärendö II ice free interval includes large climatic shifts, previously not recognized, from relatively warm conditions with Betula as the dominating pollen taxon to cold conditions with dominance of Artemisia and Gramineae and back to warmer conditions again. Correlation alternatives of the north Swedish ice free intervals Tärendö I and II are: 1/ Brörup (MIS 5c; c. 105-93 ka BP) and Odderade (MIS 5a; c. 85-74 ka BP), respectively, or 2/ Odderade and early Middle Weichselian time (MIS 3; c. 59-40 ka BP). Of these, alternative 2 is regarded as the most likely. Interstadial sediments deposited in a Veiki moraine plateau during downwasting of a pre-Late Weichselian ice sheet include only Betula dominant pollen spectra, showing that the climate during formation of the Veiki moraine was relatively warm. According to stratigraphical correlation there are three possible alternatives for Veiki moraine formation. Either it was formed during 1/ early Tärendö I, 2/ early Tärendö II, or 3/ late Tärendö II. Alternative 3 implies growth of an intermediate ice sheet reaching the eastern limit of Veiki moraine distribution during the cold phase of Tärendö II.

The past climate in central Asia, and especially on the Tibetan Plateau (TP), is of great importance for an understanding of global climate processes and for predicting the future climate. As a major influence on the climate in this region, the Asian Summer Monsoon (ASM) and its evolutionary history are of vital importance for accurate predictions. However, neither the evolutionary pattern of the summer monsoon nor the driving mechanisms behind it are yet clearly understood. For this research, I first synthesized previously published Late Glacial to Holocene climatic records from monsoonal central Asia in order to extract the general climate signals and the associated summer monsoon intensities. New climate and vegetation sequences were then established using improved quantitative methods, focusing on fossil pollen records recovered from Tibetan lakes and also incorporating new modern datasets. The pollen-vegetation and vegetation-climate relationships on the TP were also evaluated in order to achieve a better understanding of fossil pollen records. The synthesis of previously published moisture-related palaeoclimate records in monsoonal central Asia revealed generally different temporal patterns for the two monsoonal subsystems, i.e. the Indian Summer Monsoon (ISM) and East Asian Summer Monsoon (EASM). The ISM appears to have experienced maximum wet conditions during the early Holocene, while many records from the area affected by the EASM indicate relatively dry conditions at that time, particularly in north-central China where the maximum moisture levels occurred during the middle Holocene. A detailed consideration of possible driving factors affecting the summer monsoon, including summer solar insolation and sea surface temperatures, revealed that the ISM was primarily driven by variations in northern hemisphere solar insolation, and that the EASM may have been constrained by the ISM resulting in asynchronous patterns of evolution for these two subsystems. This hypothesis is further supported by modern monsoon indices estimated using the NCEP/NCAR Reanalysis data from the last 50 years, which indicate a significant negative correlation between the two summer monsoon subsystems. By analogy with the early Holocene, intensification of the ISM during coming decades could lead to increased aridification elsewhere as a result of the asynchronous nature of the monsoon subsystems, as can already be observed in the meteorological data from the last 15 years. A quantitative climate reconstruction using fossil pollen records was achieved through analysis of sediment core recovered from Lake Donggi Cona (in the north-eastern part of the TP) which has been dated back to the Last Glacial Maximum (LGM). A new data-set of modern pollen collected from large lakes in arid to semi-arid regions of central Asia is also presented herein. The concept of "pollen source area" was introduced to modern climate calibration based on pollen from large lakes, and was applied to the fossil pollen sequence from Lake Donggi Cona. Extremely dry conditions were found to have dominated the LGM, and a subsequent gradually increasing trend in moisture during the Late Glacial period was terminated by an abrupt reversion to a dry phase that lasted for about 1000 years and coincided with the first Heinrich Event of the northern Atlantic region. Subsequent periods corresponding to the warm Bølling-Allerød period and the Younger Dryas cold event were followed by moist conditions during the early Holocene, with annual precipitation of up to about 400 mm. A slightly drier trend after 9 cal ka BP was then followed by a second wet phase during the middle Holocene that lasted until 4.5 cal ka BP. Relatively steady conditions with only slight fluctuations then dominated the late Holocene, resulting in the present climatic conditions. In order to investigate the relationship between vegetation and climate, temporal variations in the possible driving factors for vegetation change on the northern TP were examined using a high resolution late Holocene pollen record from Lake Kusai. Moving-window Redundancy Analyses (RDAs) were used to evaluate the correlations between pollen assemblages and individual sedimentary proxies. These analyses have revealed frequent fluctuations in the relative abundances of alpine steppe and alpine desert components, and in particular a decrease in the total vegetation cover at around 1500 cal a BP. The climate was found to have had an important influence on vegetation changes when conditions were relatively wet and stable. However, after the 1500 cal a BP threshold in vegetation cover was crossed the vegetation appears to have been affected more by extreme events such as dust storms or fluvial erosion than by the general climatic trends. In addition, pollen spectra over the last 600 years have been revealed by Procrustes analysis to be significantly different from those recovered from older samples, which is attributed to an increased human impact that resulted in unprecedented changes to the composition of the vegetation. Theoretical models that have been developed and widely applied to the European area (i.e. the Extended R-Value (ERV) model and the Regional Estimates of Vegetation Abundance from Large Sites (REVEALS) model) have been applied to the high alpine TP ecosystems in order to investigate the pollen-vegetation relationships, as well as for quantitative reconstructions of vegetation abundance. The modern pollen–vegetation relationships for four common pollen species on the TP have been investigated using Poaceae as the reference taxa. The ERV Submodel 2 yielded relatively high PPEs for the steppe and desert taxa (Artemisia Chenopodiaceae), and low PPEs for the Cyperaceae that are characteristic of the alpine Kobresia meadows. The plant abundances on the central and north-eastern TP were quantified by applying these PPEs to four post-Late Glacial fossil pollen sequences. The reconstructed vegetation assemblages for the four pollen sequences always yielded smaller compositional species turnovers than suggested by the pollen spectra, indicating that the strength of the previously-reported vegetation changes may therefore have been overestimated. In summary, the key findings of this thesis are that (a) the two ASM subsystems show asynchronous patterns during both the Holocene and modern time periods, (b) fossil pollen records from large lakes reflect regional signals for which the pollen source areas need to be taken into account, (c) climate is not always the main driver for vegetation change, and (d) previously reported vegetation changes on the TP may have been overestimated because they ignored inter-species variations in pollen productivity.
Das Paläoklima in Zentralasien, besonders in der Hochebene von Tibet (HT), ist von großer Bedeutung um globale Klimaprozesse zu verstehen und mögliche Voraussagung für die zukunft zu treffen. Als wichtigstes Klimaphänomen nehmen der asiatische Sommermonsun (ASM) und seine Entwicklungsgeschichte eine Schlüsselposition ein. Dennoch sind derzeit weder das Entwicklungsschema noch der antreibende Vorgang ausreichend verstanden. Dies gilt insbesondere für das Holozän, für welches große Kimaschwankungen und regionale Diskrepanzen weithin belegt sind. Deshalb habe ich zuerst holozäne Klimadaten zusammengefasst. Bereits veröffentlichte Publikationen aus den Monsungebieten Zentralasiens dienten als Grundlage, um die wichtigsten Klimasignale und die zugehörigen Intensitäten des Sommermonsuns heraus zu arbeiten. Anhand von Pollensequenzen aus tibetischen Seen erzeugte ich neue Klima- und Vegetationssequenzen, welche auf verbesserten quantitativen Methoden und rezenten Datensätzen beruhen. Außerdem wurden die Verhältnisse Pollen-Vegetation und Vegetation-Klima bewertet, um Schlussfolgerungen fossiler Pollensequenzen zu verbessern. Die Zusammenfassung der zuvor veröffentlichten, niederschlagsbezogenen Paläoklimadaten im Monsungebiet Zentralasiens ergab generell unterschiedliche Muster für die zwei Teilsysteme des ASMs, den Indischen Sommermonsun (ISM) und den Ostasiatischen Sommermonsun (OASM). Der ISM weist maximale feuchte Bedingungen während des frühen Holozöns auf, während viele Datensätze aus dem Gebiet des OASMs einen relativ trockenen Zustand anzeigen, besonders im nördlichen Zentralchina, wo maximale Niederschläge während des mittleren Holozäns registriert wurden. Genaue Betrachtungen der Antriebsfaktoren des Sommermonsuns ergaben, dass der ISM hauptsächlich durch Veränderungen der Sonneneinstrahlung auf der Nordhemisphäre angetrieben wird, während der OASM potentiell durch den ISM beherrscht wird - dies führt zu asynchronen Entwicklungen. Diese Hypothese wird durch rezente Monsunindizes gestützt. Sie weisen eine signifikant negative Korrelation zwischen den beiden Sommermonsun-Teilsystemen auf. Für die quantitative Klimarekonstruktion von Pollensequenzen wurde ein Sedimentkern aus dem See Donggi Cona im Nordosten der HT analysiert, der bis zum letzten glazialen Maximum (LGM) zurückdatiert wurde. Aufgrund der Tatsache, dass Donggi Cona ein relativ großer See ist, wird hiermit ein neuer Pollen-Klima-Kalibrierungsdatensatz auf Grundlage großer Seen in ariden und semiariden Regionen Zentralasiens vorgelegt. Das Konzept des Pollenherkunftsgebietes wurde in diese rezente, pollenbasierte Klimakalibrierung eingebracht und auf die Pollensequenz von Donggi Cona angewendet. Die Auswertung ergab, dass extrem trockene Bedingungen während des LGM (ca. 100 mm/yr) vorherrschten. Ein ansteigender Trend von Niederschlägen während des späten Glazials wurde durch einen abrupten Rückgang zu einer etwa 1000-jährigen Trockenphase beendet, welche mit Heinrich-Ereignis 1 in der Nordatlantik-Region übereinstimmt. Danach entsprechen die Klimaperioden dem warmen Bølling/Allerød und dem Kälteereignis der Jüngeren Dryas. Anschließend herrschten feuchte Bedingungen im frühen Holozän (bis zu 400 mm/yr). Ein etwas trockenerer Trend nach dem Holozänen Klimaoptimum wurde dann von einer zweiten Feuchtphase abgelöst, welche bis 4,5 cal. ka vor heute andauerte. Relativ gleichmäßige Bedingungen dominierten das späte Holozän bis heute. Die Klimadynamik seit dem LGM wurde vor allem durch Entgletscherung und Intensitätsschwankungen des ASM bestimmt. Bei der Betrachtung des Vegetation-Klima-Verhältnisses habe ich die zeitlichen Variationen der bestimmenden Faktoren hinsichtlich der Vegetationsdynamik auf der nördlichen HT untersucht. Dabei wurden hochauflösende holozäne Pollendaten des Kusai-Sees verwendet. Eine Redundanzanalyse (RDA) wurde angewendet um die Korrelation zwischen Pollenvergesellschaftungen und individuellen sedimentären Klimaanzeigern als auch die damit verbundene Signifikanz zu bewerten. Es stellte sich heraus, dass das Klima einen wichtigen Einfluss auf den Veränderungen in der Vegetation besaß, wenn die Bedingungen relativ warm und feucht waren. Trotzdem scheint es, dass, dass die Vegetation bei zu geringer Bedeckung stärker durch Extremereignisse wie Staubstürme oder fluviale Erosion beeinflusst wurde. Pollenspektren der vergangen 600 Jahre erwiesen sich als signifikant unterschiedlich verglichen mit den älterer Proben, was auf verstärkten anthropogenen Einfluss hindeutet. Dieser resultierte in einem beispiellosen Wandel in der Zusammensetzung der Vegetation. In Hinsicht auf das Pollen-Vegetation-Verhältnis und der quantitativen Rekonstruktion der Vegetationshäufigkeit habe ich theoretische Modelle, welche für europäische Regionen entwickelt und weithin angewendet wurden, respektive die Modelle "Extended R-Value" (ERV) sowie "Regional Estimates of Vegetation Abundance from Large Sites" (REVEALS), auf die hochalpinen Ökosysteme der HT überführt. Dafür wurden rezente Pollen-Vegetations-Verhältnisse von vier weit verbreiteten Pollen-Arten der HT überprüft. Poaceae wurden als Referenztaxa verwendet. Bei der Anwendung dieser Verhältnisse auf vier Pollensequenzen, welche die Paläoumweltbedingungen seit dem letzten Glazial widerspiegeln, wurden die Häufigkeiten von Pflanzen auf der zentralen und nordöstlichen HT quantifiziert. Anteile von Artimisia und Chenopodiaceae waren dabei im Vergleich zu ihren ursprünglichen Pollenprozenten deutlich verringert. Cyperaceae hingegen wies eine relative Zunahme in dieser Vegetationsrekonstruktion auf. Die rekonstruierten Vegetationsvergesellschaftungen an den Standorten der vier Pollensequenzen ergaben stets geringere Umwälzungen in der Artenzusammensetzung, als durch die Pollenspektren zu vermuten gewesen wäre. Dies kann ein Hinweis darauf sein, dass die Intensität der bislang angenommenen Vegetationsveränderungen überschätzt worden ist. Zusammengefasst sind die Hauptresultate dieser Dissertation, dass (a) die zwei ASM Teilsysteme asynchrone Muster während des Holozäns und heute aufweisen, dass (b) fossile Pollensequenzen großer Seen regionale Klimasignale widerspiegeln sofern die Herkunftsgebiete der Pollen berücksichtigt werden, dass (c) Klima nicht immer der Haupteinflussfaktor für Vegetationswandel ist und dass (d) das Ausmaß von Vegetationsveränderungen in zuvor veröffentlichten Studien auf der Hochebene von Tibet überschätzt worden sein kann, weil Diskrepanzen der Pollenproduktivität zwischen den Arten nicht einbezogen wurden.

