Nesting success is an important vital rate affecting the reproductive fitness of birds, and predation typically is the single most important factor affecting nesting success. Presumably, birds should nest in locations that maximize nest survival. If specific nest characteristics increase the probability that a nest will hatch, natural (phenotypic) selection could favour use of sites with these features, producing nonrandom patterns of nest site use. Alternatively, birds that are highly selective in nest site choices might be at a disadvantage if predators learn to forage preferentially in these locations and improve their efficiency in depredating nests; in this case, random nesting patterns could be favoured. Finally, it has been hypothesized that predation pressure can influence nest site selection patterns of entire bird communities. If predators develop a search image to hunt for bird nests, then nests that are most similar to each other, irrespective of species, should sustain higher mortality. To evaluate these hypotheses, I quantified nest site selection patterns of multiple species of ground-nesting dabbling ducks in areas where predation pressure was normally high, and compared these patterns to those on areas where predation was relaxed. Predation pressure was experimentally reduced by removing common predators of duck nests and females (mainly red foxes, coyotes, skunks and raccoons) on some study areas and not on others (controls). Predator removal and natural causes produced a 10-fold difference in duck nesting across study sites, allowing for investigation of effects of predation pressure on nest site selection of ducks. Coarse scale habitat selection patterns were similar to results reported in previous studies; blue-winged teal and northern shoveler were found more often in native grassland than in other habitat types, while gadwall and mallard nests occurred more frequently in shrub patches when compared with other habitat patches. A difference in nest site characteristics was observed between hatched and depredated nests for gadwall and northern shoveler but not for blue-winged teal and mallard. However, in all species, the nest site selection patterns were non-random. Thus, the process of nest predation did not shape patterns of nest site choice. Contrary to predictions, inter-specific overlap in nest site features was not related to predation pressure: nests that overlapped most with features of other species did not suffer higher predation, nor did inter-specific overlap in nest characteristics decrease during the nesting season. These findings were inconsistent with the hypothesis that community-level patterns of nest site use are differentiated as a result of predation pressure. Long-term work on nest site use by individually marked females of numerous ground-nesting bird species would be informative, as would experimental studies of other hypotheses about factors affecting nest site choices in birds.

Nesting success is an important vital rate affecting the reproductive fitness of birds, and predation typically is the single most important factor affecting nesting success. Presumably, birds should nest in locations that maximize nest survival. If specific nest characteristics increase the probability that a nest will hatch, natural (phenotypic) selection could favour use of sites with these features, producing nonrandom patterns of nest site use. Alternatively, birds that are highly selective in nest site choices might be at a disadvantage if predators learn to forage preferentially in these locations and improve their efficiency in depredating nests; in this case, random nesting patterns could be favoured. Finally, it has been hypothesized that predation pressure can influence nest site selection patterns of entire bird communities. If predators develop a search image to hunt for bird nests, then nests that are most similar to each other, irrespective of species, should sustain higher mortality. To evaluate these hypotheses, I quantified nest site selection patterns of multiple species of ground-nesting dabbling ducks in areas where predation pressure was normally high, and compared these patterns to those on areas where predation was relaxed. Predation pressure was experimentally reduced by removing common predators of duck nests and females (mainly red foxes, coyotes, skunks and raccoons) on some study areas and not on others (controls). Predator removal and natural causes produced a 10-fold difference in duck nesting across study sites, allowing for investigation of effects of predation pressure on nest site selection of ducks. Coarse scale habitat selection patterns were similar to results reported in previous studies; blue-winged teal and northern shoveler were found more often in native grassland than in other habitat types, while gadwall and mallard nests occurred more frequently in shrub patches when compared with other habitat patches. A difference in nest site characteristics was observed between hatched and depredated nests for gadwall and northern shoveler but not for blue-winged teal and mallard. However, in all species, the nest site selection patterns were non-random. Thus, the process of nest predation did not shape patterns of nest site choice. Contrary to predictions, inter-specific overlap in nest site features was not related to predation pressure: nests that overlapped most with features of other species did not suffer higher predation, nor did inter-specific overlap in nest characteristics decrease during the nesting season. These findings were inconsistent with the hypothesis that community-level patterns of nest site use are differentiated as a result of predation pressure. Long-term work on nest site use by individually marked females of numerous ground-nesting bird species would be informative, as would experimental studies of other hypotheses about factors affecting nest site choices in birds.

