A rapid assay kit for Vibrio cholerae (Vc) was developed to detect and quantify Vc cells in oyster samples within 24 h. The kit, formulated within a two -phase (liquid and solid) 96-well plate, can detect biomarker expression of Vc when the enrichment broth and incubation temperature are optimized. The kit showed 91 % selectivity and 92 % specificity when tested with 23 inclusive Vc and 106 exclusive non-Vc strains. The kit was further optimized using 47 samples of oysters, clams, and soil. There was no significant difference in most probable number between the kit, conventional PCR and BAX PCR regardless of agar heating method (autoclaved vs. boiled). The kit’s limit of detection was below 5 cfu/g. The kit is a reliable method for the detection of V. cholerae in bivalve samples.

A thesis submitted to the School of Graduate Studies in partial fulfilment of the requirements for the degree of Master of Science in the graduate academic unit of Biology / Microparticles enter aquatic environments through many sources, including wastewater treatment plants (WWTPs), but their uptake by aquatic organisms is poorly understood. Freshwater bivalves accumulate multiple contaminants, making them potential bioindicators for MP pollution. This study aims to understand the abundance and characteristics of microparticles that accumulate in wild bivalves. Samples were collected from 5 locations along the Grand River (Ontario, Canada) in 2021-2022, including 3 municipal WWTPs where both an upstream and downstream site were sampled. At each site, fingernail clams (Sphaeriidae, n=5 composite samples), flutedshell mussels (Lasmigona costata, n=10), and surface water (n=3) were sampled. Within the mussels, the gill, digestive gland, and hemolymph tissues were targeted and compared. Microparticles were isolated and quantified via stereomicroscopy but have not yet been confirmed as plastic; as such, they will be referred to herein as microparticles. Fibers were the dominant morphology and clear, blue, and black were the most common colours, but there were some differences among sites and sample types. Most microparticles were between 80 μm and 1 mm in length. Fingernail clams contained the highest microparticle counts per mass of tissue at 35.5 ± 29.4 microparticles/g, mussel tissues ranged from 4.3 ± 4.2 microparticles/mL to 6.5 ± 8.1 microparticles/g, and water samples contained the lowest counts at 0.0055 ± 0.0028 microparticles/mL. Elevated microparticle counts at downstream sites were only seen in mussel gills and not other bivalve tissues. Surface water samples did not show elevated counts downstream of the WWTPs and microparticle exposures were similar across sites. This study provides baseline data for future monitoring and informs toxicity studies to fully assess the risk of microparticles to vulnerable freshwater bivalves and other aquatic organisms. It also suggests microparticles in freshwater bivalves are coming from sources in addition to WWTPs and are ubiquitous in the Grand River. / Thesis / Master of Science (MSc) / Microplastics are found in nearly every environment, especially freshwater ecosystems. These plastics come from a variety of sources, and this study focuses on assessing the characteristics of microparticles in freshwater clams and mussels (bivalves) that have been exposed to municipal wastewaters. Bivalves and water samples were collected from 5 locations along the Grand River (Ontario, Canada) in 2021-2022, and microparticles were extracted and analyzed from each sample. Fibers were the most abundant type of microparticle, with colours consisting mostly of clear, blue, and black. Clams had the highest number of microparticles per mass of tissue collected and the lowest counts were found in water samples. Higher microparticle counts were only seen in one (mussel gill) of the four tissues from bivalves collected downstream of wastewater outfalls. This study provides baseline data on microparticle characteristics in freshwater bivalves and will guide future studies on the toxicity of microparticles to these animals.

