Les écosystèmes marins sont soumis à des changements environnementaux rapides sous l’impact des pressions anthropiques croissantes qui menacent la persistance des espèces et des populations locales. Comprendre les effets de la variabilité génétique et des capacités de dispersion sur la persistance des espèces marines, est donc un enjeu majeur pour la conservation de la biodiversité. Mes travaux de doctorat répondent ainsi à deux objectifs principaux : (i) évaluer la distribution spatiale et les déterminants de la variation génétique de populations de poissons marins côtiers (ii) estimer les réponses des populations aux changements climatiques afin de mieux comprendre leur capacité de persistance.J’ai d’abord montré, à partir d’une synthèse bibliographique réalisée sur 31 espèces de poissons méditerranéens, que les traits écologiques liés à la mobilité et à la taille des populations influencent fortement le niveau de diversité génétique intra-populationnelle des espèces. Ensuite, j’ai étudié les déterminants de la variation génétique spatiale à partir des données récoltées sur 727 individus de rouget de roche (Mullus surmuletus) issus de 72 sites autour la Mer Méditerranée et regroupés en 47 groupes génotypés pour 1153 marqueurs SNP. Des analyses de génétique du paysage ont montré que la dispersion larvaire structure la variation génétique de l’espèce à moyenne et petite échelle spatiale (<1 000km), alors que l’isolement géographique, possiblement dû à l’histoire démographique des populations ou à l’adaptation, est le principal facteur structurant à plus large échelle. Finalement, l’étude de la variation génétique adaptative de M. surmuletus réalisée à l’aide d’un criblage génomique a mis en évidence une potentielle réponse adaptative de l’espèce au gradient Est-Ouest de salinité en Méditerranée.Dans un second temps, un modèle démo-génétique simulant la dynamique et la résilience des populations de coraux dans l’Indopacifique a montré qu’un mécanisme de « sauvetage évolutif » permet aux génotypes adaptés aux eaux les plus chaudes de diffuser entre les populations grâce à la connectivité larvaire. Ce mécanisme favorise la persistance des populations en permettant leur adaptation à des changements environnementaux qui conduiraient sans cela à des déclins, voir des extinctions locales.Finalement, l’ensemble de ces travaux ont mis en évidence la nécessité de considérer la connectivité et le potentiel évolutif des espèces dans les stratégies de conservation, afin de maximiser leur capacité de résilience et de persistance à long terme en dépit des crises environnementales de plus en plus prononcées. / World marine ecosystems are experiencing unprecedented anthropic pressures inducing rapid environmental changes that threaten the persistence of wild species and their local populations. Hence, understanding the effects of genetic variability and dispersal capacities on marine population persistence is a key issue for the conservation of biodiversity. My PhD work had two main objectives: (i) evaluate the spatial distribution and drivers of genetic variation across coastal marine fish populations, and (ii) estimate the response of populations to climate changes in order to better understand their ability to persist.First, by performing a synthesis of published literature on 31 Mediterranean fish species, I showed that ecological traits related to mobility and population size strongly influence the level of within-population genetic diversity across species. Then, I studied the drivers of spatial genetic variation using genetic data from 727 individuals of the stripped red-mullet (Mullus surmuletus) collected in 72 sites around the Mediterranean Sea, and grouped into 47 pools genotyped for 1153 single nucleotide polymorphism (SNP) markers. Seascape genetic analyses showed that larval dispersal predominantly structures M. surmuletus genetic variation at intermediate and local spatial scales (<1000 km), whereas geographic isolation, due to population demographic history or adaptation, is the main driver at larger spatial scale. Lastly, studying the adaptive genetic variation of M. surmuletus using genome scan revealed a potential adaptive response of this species to the East-West gradient in salinity across the Mediterranean Sea.Subsequently, using a demo-genetic model to simulate coral population dynamics and resilience across the Indo-pacific corals, I showed that the process of ‘evolutionary rescue’ can help genotypes adapted to warm ocean waters to move and migrate between populations thanks to larval connectivity. Evolutionary rescue can thus promote the persistence of populations by allowing them to adapt to environmental changes that would otherwise lead to population declines or even local extinctions.Finally, all of these results highlighted the need to better consider connectivity and the evolutionary potential of species in conservation strategies, in order to maximize their resilience capacity and long-term persistence in the face of more severe environmental crises.