The long history of co-existence of bacteria and their protozoan predators in aquatic environments has led to evolution of protozoa resistant bacteria (PRB). Many of these bacteria are also pathogenic to humans. However, the ecological drivers determining the occurrence of different types of PRB in aquatic environments, and the eco-evolutionary link between bacterial adaptation and the resulting implications for mammalian hosts are poorly known. This thesis examines the impact of nutrients and predation on PRB, as well as the ecological and evolutionary connection between their life in aquatic environments and mammalian hosts. In the first study seven bacterial isolates from the Baltic Sea were investigated for their plasticity of adaptation to predation. The response to predation showed large variation where some bacteria rapidly developed a degree of grazing resistance when exposed to predators. The rapid adaptation observed may result in bacterial communities being resilient or resistant to predation, and thus rapid adaptation may be a structuring force in the food web. With the aim to elucidate the link between occurrence of PRB and environmental conditions, a field study and a laboratory experiment were performed. In both studies three PRB genera were found: Mycobacterium, Pseudomonas and Rickettsia. PRB were found both in oligotrophic and eutrophic waters, indicating that waters of all nutrient states can harbor pathogenic bacteria. However, the ecological strategy of the PRB varied depending on environmental nutrient level and disturbance. Using an advanced bioinformatic analysis, it was shown that ecotypes within the same PRB genus can be linked to specific environmental conditions or the presence of specific protozoa, cyanobacteria or phytoplankton taxa. These environmental conditions or specific plankton taxa could potentially act as indicators for occurrence of PRB. Finally, using four mutants (with specific protein deletions) of the pathogenic and predation resistant Francisella tularensis ssp. holarctica, I found evidence of an eco-evolutionary connection between the bacterium´s life in aquatic and mammalian hosts (aquatic amoeba Acanthamoeba castellanii and a murine macrophage).  To a large extent F. t. holarctica use similar mechanisms to persist predation by protozoa and to resist degradation by mammal macrophages. To summarize I found a link between predation resistant bacteria in aquatic environments and bacteria that are pathogenic to mammals. Further, I showed that different environmental conditions rapidly selects for PRB with either intracellular or extracellular lifestyles. This thesis provides insights regarding environmental conditions and biomarkers that can be used for assessment of aquatic environments at risk for spreading pathogenic bacteria. / <p>Medfinansiärer var även: Swedish Ministry of Defence (A4040, A4042, A404215, A404217), Swedish Minestry of Foreign Affairs (A4952), Swedish Civil Contingencies Agency (B4055)</p>

Lake Winnipeg has been subject to intense eutrophication and invasive species such as Rainbow Smelt and Eubosmina coregoni for the last 40 years. This study demonstrated significant increases in total phosphorus, total nitrogen, chlorophyll-a, overall zooplankton abundance, and specifically Cladocera, between 1969 and the first decade of the 21st century. There were specific basin differences in the long-term changes of the Cladocera community, with the species Chydorus sphaericus and Ceriodaphnia quadrangula negatively affected by high levels of phosphorus, nitrogen and chlorophyll-a. Moreover, long-term change in the Cladocera community composition and abundance throughout the years (1969-2011) during summer was correlated with intensifying eutrophication. Additionally, weak diel vertical migration in the zooplankton community was observed for the first time in Lake Winnipeg.

Lake Winnipeg has been subject to intense eutrophication and invasive species such as Rainbow Smelt and Eubosmina coregoni for the last 40 years. This study demonstrated significant increases in total phosphorus, total nitrogen, chlorophyll-a, overall zooplankton abundance, and specifically Cladocera, between 1969 and the first decade of the 21st century. There were specific basin differences in the long-term changes of the Cladocera community, with the species Chydorus sphaericus and Ceriodaphnia quadrangula negatively affected by high levels of phosphorus, nitrogen and chlorophyll-a. Moreover, long-term change in the Cladocera community composition and abundance throughout the years (1969-2011) during summer was correlated with intensifying eutrophication. Additionally, weak diel vertical migration in the zooplankton community was observed for the first time in Lake Winnipeg.