Previously published descriptions of the pollen morphology of the Palmae are reviewed and discussed. The earliest macro fossil records for palms are summarised, while a more detailed review is given of the fossil records of palmlike pollen. Selected literature relating to pollen sharing some similarities to palm pollen in other monocotyledonous families are briefly reviewed, and the fossil pollen records for these families are examined. A brief chronological account of earlier systematic treatments of the palms is provided, as well as an outline of the systematic treatment of the family used in the present account. The pollen morphology of 1150 collections, representing 765 species of palms,f rom all but seveno f the currentlyr ecognisedg enera,h asb eene xamýined, as well as dispersedp alm-likef ossil pollen from the middle Eoceneo f the Isle of Wight, and of Java. Iii silit pollen of fossil palm flowers from the Messel oil shales (Germany)a re describedP. ost meiotic tetrad stageh asb eens tudiedf or representatives peciesin all subfamiliese xceptingt he PhytelephantoideaeP.o llen morphologyo f both recenta nd fossil pollen is describedf rom light, scanning electrona nd, selectivelyf rom transmissione lectronm icroscopy,w hile tetrad resultsa re from light and scanninge lectronm icroscopy.F ull detailso f preparation methods,t erminologya nd databaseus sedf or pollen morphological,f ossil and tetrad studies are given. Seventeena perturet ypes,p lus numerouss ubtypesa, nd twelve exine types with numerous subtypes are identified. The aperture types are shown to be broadly separablein to two groupsw hich are associatedw ith either simultaneous (tetrahedralt etrads)o r successive(t etragonalt etrads)m icros porogenessi. In generalt heset wo groups supportp resents ystematico pinion regardingt he subfamilies.S uccessivem eiosisi s dominanti n subfamiliesC alamoideaea nd Nypoideaew hile, with somer are exceptionss, imultaneousm eiosisp redominates in the remainingf our subfamiliesC: oryphoideaeC, eroxyloideaeA, recoideaea nd PhytelephantoideaeP.o llenu ltrastructurei s treatedi n detail only for simple tectate exines where it is important for further definition. Six types and a number of subtypesa re described.T he systematicd istributionso f aperturea nd exine types are summarisedA. trend towardsl arger pollen is noted, with the smallest pollen occurring in the least specialised subfamily, the Coryphoideae, while very large-sized pollen are characteristic of subfamily Phytelephantoideae. Monosulcate, disulcate and zonosulcate pollen are described from fossil material and closest affinities with recent palms suggested. Pollen morphology of recent palms is summarised and discussed, and compared with pollen of selected monocotyledonous families. The bearing of pollen data on recent palm systematics is considered at various levels from subfamily to species. Angiosperm pollen evolution is re-considered and evolutionary pathways for palm pollen aperture types and exine types are suggested. In the light of recent pollen morphology for the family the fossil record of palm pollen is re-evaluated. Some widely accepted affinities are challenged while previously unconsidered affinities are suggested, particularly for the mid- Cretaceous. The need is emphasized for future fossil pollen studies to look critically for pre Late Cretaceous palm-like monosulcates, which would be more informative of the early history of the family than the apparently highly evolved, easily recognisable Spini. -onocolpiles of the Late Cretaceous. Palaeogeography, environment and distribution of fossil records and depositional environment are discussed. Probable evolutionary pathways of pollen morphology, including pollen tetrad data which suggests imultaneousra thert han successivem eiosisa s the plesiomorphics tate,o ffer further evidencet hat the palmsa re indeeda n ancient group, and support the hypothesis that the palms may have originated in South America and Africa (West Gondwana)in the Late Jurassic or early Cretaceous, prior to the complete separation of these continents.