<p> This study analyzed fossil and modern freshwater bivalve mollusc shells, from in and around lakes Ontario and Erie, for the following trace metals: Cu, Ni, Zn, As, Pb, and Mn. Elliptio dilatata, Elliptio complanata, and Lampsilis radiata siliquoidea shells were analyzed by ICPMS for differences in shell metal levels between species and genera, through time and due to anthropogenic inputs. </p> <p> Regardless of age, all three species showed high concentrations of Zn and Mn, and little or no changes in Cu, Ni, Zn, and Pb concentrations with time. E. comp1anata shells were generally poorer in Pb, but richer in As and Mn, than were the E. dilatata and L. radiata siliquoidea shells. Fossil Elliptio samples did not posses low background, or baseline, trace metal concentrations. These samples were richer in As, Pb, and Mn than were modern samples from post-industrial environments. Among the modern shells, the E. complanata showed no differences in metal concentrations between samples from high- and low-contamination· sites, while the L. radiata siliquoidea showed changes in Ni, As, and Mn concentrations among the same sites. Modern L. radiata siliquoidea may be more likely to represent environmental metal changes than are modern E. complanata. Historical change in environmental metal concentrations of the Great Lakes region is not recorded as a simple change in shell metal concentrations of these freshwater bivalve molluscs. </p> / Thesis / Bachelor of Science (BSc)

Experiments were conducted on the effectiveness of exposure to simultaneous temperature shock with chlorination, monochloramine, and ammonia as control agents of the Asiatic clam, Corbicula sp. Control procedures were evaluated based on lethal and sublethal responses (e.g., glycogen, tissue water, dry weight index, and siphoning activity) of clams during 30-day laboratory artificial stream studies. Studies also were conducted comparing sublethal responses (e.g., glycogen, tissue water, soluble protein, and siphoning activity) of clams to copper, a component of power plant effluents, during 30-day laboratory, site-specific, and in-situ copper exposures. This was done to evaluate the use of the Asiatic clam as a biomonitoring organism of copper contamination. Regarding temperature and chlorine interactions, it was demonstrated that an increase of 10° C was needed to increase significantly adult and juvenile mortality in the presence of chlorine (0.30 mg/l TRC) during winter and summer. Naturally high temperatures also increased adult mortality during in-plant chlorination procedures, with the highest mortality occurring during the spring. Significant decreases in the dry weight condition index were observed for adults chlorinated at 5° increases during winter and at 10° C increases for control (non-chlorinated) clams during both winter and summer. Similarly, glycogen content responded with a temperature-dependent decrease in both control and chlorinated clams during the summer. In addition, exposure to increased temperatures significantly increased the siphoning activity of control adults during summer and juveniles during winter. Chlorinated clams experienced near total inhibition of siphoning activity at all temperatures tested, except for adults exposed at 33° C. Increased dsiphoning activity, decreased glycogen content, and possibly ammonia accumulation in the mantle cavity were believed to be responsible for the increased mortality of clams chlorinated at higher temperatures. Total residual chlorine, with < 90% as monochloramine, was found to be equally toxic to adults and more toxic to juveniles compared to total residual chlorine containing higher amounts of free residual chlorine. Since free residual chlorine is considered to be more toxic than combined residual chlorine (e.g., monochloramine), questions were raised as to which form of chlorine was actually exposed to the tissues of adducted Asiatic clams. Ammonia was considerably less toxic to adults but more toxic to juveniles compared to chlorine. Both monochloramine and ammonia caused significant reductions in clam glycogen content and siphoning activity. The siphoning activity of clams exposed to ammonia, although significantly reduced, was considerably higher than siphoning activities observed for monochlorinated and chlorinated clams. Clam tissue water content decreased in the presence of ammonia but remained unaffected in the presence of monochloramine. Ammonia toxicity to adult clams was highly pH dependent but may be useful in controlling larval stages of Asiatic clams. More definitive research is needed to evaluate fully the potential of monochlorination as a biofouling control agent. Clams were more sensitive to copper exposures, with respect to glycogen content, in field-located (i.e. site-specific) artificial streams than in laboratory artificial streams. Specifically, the "no observable effect concentration" was between 5.5 and 8.4 μg Cu/1 during the 30-day site-specific studies compared to 17.2-32.1 μg Cu/1 in the laboratory. Copper significantly increased clam tissue water content during the Clinch River and June site-specific studies. However, clam soluble protein content demonstrated no consistent dose-dependent response during the laboratory or site-specific studies. Glycogen and tissue water content, although subject to some seasonal influences, are recommended for use in Corbicula for future site-specific and in-situ long-term toxicity experiments. / Master of Science

