Dans la première partie de ma thèse, je fournis un programme informatique qui permet aux utilisateurs de déterminer dans quelles circonstances ils doivent mesurer le mouvement des particules. J’explique comment ces mesures peuvent être effectuées et fournissent un programme pour analyser ce type de données. La partie principale de ma thèse comprend des expériences portant sur l'impact de l'exposition répétée au bruit du trafic, la source anthropique la plus courante de bruit dans l'environnement marin, sur les poissons et les invertébrés pendant leur développement. Je démontre qu’une variété de comportements a été touchée par le bruit. J’ai aussi trouvé que le bruit prévisible peut conduire à des impacts différents sur le développement par rapport au bruit imprévisible, mais que certaines espèces de poissons peuvent être en mesure de s'habituer au bruit du trafic, tandis que d'autres non. En outre, je trouve que le développement et la survie des limaces de mer peuvent être impactés négativement par le bruit des bateaux. Les poissons et les invertébrés constituent une source de nourriture vitale pour des millions de personnes et constituent des liens essentiels dans de nombreux réseaux trophiques. L'étude de leur comportement, de développement et de remise en forme peut nous donner un aperçu des impacts de la population et le niveau de bruit de la communauté qui sont pertinents pour la survie des espèces et l'évolution. Le développement de certaines des nouvelles idées et techniques abordées dans cette thèse nous permettra de faire progresser ce domaine vital de la recherche. / As the first part of my thesis, I provide a computer program which allows users to determine under what circumstances they should measure particle motion; I explain how these measurements can be made and provide a program for analysing this type of data. The main part of my thesis comprises experiments investigating the impact of repeated exposure to traffic noise, the most common anthropogenic source of noise in the marine environment, on fishes and invertebrates during development. In all three chapters involving experiments on fish in tanks and in the field, I found that a variety of behaviours were impacted by traffic noise playback. I also found that predictable noise can lead to different impacts on development compared to unpredictable noise, but that some species of fish may be able to habituate to traffic noise, while others suffer lower survival. Further, I found that the development and survival of seahares can be negatively impacted by traffic-noise playback. Fishes and invertebrates provide a vital food source to millions of people and form crucial links in many food webs; studying their behaviour, development and fitness can give us an insight into population and community level impacts of noise that are relevant to species survival and evolution. Developing some of the novel ideas and techniques discussed in this thesis will enable us to advance this vital area of research.

Devido à importância dos macroinvertebrados bentônicos como bioindicadores da qualidade ambiental e às vantagens de seu emprego como tal, estes organismos foram utilizados para avaliar a possível existência de impacto antropogênico às nascentes localizadas no Parque Estadual do Jaraguá (São Paulo, SP). Para isso, selecionaram-se quatro nascentes, em cada uma das quais foram nas quais foram coletadas amostras de água em cada nascente para a análise de coliformes fecais e das concentrações de nitrogênio e fósforo totais. A coleta de macroinvertebrados bentônicos foi realizada, com o auxílio de um delimitador Surber (área de 0,04m2, malha de 500 ?m), em poções e corredeiras da cada nascente. Este trabalho divide-se em dois capítulos. O primeiro capítulo trata da estrutura da comunidade de invertebrados bentônicos nas nascentes do Parque Estadual do Jaraguá e mostra uma diferenciação entre poções e corredeiras, sendo que as famílias Cyclopidae, Talitridae, Leptoceridae, Psychodidae e Stratiomyidae foram exclusivas de poções, enquanto