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Coral reef environments are important marine ecosystem and they are in decline due to climate change. Monitoring coral reefs is crucial but has its challenges since coral reefs are dynamic and data is sensitive to weather conditions. This often leads to difficulties for acquiring accurate data. Coral reef surveys are normally done during ideal conditions which are not always available when researchers are present. That is only one of several challenging aspects in coral reef classification. This study explores the possibilities of applying deep learning to classify drone imagery from coral reefs as a promising new approach for coral reef classification, but also as a new approach for producing geophysical output. This study also explores if it is possible to classify non ideal shore imagery. The possibility to work with non ideal imagery would provide more options for the analysis of coral reef surveys. The images are classified using a segmentation approach with a convolutional neural network. The binary classifications achieve high accuracies of 94% and 96% and IoU values of 77% and 71%. From the segmented output a coral density map is derived. The production of the coral density map is the one of the final steps towards producing promising geophysical output. The classification of non ideal imagery led to some difficulties, but it should be possible to fully correctly classify those as well, which can be discussed in further research

Coral reef environments are important marine ecosystem and they are in decline due to climate change. Monitoring coral reefs is crucial but has its challenges since coral reefs are dynamic and data is sensitive to weather conditions. This often leads to difficulties for acquiring accurate data. Coral reef surveys are normally done during ideal conditions which are not always available when researchers are present. That is only one of several challenging aspects in coral reef classification. This study explores the possibilities of applying deep learning to classify drone imagery from coral reefs as a promising new approach for coral reef classification, but also as a new approach for producing geophysical output. This study also explores if it is possible to classify non ideal shore imagery. The possibility to work with non ideal imagery would provide more options for the analysis of coral reef surveys. The images are classified using a segmentation approach with a convolutional neural network. The binary classifications achieve high accuracies of 94% and 96% and IoU values of 77% and 71%. From the segmented output a coral density map is derived. The production of the coral density map is the one of the final steps towards producing promising geophysical output. The classification of non ideal imagery led to some difficulties, but it should be possible to fully correctly classify those as well, which can be discussed in further research

The number of designated Protected Areas (PAs) worldwide has been increasing fast over the past decades and currently 15.1% of the land and 7.9% of the ocean’s surface are under protection. However, the mere designation of a PA does not guarantee any degree of protection. Where the IUCN Categorizing system classifies PAs solely based on the management strategy on paper, the actual effects of this management remain undetermined. Over the past years, thousands of PA effectiveness methodologies have been developed and applied to PAs from all over the world. However, the majority of the existing assessments are not entirely fit for a quick and easy assessment of the actual quality of the protection in place. Therefore, we propose a new method that assesses the effects of the PA management and thereby reflects the actual degree of protection within the borders of a PA. We present the Protection Level Index (PLI), an index (ranging from 0 to 1) that is based on the scores for 12 equally weighted managerial, socio-economic and ecological sub-indices that are based on both the results from a questionnaire and an analysis of the spatial characteristics of the PA in a GIS. One of the great advantages of PLI is that it omits pre-defining universal optimal conditions and instead allows the PA manager(s) to put numerical quantifications into context. PLI has been tested for 7 European PAs covering a wide range of environmental regimes. The results indicate that some the sub-indices are closely related to each other and that despite the dissimilarities between the 7 PAs, they all have a similar final PLI score in the midrange around 0.63. This emphasizes the unbiased character of PLI, which makes it an ideal protected area management effectiveness method that can be applied to any PA worldwide.

Global climate has been rapidly changing due to on-going anthropogenic CO2 input to the atmosphere, causing the Antarctic Ice Sheet (AIS) to retreat and subsequently cause global sea level rise. AIS melting is heavily dependent on ocean-ice interactions. To be able to more accurately predict the future behaviour of the AIS - with respect to the ocean-driven melting - studying the interactions between AIS and ocean during past intervals of rapid climate warming can provide insights into mechanisms and feedbacks. One interval in the past when climate rapidly warmed is the Miocene Climatic Optimum (18 to 16 Ma), when the Southern Ocean was several degrees warmer in comparison to present sea surface temperatures. This research hence is a palaeoceanographic reconstruction of the Ross Sea in the early to middle Miocene and is performed using samples made into microscopic slides from the Ross Sea at Site U1521, recently retrieved during IODP. Dinoflagellate cyst assemblages suggest a highly dynamic marine-based Ross Sea ice sheet before and throughout the MCO and a clear warming trend towards the MCO. The studied interval starts with the reworking period indicating a period of increased glacial activity. Before the onset of the MCO the Ross Sea is mostly dominated by gonyaulacoid dinocysts suggesting a low SST and a locally ice-free sea to allow light to penetrate and stimulate photosynthesis. The onset of the MCO is indicated by the chert layer with dominance of heterotrophic dinocysts, indicating upwelling of nutrient rich water and ice sheet retreat with a higher Ross Sea SST. A small cooling trend is visible after the onset with fluctuating sea surface temperatures, indicated by autotrophic gonyaulacoid dominance, until the MCO where temperatures rise and heterotrophic dinocysts become abundant again.