Geographical variation in taxa must be considered in evolutionary studies. The purpose of the present study is to demonstrate how geographical variation can be measured and documented for a taxon for one slice of time. Future evolutionary studies should document geographical variation for the entire geographical range of the species involved at several points of time throughout its total stratigraphic range. Thus the variation that is present at one time horizon may be separated from the variation that occurs through time. This work consists of a study of geographical variation in the genus Astarte (Phylum Mollusca: Class Bivalvia) from the Yorktown and Jackson Bluff Formations (early Pliocene) of the Atlantic Coastal Plain. Factor analysis, multivariate analysis of variance, and discriminant analysis were performed on measurements of specimens of Astarte from ten localities. There are significant differences in the morphologies of individuals among localities. These differences are due to the presence of different species of Astarte and to variation in size and external ornamentation within the same species. Seven species recognized from literature on Pliocene Astarte were identified among the individuals of the ten localities, but the statistical results indicate that these seven species may be grouped into three "types" that mayor may not represent species. The three types occur together in some localities, suggesting that they are distinct species living in sympatry. Factors influencing geographical variation include larval dispersal strategy and the effect of the environment. / Master of Science

Nos moluscos da classe Bivalvia, a margem do manto (ou palial) é geralmente organizada em três pregas e representa um ponto chave na compreensão da irradiação evolutiva do grupo e na conquista de novos nichos ecológicos. Na subclasse Pteriomorphia, agrupamento que reúne bivalves como ostras, vieiras e mexilhões, a margem do manto é amplamente diversa. Além disso, algumas linhas de evidência apontam para a associação entre estruturas paliais e diversificação de hábitos de vida, de modo que essa região anatômica representa uma importante fonte de dados para estudos de adaptação e correlação fenótipo-ambiente. A pesquisa desenvolvida investigou a diversidade morfológica da margem do manto em Pteriomorphia, por meio de abordagens comparativas e funcionais, a fim de inferir a evolução dessa região anatômica e testar hipóteses de homologia, convergência e correlação. A metodologia abrangeu: (1) inferência filogenética de Pteriomorphia com base em 187 espécies e até cinco genes; (2) morfologia comparada de 209 espécies utilizando-se espécimes depositados em coleções científicas, levantamento de caracteres chave do manto e emprego de métodos filogenéticos comparativos; e (3) anatomia detalhada da margem do manto em representantes de 12 espécies das principais famílias de Pteriomorphia, que foram coletados e analisados por meio de histologia, microscopia eletrônica de varredura e microscopia confocal. A análise filogenética de Pteriomorphia indica que o grupo é monofilético e organizado em quatro ordens contidas em dois clados principais (Arcida+Pectinida e Ostreida+Mytilida). A evolução da margem do manto abrange o surgimento de cinco tipos de órgãos fotorreceptores em diferentes linhagens epifaunais, com subsequente perda desses órgãos principalmente em grupos que se tornaram infaunais. Convergências evolutivas foram recorrentes na irradiação dos Pteriomorphia, como é o caso dos tentáculos paliais. Algumas dessas convergências estão correlacionadas a transições para o hábito de vida infaunal, como demonstrado pela hipertrofia da prega interna do manto em representantes de Arcida e Mytilida. A caracterização da inervação, musculatura, atividade secretora e ciliação da margem do manto contribuiu para a compreensão da anatomia funcional das pregas, ocelos, tentáculos, glândulas e demais estruturas associadas. Em suma, os resultados obtidos permitem compreender a evolução da margem do manto em Pteriomorphia associada a mudanças nos hábitos de vida, fornecendo evidências importantes para se explorar questões macroecológicas na irradiação dos bivalves e do bentos marinho como um todo / The mantle margin in bivalve mollusks typically comprises three folds, being considered a key element in