L’Océan austral est l’un des pivot des écosystèmes et du climat de notre planète, qui concentre plus de 20% de la productivité primaire marine mondiale. La complexité de ses réseaux trophiques et son inaccessibilité rendent plus encore qu’ailleurs nécessaire l’utilisation d’espèces bio-indicatrices. Plusieurs espèces de manchots (comme le Manchot Royal et le Manchot Empereur) sont ainsi l’objet de programmes de suivi à long terme. Dans cette étude, nous utilisons les données offertes par la génomique des populations (« RAD-sequencing » couvrant le génome de centaines d'individus issus couvrant la distribution de ces deux espèces) et les représentations numériques du climat de l’IPCC-CMIP5 pour calibrer dans le temps long les analyses démographique plus précises réalisées à l'échelle de quelques générations dans le cadre de suivis démographiques, et mieux comprendre la réponse des manchots au changement climatique. Au-delà de ses conséquences immédiates pour l’étude des Manchots en tant que sentinelles de l’Océan Austral, cette étude montre l’intérêt d’une plus forte intégration de la génomique des populations dans les études démographiques et comportementales. / The Southern Ocean plays a central role in the regulation of the Earth’s climate and ecosystems, and accounts for more than 20% of the world’s marine productivity. The complexity of its trohpic networks and its sheer inaccessibility make the use of bioindicator species more necessary there than anywhere else. Several penguin species (such as the King and the Emperor penguin) are therefore the focus of long-term monitoring programs.In this study, we use the information from population genomics (« RAD-sequencing » data covering the genome of hundreds of individuals from the two species’ full distribution) and from IPCC-CMIP5 numerical climate models to calibrate in the long time the more precise demographic analyses realised in the framework of field surveys, and understand penguin responses to cliamte change. Beyond its implications for the study of penguins as sentinels of the Southern Ocean, our work demonstrates the interest of a stronger integration of population genomics in demographic and behavioural investigation.

South African southern right whales (SRWs; Eubalaena australis) have been studied intensively since 1969, and annual aerial surveys between 1971 and 2006 indicate a predominant 6.9% annual population growth rate – a conservation success story after the species’ legal protection from commercial whaling in 1935. However, the prevalence of South African SRW unaccompanied adults (non-calving adults) and cow-calf pairs dropped sharply after 2009 and 2015, respectively. Additionally, the calving interval of many female South African SRWs has shifted from a three-year cycle to a four- or five-year cycle, since 2010, suggesting calving failure. This has resulted in a decrease in the population growth rate from 6.9% between 1971 and 2006, to 6.5% in 2017. SRWs are capital breeders that meet migratory and reproductive costs through seasonal energy intake, leading to strong links between their calving and foraging success. The anomalous trends in the South African SRW population have therefore raised concern about the ecological status of its broad feeding range in the Southern Ocean and ultimately about its continued population recovery. This necessitated investigation firstly into the influence of large-scale global climate drivers, Antarctic winter sea-ice extent and summer ocean productivity on the calving output of the South African SRW population. Auto-regressive integrated moving average models revealed significant model performance improvement through the inclusion of the Oceanic Niño Index (a key measure of El Niño events), the Antarctic Oscillation (the leading mode of atmospheric variability in the Southern Ocean) and chlorophyll a concentrations. The findings indicate that the South African SRW calving output appears closely influenced by not only the species’ life cycle, but also by foraging ground productivity and global climate. Secondly, the foraging strategies of South African SRWs during the 1990s (i.e. a period of high calving rates) and the late 2010s (i.e. a period of low calving rates), were assessed, through the analyses of stable carbon (δ13C) and nitrogen (δ15N) isotope values in SRW skin biopsy samples (n = 122). Results show that South African SRWs underwent a dramatic northward shift in foraging location, as well as a diversification in foraging strategy, between the 1990s and 2010s. Bayesian mixing models suggest that during the 1990s, the population foraged on prey with isotopic values similar to krill from around South Georgia. By