La compréhension et la gestion des écosystèmes requièrent un maximum de connaissances sur les dynamiques de populations. Depuis 2007, la taille de la sardine (Sardina pilchardus) et de l’anchois (Engraulis encrasicolus) dans le Golfe du Lion a chuté tandis qu’au même moment, la population de sprat, qui a une faible valeur commerciale, a fortement augmenté. Les très forts enjeux économiques autour de ces espèces ont conduit au projet de recherche « EcoPelGol » dans lequel se situe cette étude portant sur les changements observés. La condition corporelle, la croissance ainsi que la structure en âge et en taille des sardines, des anchois et en partie des sprats ont été analysées sur les vingt dernières années. Alors qu’en 2005-2007, la situation semblait optimale pour les anchois et les sardines (taille et condition élevées), celle-ci s’est considérablement dégradée depuis 2008, l’anchois et la sardine étant significativement plus petits et plus maigres. De plus, une diminution de l’âge et de la croissance a été observée chez la sardine. Nous avons ensuite caractérisé les fluctuations des débarquements historiques (1865-2013) de l’anchois, de la sardine et du maquereau. La chute récente des débarquements a été mise en exergue, avec une situation inédite où la sardine est actuellement moins débarquée qu’avant les années 60, date à laquelle les débarquements ont fortement augmenté suite à un accroissement conséquent de l’effort de pêche. Bien que la majorité de la variance dans les séries de débarquements semble être engendré par les changements de l’effort de pêche, nous avons également observé une relation entre les débarquements et l’indice « Atlantic Multidecadal Oscillation » pour l’anchois et la sardine et avec le « Western Mediterranean Oscillation » pour l'anchois. Dans une troisième analyse, la pression de prédation du thon rouge sur l’anchois, la sardine et le sprat a été estimée pour voir si l’accroissement de la population du thon depuis 2007 lié à de nouvelle mesures de gestion a pu impacté les poissons petits pélagiques. Mais bien que la sardine et l’anchois soient les proies principales du thon, moins de 2% de leurs populations ont été consommés chaque année entre 2011-2013, et ce, sans sélectivité sur la taille de ces proies de la part du thon. Ainsi, le thon rouge n’a pas pu avoir un impact significatif sur la structure en taille ou les abondances des petits pélagiques. Dans le chapitre final, nous avons considéré la possible influence de pathogènes. Des analyses globales dirigées vers la détection des parasites, des bactéries et des virus ont été effectuées tout au long de l’année et ont révélées la présence ponctuelle et relativement faible de bactéries des genres Tenacibaculum et Vibrio et celle systématique de microparasites. Malgré l’impossibilité d’exclure leur pathogénicité, aucune lésion tissulaire n’a été attribuée à ces organismes, réduisant fortement la probabilité d’une épizootie. Nos travaux indiquent que les mécanismes « top-down », des pathogènes ou encore la pêche ne sont probablement pas les facteurs clés pour expliquer les changements observés chez les poissons petites pélagiques. À l'opposé, certains paramètres environnementaux ont expliqué une partie de la variabilité dans la condition corporelle des poissons et leurs débarquements. Nous concluons donc qu’un contrôle « bottom-up », et particulièrement un changement dans la quantité et/ou qualité du zooplancton, peut être la cause des phénomènes dans les populations des poissons petits pélagiques. Si cette thèse permet une avancée dans la compréhension de leur dynamique, des analyses complémentaires seront nécessaires pour confirmer notre hypothèse principale et pour estimer l’influence des autres facteurs agissant potentiellement en synergie. / Knowledge on population dynamics is key to the improvement of management and the understanding of ecosystem functioning. Since 2007, the size of sardine (Sardina pilchardus) and anchovy (Engraulis encrasicolus) in the Gulf of Lions (NW Mediterranean) has severely decreased, which has strongly affected the fisheries. Simultaneously, the commercially uninteresting sprat population increased remarkably. As the economic and ecological stakes are high, the EcoPelGol project of which this PhD is part was established. We first analysed the sardine, anchovy and (partially) sprat population for changes in body condition, growth and size and age structure over the last 20 years. We concluded that sardine and anchovy have had from 2008 onwards a distinctively poor body condition and size, and that sardine have also showed a concurrent decrease in age and growth. In contrast, both species were in optimal and average “health” during 