Prospects for improving the representation of coastal and shelf seas in global ocean models

Accurately representing coastal and shelf seas in global ocean models represents one of the grand challenges of Earth system science. They are regions of immense societal importance through the goods and services they provide, hazards they pose and their role in global-scale processes and cycles, e.g. carbon fluxes and dense water formation. However, they are poorly represented in the current generation of global ocean models. In this contribution, we aim to briefly characterise the problem, and then to identify the important physical processes, and their scales, needed to address this issue in the context of the options available to resolve these scales globally and the evolving computational landscape. We find barotropic and topographic scales are well resolved by the current state-of-the-art model resolutions, e.g. nominal 1∕12°, and still reasonably well resolved at 1∕4°; here, the focus is on process representation. We identify tides, vertical coordinates, river inflows and mixing schemes as four areas where modelling approaches can readily be transferred from regional to global modelling with substantial benefit. In terms of finer-scale processes, we find that a 1∕12° global model resolves the first baroclinic Rossby radius for only  ∼ 8% of regions  < 500m deep, but this increases to  ∼ 70% for a 1∕72° model, so resolving scales globally requires substantially finer resolution than the current state of the art. We quantify the benefit of improved resolution and process representation using 1∕12° global- and basin-scale northern North Atlantic nucleus for a European model of the ocean (NEMO) simulations; the latter includes tides and a k-ε vertical mixing scheme. These are compared with global stratification observations and 19 models from CMIP5. In terms of correlation and basin-wide rms error, the high-resolution models outperform all these CMIP5 models. The model with tides shows improved seasonal cycles compared to the high-resolution model without tides. The benefits of resolution are particularly apparent in eastern boundary upwelling zones. To explore the balance between the size of a globally refined model and that of multiscale modelling options (e.g. finite element, finite volume or a two-way nesting approach), we consider a simple scale analysis and a conceptual grid refining approach. We put this analysis in the context of evolving computer systems, discussing model turnaround time, scalability and resource costs. Using a simple cost model compared to a reference configuration (taken to be a 1∕4° global model in 2011) and the increasing performance of the UK Research Councils' computer facility, we estimate an unstructured mesh multiscale approach, resolving process scales down to 1.5km, would use a comparable share of the computer resource by 2021, the two-way nested multiscale approach by 2022, and a 1∕72° global model by 2026. However, we also note that a 1∕12° global model would not have a comparable computational cost to a 1° global model in 2017 until 2027. Hence, we conclude that for computationally expensive models (e.g. for oceanographic research or operational oceanography), resolving scales to  ∼ 1.5km would be routinely practical in about a decade given substantial effort on numerical and computational development. For complex Earth system models, this extends to about 2 decades, suggesting the focus here needs to be on improved process parameterisation to meet these challenges

Análise de redes da paisagem submarina de canhão : implicações para o planeamento e gestão da biodiversidade

