Les mammifères marins sont des espèces clés des écosystèmes. Ils subissent un nombre important de modifications de leur milieu qui nécessitent la mise en place de stratégie de conservation. Pour cela la connaissance de la structure des populations est primordiale. Une étude de génétique des populations a été menée sur deux espèces emblématiques de la mer d'Iroise. Pour le marsouin commun, espèce connaissant un retour le long des côtes françaises, nos travaux montrent, de manière inattendue, que ce retour est le résultat de deux déplacements différents et qu'il y a une hybridation entre les individus issus de la population de la péninsule Ibérique et ceux du Nord de l'Europe. Ces déplacements sont certainement liés à des modifications de la disponibilité des proies suite à des changements du milieu. Pour le phoque gris, nos résultats montrent une grande richesse génétique, avec une structure ancestrale pour la région de contrôle mitochondriale et une panmixie pour les loci microsatellites, indiquant la présence d'une population à l'échelle du plateau celtique. Une différenciation est observée entre les années d'échouages paires et impaires ainsi qu'une signature génétique potentielle d'individu issus d'une autre population. Enfin nous avons mené une étude pilote pour un observatoire de la biodiversité génétique des mammifères marins par la technique de code barres ADN. Cette étude montre que cet observatoire serait une manière innovante et pertinente pour suivre la biologie des mammifères marins. L'ensemble de nos résultats permettent de mieux comprendre les modifications de l'écosystème et sont un support à la mise en place de stratégie de conservation. / Marine mammals are key species of ecosystems. They undergo numerous environment modifications which require conservation plans. For that, the knowledge about population structure is primary. Studies of population genetic were led about two flagship species of the Iroise Sea. For the harbour porpoise, a specie who know a return along french coasts, our works unexpectedly show this return is the result of two movements and an hybridization between individuals of the Iberia population and those of North Europe population. These movements are, probably, linked to modifications of prey's availability caused by environment changes. For the grey seal, our works show a great genetic richness, with an ancestral structure for the mitochondrial control region and a panmixia for the microsatellites loci, which are signs of a population at the scale of Celtic Shelf. A differentiation was observed between the stranding years even and odd and a possible genetic signal of individuals from another population. Finally we led a pilot study for marine mammal genetic biodiversity observatory with the DNA barcoding technique. This study shows this observatory may be a relevant and innovative means to follow the marine mammal biology. All our results bring new information about ecosystem variations and are a help for the establishment of conservation strategy.

Seal-based tourism in the Umeå archipelago Its possibilities and problems Marcus Vidberg Abstract Seal-based tourism is something that can be found throughout the world, including Sweden, which led to the question of why there is a lack of it in the region of Umeå. Studying the ecological conditions in the area has led to the conclusion that the Umeå archipelago has all the prerequisites for establishing a seal-based activity, meaning that there are more circumstances surrounding the possibilities of seal-based tourism. To fully understand the topic, one needs to study it from several different points of view, including the ecological, economical and socio-cultural aspects. There are a lot of different opinions surrounding the seals that need to be taken in to account before one reaches a conclusion. Furthermore it is also necessary to study the topic of tourism; globally, locally and its development. With a growing demand for nature-based tourism around the world, shouldn’t it be possible to establish a seal-based one in the Swedish north? The report also studies the already established operations throughout Sweden, to try to understand why the activities are located in some regions but not in others. The conclusion that has been reached in this report is that the ecological circumstances for a seal-based tourism exists in the Umeå archipelago, but a seal-based operation might find its biggest straits to be the economical and socio-cultural conditions.