Espace mythique et peuplé de légendes, espace physique complexe changeant, l’océan est soumis aux enjeux géopolitiques et à une extension progressive de l’homme à la manière d’un front pionnier (en surface et en profondeur). La territorialisation croissante des espaces maritimes, déjà prouvée sur les mers côtières, prend un angle particulier sur le domaine hauturier du fait de son immensité et de son éphémérité. Pour analyser ce processus, nous nous sommes intéressés à la navigation à voile, pratique de loisir et professionnelle, dans l’océan Atlantique. Cette pratique offre une vision intéressante du fait de la relation particulière entretenue entre l’homme, le voilier et l’océan et de la dualité entre tradition et technologie. La fin du XXème et le XXIème siècle constituent une époque charnière où les regards sur l’océan risquent d’être modifiés. Elle s’inscrit de plus dans le phénomène de mobilité croissante des sociétés, en quête ou non de rapidité, et démontre la réticularité croissante de cet espace, également liée à la mondialisation. Nous tâcherons de définir la notion de territoire en haute mer et de distinguer l’existence de « merritoires ». La connaissance des routes transatlantiques permet de dégager des centralités, périphéries et marges atlantiques. Elles constituent des réseaux territorialisés mettant en relation différents lieux où se révèle l’identité des navigateurs. Le long de ces trajets se greffent des paysages marins « itinérants », des repères, des discontinuités spatio-temporelles, des rites et représentations dégageant des disparités spatiales et une structuration de l’Océan Atlantique. / Mythical space filled with legends, complex changing physical space, the ocean is subject to geopolitical issues and a gradual extension of use by men pioneering both on the surface and the great depths. The increasing territorialisation of maritime areas, more and more common in coastal seas, takes a particular perspective on the offshore seas because of its vastness and its ephemerality. To analyze this regionalization process, we focus on sailing in the Atlantic Ocean, both a leisure and professional practice. This practice offers an interesting aspect due to the special relationship between human beings, their boat and the ocean and due to the duality between tradition and technology. The late twentieth and the twenty-first century is a turning point where the way we look at the ocean is likely to change.Moreover, it lies within an increasing mobility phenomenon of societies, searching or not for speed, and demonstrates the increasing reticularity (networkness) of this space, also linked to globalisation. We will try to define the concept of territory in the high seas and to distinguish the existence of « maritories ». The knowledge of the transatlantic routes allows to define Atlantic centralities, peripheries and margins. They represent territorialised network putting into relation the different places where the identity of the sailors can be revealed. Along these routes some « itinerant »seascape, marks, spatial and temporal discontinuities, rituals and représentations are built, creating a possibility to structure the Atlantic Ocean.

No description available.

Coral communities have begun to form under small inlet-style bridges along the causeway connecting Cayo Coco to Cayo Guillermo. To understand how these bridge-reefs formed and characterize their attributes relative to surrounding communities, a combination of ecological observations and 13C isotopes were analyzed from the bridges and surrounding reefs, mangrove channels and seagrass patches. Hierarchical Cluster Analysis, Detrended Correspondence Analysis and Canonical Correspondence Analysis were carried out to group which physical attributes contributed to the coral communities in the bridge-reefs and also which habitats they were most similar to, with respect to coral and benthic composition. Bridge reef coral assemblages resembled shallow patch reefs and mangrove channels, while benthic coverage was similar to mangrove channels. Organic matter was from combined seagrass and mangrove sources, with mangrove dominating in some regions more than others. This work demonstrates that habitats within the seascape are inter-related through varying mechanisms and development is multi-dimensional.

Coral communities have begun to form under small inlet-style bridges along the causeway connecting Cayo Coco to Cayo Guillermo. To understand how these bridge-reefs formed and characterize their attributes relative to surrounding communities, a combination of ecological observations and 13C isotopes were analyzed from the bridges and surrounding reefs, mangrove channels and seagrass patches. Hierarchical Cluster Analysis, Detrended Correspondence Analysis and Canonical Correspondence Analysis were carried out to group which physical attributes contributed to the coral communities in the bridge-reefs and also which habitats they were most similar to, with respect to coral and benthic composition. Bridge reef coral assemblages resembled shallow patch reefs and mangrove channels, while benthic coverage was similar to mangrove channels. Organic matter was from combined seagrass and mangrove sources, with mangrove dominating in some regions more than others. This work demonstrates that habitats within the seascape are inter-related through varying mechanisms and development is multi-dimensional.