Chemosymbiotic invertebrates obtain nutrition from harbouring bacteria that oxidize reduced chemicals to produce energy for carbon fixation. This allows the animals to thrive in the extreme conditions of the deep sea, because the high concentrations of sulphide (thiotrophy) and methane (methanotrophy) at cold seeps and hydrothermal vents can be utilized by the symbiotic bacteria. This research investigates whether the key role of chemosymbiosis in shaping modern deep sea ecosystems can be traced through geological time, by using the stable isotope composition (δ13C, δ15N, δ34S) of organic matter in invertebrate shells. Shell-bound organic matter (SBOM) was isolated using various shell removal techniques, and method comparison suggests that the original isotopic signal is least affect by using EDTA or acetic acid. Multi-isotope analysis of SBOM obtained from (deep sea) molluscs and brachiopods confirms that the main types of chemosymbiosis can be differentiated from non-symbiotic heterotrophic nutritional strategies. In particular chemosymbiotic SBOM δ13C is characteristically depleted, with defined ranges for the presence of either methanotrophic or thiotrophic symbionts across environmental settings. In suspected thiotrophic taxa from ancient cold seeps, the preservation of this modern range (SBOM δ13C -35‰ to -29‰) is limited to young subfossil specimens, but the upper threshold is only exceeded in pre-Pliocene samples. Moreover, the protected intra-crystalline SBOM pool retains a distinct δ13C signal up to the Miocene, and available δ34S and δ15N data of intra-crystalline SBOM do not overlap between heterotrophy and thiotrophy. For methanotrophy (δ13C -65‰ to -36‰ at modern cold seeps) a residual δ13C biosignature does appear to be present in total SBOM from Miocene samples. This encouraging finding, together with the discovery of intra-crystalline original proteins in a fossil of Cretaceous age, suggests that future work on other well-preserved specimens could trace the evolution of chemosymbiosis deep into geological time.

The three projects described herein focus on two instances of exceptional preservation and on potential source of bias in the fossil record. The occurrence of exceptionally preserved fossil assemblages and the existence of systematic bias in the fossil record from a variety of sources represent opposing forces acting on the information quality of the fossil record. Exceptionally preserved assemblages capture features of anatomy and components of assemblages not normally recorded in the fossil record. Systematic biases affecting the fossil record do the opposite, skewing our perception of patterns of diversity, the relative dominance of clades and changes in ecosystems through time. Chapter one presents the results of an analog modeling analysis to assess whether and how a newly proposed potential mechanism, the preferential sampling of larger specimens during fossil sampling due to the greater likelihood of larger specimens being intersected by a fracture surface, contributes to the lithification bias. Chapters two and three focus on the exceptionally preserved vermiform fossils from the Winneshiek Lagerstätte in northeastern Iowa and microfossils from the Doushantuo Formation of South China, respectively. Chapter two aims at resolving the identity of the Winneshiek vermiform fossils and presents evidence that these structures represent phosphatized bromalites, an ichnologic category that includes coprolites and cololites. Chapter three presents a biostratigraphy study of exceptionally preserved microfossils at three sections of the Doushantuo Formation in South China. Acanthomorphic acritarchs represent a promising tool for subdivision and correlation of the Doushantuo Formation of South China and Ediacaran strata around the world. However, the occurrence of acanthomorphic acritarchs within the Doushantuo Formation is controlled by the availability of early diagenetic chert nodules that host microfossils such as acanthomorphic acritarchs. One of these sections contains the rare occurrence of early diagenetic cherts in an upper slope section. This new biostratigraphic data adds to the growing body of integrated chemostratigraphic and biostratigraphic data from the Doushantuo Formation. By understanding both exceptional preservation and sources of bias in the fossil record it is possible to separate artifact and noise from the true signal of the history of life.
PHD

Predation is considered a powerful ecological force influencing community structure, diversity, and abundance. Paleoecology offers a unique perspective, allowing us to examine ecological processes such as predation over evolutionary timescales. The three studies summarized below include two case studies testing the role of predation in evolution and one method-oriented project, which explores new tools with which to examine predator-prey interactions in the fossil record. Considering the importance of community interactions in the current global biodiversity crisis, understanding ecological and evolutionary dimensions of predation is critical to conservation biology and ecology, as predators are thought to play a vital role in maintaining ecosystem health and biodiversity. Predation has been dismissed as a causal mechanism for some major prey groups. For example, the evolutionary decline and cryptic or antitropical distribution of brachiopods is often explained as due to the potentially low energetic value and suspected non-palatability or toxicity of brachiopod tissues. Here we demonstrate that multiple invertebrate marine predators (crustaceans, echinoderms, and gastropods) are willing and able to consume brachiopods, and that predation pressure on the living brachiopod population may be consequential. Examination of the fossil record is consistent with this interpretation: evidence for drilling and repair of brachiopod shells is found throughout the fossil record in multiple orders. This suggests that although brachiopods may be unwanted prey in the presence of energetically more desirable targets, they do appear to be edible and are subject to intense predator-prey interactions. Limpets are important prey for some crab species, yet little is known about the role of durophagy in the evolution of the limpet shell. Feeding trials using three common species of Pacific Northwest limpets (Lottia digitalis, L. pelta and Tectura scutum) were conducted to assess how different shell morphologies affect mortality and handling time. We predicted that large size, shell ornament, and low-spires would result in either increased survivorship, and/or longer handling times. Contrary to our expectation that ridges resist predation, individuals with smooth morphologies experienced significantly lower mortality, as did those with low-spires. As species possessing high-spires and ridges typically occur high in the intertidal where predation risk due to crabs is relatively low, these morphologies are likely adaptions to physical factors such as thermal stress. One of the major caveats of using gastropod drill holes to assess predator-prey interactions in both the modern and the ancient is the correct identification of drill holes of predatory origin. By examining known predatory drill holes using environmental scanning electron microscopy, we aim to refine the development of a novel technique for augmenting their identification, and to explore the relationship between predator body size, predatory radula dentition, and radular microrasping marks observed on the shells of prey organisms. Electron micrographs were used to measure the spacing of microrasping marks produced by the radula, and the intercusp spacing of the radula dentition. A relationship between predator body size and microrasping marks makes it possible to infer predator size from these microtraces in both modern and fossil specimens, augmenting our ability to examine predator-prey interactions throughout the history of this important ecological interaction. Proxies for predation intensity such as predation traces or antipredatory morphologies provide an invaluable method to examine predation in both modern communities, and the fossil record. Our understanding of the importance of predation in regulating biodiversity and in evolution will continue to grow with the development of new methodologies, and a comprehensive understanding of predatory defenses.
Ph. D.