contrast, in the 2010s, it is inferred that the population foraged on prey with isotopic values consistent with prey found in the waters of the Subtropical Convergence, Polar Front, and Marion Island. This shift could represent a new strategy to cope with changes in the availability of preferred prey or changes in habitat productivity. However, the co-occurring reproductive declines show that altering foraging strategies may not be sufficient to successfully adapt to a changing ocean. Overall, the results of this dissertation advocate that South African SRWs have recently been affected by environmental change at their foraging grounds, in turn affecting their reproductive success. Their predictive coastal presence and the existing long-term monitoring suggest that the species should be regarded as an indicator species – illustrative of climate change impacts in Southern Ocean ecosystems. / Dissertation (MSc ((Zoology))--University of Pretoria, 2020. / Zoology and Entomology / MSc (Zoology) / Restricted

This project used a variety of genetic markers to investigate the evolution and population genetics of hydrothermal vent fauna that were recovered from the Scotia Sea, in the Atlantic sector of the Southern Ocean. The origins of one of these species, an undescribed species of Kiwa sp. found on the East Scotia Ridge (ESR) and its constituent family Kiwaidae, a group of vent and seep-associated decapod squat lobsters (infraorder Anomura) was investigated using a concatenated nine-gene dataset and key divergences were dated using fossil calibrations. These results confirm earlier research showing Kiwaidae reside in the superfamily Chirostyloidea, but form a monophyletic clade with the non-chemosynthetic family Chirostylidae and not Eumunididae. Chirostyloid families diverged in the Cretaceous, although extant Kiwaidae radiated in the Eocene, consistent with many other chemosynthetic taxa that appear recently derived. The basal tree position of Pacific species (and the Alaska location of a likely stem-lineage kiwaid fossil) suggests kiwaids originated in the East Pacific. Within a Southern Hemisphere clade, the divergence between the southeastern Pacific K. hirsuta and a non-Pacific lineage (Kiwa sp. ESR and Southwest Indian Ridge kiwaids) is no earlier than 25.9 Ma, consistent with a spread from the Pacific into the Scotia Sea and beyond via now-extinct active ridge connections or mediated by a Miocene onset of the Antarctic Circumpolar Current (ACC) through a newly-opened Drake Passage. This project also investigated the population genetics of three undescribed species found at two vent fields ~ 440 km apart at either end of the ESR: Kiwa sp., a peltospirid gastropod and Lepetodrilus sp. limpets. Lepetodrilus sp. was also found at the Kemp Caldera, a submerged part of the South Sandwich Islands (SSI). Analyses of cytochrome c oxidase subunit 1 (COI) as well as microsatellite loci developed from Roche 454 sequence libraries revealed no differentiation along the ESR for all three species consistent with panmixia, or the dominance of non-equilibrium processes between vent field colonies within a metapopulation, possibly enhanced further by cold-induced arrested larval development. Despite apparent connectivity along the ESR, both COI and microsatellites revealed differentiation between ESR limpets and Kemp Caldera limpets ~ 95 km to the east, possibly owing to the hydrographic isolation of the caldera. Both COI and microsatellite diversity patterns were consistent with recent (< 1 Ma) demographic expansions for all three species (although the influence of selection sweeps on COI cannot be discounted); a pattern observed worldwide at vent communities and may reflect demographic instability over time as a consequence of the stochastic birth and death of vent colonies within a metapopulation. Different COI bottleneck ages between the three species (excluding the influence of possible selection) as well as the absence of kiwaids and peltospirids at Kemp, have been attributed to differences in life history, in particular larval morphology and presumed dispersal strategy. These results highlight the role of larval dispersal of vent fauna along active spreading ridges, both in maintaining vent metapopulations across vent colonies prone to stochastic birth and extinction in the short term, but also in the spread of taxa globally and the formation of biogeographic provinces. The likelihood that the three species presented here exist at vents east of the ESR and SSI, prompts further exploration along ridges in the South Atlantic, in order to investigate the effect of the ACC in enhancing gene flow and delineating biogeographic provinces.