During the Late Bronze Age, the number of metal objects in the Baltic Sea region increased tremendously.  Mobility and interaction in this northern inland sea intensified. This occurred in a period of prehistory when the ship was the predominant symbol in southern Scandinavia. The ship can be found in rock carvings, on bronze objects and by way of erected stone monuments: stone ship settings. These stone ships are mainly to be found in the Baltic Sea region, with a marked concentration on Gotland. The stone ship settings and their landscape context are the focus of this dissertation. The objective is to clarify whether it is possible to find evidence of social groupings of people in the Nordic Late Bronze Age (1100-500 BC), by focusing on the stone ship monument, adopting a maritime approach. These people might have been part of a maritime institution specializing in trade and long distance journeys during this period, thus achieving a more advanced maritime way of life in the Baltic Sea. Are the ship settings an expression of these specific groups of people, who utilized their practices to position and articulate themselves in the landscape? If such maritime institutions can in fact be traced, there must also be uniformly structured locations for these groups of people to meet in, some kind of antecedents of harbours. By taking an inland sea, the Baltic Sea, as a geographical demarcation, a different perspective of prehistory is attained. The area in the Late Bronze Age and earliest Iron Age (950/900-200 BC) differed from the Nordic Bronze Age sphere. The communities around the Baltic Sea, through the establishment and sharing of mutual interests, seem to have reached a certain degree of consensus. This concordance might well be largely explained by the complex dependency on metal. Such a manifestation would not have been possible without an infrastructure or network, in this case a maritime one. This is something which has previously been overlooked in discussions on the Bronze Age in the Baltic Sea.

The role of mangroves as essential fish habitat has been a focus of extensive research. However, recent evidence has shown that this role should not be evaluated in isolation from surrounding habitats such as seagrass beds and hard-bottom communities. For example, submerged aquatic vegetation (SAV) communities provide potential sources of food and shelter for fish species that may reside in the mangroves, but may also undergo ontogenetic migrations and daily home-range movements into neighboring habitats. The connectivity between the mangrove fish community and the surrounding seascape may be influenced by the level of patchiness, fragmentation, and spatial heterogeneity of adjacent SAV habitats (i.e., SAV seascape structure). The spatial patterns and heterogeneity of SAV seascape structures are driven by internal and external regulatory mechanisms operating at different spatial and temporal scales. In addition, it is likely that many fish species inhabiting the mangrove zones have different home ranges, and foraging and migratory patterns; therefore, different mangrove fish species may respond to seascape heterogeneity at different scales. There are few studies that have assessed the influence and connectivity of benthic habitats adjacent to mangroves for estuarine fish populations at multiple scales. The present research used an exploratory seascape approach in Biscayne Bay (Florida, USA) to evaluate patterns in the patch composition and configuration of SAV communities, and to examine relationships between seascape structural metrics and the abundance, diversity, and distribution of fishes that utilize the adjacent mangrove shoreline as nursery and/or adult habitat. This seascape approach consisted of: a) the multi-scale characterization of the SAV distribution across the seascape with metrics developed in Landscape Ecology, Geographic Information Systems and Remote Sensing; b) multivariate analyses to identify groups with significantly distinct SAV seascape structures within the most heterogeneous scale, and identify possible mechanisms driving the observed SAV seascape structures; and c) an assessment of the mangrove fish community responses to SAV seascape structures. By applying a set of multivariate analyses (e.g., ANOSIM, MDS plots, hierarchical clustering), the buffer within 200 m from shore was identified as the scale with the highest structural heterogeneity. At this scale, two major SAV seascape structures (i.e., areas with similar SAV spatial arrangement and composition) were identified: a fragmented SAV seascape (FSS) structure and a continuous SAV seascape (CSS) structure. Areas with CSS were characterized by large, uniform SAV patches. In contrast, areas with FSS were characterized by a higher density of smaller, more complex SAV patches. Furthermore, the areas with CSS and FSS structures clustered in zones of the bay with distinct salinity properties. The areas with CSS structures were mostly located in zones characterized by high and stable salinity. However, the areas with FSS concentrated in zones that are influenced by freshwater discharges from canals and with low and variable salinity. The responses of fish diversity metrics were not constrained to the scale at which the greatest spatial heterogeneity of SAV seascape structures was observed (i.e., the seascape composition and configuration within 200 m from shore), but was related to SAV seascape characteristics across different scales. The majority of the variability of the fish diversity metrics in the mangrove shoreline was explained by SAV seascape structures within the smaller scales (i.e., 100-400 m from shore), and SAV seascape structures that represented the level of fragmentation and/or the percent of suitable habitat. Different conceptual models were proposed to illustrate and understand the ecological dynamics behind the relationship between the diversity of the mangrove fish community and the structure of the adjacent SAV seascape. In general, the diversity and abundance of fishes is influenced by the type and level of fragmentation of the SAV seascape, which, in turn, influence the proportion of the seascape used for foraging and refuge by fish. In conclusion, this research quantified how the release of large pulses of freshwater into near-shore habitats of coastal lagoons can influence the seascape structure of SAV communities. Namely, freshwater inputs produce fragmentation in otherwise fairly homogeneous SAV meadows. The outcome of this research highlights the importance of seascape characteristics as indicators of ecosystem-level modifications and alterations affecting the spatial distribution, assemblage, and diversity of marine nearshore habitats in coastal regions heavily influenced by human activities. In addition, the results illustrated the cascading effects and synergistic influences of near-shore habitat spatial assemblages on the composition and diversity of estuarine fish communities. Lastly, and very importantly, the relationships established in this project provide quantitative and qualitative information on patterns of species-habitat associations needed for the improved synergistic management and protection of coastal habitats and fisheries resources.