In this thesis I present work using the MOPED algorithm to extract in a non-parametric fashion star formation histories and galaxy masses from the spectra of galaxies in the Sloan Digital Sky Survey. The recovered parameters for all galaxies are combined to give insight into the processes of star and galaxy formation on both individual galaxy and cosmic scales. The MOPED algorithm allows use of the entire spectral range, rather than concentrating on specific features, and can be used to estimate the complete star formation history without prior assumptions about its form. By combining the star formation histories of 96,545 galaxies in the redshift range 0 < z < 0:34 the cosmic star formation rate is determined from the present day to z ~ 6. The results show that the peak of star formation occurred at z ~ 0:6, and that 26% of the mass of stars in the present-day Universe was formed at z ~ 2. The average metallicity rises from Z/Z= 0:44 at high redshift to a peak of 0:8 at z ~ 1 before declining to a level around 0.25 atthe present day. Although the peak in star formation is more recent than previously thought, the sample used includes galaxies with a range of masses not accessible to traditional studies, down to a limit of L ~ 2 x 10-3L*. By cutting the sample into ranges of mass it can be seen that the redshift at which starformation activity peaks is an essentially monotonically increasing function of final stellar mass. The time of the peak in star formation ranges from z > 2 for the highest mass galaxies (MS < 1012M) to z ~ 0:2 for the lowest (MS < 1010M). A typical L* galaxy appears to have its peak at around z » 0:8. These differences in star formation with mass reconcile the redshift of the peak found in this work with the previous estimates, generally deep surveys only probe the SFR of galaxies with MS < ML*. The stellar mass calculated using the reconstructed spectra eliminates contamination from either emission lines or AGN components. Using these masses it is possible to construct the mass function for the stellar mass component of galaxies which give excellent agreement with previous works, but extend their range by more than two decades in mass to 10 7.5 < Ms/h-2M < 1012. I present both a standard Schechter fit and a fit modified to include an extra, high-mass contribution, possibly from cluster cD galaxies. The Schechter fit parameters are phi* = (7:8 +/- 0:1) £ 10-3h3Mpc-3, M* = (7.64 +/- 0.09) x 10*10h-2M and alpha = -1.159 +/- 0.008. The sample also yields an estimate for the contribution from baryons in stars to the critical density of omega b*h = (2.39+/-0.08)x10-3, in good agreement with other indicators. No evolution of the mass function in the redshift range 0:05 < z < 0:34 is apparent, indicating that almost all stars were already formed at z » 0:34 with little or no star formation activity since then and that the evolution seen in the luminosity function must be largely due to stellar fading. The star formation history can be interpreted as a measure of how gas was transformed into stars as a function of time and stellar mass: the Baryonic Conversion Tree (BCT). There is a clear correlation between early star formation activity and present-day stellar mass: the more massive galaxies have formed about 80% of their stars at z > 1, while for the less massive ones the value is only about 20%. Comparing the BCT to the dark matter merger tree indicates that star formation efficiency at z > 1 had to be high (as much as 10%) in galaxies with present-day stellar mass larger than 2 x 10*11M, if this early star formation occurred in the main progenitor. The LCDM paradigm can accommodate a large number of red objects; it is the high efficiency in the conversion from gas to stars that needs to be explained. On the other hand, in galaxies with present-day stellar mass less than 10*11M, efficient star formation seems to have been triggered at z ~ 0:2. This work shows that there is a characteristic mass (M » 10*10M) for feedback efficiency (or lack of star formation). For galaxies with masses lower than this, feedback (or star formation suppression) is very efficient while for higher masses it is not. The BCT, determined here for the first time, should be an important observable with which to confront theoretical models of galaxy formation.

Several questions regarding the nature of extinction in the fossil record of marine invertebrates were investigated using statistical methods and familial diversity data. First, a series of analyses were performed to determine whether the magnitudes of mass extinctions were statistically distinguishable from the magnitudes of background extinctions. The expected proportions of familial extinction for each order in a stage (based on an estimate of the ordinal probability of familial extinction for each of 134 orders) were compared to the observed proportions of familial extinction in the stage using a simple X2 goodness-of-fit test. The results indicate that eight stages in the Phanerozoic had a statistically significant excess of extinction. A second set of X2 analyses was done using estimates of per taxon familial extinction rates for the orders, rather than familial extinction probabilities. The X2 tests resulted in four additional stages that contained a statistically significant surplus of familial extinction. To test the results further, a set of bootstrapping analyses was done for each of five different extinction metrics. Two stages, the Ashgillian and the Dzhulfian, had a statistically significant excess of extinction in both Xl analyses and in four out of five of the bootstrapping analyses. Two additional stages, the Guadelupian and the Maestrichtian, had a statistically significant magnitude of extinction in every analysis. Thus, the results provide strong support for the argument that mass extinctions comprise a distinct group of evolutionary phenomena.

Familial extinction rates have declined from the early Phanerozoic to the Recent. Some have suggested that familial extinction rates have been constant through time within most major taxonomic groups and that the decline in familial extinction rates is the result of the successive elimination of groups with relatively high familial extinction rates (a process referred to as taxon sorting). A model of total familial extinction rates through time based on stationary probabilities of familial extinction within orders closely mimics the observed decline in total familial extinction rates supporting the taxon sorting hypothesis. Linear regressions of the familial extinction probabilities of orders versus the geologic time of both their first and their last occurrences suggest that the observed decline in extinction rates resulted from the early elimination of orders with characteristically high probabilities of extinction, and the later origination of orders with relatively low probabilities of extinction. In addition, a statistical analysis comparing the evolutionary volatility of extinct versus extant taxa suggests that extinct orders had greater volatility in their diversity histories which may have contributed to their early demise.

The taxonomic selectivity of both background and mass extinctions was investigated using simple X2 analyses. The results suggest that familial extinction during mass extinctions was taxonomically more selective than extinction during background extinctions. In addition, the magnitude of familial extinction experienced by an order in a stage was compared to the familial extinction probability estimated for the order using the binomial theorem. Then, those orders that suffered an unusual excess of familial extinction during particular stratigraphic stages were separated from the remaining orders in the stage. The results suggest that sessile filter feeders (particularly those groups important in ancient reefs) and pelagic groups suffered the greatest during intervals of mass extinction.

Finally, the potential relationship of familial diversity to both sea level and I7Sr/86Sr ratios was statistically examined using linear regression techniques. No statistically significant correlation was found between sea level and familial diversity. However, a significant correlation was discovered between diversity and I7Sr /86Sr ratios. Strontium ratios are believed to be an indirect measure of the aerial extent of exposed continental crust. Thus, the relationship between 17 Sr/86Sr ratios and diversity suggests that familial diversity has been a function of 1) the aerial extent of epeiric seas and 2) the amount of clastic material being supplied to these seas. The last factor could have affected familial diversity by restricting normally diverse, shallow carbonate environments.
Master of Science