Afin d'étudier les processus biogéochimiques de l'Océan Austral, des balises posées sur des éléphants de mer ont permis de récolter en 2009-2010 des profils de variables océanographiques (Chlorophylle a (Chl a), température, salinité, lumière) dans une zone s'étalant du sud des îles Kerguelen jusqu'au continent Antarctique. Cette thèse se penche en particulier sur les données de Chl a, car celle-ci est contenue dans les organismes photosynthétiques qui jouent un rôle essentiel de pompe à carbone. Mais les profils verticaux de Chl a, récoltés peu fréquemment, ne permettent pas d'obtenir une cartographie de cette variable dans cette zone de l'océan. Cependant, nous disposons de profils de lumière, échantillonnés plus souvent. L'objectif était alors de développer une méthodologie permettant de reconstruire de manière indirecte les profils de Chl a à partir des profils de lumière, et qui prenne en compte les caractéristiques de ce type de données qui se présentent naturellement comme des données fonctionnelles. Pour cela, nous avons abordé la décomposition des profils à reconstruire ou explicatifs sur une base de splines, ainsi que les questions d'ajustement associées. Un modèle linéaire fonctionnel a été utilisé, permettant de prédire des profils de Chl a à partir des dérivées des profils de lumière. Il est montré que l'utilisation d'un tel modèle permet d'obtenir une bonne qualité de reconstruction pour accéder aux variations hautes fréquences des profils de Chl a à fine échelle. Enfin, une interpolation par krigeage fonctionnel permet de prédire la concentration en Chl a de nuit, car les mesures de lumière acquises à ce moment-là ne peuvent pas être exploitées. / To study biogeochemical processes in the Southern Ocean, tags placed on elephant seals allowed to collect during 2009-2010 oceanographic variables profiles (Chlorophyll a (Chl a), temperature, salinity, light) in an area ranging from southern Kerguelen until the Antarctic continent. This thesis focuses on Chl a data as it is contained in photosynthetic organisms and these ones play an essential role in the oceanic carbon cycle. The infrequently collected vertical Chl a profiles don't provide a mapping of this variable in this area of the ocean. However, we have light profiles sampled more often. The aim of this thesis was then to develop a methodology for reconstructing indirectly Chl a profiles from light profiles, and that takes into account characteristics of this kind of data that naturally occur as functional data. For this, we adressed the profiles decomposition to rebuild or explanations on splines basis, as well as issues related adjustment. A functional linear model was used to predict Chl a profiles from light profiles derivatives. It was shown that the use of such a model provides a good quality of reconstruction to access high frequency variations of Chl a profiles at fine scale. Finally, a functional kriging interpolation predicted the Chl a concentration during night, as light measurements acquired at that time can't be exploited. In the future, the methodology aims to be applied to any type of functional data.

A complexa interação que ocorre entre os processos oceânicos e atmosféricos no Oceano Austral afeta a circulação oceânica global em diferentes camadas. O Mar de Weddell e o Mar de Ross possuem reconhecida importância na formação da Água de Fundo Antártica (AABW). O objetivo principal deste trabalho é caracterizar as massas de água dos Mares de Weddell e Ross, através dos dados mais recentes de reanálise oceânica SODA (Simple Ocean Data Assimilation). Através da técnica de separação de massas de água Análise Multiparamétrica Ótima (AMO) foi possível a identificação de 3 principais massas de água no Mar de Ross: Água Profunda Circumpolar Superior (UCDW), Água Profunda Circumpolar Inferior (LCDW) e Água de Plataforma de Baixa Salinidade (LSSW). A UCDW foi a que apresentou a maior variabilidade, não atingindo a Plataforma de gelo do MR durante os anos de 1950-1974. No Mar de Weddell foi possível a identificação das seguintes massas de água: Água Profunda Cálida (WDW), Água Profunda do Mar de Weddell (WSDW) e Água de Fundo do Mar de Weddell (WSBW). A WDW atingiu valores >70% à 800m. A WSDW possui em seu núcleo valores > 90% entre 2000 e 3500m. A WSBW, apresenta ~100% em profundidades > 4000m. / The complex interaction that occurs between the oceanic and atmospheric processes in the Southern Ocean affects global ocean circulation in different layers. The Weddell and Ross Seas have recognized importance in the formation of Antarctic Bottom Water (AABW). This work aims to characterize the water masses of the Weddell and Ross Seas, using the latest ocean data reanalysis SODA (Simple Ocean Data Assimilation). Through the water masses separation technique, Optimum Multiparameter Analysis (OMP), it was possible to identify three main water masses in Ross Sea: Upper Circumpolar Deep Water (UCDW), Lower Circumpolar Deep Water (LCDW) and Low Salinity Shelf Water (LSSW). UCDW showed the greatest variability, not reaching the Ross Sea Ice Shelf during the years 1950-1974. It was possible to identify the following water masses in Weddell Sea: Warm Deep Water (WDW), Weddell Sea Deep Water (WSDW) and Weddell Sea Bottom Water (WSBW). WDW reached values up to 70% in 800m. WSDW has in its core values > 90% between 2000 and 3500m. WSBW presents a contribution up to 100% at depths > 4000m.