À l'interface bentho-pélagique, les herbiers marins présentent une multitude de rôles écosystémiques. Historiquement, les scientifiques et décideurs de La Réunion se sont focalisés sur l'écosystème récifal. Néanmoins, des prairies monospécifiques à Syringodium isoetifolium sont présentes de manière pérenne (3 hectares) au sein du complexe récifal de l'Ermitage / La Saline (côte ouest). L'objectif principal de cette étude était d'apporter les premières données sur l'écologie de ces herbiers marins. Ainsi, une approche pluridisciplinaire a été développée : 1. L'étude de la dynamique spatiale du paysage herbier sur 65 ans (dès 1950), et à l'échelle saisonnière (2013-2015) qui a permis de définir le rôle majeur des forçages hydrodynamiques et de l'eutrophisation. 2. L'analyse de la productivité de l'écosystème herbier et sa réponse métabolique face à des apports nutritifs, révèle des bilans métaboliques opposés (autotrophie/hétérotrophie) en fonction des conditions environnementales, ainsi qu'un rôle de tampon sur les flux de nutriments. 3. Des analyses isotopiques (δ13C et δ15N) ont permis d'identifier les sources de matière entrant dans l'écosystème et alimentant les réseaux trophiques associés aux herbiers. L'étude a permis d'établir un lien trophique entre Holothuria leucospilota et les herbiers marins ainsi qu'un rôle essentiel dans le maintien des populations de poisson herbivores récifaux. 4. Des enquêtes locales ont révélé une méconnaissance de cet écosystème malgré leur potentiel économique et écologique. À la lumière de ces travaux de thèse, la prise en considération des herbiers marins dans la gestion du milieu marin réunionnais est nécessaire. / Located at the benthos-pelagos interface, seagrass beds have many ecosystemic roles such as coastal protection or biodiversity. Historically, scientists and decision-makers at Reunion Island have been focusing on reef ecosystems. However, for several decades, monospecific (Syringodium isoetifolium) seagrass beds have been observed (3 hectares – 2013) within Ermitage / La Saline reef (West coast). The main objective of this study was to give the first data on seagrass ecology at Reunion Island. Therefore, a multi-disciplinary study was developed. First, seascape ecology of seagrasses is analyzed at decadal (since 1950) and seasonal scales (2013-2015). Physical settings (swell) and eutrophication were driving factors on the spatial dynamics of seagrass beds. Second, seagrass community metabolism and response to nutrient loads (nitrate and phosphate) show variations in metabolic budget (autotrophy to heterotrophy) and make seagrass beds a nutrient sink following the environmental conditions. Third, stable isotope analysis (δ13C and δ15N) identified sources of particulate matter entering the ecosystem and fueling food webs. The trophic roles of seagrass beds are assessed for echinoderm and herbivorous fish communities. This study highlighted a trophic link between seagrass and Holothuria leucospilota, and proved some species to be heavily dependent on seagrass ecosystem (Leptoscarus vaigiensis, Siganus sutor). Finally, interviews showed a lack of knowledge about this ecosystem despite crucial economic and ecologic roles. Considering their major functions, seagrass beds have to be considered in future management of the coastal marine systems at Reunion Island.