Palaeomacroecology is the study of large scale patterns of species diversity in the fossil record, encompassing a variety of subtopics. This thesis also addresses a variety of these subtopics, making it difficult to define under one heading.The first portion of the thesis deals with a new package of software tools for the analysis of large scale datasets, with a specific focus towards palaeoecology and palaeogeography. These software tools have been combined into a package called fossil that has been released on the Comprehensive R Archive Network (CRAN), and is already being used by other palaeoecologists. While the majority of these tools had a basis in previous statistical methods, I have also independently developed a clustering algorithm for use with biogeographic datasets. This clustering algorithm is relational, non-Euclidean and non-hierarchical and as such is called Non-Euclidean Relational Clustering (NERC). NERC eliminates several of the assumptions common to most other clustering methods that are often violated by biogeographic data.The next portion of my thesis describes a new Triassic aged flora from Axel Heiberg Island in Nunavut. Macroecological studies typically use large databases compiled from individual samples; therefore, these individual samples represent the foundation on which macroecological analyses rest, and collection and description of new fossil bearing sites is vital to the advancement of palaeomacroecology.Chapter 5 is an analysis of the provinciality and beta diversity of dinosaurs in the Late Cretaceous of North America. This analysis found that contrary to previous studies, dinosaur genera were widespread across the continent and not restricted to small geographic ranges. Chapter 6 is the final culmination of my thesis, and where I see palaeomacroecology headed in the future. It is an analysis of how latitudinal diversity gradients in plants have changed through time. The analysis assesses the impact of changing climate in creating and sustaining the latitudinal diversity gradient, and lends support to the idea that temperatures are important drivers of the gradient.The final chapter is a summary of where palaeomacroecology has been, and where its future work might be best focused. While the field of palaeontology is vital to our understanding of large scale, especially temporally, patterns of species diversity, the field of palaeontology has an opportunity to advance our understanding at an even more rapid pace provided we ask the appropriate questions of our data.
La palaeomacroecology est l'etude des modeles a grande echelle de la diversite des especes dans les archives fossiles, et inclue une variete de sous-themes. Cette these adresse aussi une variete de ces sous-themes, ce qui en fait diffucult de definir sous une seule rubrique. La premiere partie de la these discute d'un nouvel ensemble d'outils logiciels pour l'analyse des ensembles de donnees a grande echelle, avec une attention particuliere a la paleoecologie et la paleogeographie. Ces outils logiciels ont ete combines dans un paquet appele fossil qui a ete publie sur le reseau Comprehensive R Archive Network (CRAN), et est deja utilise par d'autres palaeoecologists. Bien que la majorite de ces outils avait une base en preious methodes statistiques, j'ai aussi developpe independamment un algorithm de regroupement pour une utilisation avec des bases de donnees biogeographiques. Cet algorithme de regroupement est relationnelle, non-euclidienne et non-hierarchique et en tant que telle est appele Non-Euclidean Relational Clustering (NERC). NERC elimine plusieurs des hypotheses communes a la plupart des autres methodes de classification, et qui sont souvent violees par des donnees biogeographiques.La partie suivante de ma these decrit une nouvelle flore du Trias a l'ile Axel Heiberg, au Nunavut. Les etudes macroecologiques utilisent generalement de grandes bases de donnees compilees a partir des echantillons individuels et, par consequent, ces echantillons individuels representent le fondement del'analyse macroecologique, et la collecte et la description des nouveaux sites fossiliferes est indispensable a l'avancement de la palaeomacroecologie.Le Chapitre 5 est une analyse du provincialisme et de la diversite beta des dinosaures aux Cretace superieur en Amerique du Nord. Contrairement aux etudes precedentes, cette analyse a revele que les genres de dinosaures ont ete beaucoup plus repondus a travers le continent et ne se limitement pas a de petites aires geographiques. Le Chapitre 6 est l'aboutissement final de ma these, ou je vois dans quelle direction se dirige a la palaeomacroecologie. Il s'agit d'une analyse de la facon dont les gradients de diversite des plantes ont change au fil du temps. L'analyse evalue le role des changements climatiques dans la creation et le maintien du gradient latitudinal de diversite, et soutient l'idee que les temperatures sont d'importants moteurs de ce gradient.Le dernier chapitre resume l'evolution palaeomacroecologie dans quelle direction les travaux futurs devraient etre orientes. Bien que le domaine de la paleontologie sait vital pour notre comprehension des modeles de la diversite des especes a grande echelle, en particulier celle temporelle, le domaine de la paleontologie a une occasion de faire progresser notre comprehension a un rythme encore plus rapide, a condition de poser les bonnes questions.

Macroevolution and macroecology are concerned with the patterns in evolutionary and ecological data, respectively, which arise when observing multiple species over time and/or space. Species extinction and species pool functional composition are the macroevolutionary and macroecological patterns at the heart of this dissertation. The hypotheses and analyses in the three studies forming this dissertaiton were all framed in terms of how species functional traits can shape these emergent patterns.

In my first study, I analyzed the Cenozoic fossil record of North American mammals to test two long standing hypotheses: the survival of the unspecialized hypothesis, and the Law of Constant Extinction. My analysis centers around a model of species duration as a function of multiple species traits, species’ phylogenetic relatedness, and species’ origination cohort. My results support the conclusion that generalist species will, on average, have a greater duration than more specialized species. I also find that species extinction risk increases with species duration, a result that is counter the Law of Constant Extinction. Additionally, I find that only some of the factors associated with extinction risk for Modern mammals could be considered risk factors for mammals from the rest of the Cenozoic, indicating a difference between the modern biodiversity crisis and “normal” extinction dynamics.

My second study also deals with the survival of the unspecialized and the Law of Constant Extinction, but focuses on a different system: post-Cambrian Paleozoic brachiopods. An additional aspect of this study is an analysis of the relationship between extinction intensity and the strength of trait selection. I find support for greater survival among environmental generalists than specialists. I also find evidence that for geographic range and environmental preference, as extinction intensity increases, the selective importance of these traits increases. This result is evidence for a qualitative difference between background and mass extinction. The final study is an analysis of the changing functional composition of the North American mammal regional species pool over the last 65 million years. The goals of this analysis are to understand when functional groups are enriched or depleted, and how changes to environmental context may shape these changes. I find that mammal diversity is more strongly shaped by changes to origination probability rather than changes to extinction probability. I also find that all arboreal ecotypes declined throughout the Paleogene and disappeared from the species pool by the Neogene. Additionally, I found that most herbivore ecotypes expand their relative contribution to functional diversity over time.

My desire with this dissertation is to present the types of analyses and results that are possible through a synthesis of macroevolution and macroecology. The first step to building any dialogue is to agree on a common language and I’ve emphasised an expressive statistical framework with which to phrase our questions in a common tongue. My hope is that this studies serve as an example of how to use paleontological data to unite questions about the processes underlying macroevolutionary and macroecological patterns.

Thesis (M.A.) University of Missouri-Columbia, 2006.
The entire dissertation/thesis text is included in the research.pdf file; the official abstract appears in the short.pdf file (which also appears in the research.pdf); a non-technical general description, or public abstract, appears in the public.pdf file. Title from title screen of research.pdf file viewed on (May 20, 2007) Vita. Includes bibliographical references.

Plant-feeding insects are the most species-rich group on the planet today. Models have been proposed to explain this diversity, but few use the fossil record to evaluate hypotheses. I conduct studies in modern systems to examine (1) taphonomic biases in insect preservation and how this may affect our understanding of insect diversity trends through time and (2) patterns of herbivory in modern ecosystems to improve the comparability of fossil and modern datasets. I then use the Cenozoic fossil record to examine the history of ecological associations between insects and plants and how these interactions respond to environmental change. I conducted an actualistic study on the preservation of beetles in Willcox Playa, an ephemeral lake in SE Arizona. I compared the insect death assemblage in shoreline sediments to the living beetle assemblage. The sediments captured 56% of the live-collected beetle families, and 28% of the live-collected beetle genera. The relative abundances of living beetles were not reflected in the death assemblage. Beetle diet, feeding habitat, and size influenced the composition of the death assemblage. Necrophagous, ground-dwelling and smaller beetles were over-represented in the death assemblage. Such biases should be considered in insect paleoepology and in studies of diversity change. Annual variation in herbivory was compared within and between two lowland neotropical forests Costa Rica. Herbivory did not vary significantly within sites between years, but was significantly different: between sites. Modern herbivory data collected with discrete sampling techniques is compartable to herbivory data from fossil forests. Herbivory data from one-time collections of leaf litter are most suitable for comparison with fossil herbivory. I compared herbivory between two Eocene floras and between the Eocene floras and six modern floras. A decline in levels of herbivory corresponds with a decline in temperature from the middle to the late Eocene. Fossil herbivore damage was significantly lower than modern herbivore damage. This pattern may result from taphonomic bias, environmental differences between the fossil and modern sites or evolutionary change.

Hominins (the clade including modern humans and their fossil ancestors) were a taxonomically and morphologically diverse group during the Plio-Pleistocene, and their evolution documents the only known transition to obligate bipedalism in primates. However,many aspects of their shared evolutionary history remain frustratingly unclear due to uncertainty about whether change in the fossil record reflects genuine evolutionary change or variation in our sampling of the rock record. Here, a comprehensive assessment of the quality of the early African hominin fossil record is presented. A specimen database of all early African hominin fossils (>5000) has been compiled including taxonomic, geological, anatomical, and bibliographic information. Using a range of sampling metrics (fossil-bearing formations, collection effort, sampled area, and ghost lineage diversity), it is shown that the pulsedlike pattern of uncorrected (taxic) hominin diversity is almost entirely controlled by rock availability. By contrasting taxic with phylogenetically corrected diversity, hominin diversification appears unconstrained through the lateMiocene and Pliocene, with diversity constantly increasing until a single peak is reached in the early Pleistocene. Phylogenetically corrected diversity shows no discernible link with sampling metrics and there is no direct evidence that shifts in climatic conditions drove diversification. A study of specimen completeness through geological time shows that while sampling metrics (specifically sustained collection effort at rich deposits) have a major influence on patterns of specimen completeness, specimen completeness has only a moderate influence on diversity patterns. It also shows that specimen completeness is poorest during the period most pertinent to human origins, the estimated Pan-Homo divergence date, in large part due to under-sampling (< 4% of Africa by sampled area). In combination, this work illustrates that the hominin fossil record is by no means an unbiased depiction of evolutionary events, and therefore its quality and incompleteness should be fully understood before any interpretation of macroevolutionary patterns.