the evolutionary radiation of the class and occupancy of novel ecological niches. In the subclass Pteriomorphia, which includes oysters, scallops, and mussels, the mantle margin is significantly diverse. In addition, several lines of evidence suggest the association between mantle structures and diversification of lifestyles, making the mantle margin a suitable anatomical region for studies focused on adaptations and phenotype-environment correlations. The present investigation evaluated the morphological diversity of the mantle margin in Pteriomorphia, by means of comparative and functional approaches, to infer the evolution of this anatomical region, and test hypotheses of homology, convergence and correlation. The methodology included: (1) phylogenetic inference of Pteriomorphia based on 187 taxa and up to five genes; (2) comparative morphology of 209 species based on observations of archived specimens, survey of key mantle traits and subsequent use of phylogenetic comparative methods; and (3) detailed anatomy of the mantle margin in representatives of 12 species from the most diverse pteriomorphian families, which were collected and analyzed by means of histology, scanning electron microscopy and confocal microscopy. Phylogenetic analyses of Pteriomorphia corroborate its monophyly and indicate it is comprised of four orders divided in two main clades (Arcida+Pectinida and Ostreida+Mytilida). The inferred evolution of the mantle margin suggests the origin of five types of photoreceptor organs in independent epifaunal lineages, with subsequent loss of eyespots mostly in groups that became infaunal. Evolutionary convergences were pervasive in pteriomorphian radiation, as illustrated by multiple gains of mantle tentacles. Some convergences are correlated with transitions to infaunal lifestyles, as demonstrated by the hypertrophy of the inner mantle fold in lineages within Arcida and Mytilida. In addition, the detailed investigation of musculature, innervation, secretory activity and cilia of the mantle margin permitted inferring possible functions performed by mantle folds, eyespots, tentacles, glands and further associated structures. Altogether, the results shed light on the evolution of the mantle margin in Pteriomorphia in association with lifestyle shifts, therefore providing bases to explore macroecological questions in the evolutionary radiation of bivalves and the marine benthos as a whole

O atual conhecimento sobre a margem do manto em moluscos bivalves é extenso, incluindo informações sobre morfologia, função e diversidade. Bivalves da família Pectinidae, também conhecidos como vieiras, possuem complexa margem palial, organizada em três pregas, incluindo olhos e tentáculos. Questões acerca do desenvolvimento da margem do manto em bivalves continuam amplamente incompreendidas, assim como a relação entre características paliais ao longo dos diferentes estádios do ciclo de vida. Neste contexto, a presente investigação utilizou a espécie de vieira Nodipecten nodosus como modelo para compreensão da morfogênese da margem palial em Pectinidae, com ênfase na origem e diferenciação das pregas paliais e estruturas associadas. Para contemplar esses objetivos, espécimes em diferentes estádios de desenvolvimento larval e pós-metamórfico foram analisados por meio de técnicas integradas de microscopia (i.e., histologia, microscopia eletrônica de varredura e transmissão, e imunocitoquímica aplicada à microscopia confocal). Inicialmente, a margem palial em larvas véliger de N. nodosus não é pregueada, porém, ao longo do desenvolvimento, dois processos de evaginação são determinantes na formação das pregas paliais. O primeiro ocorre no estádio de pedivéliger, originando as pregas externa e interna, bem como o sulco do perióstraco. O segundo ocorre após a metamorfose, sendo responsável pela origem da prega palial mediana a partir da porção interna da prega interna. Os sistemas muscular e nervoso da margem palial têm origem durante o período larval, tornando-se amplamente desenvolvidos posteriormente. Estruturas associadas, como tentáculos e olhos paliais, são formadas apenas após a metamorfose, e compõem a complexa condição final da margem do manto em Pectinidae. Os diferentes tipos tentaculares possuem desenvolvimento e anatomia similar, entretanto diferem quanto ao tamanho, tipo de musculatura, organização ciliar e presença de células glandulares. Os olhos paliais em formação diferenciam-se gradualmente em sentido proximal-distal, essas características morfológicas sugerindo um nível simples de fotopercepção direcional como condição inicial. Os dados aqui apresentados para N. nodosus permitiram propor um modelo geral para o desenvolvimento da margem palial em Pectinidae, além de contribuir para o entendimento da morfogênese dessa região em Bivalvia / Current knowledge of the bivalve mantle margin is extensive, covering several aspects of its