La plasticité comportementale et les interactions entre organismes sont connues pour avoir une influence sur l’utilisation de l’espace, notamment la sélection de l’habitat de chasse. Dans l’Atlantique Nord-Est, les phoques gris et veaux marins vivent en sympatrie. Ces deux espèces sont réparties dans différentes colonies où les interactions entre organismes (liées à la taille de la colonie et à la présence simultanée ou non des deux espèces) ainsi que la disponibilité de l’habitat (et donc des proies) varient localement. L’objectif de cette thèse était d’étudier l’utilisation spatiale et la sélection d’habitat de chasse à l’échelle locale de ces deux espèces dans des situations contrastées de dynamique de colonies. Pour cela, plusieurs individus de différentes colonies situées en Irlande, en Écosse et en France ont été équipés de balises GPS/GSM. Les données récoltées ont permis de caractériser leurs trajets en mer ainsi que d’identifier les zones de chasse permettant par la suite la sélection d’habitat. Contrairement aux veaux marins, qui ont réalisé des déplacements restreints aux alentours des colonies, la plupart des phoques gris se sont déplacés entre différentes colonies. Ainsi, l’étude de la sélection d’habitat à l’échelle individuelle pour les individus se déplaçant entre différentes colonies a mis en évidence l’influence de la plasticité comportementale et suggéré celle de la personnalité de l’animal. A l’échelle de la colonie, chez les deux espèces, les résultats ont mis en évidence l’influence de la disponibilité de l’habitat (et indirectement de la disponibilité des proies) ainsi que des interactions intra-spécifiques (liée à l’effet de densité dépendance) sur l’utilisation spatiale et la sélection de l’habitat de chasse. Cependant, la sélection de l’habitat de chasse était principalement liée à la distance au reposoir et la bathymétrie. Ces deux paramètres sont liés aux caractères de chasseur à place centrale et benthique des phoques. Cette étude a également mis en évidence, pour les sites où les deux espèces étaient présentes, une certaine ségrégation spatiale et des différences de sélection d’habitat entre les deux espèces. / The behavioural plasticity and the interactions between organisms are known to influence foraging habitat selection and spatial usage. In the Northeast Atlantic, greyand harbour seals live in sympatry. These two species are spread into different colonies where interactions between organisms (linked to the colony size et and the presence of one or both species) and habitat availability (linked to the prey distribution) vary locally. The objective of this PhD was to study the spatial usage and foraging habitat selection of these two species at the local scale, in contrasted situations of population dynamics. Several individuals were tagged with GPS/GSM tags in different colonies located in Ireland, Scotland and France. Telemetry data was used to characterize the seals’ trips at sea and to identify their foraging areas in order to model foraging habitat selection. While harbour seals only performed trips restricted around their haulout sites, grey seals moved between colonies. Studying habitat selection at the individual scale, for individuals moving between colonies, highlighted the influence of behavioural plasticity and suggested the influence of individual personality. At the colony scale, for both species, results highlighted the influence of habitat availability (indirectly linked to prey availability) and intra-specific interactions (linked to density dependence effects) on spatial usage and foraging habitat selection. However, the foraging habitat selection was mainly explained by the distance from the last haulout and the bathymetry. These two parameters are linked to the central place forager and benthic feeder characteristics of the seals. Furthermore, this study also highlighted, for study sites where both species occur, a spatial segregation and differences in foraging habitat selection between grey and harbourseals.

Neonatal mortality in grey seals on the Isle of May breeding colony and in a rehabilitation centre were investigated by detailed systematic post-mortem examinations (n=59), on-site bacteriology and advanced molecular diagnostic techniques for specific pathogens. Causes of death on the breeding colony included starvation (30%), omphalitis-peritonitis (26%), septicaemia (22%), stillbirth (10%) and trauma (4%) and in the rehabilitation centre starvation (44%) and septicaemia (22%). Detailed key gross and histopathological findings and pathogens are described and include the first report of Listeria monocytogenes in any marine mammal. Phocid herpes virus 1 nucleic acids were detected in nasal swabs of 58% live, free-ranging grey seal pups (n=90) and 28% yearlings (n=19), suggesting recrudescence in the latter. Previously undetected in Scotland, phocid herpes virus 2 nucleic acids were identified only in yearlings (15%); sealpox was detected in a single live stranded grey seal pup and phocine distemper virus was not detected. Given their unique characteristics and potential for acting as sentinels of coastal marine health several pathogens of putative anthropogenic origin were investigated: Toxoplasma gondii, Neospora caninum, Salmonella spp. and Campylobacter spp. Toxoplasma gondii DNA was detected in 6% dead free-ranging grey seal pups (n=50) but N. caninum was not found. Salmonella (20%) and Campylobacter (50%) were isolated from rectal swabs of live and dead grey seal pups and Campylobacter was significantly associated with moderate to severe colitis implying pathogenicity. These findings imply a land-sea-land transfer of T. gondii and early exposure of pups to this parasite. Extensive genetic fingerprinting suggested an exchange of Salmonella between grey seal, cattle and human populations and that the Campylobacter isolates may share the same origin as human clinical isolates. This work provides a solid base line study of diseases present in grey seal pups and demonstrates that they are useful indicators of coastal marine microbial contamination.