The coastal regions in Greece have long been a topic of discussion, since vast regions of coast has changed drastically from the Neolithic period until our modern-day perception of them. Coastal reconstructions with data from drilling cores help geoarchaeologists get a better understanding of how the prehistoric settlements related the coast, and how the landscape and seascape around them looked. This thesis aims to better understand the coastal reconstructions of Asine, Peloponnese made by Eberhard Zangger and how archaeological finds can be used as a complementary material in creating these reconstructive maps. The insides of the drilling cores, their placement and the quantity of them are important factors for a geoarchaeological study, and this paper aims to better understand the quality of the coastal reconstructions of Asine. With new archaeological finds of Neolithic ceramics in the Asine area, together with early Helladic finds, this paper explores the possible uncertainty of the modern reconstructions. This paper reaches its natural conclusion in the Hellenistic Asine, where the theory of a harbor in the area is discussed from different possibilities of coastal reconstructions, and how Zanggers reconstruction relates to the Hellenistic architectural remains. The discussion also brings other comparative studies in light and differences between Zanggers coastal reconstructions and other reconstructions of similar nature are confronted.

Submitted by Cláudia Bueno (claudiamoura18@gmail.com) on 2016-05-19T19:46:17Z No. of bitstreams: 2 Dissertação - André Felipe Alves de Andrade - 2016.pdf: 2007118 bytes, checksum: 69341ce5bc6c459857d1feff5d92366e (MD5) license_rdf: 23148 bytes, checksum: 9da0b6dfac957114c6a7714714b86306 (MD5) / Approved for entry into archive by Luciana Ferreira (lucgeral@gmail.com) on 2016-05-20T13:54:17Z (GMT) No. of bitstreams: 2 Dissertação - André Felipe Alves de Andrade - 2016.pdf: 2007118 bytes, checksum: 69341ce5bc6c459857d1feff5d92366e (MD5) license_rdf: 23148 bytes, checksum: 9da0b6dfac957114c6a7714714b86306 (MD5) / Made available in DSpace on 2016-05-20T13:54:17Z (GMT). No. of bitstreams: 2 Dissertação - André Felipe Alves de Andrade - 2016.pdf: 2007118 bytes, checksum: 69341ce5bc6c459857d1feff5d92366e (MD5) license_rdf: 23148 bytes, checksum: 9da0b6dfac957114c6a7714714b86306 (MD5) Previous issue date: 2016-02-26 / Coordenação de Aperfeiçoamento de Pessoal de Nível Superior - CAPES / Coral reefs are of extreme importance to both nature and society, due to being responsible for several services and harbouring hundreds of species. Despite such critical importance, reef corals current suffered heavy losses since the Anthropocene, with 20% of world´s corals damaged beyond recovery due to human pressure and coastal development. This scenario is even worse, since corals are especially vulnerable to climate change and the entire ecosystem could go extinct by 2050. In this study we focus on comparing the already established impacts from human development and the yet happen losses from climate change on Brazilian corals, a unique fauna that still have gaps in knowledge. We created environmental suitability models for 24 species and quantified individual losses from both climate change and human activities. From the individual results we derived an overall pattern, in which we found out that future losses from climate alteration are equivalent to current losses from human activities. We then used the spatial distribution of those activities and key areas for conservation, determined with software Zonation, to select six areas in the Brazilian exclusive economic zone where proactive and reactive conservation strategies should be implanted, given its importance to biodiversity and concentrated anthropogenic impacts. Overall suitability losses were of approximately 30% for both sources and 60% of the areas will continue to be suitable in the future. Therefore, Brazilian corals will experience heavy losses from climate, especially the loss of highly suitable areas, which are compared to effects from human economic activities. Coral situation is likely to be even worse, if we were to consider bleaching, ocean acidification and diseases, events expected to increase with the rising temperature. / Ecological Niche Modelling (ENM) is widely used for conservation purposes, predicting species invasion, evolutionary aspects and a whole array of applications. However, for most cases, evaluating the efficiency of those models poses as problematic, as commonly used methods (i.e. random methods) do not assure the required independence between data used to create the model and data used to evaluate the model. We developed a new transferabilitybased framework that ensures the much-needed independence between subsets. We created an alternate approach that geographically splits occurrence datasets, while intrinsically controls issues related to previous transferability approaches, such as overfitting, extrapolation and sampling bias. We used 26 Atlantic coral species to perform three different geographical divisions quantifying the effect of different splits on model predictive efficiency. We demonstrate that transferability should be used as an effective method to evaluate ENMs. Geographical split of the area in deciles proved as a reliable evaluation method, assuring independence between datasets and being less prone to common transferability issues. Our odds-and-evens framework provides improvements to the ongoing debate of ENMs evaluating by its transferability. This new method corrects the issue of artificiality causing sampling bias and overfitting, common in previous methodologies, while also is less prone to extrapolation issues, a common problem in transferability approaches. Moreover, the framework appears as a feasible and useful alternative to the problematic and commonly used random partition of datasets evaluation.