morphology, function and diversity. Bivalves from the family Pectinidae, also known as scallops, bear three pallial folds at the mantle margin, including complex structures, such as tentacles and eyes. The development of the bivalve mantle margin is still poorly understood, the morphogenesis and functional anatomy of mantle margin features during developmental stages being enigmatic. The present investigation used the scallop Nodipecten nodosus (L. 1758) as a model species to understand mantle margin morphogenesis in the Pectinidae, with emphasis on the origin and differentiation of pallial folds and associated pallial structures. To achieve these goals, specimens from larval and postmetamorphic stages were thoroughly analyzed by means of integrative microscopy techniques (i.e., histology, scanning and transmission electron microcopy, and immunocytochemistry combined with confocal microscopy). In veliger larvae of N. nodosus, the mantle margin is initially unfolded, two folding processes being crucial for pallial fold establishment during further development. The first one occurs by the pediveliger stage, forming the outer and inner folds, as well as the periostracal groove. The second folding process takes place after metamorphosis and is responsible for the formation of the middle pallial fold from the inner region of the inner mantle fold. The emergence of muscular and nervous systems in the mantle margin occurs early during development, at the larval stage. Associated pallial structures, including tentacles and eyes, develop only after metamorphosis, and contribute to the complex final condition of the mantle margin in Pectinidae. Although different tentacular types have similar development and anatomy, they differ in size, muscle type, ciliary organization, and gland cells distribution. Developing pallial eyes exhibit gradual differentiation in a proximal-distal direction, and their morphological features suggest a simple level of directional photoreception as the initial ocular condition in juveniles. The present investigation conducted with N. nodosus provided a general model to understand mantle margin development in the Pectinidae, as well as insights into the morphogenesis of this region in the Bivalvia

Le recrutement est un processus clé du cycle de vie des invertébrés marins benthiques, dont les bivalves. Si la phase larvaire et l’étape de fixation/métamorphose sont largement étudiées, les processus post-fixation, dont font partie les migrations secondaires, restent relativement ignorés ou du moins sous-estimés.Ces migrations secondaires ou post-fixations résultent de processus hydrodynamiques modulés par des réponses éco-éthologiques.Le présent projet proposait d’étudier les mécanismes de migrations secondaires des recrues de bivalves en développant une approche éco-étho-physiologique afin de répondre à trois objectifs : i) Estimer le poids potentiel des migrations secondaires dans les habitats de sédiments grossiers ii) Identifier des facteurs environnementaux, et plus spécifiquement ceux de l’environnement trophique en relation avec l’hydrodynamisme, qui contrôlent ces processus iii) Évaluer les potentielles interactions entre migrations secondaires et physiologie des recrues. Dans un premier temps, nous avons développé une étude in-situ des migrations secondaires des recrues de bivalves dans un habitat de sédiments grossiers dans l’archipel de Chausey (Normandie, France) via l’utilisation de pièges à recrues. En parallèle, un suivi de nombreux paramètres environnementaux (conditions hydrologiques, hydrodynamiques et trophiques) a été mis en place. Puis, nous avons étudié en conditions expérimentales, le potentiel de dispersion post-fixation de différentes espèces de bivalves exploitées et l’influence de la physiologie (en termes de réserves énergétiques) sur les migrations secondaires. Pour ce faire, nous avons utilisé des outils innovants, tels un tube de vitesse de chute et un canal hydrodynamique tout en développant la zootechnie de l’élevage larvaire et poste-larvaire de la praire, Venus verrusosa. Nos résultats mettent en évidence l’importance des migrations secondaires des recrues de bivalves dans les habitats de sédiments grossiers avec près de 24 taxons différents de bivalves identifiés en migration. Certaines de ces migrations post-fixations correspondraient à des changements ontogéniques d’habitats, et les habitats de sédiments grossiers constitueraient une zone de nurserie pour plusieurs espèces. De plus, ce projet démontre, pour la première fois, le rôle de la physiologie et de l’environnement trophique dans le contrôle des migrations secondaires et cela à différents niveaux. Nous avons observé une synchronisation entre un événement massif de migrations secondaires actives et un changement de la composition de la communauté phytoplanctonique, plus particulièrement un bloom de nanoeucaryotes. Cette réponse des recrues de