Submarine canyons are complex and heterogeneous geomorphologic structures highly relevant for the biodiversity and productivity of continental margins. These marine ecosystems play a key role providing invaluable goods and services for human well-being but are also increasingly subjected to the effects of anthropogenic pressure and climate change. The natural isolation of canyons may act synergistically with these changes with implications for population connectivity and the maintenance of biodiversity. The understanding of the causes and ecological consequences of such changes requires holistic and interdisciplinary approaches. I mapped the landscape of submarine canyon research based on a comprehensive bibliographic data set and using data mining techniques and network analysis. The existing knowledge clusters, historical trends, emergent topics and knowledge gaps in canyon research were identified and characterized. Topics such as “Geology & Geophysics”, “Oceanographic Processes” and “Biology & Ecology” were among the most studied while, for instance, “Biogeochemistry” and ecological modelling were among the less explored. Topics regarding anthropogenic impacts and climate-driven processes were only detected on publication of the last decade. The knowledge network reflects a latent interdisciplinarity in canyon research that developed mostly in the new millennium, supported by a well implemented and international collaboration network. The research efforts have been mainly directed towards only a few canyon systems and a thematic bias was identified, with specific topics addressed preferentially in particular canyons. This spatial and thematic bias, together with the paucity of truly inter-disciplinary studies, may be the most important limitation to the integrated knowledge and development of canyon research and hinders a global, more comprehensive understanding of canyon patterns and processes. The scientific landscape mapping and the complementary results are made available online as an open and interactive platform. In order to assess the importance of submarine canyons for the conservation and management on the deep sea, a study area and a modelling species were selected: the Mediterranean Sea and Lophelia pertusa, a cold-water coral species. The Mediterranean Sea encompasses several submarine canyon systems and L. pertusa is an ecosystem engineering species that occurs frequently in these geomorphological features and provides refuge, nursery grounds and physical support for a remarkable diversity of other life forms. Considering that the distribution of L. pertusa in the Mediterranean Sea is probably underestimated and that this information is crucial to assess the relevance of canyons in the Mediterranean seascape, I estimated the habitat suitability and draw uncertainty maps for this region based on environmental predictors and an ensemble approach of three machine-learning algorithms. The results suggest that in the Mediterranean Sea, L. pertusa encounters environmental settings close to its physiological limits but, despite the highly variable quality of the seascape, submarine canyons were identified as high suitability areas, especially across the Western and Central Mediterranean margins. In addition to the environmental suitability, the ecosystem connectivity determines the species distribution, the metapopulation dynamics and population resilience. I simulated the transport of L. pertusa larvae in the Mediterranean Sea using a biophysical model to estimate their potential dispersal as well as a network analysis to evaluate the habitat availability based on parameters such as suitability, spatial configuration of the seascape and the oceanographic conditions variability. The results suggest that connectivity among Mediterranean ecoregions is weak and that the intensification of climate-driven events (e.g., dense shelf water cascading) may worsen this scenario. However, the potential exchange of larvae between colonies within the same ecoregion was significant, favoring population resilience to local disturbances. Habitat areas with high quality and larval flux were identified as a priority for the conservation of L. pertusa, and subsequently also for their associated fauna. Once again, I showed that habitat areas on submarine canyons may play an important role in the connectivity of L. pertusa Mediterranean populations. However, these habitat areas are subjected to intense anthropogenic pressures, which allied to the effects of climate change, may impose greater challenges to their conservation. Apart from three French marine protected areas in the Gulf of Lion, the development of conservation efforts considering submarine canyon in the Mediterranean Sea is negligible. The knowledge produced in this thesis provides scientific evidence to support decision-making in conservation and planning of marine protected areas networks in the Mediterranean Sea and illustrates the relevance of submarine canyon for the management and conservation of deep-sea biodiversity.Os canhões submarinos são estruturas geomorfológicas complexas localizadas nas margens continentais. São reconhecidos como zonas importantes de biodiversidade no mar profundo onde os níveis de produtividade biológica são de modo geral superiores às áreas adjacentes. Estes ecossistemas marinhos desempenham um papel fundamental na prestação de bens e serviços essenciais ao bem-estar humano. Não obstante, estes ecossistemas estão cada vez mais sujeitos a efeitos nefastos que advêm de ações diretas das atividades humanas, mas também, resultantes de alterações climáticas. O isolamento natural dos canhões submarinos em conjunto com estas mudanças, pode ter implicações para a conectividade das populações biológicas que os habitam, bem como para a manutenção da biodiversidade associada. Avaliar as causas e efeitos ecológicos de tais mudanças só será possível através de uma abordagem holística e interdisciplinar. Partindo de uma base de dados bibliográfica abrangente de publicações dedicadas ao estudo de canhões submarinos, usei técnicas de data mining e de análise de redes para mapear o conhecimento reunido até agora. Foram identificados clusters de conhecimento, a evolução histórica da investigação em canhões submarinos, bem como, os tópicos emergentes e lacunas no conhecimento sobre estas estruturas. Os tópicos mais desenvolvidos dizem respeito a áreas associadas à “Geologia e Geofísica”, “Processos Oceanográficos” e “Biologia e Ecologia”. Por outro lado, temas como “Biogeoquímica” e modelação ecológica estão entre os menos explorados. Estudos referentes a impactos antropogénicos nestes ecossistemas e alterações induzidas por processos climáticos foram detetados apenas em publicação datadas da última década. A rede de tópicos gerada reflete uma interdisciplinaridade latente na investigação associada a canhões que se desenvolveu principalmente durante o século XXI, apoiada por colaborações internacionais da comunidade científica. No entanto, a investigação científica em canhões submarinos apresenta uma tendência clara direccionada para determinados temas e áreas geográficas. Tópicos específicos são abordados preferencialmente em determinados canhões, enquanto que um número muito pequeno destas estruturas concentra a maior parte dos trabalhos desenvolvidos. Este resultado juntamente com o número reduzido de estudos interdisciplinares, foi a mais importante limitação detetada que poderá dificultar a integração do conhecimento já reunido sobre estas estruturas, impedido uma compreensão mais abrangente dos padrões e processos associados aos canhões submarinos. Os resultados alcançados foram disponibilizados numa plataforma online aberta para exploração interativa e direcionada dos conteúdos. No sentido de avaliar a importância dos canhões para a conservação e gestão da biodiversidade no mar profundo, foi definida como área de estudo o Mar Mediterrâneo e selecionada como espécie modelo, um coral de água fria: Lophelia pertusa. O Mar Mediterrâneo engloba vários sistemas de canhões submarinos enquanto que L. pertusa é uma espécie engenheira de ecossistemas que cria refúgio, áreas de berçário e habitat para uma panóplia de outras espécies, ocorrendo frequentemente em canhões. Uma vez que a distribuição de L. pertusa no Mar Mediterrâneo está provavelmente subestimada e que esta informação é fundamental para avaliar a relevância dos canhões na área de estudo, desenvolvi um modelo de nicho ecológico baseado em variáveis ambientais e uma abordagem conjunta de três algoritmos. Os resultados obtidos foram mapas de adequação ambiental, bem como, de avaliação da capacidade de previsão do modelo. Os resultados sugerem que no mar Mediterrâneo, esta espécie de coral encontra condições ambientais próximas dos seus limites fisiológicos. Apesar disso, áreas com condições favoráveis à ocorrência de L. pertusa foram detetadas em canhões submarinos, principalmente no Mediterrâneo Ocidental e Central. A par da qualidade dos habitats, a distribuição dos organismos, a dinâmica metapopulacional e a resiliência das populações a perturbações estão fortemente relacionadas com a conectividade dos ecossistemas. Neste contexto, simulei o transporte de larvas de L. pertusa no Mar Mediterrâneo usando um modelo biofísico para estimar o seu potencial de dispersão. Com os resultados do modelo e usando análises de rede, avaliei a disponibilidade de habitat com base em parâmetros como a qualidade, configuração espacial da paisagem marinha e variabilidade oceanográfica. Os resultados sugerem que a conectividade entre as eco-regiões do Mar Mediterrâneo é baixa e que a intensificação de eventos impulsionados por condições climáticas (por exemplo, dense shelf water cascading) pode agravar este cenário. No entanto, a potencial troca de larvas entre colónias dentro da mesma eco-região foi significativa, podendo favorecer a resiliência das populações a perturbações locais. Áreas de habitat com boa qualidade e com fluxo de larvas foram identificadas como prioritárias para a conservação de L. pertusa, com benefícios eventuais também para a fauna associada a este coral. Mais uma vez, áreas de habitat incluídas em canhões submarinos foram identificadas como as mais relevantes no Mar Mediterrâneo, devendo desempenhar um papel importante na conectividade de populações desta espécie. Contudo, estas áreas estão igualmente sujeitas de forma intensa a atividades humanas com efeitos prejudiciais nos ecossistemas, e que, aliadas aos efeitos das alterações climáticas, podem dificultar a implementação de medidas de conservação eficazes. Com a exceção de três áreas marinhas protegidas francesas no Golfo do Leão, o desenvolvimento de esforços de conservação no Mar Mediterrâneo que incluam áreas com canhões submarinos é ainda negligenciável. Os resultados apresentados nesta tese fornecem evidências científicas que poderão apoiar medidas de conservação e gestão com vista à criação de redes de áreas marinhas protegidas no Mar Mediterrâneo. Neste sentido, proponho os canhões submarinos como áreas prioritárias para a conservação da biodiversidade de mar profundo na área de estudo.PEst-C/MAR/LA0017/2013 e UID/AMB/50017/2013Programa Doutoral em Biologia e Ecologia das Alterações Globai