Perlidae e Simuliidae foram exclusivas de corredeiras, sendo que abundância relativa de Chironomidae foi elevada em ambos os habitats. No segundo capítulo, foram testadas onze métricas para a análise da qualidade ambiental das nascentes do Parque Estadual do Jaraguá (São Paulo, SP), das quais apenas quatro (diversidade de Shannon-Wiener, dominância, EPT/Total e IBFM) mostraram-se úteis para a diferenciação das nascentes não impactadas e impactadas. / Due to the importance of benthic macroinvertebrates to assess water quality and the advantages of their utilization as bioindicators, these organisms were employed to assess the possible antropogenic impact in four streams located in Jaraguá State Park (São Paulo, SP). In each stream the benthic macroinvertebrates were collected in 5 pools and 5 riffles with a Surber sampler (0,04m2, 500 ?m mesh size). This study is divided in two chapters. The first compares the benthic macroinvertebrate community structure between pools and riffles. The families Cyclopidae, Talitridae, Leptoceridae, Psychodidae and Stratiomyidae were present exclusively in pools, while Perlidae and Simuliidae were exclusive of riffles. In both habitats, Chironomidae relative abundance was high. In the second chapter, eleven metrics were tested for the analysis of environmental quality of streams. Four of them (Shannon-Wiener diversity, dominance, EPT/Total, and IBMF) showed differences related to the degree of impact anthropogenic on streams and were used to compose a multimetric index

Model projections of future climate change require that coupled climate-vegetation models are developed and validated, i.e. these models should be able to reproduce past climate and vegetation change. Records of pollen deposited in lake bottoms and peat bogs can provide the information needed to validate these models. The aim of this thesis was i) to explore the modern relationships between pollen and vegetation in northern and temperate China and estimate pollen productivity of major plant taxa, and ii) to use the results of i) to produce the first reconstruction of plant cover in China over the last 10 000 years for the purpose of climate modelling. A study of the modern pollen-vegetation-climate relationships was performed in northwestern China (Paper I). Pollen productivity for 18 major plants of cultural landscapes in central-eastern China was estimated (Paper II). Based on a synthesis and evaluation of all existing estimates of pollen productivity in the study region, a standard dataset of pollen productivity for 31 plant taxa is proposed (Paper III). This dataset was used to achieve pollen-based REVEALS reconstructions of plant cover over the last 10 000 years in 35 regions of northern and temperate China (Paper IV). The major findings can be summarized as follows. Paper I: Annual precipitation (Pann) is the major climatic factor influencing pollen assemblages, followed by July precipitation (PJul). The shared effect of combinations of two climatic factors explains a larger portion of the variation in pollen data than individual variables. Paper II: Of the 16 reliable pollen productivities estimated, the estimates for 8 taxa are new, Castanea, Cupressaceae, Robinia/Sophora, Anthemis type/Aster type, Cannabis/Humulus, Caryophyllaceae, Cruciferae, and Galium type. Trees have in general larger pollen productivity than herbs. Paper III: Of the total 31 taxa for which estimates of pollen productivity are available in China, 13 taxa have more than 1 value. All or most of these values are similar for Artemisia, Cyperaceae, Larix, Quercus and Pinus. Eight taxa have very variable estimates. Paper IV: The REVEALS plant percentage-cover strongly differs from the pollen percentages, and they provide new important insights on past changes in plant composition and vegetation dynamics.