bivalves à un signal trophique pélagique («trophic migration trigger», TMT), pourrait être due au coût énergétique supplémentaire associé aux comportements actifs de migration. En effet, nous avons ensuite constaté en conditions expérimentales que la capacité des recrues à contrôler leur dispersion par leur comportement est directement corrélée avec leur profil physiologique. Les recrues avec le plus de réserves énergétiques ont une meilleure capacité d’accroître leur potentiel de dispersion par leur comportement. Aussi les recrues migreraient quand leur principale source de nourriture est disponible dans le milieu afin de mieux supporter le coût des comportements de migrations secondaires actives comme la dérive byssopélagique. De plus, le potentiel de migration post-fixation apparait comme fortement lié à la synchronicité entre la période d’arrivée de la larve sur le sédiment et le cycle de marée (morte-eau ou vive-eau), mais également aux taux de croissance post-larvaires qui dépendent eux-mêmes de l’environnement trophique. Les patrons de migrations secondaires des recrues bivalves résultent donc d'un étroit couplage physico-biologique impliquant l'hydrodynamique, mais aussi des réponses éco-éthologiques modulées par des processus physiologiques en lien avec l’environnement trophique. / Recruitment is a key process in the life-cycle of benthic marine invertebrates, and most of bivalve species. It includes the larval phase, the settlement and secondary dispersal mechanisms which lead to a gradual sedentary lifestyle until the recruits begin a strict benthic life. Although the larval phase and the settlement/metamorphosis stage are well studied, post-settlement migrations remain relatively unknown or at least underestimated. These migrations are the result of hydrodynamic processes modulated by eco-ethological responses in the benthic boundary layer that can radically change primary fixation patterns and have a major impact on the life cycle of a bivalve.This project proposed to study secondary migrations mechanisms of bivalve recruits by developing an eco-etho-physiological approach in order to answer three objectives: I) estimate the potential weight of the secondary migrations in coarse sediments habitats, ii) identify environmental factors, and more specifically those of the trophic environment in relation to hydrodynamics conditions, which control these processes, iii) evaluate the potential interactions between secondary migrations and recruits physiology.Firstly, we developed an in-situ study of secondary migrations of bivalve recruits in a coarse sediment habitat in the Chausey Archipelago (Normandy, France) by using recruit traps and monitoring environmental parameters (hydrological, hydrodynamic and trophic conditions). Then, we studied in experimental conditions post-settlement dispersal potential of different exploited bivalve species as well as the influence of physiology (in terms of energy reserves) on secondary migrations with a fall velocity tube, a benthic flume and by developing the larval and post-larval rearing of the warty venus, Venus verrucosa. Our results highlight the importance of secondary migrations of bivalve recruits in coarse sediment habitats with nearly 24 different taxa of bivalves identified in migration. Some of these post-settlement migrations would correspond to ontogenic change of habitat, and so coarse sediment habitats would constitute a nursery zone for several species. For the first time, this project demonstrates, at different levels, the role of physiology and trophic environment in the control of secondary migrations. We observed synchronization between a massive active secondary migration event with a change in the composition of the phytoplankton community and more particularly a bloom of nanoeukaryotes. This response of bivalve recruits to a ‘’trophic migration trigger’’ (TMT) could be due to the additional energy cost of active migration behaviors. Indeed, we highlighted, in experimental conditions, that the ability of recruits to control their dispersal by their behavior is directly correlated with their physiological profile. Recruits with the most energy reserves are the most able to increase their dispersal potential by their behavior. Also recruits would migrate when their main food source is available in the environment in order to support the cost of active secondary migration behaviors such as bysso-pelagic drift. In addition, post-fixation migration potential appears to be strongly related to the synchronicity between the settlement period and the tidal cycle (spring tide or neap tide), but also to post-settlement growth rates which depend on trophic conditions. Patterns of secondary migrations result from a close physico-biological coupling involving hydrodynamics factors but also eco-ethological responses modulated by physiological processes related to the trophic environment.