2005-2007 and 1992-2004, respectively. Subsequently, historical landings of sardine, anchovy and mackerel were considered (1865-2013), of which the fluctuations were characterised and statistically related to environmental variables. The recent dramatic landings decrease was put into perspective, as for example sardine is now for the first time landed less than before the 1960s, when a big probably effort-related upsurge occurred. Despite most of the variability being explained by what looks like changes in fishing effort, a link was found between the sardine and anchovy landings and the Atlantic Multidecadal Oscillation and the anchovy landings and the Western Mediterranean Oscillation. Next, as a management associated bluefin tuna increase also happened since 2007, its predation pressure on all three small pelagic species was estimated. We concluded that although sardine and anchovy are bluefin tuna’s main prey items, less than 2% of each population (including sprat) was consumed annually during 2011-2013 and that there was no clear size selectivity. Thus, tuna could not have had a noticeable impact on the population abundance or size structure of the small pelagics. In the last chapter, an epizootic disease was considered. An all-embracing approach directed towards the all-year round detection of both general and specific parasites, bacteria and viruses revealed the mostly temporal and not necessarily high occurrence of only three groups: microparasites, Vibrio spp. (sometimes determined as Vibrio alginolyticus) and bacteria of the genus Tenacibaculum. Although we could not exclude their pathogenicity, significant tissue damage at a cellular or macroscopic level was never observed, making the disease hypothesis less likely. Thus, we considered several hypotheses and indicated that top-down control (through Bluefin tuna predation), pathogens and fisheries are unlikely to be main drivers. In contrast, some environmental parameters explained a part of the variability in fish condition and landings. After a final discussion on all probable theories we concluded that a bottom-up control, such as especially a planktonic change in quantity and/or quality, might be on the basis of the observed changes. Although this work is a great step towards the understanding of the small pelagic dynamics in the Gulf of Lions, further investigations will still be needed to confirm our main hypothesis and to estimate the potential synergetic effect of other drivers.

Post-pelagic juvenile and subadult Kemp's ridley sea turtles (Lepidochelys kempii) (20-40 cm straight carapace length) utilize nearshore waters of the northwestern Gulf of Mexico as nursery or developmental feeding grounds. This study utilizes 10 years of entanglement netting data to characterize long-term abundance and distribution of Kemp's ridley sea turtles at index habitats in this region. Netting surveys were conducted during April-October 1993-2002, primarily at Sabine Pass, Texas and Calcasieu Pass, Louisiana. Additionally, this study takes an ecosystem-based approach to understanding factors influencing Kemp's ridley in-water abundance and distribution via the development of a conceptual model incorporating data on nesting dynamics, environmental conditions, prey availability, and predation pressure. Overall monthly mean ridley catch-per-unit-effort (CPUE) peaked in the beginning of summer (April-June), probably in response to rising water temperatures and seasonal occurrence of blue crab prey. Annual mean ridley CPUE across all study areas peaked in 1994, 1997, 1999 and 2002, suggesting a 2-3 year cycle in abundance that may be related to patterns in clutch size or hatch success at the Rancho Nuevo, Mexico nesting beach. However, ridley CPUE in nearshore waters remained relatively constant or decreased slightly even as number of hatchlings released from Rancho Nuevo increased exponentially. Annual declines in Texas strandings since 1994 and subsequent increases in Florida counterparts since 1995 suggest a shift in ridley distribution from the western to eastern Gulf in recent years. Significant declines in ridley CPUE at Sabine Pass since 1997 coincided with a concurrent reduction in blue crab size, but a similar trend was not detected at Calcasieu Pass. Kemp's ridley occurrence at study sites was not significantly related to shrimping activity/by-catch. There also were no biologically significant relationships between Kemp's ridley CPUE and abiotic factors, nor were ridleys deterred from utilizing areas frequented by bull sharks. Overall, nesting dynamics and prey availability were conceptual model components appearing to have the greatest influence on nearshore ridley occurrence.