The effects of intrinsic traits on the diversification dynamics have been extensively investigated, with several traits being associated with increase in diversification. On the other hand, the possible negative effects of traits on the diversification of a lineage have been for the most part overlooked. Here we used both the fossil record and molecular data to study the diversification dynamics of Placentalia, focusing on the orders in decline of diversity, and investigated different mechanisms that might control the evolutionary success of the 21 placental orders. More specifically we: 1- determined which of the 21 orders of Placentalia are in decline of diversity (i.e., Decline model); 2- investigated whether the Decline model has a phylogenetic signal; 3- tested the hypothesis that the differences in body size are related to the Decline model; 4- tested the hypothesis that the orders in Decline have lower morphological disparity; 5- investigated whether the orders in decline of diversity, inferred from the fossil record, are the ones with higher extinction risk nowadays. Our analysis indicate that the majority of the orders of placental mammals have a pattern consistent with the Decline model and, although the Decline model is not equally distributed among the placental superorders, there was no significant phylogenetic signal for the orders in diversity decline. We found a positive correlation between the Decline model and the average body size which is in line with previous studies on body size evolution. We argue that such results suggest a complex evolutionary dynamics: larger body size appears to be an evolutionary attractor with lineages showing a tendency to increase in size, however, the increase in body size would be counterbalanced by a higher propensity to Decline. Moreover, we found a the negative correlation between the Decline model and morphological variation. We suggest that such results could indicate two possible scenario: (i) the low morphological variation would cause lineages to loose diversity; (ii) the low morphological variation would be the product of decrease in diversity through extinction selectivity. Finally, we found no correlation between the extinction risk of extant species and the deep time diversity decline, which suggests that the drivers of the current and the past Decline are not the same
O efeito de caracteres intrínsecos na dinâmica de diversificação foram extensamente investigados e diversos caracteres foram associados com aumentos na diversificação. Contudo, os possíveis efeitos negativos de um caractere sobre a diversificação de uma linhagem foram em grande parte ignorados. No presente trabalho integramos o registro fóssil com dados moleculares para estudar a dinâmica de diversificação de Placentalia, focando nas ordens em declínio de diversidade, e investigamos possíveis mecanismos responsáveis por gerar os padrões de diversificação encontrados. Mais especificamente nós: 1- determinamos quais das 21 ordens de Placentalia estão em declínio de diversidade (i.e., Declínio); 2- investigamos se o Declínio apresenta um sinal filogenético; 3- testamos a hipótese de que o tamanho do corpo está relacionado com o Declínio; 4- testamos a hipótese de que as ordens em Declínio possum menor disparidade morfológica; 5- investigamos se as ordens em Declínio, inferido a partir do registro fóssil, são as mesas com maior risco de extinção na atualidade. Nossas análises indicam que a maioria das ordens de mamíferos placentários apresentam um signal consistente com o Declínio e, embora o Declínio não esteja igualmente distribuído entre as superorderns de Placentalia, não há um signal filogenético significativo para as ordens em Declínio. Nossos resultados indicam uma correlação positiva entre o Declínio e o tamanho corporal médio de cada ordem que está de acordo com estudos prévios sobre evolução do tamanho do corpo. Argumentamos que estes resultados sugerem uma dinâmica de evolução complexa: tamanho corpóreo grande seria um atrator evolutivo que gera a tendência das linhagens aumentarem de tamanho, todavia, o aumento do tamanho do corpo seria contrabalançado pela maior susceptibilidade ao Declínio. Outrossim, encontramos uma correlação negativa entre o Declínio e a variação morfológica. Argumentamos que essa correlação poderia indicar dois possíveis cenários: (i) a baixa variação morfológica seria responsável pela redução no número de linhagens e tornaria as ordens mais susceptíveis ao declínio de diversidade; (ii) a baixa variação morfológica teria sido gerada pela diminuição da diversidade. Por último, o risco de extinção das espécies atuais não está correlacionado com o Declínio, o que sugere que os mecanismos responsáveis pelo Declínio no passado e no presente não são os mesmos.

The horse (Equus caballus) is an economically and scientifically important species of mammal. The horse genome (and that of other mammals) contains thousands of sequences derived from retroviruses, called endogenous retroviruses (ERVs). These sequences are highly informative about the long-term interactions of retroviruses and hosts. They are also interesting because they have influenced the evolution of mammalian genomes in various ways. Horses belong to the family Equidae in the order Perissodactyla - comprising 16 extant species of strict herbivores adapted for running and dietary specialisation. This PhD thesis describes my work developing and applying a novel bioinformatics approach for characterising ERVs. I used this approach to characterise ERVs in genomes of Hippomorpha species in relation to those found in a representative of the Ceratomorpha - the white rhinoceros (Ceratotherium simum). Through comparative analysis of these three genomes, I derive a calibrated timeline describing the process through which ERV diversity has been generated in the equine germline. My project has provided an overview of retrotranspositional activity in perissodactyl ERV lineages and identified individual ERV loci that show evidence of involvement in physiological processes and/or pathological conditions. The dataset generated in this project will be of great utility for future studies aiming to investigate the potential functional roles of equine ERVs and their impact on equine evolution.

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

Thesis: S.B., Massachusetts Institute of Technology, Department of Earth, Atmospheric, and Planetary Sciences, May, 2020
Cataloged from the official PDF of thesis.
Includes bibliographical references (pages [24]-[29]).
Filamentous cyanobacteria that built macroscopic tufted mats in Proterozoic peritidal environments were fossilized by silicification, but the environmental and biological factors that shaped these structures and enabled this type of preservation are not well understood. Recent work has shown that coccoidal cyanobacteria can become fossilized because they can sequester silica from seawater that is undersaturated with respect to silica. Here, we use taphonomy experiments to demonstrate that filamentous cyanobacteria that form tufted and conical mats are also able to mediate the precipitation of silica in seawater that is undersaturated with respect to silica as well. These results show that different marine cyanobacteria and their macroscopic structures have a high potential to be preserved by silicification. We find that the exterior of macroscopic structures such as tufts and pillars are preferentially silicified, and more completely silicified at silica concentrations below saturation in seawater. The interior of these structures may be preserved by later diagenetic minerals. These results are consistent with microfossil assemblages found in early diagenetic chert deposits throughout the Proterozoic. The data suggest abundant Ca-rich sulfated polysaccharides in the exopolymeric substance (EPS), which are likely the site of silicification. Interactions among similar organisms, seawater chemistry, and silica in evaporative environments may account for the two-billion-year long record of exceptionally silicified filamentous and coccoidal cyanobacteria and their macroscopic aggregates in peritidal environments.
by Kyle J. Morgenstein.
S.B.
S.B. Massachusetts Institute of Technology, Department of Earth, Atmospheric, and Planetary Sciences

The idea of studying the colour of organisms in the fossil record has for a long timeseemed nothing more than the far flung dreams of a few idealistic palaeontologists.The last 5 years however have brought sweeping advances in this area, such that theidea is no longer hypothetical but an actual possibilty. Recent studies on the preserva-tion of fossilised pigment containing organelles, melanosomes, have hailed a new eraof palaeontological study and reconstruction. In this work geochemical techniques areapplied to study such structures in fossil feathers and an amphibian, to determine thenecessary level of confidence that these structures are not bacterial, discuss the relativeadvantages and disadvantages of the techniques used in the study of fossil melanin, andextend the study of fossil colour to other pigments in fossil algae. Fourier transforminfrared spectroscopy (FTIR) data is shown to provide some of the most consistentevidence of the presence of melanin, however it does not enable us to adequately dis-tinguish between the two major types, eu- and pheomelanin. Determining the presenceof bacteria in fossil stromatolites is shown to be most effective by using tetra-methylammonium hydroxide assisted pyrolysis gas chromatography mass spectrometry (Py-GCMS) to look for the distribution pattern of fatty acid methyl esters. Such analysisshows that samples identified as bacterial have identical patterns that differ signifi-cantly from those of fossil plants and animals. Such a biomarker is shown to be morereliable than hopanes, further commonly used bacterial biomarkers. The combination of FTIR and Py-GCMS suggest the presence of the red algal pigment phycoerythrin inthe Jurassic fossil Solenopora jurassica, strengthening its identification as a calcareousalga.