<p>An influence at one trophic level can result in dynamic impacts also on other components of a food web. These dynamics are known as trophic cascades, and can be both top-down and bottom-up. After a near-collapse of the Baltic cod <i>Gadus morhua</i> stock in the 1980s, its main prey sprat <i>Sprattus sprattus</i> increased dramatically. The main food of sprat, marine copepods, decreased during the same time period, likely a combined effect of increased predation pressure from sprat and decreasing salinities. This shortage of food for sprat resulted in decreasing quality of sprat as a food source for common guillemots <i>Uria aalge</i>. However, a recent increase in fishing for sprat has again resulted in better feeding conditions for guillemots.</p><p>Human impacts on this simple food web can be complex. In the early 20th century, marine mammals were abundant and nutrient levels were low in the Baltic Sea. This thesis illustrate that this situation corresponded to lower fish biomass. A reduction of seals early in the century led to reduced top-down control, which resulted in increasing fish stocks. Later, in the 1950s, the largest inflow of salt water during the century mobilized accumulated phosphorus from the deep sediments, which stimulated nitrogen fixation. Combined with increasing anthropogenic nutrient loads, this led to increased primary production and a rapid change from an oligotrophic to a eutrophicated state. This change can be termed a regime shift, which also stimulated fish production. Subsequent over-fishing of cod likely caused a second regime shift, from a cod- to a clupeid- dominated state, which led to the described effects on the common guillemots.</p><p>Several factors affect the life-history of this long-lived seabird. Bycatches in gillnet fisheries is one factor directly affecting guillemot survival, and the proportion of bycatches increased during a period of increasing fishing effort. Surprisingly, avian cholera, a previously undocumented disease in common guillemots, was found at times to cause considerable adult mortality. Common guillemot life-history information can communicate the diversity of factors influencing marine ecosystems – hopefully this can increase our understanding of how complex even "simple" food webs are.</p>

An influence at one trophic level can result in dynamic impacts also on other components of a food web. These dynamics are known as trophic cascades, and can be both top-down and bottom-up. After a near-collapse of the Baltic cod Gadus morhua stock in the 1980s, its main prey sprat Sprattus sprattus increased dramatically. The main food of sprat, marine copepods, decreased during the same time period, likely a combined effect of increased predation pressure from sprat and decreasing salinities. This shortage of food for sprat resulted in decreasing quality of sprat as a food source for common guillemots Uria aalge. However, a recent increase in fishing for sprat has again resulted in better feeding conditions for guillemots. Human impacts on this simple food web can be complex. In the early 20th century, marine mammals were abundant and nutrient levels were low in the Baltic Sea. This thesis illustrate that this situation corresponded to lower fish biomass. A reduction of seals early in the century led to reduced top-down control, which resulted in increasing fish stocks. Later, in the 1950s, the largest inflow of salt water during the century mobilized accumulated phosphorus from the deep sediments, which stimulated nitrogen fixation. Combined with increasing anthropogenic nutrient loads, this led to increased primary production and a rapid change from an oligotrophic to a eutrophicated state. This change can be termed a regime shift, which also stimulated fish production. Subsequent over-fishing of cod likely caused a second regime shift, from a cod- to a clupeid- dominated state, which led to the described effects on the common guillemots. Several factors affect the life-history of this long-lived seabird. Bycatches in gillnet fisheries is one factor directly affecting guillemot survival, and the proportion of bycatches increased during a period of increasing fishing effort. Surprisingly, avian cholera, a previously undocumented disease in common guillemots, was found at times to cause considerable adult mortality. Common guillemot life-history information can communicate the diversity of factors influencing marine ecosystems – hopefully this can increase our understanding of how complex even "simple" food webs are.