O oceano desempenha papel fundamental na configuração e manutenção do clima da Terra, sendo considerado um dos componentes principais do sistema climático.Diversos estudo foram conduzidos para avaliar as mudanças nos processos climáticos e como o clima, em contrapartida, é afetado por tais mudanças. O presente trabalho visa investigar o impacto das mudanças climáticas na formação de massas de água do oceano austral. Foram analisados resultados de simulação numérica para os séculos XX e XXI pelo modelo CCSM3 para os cenários 20c3m e SRESA1B do IPCC. Através da técnica de separação de mássas de água Análise Otimizada de Parâmetros Múltiplos (OMP) foram identificadas 3 massas de água no Mar de Ross: Água Profunda Circumpolar (CDW); Água da Plataforma de Gelo (ISW); Água de Plataforma de Baixa Salinidade (LSSW). A ISW, precursora da Água de Fundo Antártica (AABW), apresenta maior variação espacial tornando-se mais rasa no século XX e assumindo camadas mais profundas no século XXI. A variação da ISW está relacionada à variação do Modo Anular Sul (SAM) e à variação do gelo marinho. / It has been known for a long time that the ocean plays the most important role on Earth\'s heat budget, what turns it into a major component of the global climate system. Therefore, many studies have been made to assess whether features of climate processes are changing and how may climate itself be affected by these changes. This work aims to look at the impact of climate changes on water masses formation in the Southern Ocean. Results from the 20th century and SRESA1b CCSM3/NCAR simulation (1870 to 2100) were analyzed using the Optimum Multiparameter Analysis (OMP) to separate water masses. Three water masses were identified in the Ross Sea: Circumpolar Deep Water (CDW); Ice Shelf Water (ISW); Low Salinity Shelf Water (LSSW). Simulation results have shown that the ISW gets shallower during the 20th century and then, during the 21stcentury, it gets deeper and occupies the deepest layer by 2100 while it flows towards higher latitudes as AABW. Much closely to what has been shown by observational studies, water masses formation in the Southern Ocean is intrinsically linked to atmospheric vaiability modes, such as the southern annular mode--SAM, and to sea ice variation.

L'océan Austral joue un rôle crucial dans la régulation du système climatique en absorbant de grandes quantités de CO2 atmosphérique. Toutefois de nombreuses incertitudes demeurent quant à l'évolution récente du puits de carbone austral notamment en raison du manque d'observations et des lacunes des modèles océaniques dans la représentation de processus dynamiques comme les tourbillons. Depuis quelques décennies notamment, l'efficacité du puits de carbone austral diminuerait en raison d'une intensification des vents liée à une tendance positive du Mode Annulaire Austral (SAM). L'objectif de ces travaux de thèse est de décrire et comprendre la variabilité spatiale et temporelle récente des flux air-mer de CO2 dans l'océan Austral. Pour cela, des simulations de sensibilité aux phases positives du SAM sont réalisées dans une configuration régionale de l'océan Austral (sud de 30°S), basée sur un modèle couplé dynamique-biogéochimie forcé par l'atmosphère et résolvant partiellement la méso-échelle océanique. Dans l'océan Austral, la réponse des flux de CO2 au SAM correspond à un dégazage intense de CO2 dans la zone antarctique dû à une augmentation des concentrations de surface de carbone inorganique dissous (DIC). Cette augmentation est pilotée par la dynamique de la couche de mélange et alimentée par un transport méridien de DIC qui résulte essentiellement de la compétition entre circulation induite par les vents et par les méandres stationnaires. Ces travaux montrent l'apport d'une augmentation de la résolution numérique des modèles pour la simulation des flux de CO2. / By taking up large amounts of atmospheric CO2, the Southern Ocean helps to regulate the climate system. Southern Ocean carbon sink is poorly constrained, in part because data coverage is sparse and also because ocean models that have been used in such assessments fail to explicitly resolve key physical features such as mesoscale eddies. In recent decades, the growth of the Southern Ocean carbon sink may have been partly counteracted due to a loss of natural CO2 from the ocean driven by an intensification of westerlies, related to a positive trend in the Southern Annular Mode (SAM). This thesis focuses on documenting and understanding recent spatial and temporal variability of air-sea CO2 fluxes in the Southern Ocean. Sensitivity to positive phases of the SAM are tested by making simulations with a regional model of the Southern Ocean (south of 30°S) that couples biogeochemistry to the dynamics, is forced by atmosphere reanalysis data, and partially resolves the mesoscale. The resulting response of Southern Ocean CO2 fluxes to the SAM is dominated by a strong CO2 efflux to the atmosphere from the Antarctic Zone due to an increase in surface dissolved inorganic carbon (DIC). This increase is driven by the mixed-layer dynamics and is supplied by a meridional transport of DIC, a competition between the wind-driven circulation and the standing eddy-induced circulation. This work discusses the effect of increasing model resolution on simulated air-sea CO2 fluxes.