The number of designated Protected Areas (PAs) worldwide has been increasing fast over the past decades and currently 15.1% of the land and 7.9% of the ocean’s surface are under protection. However, the mere designation of a PA does not guarantee any degree of protection. Where the IUCN Categorizing system classifies PAs solely based on the management strategy on paper, the actual effects of this management remain undetermined. Over the past years, thousands of PA effectiveness methodologies have been developed and applied to PAs from all over the world. However, the majority of the existing assessments are not entirely fit for a quick and easy assessment of the actual quality of the protection in place. Therefore, we propose a new method that assesses the effects of the PA management and thereby reflects the actual degree of protection within the borders of a PA. We present the Protection Level Index (PLI), an index (ranging from 0 to 1) that is based on the scores for 12 equally weighted managerial, socio-economic and ecological sub-indices that are based on both the results from a questionnaire and an analysis of the spatial characteristics of the PA in a GIS. One of the great advantages of PLI is that it omits pre-defining universal optimal conditions and instead allows the PA manager(s) to put numerical quantifications into context. PLI has been tested for 7 European PAs covering a wide range of environmental regimes. The results indicate that some the sub-indices are closely related to each other and that despite the dissimilarities between the 7 PAs, they all have a similar final PLI score in the midrange around 0.63. This emphasizes the unbiased character of PLI, which makes it an ideal protected area management effectiveness method that can be applied to any PA worldwide.

Global climate has been rapidly changing due to on-going anthropogenic CO2 input to the atmosphere, causing the Antarctic Ice Sheet (AIS) to retreat and subsequently cause global sea level rise. AIS melting is heavily dependent on ocean-ice interactions. To be able to more accurately predict the future behaviour of the AIS - with respect to the ocean-driven melting - studying the interactions between AIS and ocean during past intervals of rapid climate warming can provide insights into mechanisms and feedbacks. One interval in the past when climate rapidly warmed is the Miocene Climatic Optimum (18 to 16 Ma), when the Southern Ocean was several degrees warmer in comparison to present sea surface temperatures. This research hence is a palaeoceanographic reconstruction of the Ross Sea in the early to middle Miocene and is performed using samples made into microscopic slides from the Ross Sea at Site U1521, recently retrieved during IODP. Dinoflagellate cyst assemblages suggest a highly dynamic marine-based Ross Sea ice sheet before and throughout the MCO and a clear warming trend towards the MCO. The studied interval starts with the reworking period indicating a period of increased glacial activity. Before the onset of the MCO the Ross Sea is mostly dominated by gonyaulacoid dinocysts suggesting a low SST and a locally ice-free sea to allow light to penetrate and stimulate photosynthesis. The onset of the MCO is indicated by the chert layer with dominance of heterotrophic dinocysts, indicating upwelling of nutrient rich water and ice sheet retreat with a higher Ross Sea SST. A small cooling trend is visible after the onset with fluctuating sea surface temperatures, indicated by autotrophic gonyaulacoid dominance, until the MCO where temperatures rise and heterotrophic dinocysts become abundant again.

Plastic pollution poses one of the most urgent threats of present time to the marine environment. Global plastic production is growing exponentially and causing an unprecedented increase in the amount of mismanaged plastic waste available to enter the world’s oceans. Microplastic particles with a density lower than that of seawater float on the ocean surface and tend to accumulate in the Subtropical Gyres of all ocean basins due to geostrophic and Ekman currents and Stokes drift. This work develops a method to analyse the possible pathways followed by particles that were sampled in the South Atlantic Subtropical Gyre in order to identify their sources. To do so, particle trajectories were computed by means of Lagrangian simulations backward in time and for each particle the probability of being sourced from nine selected cities bordering the South Atlantic Ocean was calculated. Probability calculations were performed following both an exponential and a quadratic modelling approach on two different datasets. Both models were implemented in such a way that the probability decreased with an increase in distance between the particle and the potential source. The probabilities were also a function of the source uncertainty distance, a parameter representing the uncertain distance at which a particle could be identified as being sourced from a given location. The consistency between the results obtained from two modelling approaches and the different datasets allowed to pinpoint the Rio de la Plata estuary (comprising Montevideo and Buenos Aires), Cape Town and Rio de Janeiro as the most likely sources of microplastics to the South Atlantic Subtropical Gyre. Additionally, from sensitivity analysis the most meaningful source uncertainty distance was determined to range between 25 and 100 km. The methodology developed to calculate land source probabilities is fully transferable and could be used regardless of the study domain and the source locations that want to be address