O histórico de contaminação por metais no Vale do Rio Ribeira de Iguape é bem conhecido, com evidências de transporte destes contaminantes ao Complexo Estuarino Lagunar de Cananéia-Iguape (CELCI), adsorvidos ao material em suspensão. Assim, os metais podem alcançar o setor sul do CELCI, podendo acumular nos sedimentos e nos organismos filtradores. Neste estudo foi realizada uma avaliação de risco ecológico no CELCI associado à presença de metais oriundos das antigas áreas de mineração do Alto Ribeira, utilizando diferentes linhas de evidência. Os resultados foram avaliados de forma integrada, incluindo análises geoquímicas e biológicas (ensaios de toxicidade aguda, medidas de bioacumulação e biomarcadores bioquímicos em brânquias de bivalves). Os sedimentos apresentaram níveis moderados a altos de metais e toxicidade aguda, a qual foi associada, especialmente, com as concentrações de Cu, Pb e Zn. Da mesma forma estes metais foram encontrados em concentrações altas nos tecidos de bivalves. Os biomarcadores bioquímicos (MT, GSH, GST, GPx, GR, AChE, LPO e danos em DNA) indicaram a ocorrência de efeitos significativos nos bivalves. Portanto, os resultados mostram que os metais estão sendo carreados para a porção sul do estuário, causando bioacumulação e efeitos nos organismos aquáticos e, portanto, gerando riscos ecológicos para o CELCI. / The historic of contamination by metals in the Valley of Ribeira de Iguape River is well known, and there are evidences that these chemicals are carried to the Estuarine Complex of Cananeia-Iguape (ECCI), adsorbed on the suspended particles. Metals can thus reach the south of the ECCI, where they may accumulate in the sediments and filter feeding organisms. This study aimed to evaluate the ecological risks associated to the metals originated from the former mining areas of the upstream Ribeira de Iguape River, by using different lines of evidence, which included geochemical and biological analysis (acute toxicity tests, bioaccumulation and biochemical biomarkers in bivalves\' gills). The sediments presented moderate to high levels of metals and acute toxicity, which was correlated with the concentrations of metals (Cu, Pb and Zn). These elements were found in high concentrations in the bivalves soft tissues. The biochemical biomarkers (MT, GSH, GST, GPx, GR, AChE, LPO, and DNA damage) indicated the occurrence of significant effects in the bivalves. Therefore, the results showed that metals are carried into the South portion of the estuary, accumulating in the biota and causing negative effects to the aquatic organisms, producing thus ecological risks to the ECCI.

Les rudistes bivalves forment un groupe monophylétique qui s’étend dans le registre fossile de 160 à 66 millions d’années. L’objectif de cette thèse est de porter un nouveau regard sur l’histoire évolutionnaire de ce groupe dans le cadre de la théorie cladistique. Dans une première partie sont posées les bases théoriques, méthodologiques et techniques de l’analyse à trois éléments. Le concept de triplet permet de proposer des arguments sur la pertinence des arbres consensus. La méthode d’analyse à trois éléments est ensuite comparée à la méthode de parcimonie grâce à des arguments théoriques et méthodologiques, ainsi que par des simulations basées sur des modèles d’évolution. Dans une seconde partie, nous appliquons la théorie et la méthode à la reconstruction de l’histoire des rudistes. Le genre Ichthyosarcolites est révisé, et des analyses statistiques permettent de tester la pertinence des hypothèses d’homologie basée sur la forme de la coquille. Les hypothèses d’homologie sont revues et de nouveaux caractères basés sur les myophores et les canaux palléaux sont formalisés pour l’ensemble des Hippuritida. La nouvelle phylogénie qui en découle est cohérente avec l’âge géologique et permet de raffiner l’histoire évolutive des rudistes au Crétacé. L’étude de couches Cénomaniennes du Bassin Sud-Provençal (Var, France) nous permettent de faire un lien entre l’histoire de la diversification des rudistes et leur paléoécologie. / The rudist bivalves form a monophyletic group that extends in the fossil record from 160 to 66 million years. The objective of this thesis is to propose new insights at the evolutionary history of this group within the framework of cladistic theory. In the first part, we lay the theoretical, methodological and technical foundations of the three-item analysis. The concept of triplet allows us to propose arguments on the relevance of consensus trees in cladistics. The three-item analysis method is then compared to the method of parsimony using theoretical and methodological arguments, and simulations based on evolutionary models. In a second part, we apply the theory and method to the reconstruction of the rudist history. The genus Ichthyosarcolites is reviewed, and statistical analyses are used to test the relevance of homology hypotheses based on shell shape. Hypotheses of homology and new characters based on myophores and pallial canals are tested on the Hippuritida. The new, resulting phylogeny is consistent with known geological occurrences of the group and further our understanding of rudist evolutionary history during the Cretaceous. The study of Cenomanian outcrops of the South Provence Basin (Var, France) allows us to make a link between the history of the diversification of rudists and their paleoecology.