O hidrÃide calcÃrio do gÃnero Mil/epora ocorre em regiÃes tropicais de todo o planeta como um componente regular dos recifes de coral. MilÃporas sÃo encontradas em profundidades menores que 1 atà 40 m. Os corais vivos criam uma sÃrie rica de habitats para um grande nÃmero de espÃcies fornecendo substrato para os organismos sedentÃrios e alimento ou abrigo para os organismos mÃveis. O objetivo deste estudo foi identificar e quantificar toda a macrofauna encontrada em colÃnias de Mil/epora a/cicornis na Ãrea de ProteÃÃo Estadual dos Recifes de Coral (RN). As 26 amostras foram coletadas manualmente atravÃs de mergulho autÃnomo, em profundidades de 1 a 3 m. No perÃodo de julho e novembro de 2004 e fevereiro de 2005, as colÃnias foram envolvidas por sacos plÃsticos e, em seguida, extraÃdas do substrato com o auxÃlio de martelo e talhadeira. Posteriormente, as amostras foram fixadas com formalina 4%. No laboratÃrio, as colÃnias foram analisadas para a retirada dos epibiontes e, em seguida, cuidadosamente fragmentadas para a remoÃÃo da fauna perfurante. Foram registrados 1.234 indivÃduos e 95 espÃcies de organismos nÃo coloniais dos grupos Crustacea, Echinodermata, Mollusca, Nemertea, Polychaeta e Sipuncula, e 86 colÃnias e 26 espÃcies de organismos coloniais dos tÃxons Cnidaria, Porifera e Tunicata. Os crustÃceos apresentaram o maior nÃmero de indivÃduos e espÃcies, seguidos por poliquetas e moluscos. Segundo coeficiente de correlaÃÃo de Spearman, o nÃmero de indivÃduos e espÃcies dos organismos nÃo coloniais associados aumenta com o crescimento da colÃnia. Em relaÃÃo à fauna colonial, os tunicados possuÃram maior nÃmero de colÃnias e os porÃferas, maior nÃmero de espÃcies. A epifauna dos grupos coloniais e nÃo coloniais foi mais numerosa que a endofauna. ComparaÃÃes entre milÃporas e corais escleractÃnios podem ser traÃadas devido a uma possÃvel convergÃncia funcional desses tÃxons. à possÃvel supor que as associaÃÃes com corais nÃo dependem exclusivamente da espÃcie hospedeira, pois espÃcies distintas habitam a mesma espÃcie de coral em regiÃes diferentes. Provavelmente o substrato exerÃe papel mais importante, cujas formas promovem a formaÃÃo de habitats distintos. / The limestone of the genus hidrÃide Mil / epora occurs in tropical regions around the planet as a regular component of coral reefs. MilÃporas are found at depths less than 1 to 40 m. The live coral create a rich variety of habitats for many species by providing substrate for sedentary organisms and food or shelter for the bodies moving. The aim of this study was to identify and quantify all the macrofauna found in colonies of Mil / epora a / cicornis Area of Protection of Coral Reefs of the State (RN). The 26 samples were collected manually through autonomous diving in depths from 1 to 3 m. In the period from July to November 2004 and February 2005, the colonies were surrounded by plastic bags and then extracted from the substrate with the aid of hammer and chisel. Subsequently, the samples were fixed with formalin 4%. In the laboratory, the colonies were tested for the withdrawal of epibiontes and then carefully to remove fragmented fauna Perforating. 1234 individuals were recorded and 95 species of non-colonial groups of Crustacea, Echinodermata, Mollusca, Nemertea, and Sipuncula Polychaeta, and 86 colonies and 26 species of organisms colonial taxa of Cnidaria, Porifera and Tunicata. The crustaceans had the highest number of individuals and species, followed by polychaetes and molluscs. According to Spearman correlation coefficient, the number of individuals and species of non-colonial increases associated with the growth of the colony. Regarding colonial fauna, tunicates owned the largest number of colonies and Porifera, greater number of species. The epifauna of non-colonial and colonial groups was larger that endofauna. Comparisons between milÃporas and coral escleractÃnios can be drawn due to a possible functional convergence of these taxa. You can assume that the associations with corals do not depend exclusively on the host species, as different species inhabit the same species of coral in different regions. Probably the most important role exercise substrate, which forms promote the formation of distinct habitats.