Les modifications environnementales qui affectent aujourd'hui les milieux marins recouvrent des problématiques scientifiques et sociétales majeures, d'autant que ces changements devraient s'accélérer au cours du 21ème siècle. Comprendre et anticiper la réponse de la biodiversité marine à ces changements représente un enjeu scientifique d'actualité. Les approches biogéographiques et macroécologiques constituent un cadre scientifique dans lequel il est possible d'étudier, de décrire, et de comprendre les motifs de distribution des espèces à large échelle et d'estimer leur évolution possible face aux changements environnementaux. C'est notamment le cas dans l'océan Austral où les effets du changement climatique se font déjà sentir et où les modifications environnementales associées pourraient avoir des effets profonds sur la structure et le fonctionnement des écosystèmes. Malgré de récents efforts d'échantillonnage, nos connaissances sur la distribution des espèces dans l’océan Austral comptent encore de nombreuses lacunes attribuables au caractère récent des découvertes, à l'isolement et à l'éloignement de cet océan d'accès difficiles. Dans ce contexte, les objectifs de cette thèse consistaient à mieux comprendre les motifs de distribution d'espèces à l’échelle de l’océan Austral, à mettre en évidence les facteurs qui en sont à l’origine et enfin, à évaluer l’impact du changement climatique sur leur distribution. Pour cela, différents types de modèles de niche écologique (MNE) ont été employés. Les échinides (oursins), organismes communs des communautés benthiques de l’océan Austral ont servi de modèle d'étude pour ce travail. / Current environmental changes, which impact marine environments, cover major scientific and societal issues, especially as these environmental changes are expected to accelerate along the 21st century. Understanding and forecasting the response of marine biodiversity to these changes is a pregnant scientific issue. Biogeographic and macroecological approaches provide a scientific framework for that purpose. They allow describing and understanding species distribution patterns at large spatial scale as well as estimating their potential shift with regards to environmental change. This is particularly true in the Southern Ocean, where the effects of climate change are already occurring and where environmental changes could have a deep and manifold impact on the structure and functioning of marine ecosystems. Despite recent sampling efforts, our knowledge of the Southern Ocean species distributions still faces many shortcomings due to the rather recent discovery of this ocean, its isolation and remoteness along with difficult access conditions. In this context, the aims of this thesis are to better understand the factors that drive species distribution patterns at the Southern Ocean scale, and to assess the impact of climate change on their distribution. For this purpose, different types of Species Distribution Models (SDM) have been used. Echinoids (sea urchins), which are common organisms of benthic communities in the Southern Ocean, have been used as a biological model for this work.