Les comportements dirigés vers soi (CDS) tels que l'autotoilettage, les grattements et les bâillements peuvent être des indicateurs indirects de stress chez les mammifères. Comprendre si ces comportements associés au stress coïncident avec des facteurs de stress sociaux ou écologiques devrait permettre d'identifier les éléments de la vie en groupe qui causent plus de stress chez les femelles. Pour déterminer les pressions de la vie en groupe pouvant générer du stress chez les femelles Colobus vellerosus à Boabeng-Fiema Monkey Sanctuary (BFMS), au Ghana, j’ai cherché à savoir si les CDS variaient selon : H1) La compétition alimentaire, qui peut augmenter en intensité avec le nombre de congénères qui sont en compétition pour les mêmes ressources nutritionnelles ; H2) La pression de prédation, qui peut augmenter avec un nombre total d'individus moins élevé, car cela réduit la détection des prédateurs; H3) Le risque d'infanticide, qui augmente avec le nombre de mâles adultes et les renversements de pouvoir par les mâles, car les relations de dominance masculine sont souvent contestées dans les groupes multimâles ; et H4) La pression de copulation, qui augmente lorsque les femelles sont en oestrus et s'engagent dans des comportements sexuels, ce qui peut conduire les mâles à être agressifs et coercitifs envers elles. Pour ce faire, j'ai utilisé des données longitudinales sur les grattements, l’autotoilettage et les bâillements collectées auprès de 64 femelles adultes à BFMS de 2004 à 2019. J'ai comparé les taux mensuels de CDS des femelles en fonction de la taille des groupes, de l'interaction entre le nombre de mâles et la survenue ou non d'un renversement par les mâles, et de la présence de comportements sexuels féminins. Alors que l'autotoilettage et le bâillement ne variaient pas de manière significative en fonction de nos variables, les femelles se grattaient davantage au cours des mois où il y avait plus de mâles et/ou un renversement (équations d'estimation généralisées : P < 0,05), ainsi que lorsqu'elles ont exprimé plus de comportements sexuels (P < 0,05). Ces résultats soutiennent les hypothèses du risque d'infanticide et de la pression de copulation suggérant que les stratégies reproductives des mâles expliquent le mieux le stress chez les femelles. Ceci apporte une évidence supplémentaire que la pression d'infanticide, déjà connue pour influencer la composition des groupes et le développement de la progéniture chez C. vellerosus, affecte les comportements des femelles et leur réponse au stress. Cela permet donc une meilleure compréhension de la socialité chez les primates par l’étude des facteurs de stress vécus par les femelles qui déterminent, dans une certaine mesure, la formation des groupes. / Self-directed behaviors (SDB) such as self-grooming, scratching, and yawning can be indirect stress indicators in mammals. Understanding whether behaviors associated with stress co-occur with social or ecological pressures can help identify the elements of group life that cause more stress for females. To determine which pressures of group-living may lead to stress in female Colobus vellerosus at Boabeng-Fiema Monkey Sanctuary (BFMS), Ghana, I investigated whether SDBs varied according to: H1) Feeding competition, which may increase in intensity with the number of conspecifics competing for the same nutritional resources; H2) Predation pressure, which may increase with fewer total individuals, as this reduces predator detection; H3) Infanticide risk, which increases during male group take-over and with the number of adult males because male dominance relationships are often contested in multi-male groups in this population; and H4) Mating pressure, which increases when females are in estrus and engage in copulations, and may lead to males being aggressive and coercive toward females. I used longitudinal data on three SDBs, namely scratching, self-grooming and yawning, by 64 adult females at BFMS from 2004 to 2019. I compared female monthly SDB rates according to group size, an interaction effect between the number of males and whether a male group takeover occurred, and the presence of female sexual behaviors. While self-grooming and yawning did not vary significantly with the predictor variables, females scratched themselves more during months in which more males were present and/or a takeover occurred (Generalized Estimating Equations: P < 0.05), as well as when more sexual behaviors occurred (P < 0.05). The results support the infanticide risk and mating pressure hypotheses and suggest that the reproductive strategies of adult males best explain female stress. This provides further evidence that infanticide pressure, already known to influence group composition and offspring development in C. vellerosus, affects female behaviors and their stress response. This allows a better understanding of sociality in primates by studying the stressors experienced by females that determine, to some extent, group formation.