Atmospheric aerosols deteriorate visibility and pose a significant risk to human health. The global fluxes of secondary organic aerosols (SOA) that form in the atmosphere from aromatic hydrocarbons are poorly constrained and highly uncertain. The lack of molecular tracers to quantify anthropogenic SOA (ASOA) in part limits the understanding of its abundance and variability, and results in a systematic underestimation of the role of ASOA in the atmosphere. The research presented in this thesis advances the knowledge about ASOA through the i) development of new and advanced methods to quantify potential ASOA tracers, ii) evaluation of their suitability as tracers for ASOA, and iii) application of the validated tracers to assess the spatial, diurnal and seasonal variation of ASOA in three urban environments. In this research, a greater understanding of the role of ASOA is gained through the expansion of tracers for SOA from aromatic hydrocarbons. An analytical method to quantify furandiones, which are produced in high yields from the photooxidation of aromatic hydrocarbons, was developed and enabled the first ambient measurements of furandiones. The optimized method allows for the simultaneous extraction of primary source tracers (e.g., polycyclic aromatic hydrocarbons, hopanes, levoglucosan) and other potential ASOA tracers (e.g., 2,3-dihydroxy-4-oxopentanoic acid [DHOPA], benzene dicarboxylic acids, and nitromonoaromatics). The systematic evaluation of potential ASOA tracers by their detectability, gas-particle partitioning, and specificity revealed that DHOPA, phthalic acid, 4-methylphthalic acids, and some nitromonoaromatics are good ASOA tracers because they are specific to aromatic hydrocarbon photooxidation, readily detected in ambient air, and substantially partition to the particle phase under ambient conditions. These tracers are thus recommended for use in field studies to estimate ASOA contributions to atmospheric aerosol relative to other sources. ASOA was determined to be a significant contributor to PM2.5 organic carbon (OC) in three urban environments. In the industrial Houston Ship Channel area in Houston, TX, ASOA contributed 28% of OC, while biogenic SOA (BSOA) contributed 11%. Diurnally, ASOA peaked during daytime and was largely associated with motor vehicle emissions. In Shenzhen, a megacity in China, 13-23% of OC mass was attributed to ASOA, three folds higher than BSOA. When China controlled the emissions from fossil fuel-related sources, the ASOA contribution to OC reduced by 42-75% and visibility remarkably improved. In downtown Atlanta, GA, ASOA contributed 29% and 16% of OC during summer and winter, respectively. ASOA dominates over BSOA during winter, while high biogenic VOC fluxes made BSOA the major SOA source in Atlanta, GA during summertime. These results indicate the high abundance of ASOA in urban air that has potential to be reduced by modification of anthropogenic activities. Overall, the work presented in this dissertation advances the knowledge about the abundance and variation of ASOA in urban atmospheres through the development of quantification methods and expansion of ASOA tracers. These tracers improve source apportionment of ASOA in receptor based models, which can ultimately aid in developing and implementing effective strategies for air quality management.

Survival is a prerequisite for successful reproduction, and is thus intertwined with fitness. Some physiological systems can improve survival, like the immune system, but compete with other processes for resources. Because animals evolved with resource limitation, it is important to understand how these resource-allocation decisions are made. To meet this end, I performed four investigations addressing how life-history characteristics shift in side-blotched lizards (Uta stansburiana) using laboratory studies and multi-year field sampling. First, I measured metabolic rates in response to different immune challenges and different energy states in male lizards. I found that, surprisingly, cutaneous biopsies were associated with a downregulation of metabolic rate, lipopolysaccharide injection did not affect metabolic rate, and the fastest-healing individuals had the largest decrease in metabolic rate, regardless of feeding treatment. In my second experiment, female lizards were challenged with a cutaneous biopsy and follicle-stimulating hormone to force a trade-off between the reproductive and immune systems. I learned that follicle-stimulating hormone increased metabolic rates and cutaneous biopsies decreased them, and that a combination of both treatments reduced metabolic rate the most. In my third experiment, I sampled wild lizards from northern populations in eastern Oregon and southern populations in southern Utah. In the first year, longer-lived northern lizards had higher circulating corticosterone concentration, decreased reproductive investment, and increased microbiocidal ability, but the subsequent year did not hold to these trends. A subsequent common-garden experiment revealed that southern lizards were faster at healing cutaneous wounds, but lost much more body mass than the northern individuals, which healed more slowly but maintained body mass. Finally, I have conducted a 5-year field investigation addressing the life-history trade-offs associated with urbanization, which reveals interesting effects of precipitation on survival and reproductive effort at urban and rural sites.