Modelling dispersal and connectivity of broadcast spawning corals in the Western Indian Ocean

Coral reef degradation is happening at an alarming rate all over the world due to multiple stressors with elevated sea surface temperature being the root cause. Using the Regional Ocean Modelling System and an individual-based model for the western Indian Ocean, this thesis explored the general circulation patterns (both large and mesoscale) important to dispersal and connectivity of broadcast corals while identifying regions that act as a source of larvae and those that receive larvae. Because habitat destruction and fragmentation through severe bleaching and mortality threaten coral reef health, projected thermal stress from Global Climate Models was explored to quantify future bleaching scenarios that might impact the reproductive timing and larval dispersal. Evaluation of the ROMS configuration for the western Indian Ocean shows that the basin-scale circulation patterns of the region are appropriately captured with the mean volume transports consistent with those derived from observation. Using the eddy detection algorithm, a description of the Southern Gyre as a key aspect of the Somali Current system was identified. The Southern Gyre is associated with barotropic instabilities associated with the northward flowing Somali Current. Rossby waves arriving at the East African coast and the strength of the monsoon winds are also responsible for the evolution and intensification of the gyre. The aggregated trajectories from the Lagrangian model highlight the dominant dispersal pathways and barriers to dispersal following release. The general circulation plays an important role in the dispersal of reef larvae over the study region. At a short pelagic larval duration, most of the released larvae settle back to or near natal reefs, but as the pelagic duration increases, the number of isolated reefs and islands decreases. Even with increased pelagic duration, some reefs (e.g., Agalega and Tromelin) are completely isolated. The mean dispersal distance from release to settlement varied across the region with larvae released along the East African coast dispersed an average of 405 km before settling while those in the Seychelles archipelago dispersed about 101 km. Different blocks of clusters were observed with 16 clusters observed when the pelagic duration is shorter (5 days), compared to seven clusters when the pelagic duration is longer (60 days). The warming trends and bleaching thermal stress shows that among the 636 reef pixels in the study region, about 56% showed positive sea surface temperature trends during the study period (1985- 2016). The frequency of bleaching level thermal stress has also increased over the same period, a tendency that climate models project to continue. Even under optimistic scenarios (such as the Representative Concentration Pathway RCP 4.5), most coral reefs are projected to experience severe bleaching and possible mortality by the 2050s. Low to moderate thermal stress are projected over reefs along the East African coast and near the northwest tip of Madagascar and thus these regions may act as potential climate refugia while increasing the potential of reefs to cope with climate change