Species distribution maps can provide important information to focus conservation efforts and enable spatial management of human activities. Two sympatric marine predators, grey seals (Halichoerus grypus) and harbour seals (Phoca vitulina), have overlapping ranges but contrasting population dynamics around the UK; whilst grey seals have generally increased, harbour seals have shown significant regional declines. A robust analytical methodology was developed to produce maps of grey and harbour seal usage estimates with corresponding uncertainty, and scales of spatial partitioning between the species were found. Throughout their range, both grey and harbour seals spend the majority of their time within 50 km of the coast. The scalability of the analytical approach was enhanced and environmental information to enable spatial predictions was included. The resultant maps have been applied to inform consent and licensing of marine renewable developments of wind farms and tidal turbines. For harbour seals around Orkney, northern Scotland, distance from haul out, proportion of sand in seabed sediment, and annual mean power were important predictors of space-use. Utilising seal usage maps, a framework was produced to allow shipping noise, an important marine anthropogenic stressor, to be explicitly incorporated into spatial planning. Potentially sensitive areas were identified through quantifying risk of exposure of shipping traffic to marine species. Individual noise exposure was predicted with associated uncertainty in an area with varying rates of co-occurrence. Across the UK, spatial overlap was highest within 50 km of the coast, close to seal haul outs. Areas identified with high risk of exposure included 11 Special Areas of Conservation (from a possible 25). Risk to harbour seal populations was highest, affecting half of all SACs associated with the species. For 20 of 28 animals in the acoustic exposure study, 95% CI for M-weighted cumulative Sound Exposure Levels had upper bounds above levels known to induce Temporary Threshold Shift. Predictions of broadband received sound pressure levels were underestimated on average by 0.7 dB re 1μPa (± 3.3). An analytical methodology was derived to allow ecological maps to be quantitatively compared. The Structural Similarity (SSIM) index was enhanced to incorporate uncertainty from underlying spatial models, and a software algorithm was developed to correct for internal edge effects so that loss of spatial information from the map comparison was limited. The application of the approach was demonstrated using a case study of sperm whales (Physeter macrocephalus, Linneaus 1758) in the Mediterranean Sea to identify areas where local-scale differences in space-use between groups and singleton whales occurred. SSIM is applicable to a broad range of spatial ecological data, providing a novel tool for map comparison.

No description available.

Management and conservation of populations of animals requires information on where they are, why they are there, and where else they could be. These objectives are typically approached by collecting data on the animals’ use of space, relating these to prevailing environmental conditions and employing these relations to predict usage at other geographical regions. Technical advances in wildlife telemetry have accomplished manifold increases in the amount and quality of available data, creating the need for a statistical framework that can use them to make population-level inferences for habitat preference and space-use. This has been slow-in-coming because wildlife telemetry data are, by definition, spatio-temporally autocorrelated, unbalanced, presence-only observations of behaviorally complex animals, responding to a multitude of cross-correlated environmental variables. I review the evolution of techniques for the analysis of space-use and habitat preference, from simple hypothesis tests to modern modeling techniques and outline the essential features of a framework that emerges naturally from these foundations. Within this framework, I discuss eight challenges, inherent in the spatial analysis of telemetry data and, for each, I propose solutions that can work in tandem. Specifically, I propose a logistic, mixed-effects approach that uses generalized additive transformations of the environmental covariates and is fitted to a response data-set comprising the telemetry and simulated observations, under a case-control design. I apply this framework to non-trivial case-studies using data from satellite-tagged grey seals (Halichoerus grypus) foraging off the east and west coast of Scotland, and northern gannets (Morus Bassanus) from Bass Rock. I find that sea bottom depth and sediment type explain little of the variation in gannet usage, but grey seals from different regions strongly prefer coarse sediment types, the ideal burrowing habitat of sandeels, their preferred prey. The results also suggest that prey aggregation within the water column might be as important as horizontal heterogeneity. More importantly, I conclude that, despite the complex behavior of the study species, flexible empirical models can capture the environmental relationships that shape population distributions.