The University of South Florida Ecological Research Area (USF Eco Area), located in west central Hillsborough County, is an approximately 306 hectare (756 acre) natural area on the Hillsborough River composed of twelve plant communities. While surrounded on three sides by urbanization, the USF Eco Area makes up the western most section of an extended natural corridor that runs approximately 88 kilometers (55 miles) east and north along the Hillsborough River. An inventory of the vascular flora and the associated ecological communities was developed to better assess the USF Eco Area for educational and research purposes as well as enhance informed decisions when evaluating its status for conservation and management purposes. The study, conducted from June 2001 through August 2005, documented 404 vascular plant taxa in 251 genera and 102 families. Three hundred and seventy-eight taxa (94%) are native to Florida of which 13 are endemic; nine are listed as endangered, threatened, or commercially exploited; four are first time recorded occurrences for Hillsborough County; and ten taxa are listed as Florida Exotic Pest Plant Council’s Category I or II invasive species. Eleven natural plant communities and one ruderal/developed plant community were documented, mapped and characterized by their unique vegetative, topographic, soil, and hydrological components based on qualitative field observations. The blackwater stream, floodplain swamp, floodplain forest, floodplain marsh, hydric hammock, seepage slope, and wet flatwoods are wetland plant communities that cover 65% of the USF Eco Area. Upland plant communities, covering the remaining 35%, are mesic flatwoods, scrubby flatwoods, sandhill, xeric hammock, and ruderal/developed.

The aim of Part One was to discover and investigate the physical and chemical properties of coal minesoils occurring within the Big South Fork National River and Recreation Area (BSF) in order to better understand the nature of these anthropogenic soils. In particular, this information was to identify which, if any, un-reclaimed or recently reclaimed minesoils were actively producing acid mine drainage (AMD) and what properties were inhibiting revegetation. Historical knowledge and maps were used to locate more than 30 un-reclaimed and reclaimed minesoil sites, which were mapped with GPS. Soil profiles were exposed on 18 sites and grab samples taken on another 12. The morphological properties of each full profile were described according to the National Soil Survey Handbook and samples were taken from each horizon. Chemical properties analyzed for include: particle size, acid-base account, pH, exchangeable aluminum, manganese oxides, soil organic carbon, cation-exchange capacity, exchangeable bases, Mehlich I-extractable elements, and total elemental concentrations. Significant differences in the following properties (averaged) were discovered between the un-reclaimed and reclaimed minesoils: slope, percent rock fragments, dominant lithology, net neutralization potential, pH, extractable aluminum, base saturation, several Mehlich I-extractable nutrients and total elemental concentrations. Hierarchical clustering analysis revealed similar findings and also highlighted instances where reclaimed minesoils were statistically more similar to un-reclaimed minesoils than to other reclaimed minesoils. This indicated that reclamation efforts may not have been completely successful on these sites. In Part Two, minesoil profiles were classified according to Soil Taxonomy and according to proposed amendments by the International Committee for Anthropogenic Soils (ICOMANTH). The ICOMANTH amendments provided more informative classifications for coal minesoils in the BSF however, shortcomings were noted. Additional recommendations were made and the minesoils were again classified according to these recommendations. Compared to both the Soil Taxonomy and the ICOMANTH classifications, those according to the proposed additional amendments revealed more of the unique properties of the minesoils studied in this project. The results of this study can aid the National Park Service with future land management of the minesoils located within the BSF boundaries and other users of drastically disturbed minesoils.

With the increasing availability of observational data from different sources at a global level, joint analysis of these data is becoming especially attractive. For such an analysis – oftentimes with little prior knowledge about local and global interactions between the different observational variables at hand – an exploratory, data-driven analysis of the data may be of particular relevance. In the present work we used generalized additive models (GAM) in an exemplary study of spatio-temporal patterns in the tropospheric NO2-distribution derived from GOME satellite observations (1996 to 2001) at global scale. We focused on identifying correlations between NO2 and local wind fields, a quantity which is of particular interest in the analysis of spatio-temporal interactions. Formulating general functional, parametric relationships between the observed NO2 distribution and local wind fields, however, is difficult – if not impossible. So, rather than following a modelbased analysis testing the data for predefined hypotheses (assuming, for example, sinusoidal seasonal trends), we used a GAM with non-parametric model terms to learn this functional relationship between NO2 and wind directly from the data. The NO2 observations showed to be affected by winddominated processes over large areas. We estimated the extent of areas affected by specific NO2 emission sources, and were able to highlight likely atmospheric transport “pathways”. General temporal trends which were also part of our model – weekly, seasonal and linear changes – showed to be in good agreement with previous studies and alternative ways of analysing the time series. Overall, using a non-parametric model provided favorable means for a rapid inspection of this large spatio-temporal NO2 data set, with less bias than parametric approaches, and allowing to visualize dynamical processes of the NO2 distribution at a global scale.