The marine microfossils of planktic foraminifers are widely used for investigating palaeoceanographic and palaeoclimatic conditions. The objective of this project was to investigate genotypic variation within planktic foraminiferal morphospecies and the spatial distribution of genotypes in the subpolar, transitional and subtropical North Atlantic. Foraminiferal genomic DNA was extracted and the ~1000 base pair 3' terminal region of the small subunit ribosomal RNA gene was amplified using the polymerase chain reaction. Using distance-based molecular phylogenetic analysis, a neighbour-joining phylogeny was reconstructed based on 31 planktic and15 benthic previously sequenced foraminifera and extended to include 15 genotype sequences obtained from the North Atlantic during this study. Bulk plankton samples were collected for preliminary examination of genotype/morphotype relationships. The molecular phylogeny is largely consistent with the foraminiferal fossil record. It supports the suggestion that the origins of planktic foraminifers are polyphyletic, as the spinose planktic foraminifers cluster separately from the non-spinose planktic foraminifers within the phylogeny. Brachn length variation within the planktic cluster reflects large differences in evolution rate between morphospecies. Within the North Atlantic, genotypic variation has been identified within the morphospecies, Globigerina bulloides, Turborotalita quinqueloba, Globigerinella siphonifera, Globigerinella calida, Globigerinoides ruber and Neogloboquadrina pachyderma. The distribution of genotypes is complex, and it has been found that genotypes, representing a single morphospecies, often co-exist within the water column. This could be indicative of cryptic speciation, suggesting that North Atlantic planktic foraminiferal diversity is much higher than fossil record interpretations have indicated. The genotypes within G. bulloides, G. siphonifera, G. calida and T. quinqueloba have different geographic distributions within the North Atlantic. It is apparent that G. bulloides Types IIa and IIb and G. siphonifera Types IIa and IIb have extensive distributions suggesting that they are more generalist in adaptation, and tolerant to a wide range of oceanic conditions.

Synapsiden erscheinen erstmals im Fossilbericht im Oberkarbon (späten Pennsylvanium) und dominierten terrestrische Ökosysteme bis zum Ende des Paläozoikums. Diese Arbeit ist die erste detaillierte Betrachtung der frühen Evolution der Synapsiden. Modifizierte Versionen zuvor publizierter Vollständigkeitsmaße werden benutzt, um die Vollständigkeit von Pelycosaurier Fossilien einzuschätzen. Zudem wird eine Reihe unterschiedlicher Methoden genutzt, um die Übereinstimmung von Fossilbericht und Phylogenese zu messen. Die Vollständigkeitsanalyse der Pelycosaurier zeigt eine negative Korrelation zwischen Diversität und dem Maß der Merkmalsvollständigkeit, was darauf hindeutet, dass viele Spezies auf unvollständig erhaltenem Material basieren. Die fehlende Korrelation zwischen dem Maß zur Merkmalsvollständigkeit (basierend auf Abschätzung der Proportion phylogenetisch erfassbarer Merkmale) und der Diversität wird auf die Entdeckungsgeschichte der Gruppe zurück geführt: Die Mehrheit der Pelycosaurier-Arten wurden zwischen den 1930er und 1960er Jahren benannt, als taxonomische Zuordnungen häufig auf Körpergrösse, Fundort und Stratigraphie anstatt auf morphologischen Merkmalen basierten. Welche Schätzungen der Artenzahl über die Erdgeschichte beinflussen, produzieren die unterschiedlichen Methoden zur Diversitätsrekonstruktion sehr ähnliche Ergebnisse. Der initialen Diversifikation der Synapsiden im Oberkarbon und Unterperm (frühes Cisuralium) folgte ein Aussterbeereignis während des Sakmariums. Ein zweites Aussterben ereignete sich an der Grenze vom Kungurium zum Roadium. Die phylogenetisch Topologie-Analyse keine signifikanten Steigerungen der Diversitätsrate der Pelycosaurier relativ zu zeitgleich lebenden Taxa. Eine breiter angelegte Auswertung der Diversitätsentwicklung paläozoischer und triassischer Amnioten liefert ein mögliches Erklärungsmodell; Veränderungen der Diversitätsraten früher Amnioten tendieren dazu, zu Zeiten erhöhter Aussterberaten aufzutreten.
Synapsids first appear in the fossil record during the late Pennsylvanian, and dominated the terrestrial realm until the end of the Palaeozoic. This thesis provides the first detailed examination of the earliest evolution of synapsids. Modifications of previously published metrics are used to assess the completeness of their specimens, and a variety of methods are employed to measure the fit of the fossil record to the phylogeny. The analysis into the completeness of pelycosaurian-grade specimens reveals a negative correlation between diversity and the Skeletal Completeness Metric, assessing the bulk of material preserved, suggesting a tendency to name many species based on poor material. The lack of correlation between the Character Completeness Metric (assessing the proportion of phylogenetic characters that can be scored) and diversity is attributed to the history of discovery in the group: the majority of pelycosaurian-grade species were named between the 1930s and 1960s, when assignments were often based on size, location and stratigraphy rather than morphological characters. The different methods of assessing diversity provide very similar results. The initial diversification of synapsids in the Late Pennsylvanian and early Cisuralian was followed by an extinction event during the Sakmarian. A second extinction event occurred across the Kungurian/Roadian boundary. The tree topology analysis found no significant increases in diversification rate occurring in pelycosaurian-grade taxa relative to their contemporaries. A broader examination of diversification patterns in Palaeozoic and Triassic amniotes reveals a possible explanation; diversification rate shifts within early amniotes tend to occur during periods of elevated extinction.

Drilling predation presents a rare opportunity to quantify ecological and evolutionary interactions in the fossil record. To date, most of this research has been done on Late Mesozoic and Cenozoic deposits, and large-scale studies have focused on temporal rather than spatial patterns. However, drilling predation occurs throughout the entire Phanerozoic, and patterns in spatial variability may mask secular trends. These issues are addressed in a series of projects presented here. An extensive survey of museum specimens and bulk materials indicate that drilling predation in Late Paleozoic brachiopod prey is relatively rare (<1% of fossil specimens are drilled) but widespread and continuously present. The intensity of drilling predation on Late Paleozoic bivalve mollusks (this is the first quantitative report of this kind) is much higher than that seen for contemporaneous brachiopod prey, but lower than what is common for Late Mesozoic and Cenozoic mollusks. Drilling intensity varies significantly between taxa and across localities, (e.g., a sample of the Pennsylvanian brachiopod Cardiarina cordata produced an estimate of 32.7%, which is an intensity similar to that seen in Cenozoic mollusks and the highest yet reported for any brachiopod). However, data for the brachiopod genus Composita, which appears to be a preferred brachiopod prey in many Late Paleozoic assemblages, show that although this genus is subject to drilling predation continuously throughout its geologic range, the over all intensity is very low (less than 1%) and at no time does the intensity ever exceed 10%. Spatial variation in Miocene assemblages from Europe is shown to be on the same order as temporal variation throughout the Cenozoic. Significant variation in drilling intensity is also documented for the Paleozoic. This emphasizes the point that to fully understand patterns of predation through time, both spatial and temporal distribution must be considered.
Ph. D.