O oceano desempenha papel fundamental na configuração e manutenção do clima da Terra, sendo considerado um dos componentes principais do sistema climático.Diversos estudo foram conduzidos para avaliar as mudanças nos processos climáticos e como o clima, em contrapartida, é afetado por tais mudanças. O presente trabalho visa investigar o impacto das mudanças climáticas na formação de massas de água do oceano austral. Foram analisados resultados de simulação numérica para os séculos XX e XXI pelo modelo CCSM3 para os cenários 20c3m e SRESA1B do IPCC. Através da técnica de separação de mássas de água Análise Otimizada de Parâmetros Múltiplos (OMP) foram identificadas 3 massas de água no Mar de Ross: Água Profunda Circumpolar (CDW); Água da Plataforma de Gelo (ISW); Água de Plataforma de Baixa Salinidade (LSSW). A ISW, precursora da Água de Fundo Antártica (AABW), apresenta maior variação espacial tornando-se mais rasa no século XX e assumindo camadas mais profundas no século XXI. A variação da ISW está relacionada à variação do Modo Anular Sul (SAM) e à variação do gelo marinho. / It has been known for a long time that the ocean plays the most important role on Earth\'s heat budget, what turns it into a major component of the global climate system. Therefore, many studies have been made to assess whether features of climate processes are changing and how may climate itself be affected by these changes. This work aims to look at the impact of climate changes on water masses formation in the Southern Ocean. Results from the 20th century and SRESA1b CCSM3/NCAR simulation (1870 to 2100) were analyzed using the Optimum Multiparameter Analysis (OMP) to separate water masses. Three water masses were identified in the Ross Sea: Circumpolar Deep Water (CDW); Ice Shelf Water (ISW); Low Salinity Shelf Water (LSSW). Simulation results have shown that the ISW gets shallower during the 20th century and then, during the 21stcentury, it gets deeper and occupies the deepest layer by 2100 while it flows towards higher latitudes as AABW. Much closely to what has been shown by observational studies, water masses formation in the Southern Ocean is intrinsically linked to atmospheric vaiability modes, such as the southern annular mode--SAM, and to sea ice variation.

L'océan Austral est une région clé pour la compréhension de la circulation océanique globale et du climat. C'est dans cette région qu'une large majorité des eaux de la planète est ventilée dans la couche de surface avant d'être réexpédiée dans l'océan profond. Ainsi la couche de surface de l'océan Austral est un élément central pour la compréhension de la circulation océanique planétaire. Malgré leur rôle fondamental dans la circulation océanique globale et dans le climat, la structure et les caractéristiques de la couche de mélange sont encore mal comprises dans la région Antarctique en raison d'un manque important d'observations in-situ. Cependant, le programme international MEOP (2004) a conduit au déploiement de milliers de capteurs hydrologiques sur des éléphants de mer, et offre une couverture spatiale de données inédites couvrant l’ensemble du cycle saisonnier. Dans cette thèse, nous exploitons ce jeu de données ainsi que d'autres plus conventionnels, afin de décrire les propriétés climatologiques et la dynamique de la couche de mélange sous la glace de mer en Antarctique. Les transferts verticaux entre la couche de mélange et l’océan plus profond, associés à la circulation de retournement y sont décrits aux échelles de temps saisonnières et inter-annuelles. Les résultats soulignent et quantifient le rôle primordial des flux d’eau douce, issus de la glace de mer et des précipitations, sur la transformation de masses d’eau sous la banquise. Nos conclusions suggèrent que des changements dans l’intensité de ces flux d’eau douce pourraient directement affecter les budgets de densité de la couche de mélange et impacter la circulation de retournement globale. / The Southern Ocean is a key region for the understanding of the global ocean circulation and for the climate as a whole. In this region, a large majority of the ocean’s water masses are ventilated in the surface layer, before being sent back to the deep ocean. The surface layer of the Southern Ocean is therefore a central element for understanding the global ocean circulation. Despite their fundamental role in the global ocean circulation and climate, the structure and characteristics of the mixed-layer are still poorly understood in the Antarctic Polar Region due to a significant lack of in-situ observations.However, the international MEOP program (2004) has led to the deployment of thousands of hydrological sensors on Elephant Seals and offers a unique spatial coverage of new data that cover the entire seasonal cycle. In this thesis, we exploit this dataset and other more conventional data, to bring a new perspective on this unknown region. Based on these observations, we describe the climatological properties and dynamics of the mixed-layer under Antarctic sea-ice. The vertical transfers between the mixed-layer and the deep ocean, associated with the meridional overturning circulation, and the hydrographic variations of the water masses in the mixed-layer, are described at seasonal and inter-annual time scales. The results highlight the critical role of freshwater fluxes, induced by sea-ice and precipitations, on the transformation of water masses under the sea-ice. Our findings suggest that changes in the intensity of these freshwater fluxes would directly affect the buoyancy budgets of the mixed-layer and impact the large-scale overturning circulation.