Ice cores are considered the gold standard for recording past climate and biogeochemical changes. However, gas records derived from ice core analysis have until now been largely limited to centennial and longer timescales because sufficient temporal resolution and analytical precision have been lacking, except during rare times when atmospheric concentrations changed rapidly. In this thesis I used a newly developed methane measurement line to make high-resolution, high-precision measurements of methane during the late Holocene (2800 years BP to present). This new measurement line is capable of an analytical precision of < 3 ppb using ~120 g samples whereas the previous highest resolution measurements attained a precision of ± 4.1 ppb using 500-1500g samples [MacFarling Meure et al., 2006]. The reduced sample size requirements as well as automation of a significant portion of the analysis process have enabled me to make >1500 discrete ice core methane measurements and construct the highest resolution records of methane available over the late Holocene. Ice core samples came from the recently completed West Antarctic Ice Sheet (WAIS) Divide ice core which has as one of its primary scientific objectives to produce the highest resolution records of greenhouse gases, and from the Greenland Ice Sheet Project (GISP2) ice core which is a proven paleoclimate archive. My thesis has the following three components. I first used a shallow ice core from WAIS Divide (WDC05A) to produce a 1000 year long methane record with a ~9 year temporal resolution. This record confirmed the existence of multidecadal scale variations that were first observed in the Law Dome, Antarctica ice core. I then explored a range of paleoclimate archives for possible mechanistic connections with methane concentrations on multidecadal timescales. In addition, I present a detailed description of the analytical methods used to obtain high-precision measurements of methane including the effects of solubility and a new chronology for the WDC05A ice core. I found that, in general, the correlations with paleoclimate proxies for temperature and precipitation were low over a range of geographic regions. Of these, the highest correlations were found from 1400-1600 C.E. during the onset of the Little Ice Age and with a drought index in the headwater region of the major East Asian rivers. Large population losses in Asia and the Americas are also coincident with methane concentration decreases indicating that anthropogenic activities may have been impacting multidecadal scale methane variability. In the second component I extended the WAIS Divide record back to 2800 years B.P. and also measured methane from GISP2D over this time interval. These records allowed me to examine the methane Inter-Polar Difference (IPD) which is created by greater northern hemispheric sources. The IPD provides an important constraint on changes in the latitudinal distribution of sources. We used this constraint and an 8-box global methane chemical transport model to examine the Early Anthropogenic Hypothesis which posits that humans began influencing climate thousands of years ago by increasing greenhouse gas emissions and preventing the onset of the next ice age. I found that most of the increase in methane sources over this time came from tropical regions with a smaller contribution coming from the extratropical northern hemisphere. Based on previous modeling estimates of natural methane source changes, I found that the increase in the southern hemisphere tropical methane emissions was likely natural and that the northern hemispheric increase in methane emissions was likely due to anthropogenic activities. These results also provide new constraints on the total magnitude of pre-industrial anthropogenic methane emissions, which I found to be between the high and low estimates that have been previously published in the literature. For the final component of my thesis I assembled a coalition of scientists to investigate the effects of layering on the process of air enclosure in ice at WAIS Divide. Air bubbles are trapped in ice 60-100m below the surface of an ice sheet as snow compacts into solid ice in a region that is known as the Lock-In Zone (LIZ). The details of this process are not known and in the absence of direct measurements previous researchers have assumed it to be a smooth process. This project utilized high-resolution methane and air content measurements as well as density of ice, δ¹⁵N of N₂, and bubble number density measurements to show that air entrapment is affected by high frequency (mm scale) layering in the density of ice within the LIZ. I show that previous parameterizations of the bubble closure process in firn models have not accounted for this variability and present a new parameterization which does. This has implications for interpreting rapid changes in trace gases measured in ice cores since variable bubble closure will impact the smoothing of those records. In particular it is essential to understand the details of this process as new high resolution ice core records from Antarctica and Greenland examine the relative timing between greenhouse gases and rapid climate changes. / Graduation date: 2013