The evolutionary origins of animal phyla are intimately linked with the Cambrian explosion, a period of radical ecological and evolutionary innovation that begins approximately 540 Mya and continues for some 20 million years, during which most major animal groups appear. Lophotrochozoa, a major group of protostome animals that includes molluscs, annelids and brachiopods, represent a significant component of the oldest known fossil records of biomineralised animals, as disclosed by the enigmatic ‘small shelly fossil’ faunas of the early Cambrian. Determining the affinities of these scleritome taxa is highly informative for examining Cambrian evolutionary patterns, since many are supposed stem-group Lophotrochozoa. The main focus of this thesis pertained to the stem-group of the Brachiopoda, a highly diverse and important clade of suspension feeding animals in the Palaeozoic era, which are still extant but with only with a fraction of past diversity. Major findings include adding support for tommotiid affinity as stem-group lophophorates. Determining morphological character homologies vital to reconstructing the brachiopod stem-group was achieved by comparing Cambrian Lagerstätten with the widespread biomineralised record of Cambrian stem-brachiopods and small shelly fossils. Polarising character changes associated with the putative transition from scleritome organisms to crown-group brachiopods was furthered by the description of an enigmatic agglutinated tubular lophophorate Yuganotheca elegans from the Chengjiang Lagerstätte, China, which possesses an unusual combination of phoronid, brachiopod and tommotiid characters. These efforts were furthered by the use of X-ray tomographic techniques that revealed novel anatomical features, including exceptionally preserved setae in the tommotiid Micrina. The evidence for a common origin of columnar brachiopod shell structures in the tommotiids is suggested and critically examined. Enigmatic and problematic early and middle Cambrian lophotrochozoans are newly described or re-described in light of new evidence, namely: the stem-brachiopod Mickwitzia occidens Walcott from the Indian Springs Lagerstätte, Nevada; a putative stem-group entoproct Cotyledion tylodes Luo and Hu from Chengjiang, China; a new enigmatic family of rhynchonelliform brachiopods exemplified by the newly described Tomteluva perturbata from the Stephen Formation, Canada; and the tommotiid Micrina etheridgei (Tate) from the Flinders Ranges, South Australia. Cladistic analyses of fossil morphological data supports a monophyletic Brachiopoda.

Dentaries of the 6 species of Myotis that occur in the eastern United States were analyzed using landmark-based geometric morphometrics. The species could be distinguished with a high degree of accuracy. Evidence was found of a phylogenetic signal in the morphology of the Neotropical and Nearctic Myotis sub-clades. There is also evidence of convergence in the morphology of the dentary among Myotis species that feed primarily by gleaning. When analyzed together there was no evidence of sexual dimorphism among the 6 eastern U.S. Myotis, but when analyzed individually some dimorphism may be present. A sample of fossil Myotis of unknown species from Bat Cave, Kentucky, was analyzed in an attempt to identify the specimens to species. Results indicate that Myotis austroriparius and M. sodalis predominate the sample, possibly with smaller numbers of M. grisescens and M. leibii. This study demonstrates the ability to differentiate Myotis taxa from historic and prehistoric sites and provides a tool for researchers to better understand and potentially conserve these species.

The Mustelinae (weasels, stoats, minks, and ferrets) are a subfamily of small, elongate-bodied mustelid carnivorans (Carnivora: Mustelidae) that originated during the Late Miocene. Mustelines are the most abundant group of carnivorans in the world today and are commonly found at Pleistocene-aged sites across their range; however, their lack of a more complete fossil record has left many questions regarding the evolution of early mustelines unanswered. Here we report a new occurrence of a musteline from the Early Pliocene age (4.9 – 4.5 Ma) Gray Fossil Site in northeastern Tennessee. Morphology of the P4 and M1 are consistent with the dental characteristics of Mustelinae, and thus this find represents the first reported pre-Pleistocene occurrence of a musteline in the eastern United States. Morphology of the specimens is distinct from the well-known Miocene ischyrictine mustelid Plionictis, but falls within the range of variation observed within the extant genera Mustela and Neovison. Linear measurements also fall within the size ranges of those genera. Distinguishing Mustela from Neovison based on morphological characters alone is very difficult and recent phylogenetic studies differentiating the two have been based exclusively on genetic evidence. Further study will hopefully allow us to place a confident identification on the musteline from Gray. The small, hypercarnivore niche of mustelines is one that was previously not recognized among fauna at the Gray Fossil Site, and improves our understanding of the site’s paleoecology.

Interpreting the taxonomic and behavioral implications of variation in the inferred limb proportions of fossil hominin taxa is contingent upon assessing how much variation exists in extant primate taxa and, by extension, how much of that variation is associated differences in their locomotor behaviors. However, the majority of evidence linking limb proportions to behavior in extant primates is based on taxonomically-restricted samples, or on species means as opposed to individual values, or does not account for field observations that capture the complexity of locomotor behavior in a primate taxon (see Napier & Napier, 1967; Fleagle, 1988; see also Preuschoft, 2002). With regards to extinct taxa, the problem is compounded by a necessary reliance on relatively few associated skeletons, most of which are incomplete, or fragmented or both.

This thesis addresses the aforementioned issues using a) multivariate methods to quantify the relationships between limb proportions and behavioral repertoires in extant anthropoids; b) machine-learning methods to select relevant extant models with which to interpret the limb proportions of extinct taxa; and c) resampling methods to evaluate hypotheses regarding major adaptive shifts in inferred locomotor behavior.

Post-mortem alteration of bivalve shells on arctic ice-scoured shelves helps illucidate the fidelity of death and fossil assemblages in these settings. Degradation rates and processes were constrained by (1) characterizing the taphonomic signature of death assemblages, (2) evaluating the live-dead fidelity of the benthos, and (3) net changes in experimentally deployed shells. Results revealed an extremely harsh taphonomic mill controlled by bioerosion, fragmentation and dissolution. Only select species accumulated in death assemblages, resulting in low taxonomic fidelity; at the habitat level 50% of the live species are found dead. 100% of the dead species are found alive, suggesting no temporal or spatial exotic contributions.
Selectively preserved species could be time-averaged over 1 000s of years based on a preliminary model, yet high damage profiles suggest shorter scales of time-averaging. Skeletons are highly degraded compared to assemblages from temperate or tropical seas and reflect only a portion the living skeletonized community.

Today’s highly endangered orangutan populations of Sumatra and Borneo offer but a glimpse into the taxonomic diversity and vast regional distribution enjoyed by orangutans and their great ape relatives in East Asia over the past 2.5 million years—a time when tropical forest pongine habitats stretched from Java to southern China. In addition to the giant terrestrial ape Gigantopithecus, other great ape genera have been proposed to have existed within this hominid community. The taxonomic diversity of this great ape faunal array is even further complicated when the purported presence of hominins at Early Pleistocene sites older than 1.85 Ma is considered. Highly acidic, the jungle floors of East Asia are notoriously bad at fossil preservation decomposing skeletal and dental evidence quickly. Fortunately, ph-neutral limestone caves have acted to offset these forces. The outcome of this peculiar taphonomy has left us with many teeth, but very little bone. With only unassociated fossil dentition to work with, modern geometric morphometrics offers scientists one of the few cutting-edge tools capable of systematically assessing this material reliably. This dissertation applies modern geometric morphometric statistical analysis to over two thousand fossil hominid teeth (Appendix A) from the Quaternary of southern China and Southeast Asia, which offers unique insight into the taxonomic diversity present in this sole Pleistocene great ape community. This study provides a much clearer understanding of the composition, paleoecology, and regional distribution of Pleistocene great ape communities of East Asia. Concordant with previous research, the main study and pilot study conducted in this dissertation showed Homo sapiens to always be morphologically and statistically distinct from extant and fossil orangutans. In turn, Pongo pygmaeus and Pongo abelii were continuously shown to be distinct from each other as well as from fossil Pongo groups. This investigation refutes hominin assignments for several teeth previously placed within early East Asian hominins (showing them to be orangutans instead) but supports the hominin status of the Jianshi upper third premolar. In combination with a published age of 1.95–2.15 million years (Ma), the hominin assignment reaffirmed here for the Jianshi dentition originally classified as human by Liu, Clarke, & Xing (2010) may offer a challenge to evolutionary models that recognize the 1.85 Ma Dmanisi hominins as the earliest hominins outside of Africa. This fact is often lost on most contemporary scientists due to their preoccupation with the 2.5 Ma Longgupo mandibular fragment, once thought to be a hominin but now assignable to an ape. Like the Jianshi upper third premolar, it is also based on a single specimen (in this case, a mandibular fragment). This dissertation supports the existence of Ciochon’s (2009) “mystery ape”. It refutes Schwartz et al., (1995) multiple Vietnamese Pongo taxa, including the proposed genus “Langsonia,” which is reassigned here to Pongo or the “mystery ape,” while placing Vietnamese fossil orangutans into either Pongo weidenreichi or Pongo devosi. Teeth from the Ralph von Koenigswald collection originally assigned to “Hemanthropus” were also determined to be representative of either the “mystery ape” or Pongo. Indeterminate “hominin” teeth were assignable to either Homo erectus, Homo sapiens, or Pongo only; no evidence was found for any other types of hominin species present in the collections examined for this study.