Last time in Earth’s history when atmospheric CO2 was comparable or slightly higher than at present was during the early Late Pliocene (3.6 to 3.0 Ma). During this generally warm period, one intense glaciation occurred (known as M2, lasting between 3.312 and 3.264 Ma), followed by the mid-Piacenzian Warm Period. The transition from M2 to the mid-Piacenzian Warm Period is often seen as an analogue for the climate of our (near) future. The end of the mid-Piacenzian Warm Period started with the less intense G20 glacial (3.025 Ma), followed by other less intense glacials. This study focuses on a marine sediment record from ODP Site 625 taken offshore the Mississippi delta, which is, therefore, expected to contain both marine and terrestrial material. The aim of this study is to reconstruct the terrestrial (hydro)climate and associated Mississippi input into the Gulf of Mexico (GoM) as well as the oceanographic changes in the Gulf of Mexico during two glacial periods: M2 and the less intense G20 using a multi-proxy approach of both lipid biomarkers and palynology. The absence of plant- and soil-derived lipid biomarkers and pollen in the sediments indicate that terrestrial material discharged to the ocean by the Mississippi did not reach the site location during the studied intervals. On the other hand, marine lipid biomarkers and dinoflagellate cysts reveal a strong influence of the Loop Current during the interval preceding M2, transporting warm and salty Caribbean waters into the Gulf of Mexico. During the cold M2 interval, TEX86 sea surface temperatures dropped from 22.7°C to 20.6°C and Uk37 sea surface temperatures from 27.2°C to 26.2°C. During the temperature drop, salinity and stratification of the water column increased, eventually resulting in hyperstratification, as indicated by the presence of P. zoharyi. Hyperstratification still lasted into the following mid-Pliocene Warm Period, at least until 3.247 Ma. Eventually, the change in dinocyst composition shows th

Plastic pollution poses one of the most urgent threats of present time to the marine environment. Global plastic production is growing exponentially and causing an unprecedented increase in the amount of mismanaged plastic waste available to enter the world’s oceans. Microplastic particles with a density lower than that of seawater float on the ocean surface and tend to accumulate in the Subtropical Gyres of all ocean basins due to geostrophic and Ekman currents and Stokes drift. This work develops a method to analyse the possible pathways followed by particles that were sampled in the South Atlantic Subtropical Gyre in order to identify their sources. To do so, particle trajectories were computed by means of Lagrangian simulations backward in time and for each particle the probability of being sourced from nine selected cities bordering the South Atlantic Ocean was calculated. Probability calculations were performed following both an exponential and a quadratic modelling approach on two different datasets. Both models were implemented in such a way that the probability decreased with an increase in distance between the particle and the potential source. The probabilities were also a function of the source uncertainty distance, a parameter representing the uncertain distance at which a particle could be identified as being sourced from a given location. The consistency between the results obtained from two modelling approaches and the different datasets allowed to pinpoint the Rio de la Plata estuary (comprising Montevideo and Buenos Aires), Cape Town and Rio de Janeiro as the most likely sources of microplastics to the South Atlantic Subtropical Gyre. Additionally, from sensitivity analysis the most meaningful source uncertainty distance was determined to range between 25 and 100 km. The methodology developed to calculate land source probabilities is fully transferable and could be used regardless of the study domain and the source locations that want to be address

Last time in Earth’s history when atmospheric CO2 was comparable or slightly higher than at present was during the early Late Pliocene (3.6 to 3.0 Ma). During this generally warm period, one intense glaciation occurred (known as M2, lasting between 3.312 and 3.264 Ma), followed by the mid-Piacenzian Warm Period. The transition from M2 to the mid-Piacenzian Warm Period is often seen as an analogue for the climate of our (near) future. The end of the mid-Piacenzian Warm Period started with the less intense G20 glacial (3.025 Ma), followed by other less intense glacials. This study focuses on a marine sediment record from ODP Site 625 taken offshore the Mississippi delta, which is, therefore, expected to contain both marine and terrestrial material. The aim of this study is to reconstruct the terrestrial (hydro)climate and associated Mississippi input into the Gulf of Mexico (GoM) as well as the oceanographic changes in the Gulf of Mexico during two glacial periods: M2 and the less intense G20 using a multi-proxy approach of both lipid biomarkers and palynology. The absence of plant- and soil-derived lipid biomarkers and pollen in the sediments indicate that terrestrial material discharged to the ocean by the Mississippi did not reach the site location during the studied intervals. On the other hand, marine lipid biomarkers and dinoflagellate cysts reveal a strong influence of the Loop Current during the interval preceding M2, transporting warm and salty Caribbean waters into the Gulf of Mexico. During the cold M2 interval, TEX86 sea surface temperatures dropped from 22.7°C to 20.6°C and Uk37 sea surface temperatures from 27.2°C to 26.2°C. During the temperature drop, salinity and stratification of the water column increased, eventually resulting in hyperstratification, as indicated by the presence of P. zoharyi. Hyperstratification still lasted into the following mid-Pliocene Warm Period, at least until 3.247 Ma. Eventually, the change in dinocyst composition shows th

Marine lakes have been proposed as a unique ecosystem to assess the physical, chemical and biological interaction within a marine community. However, study on the dynamics of past community composition and biodiversity in marine lakes is still limited. Benthic foraminifera have been considered as important environmental indicators. This study investigated the diversity and distribution of foraminiferal assemblages from two marine lake sediment cores (MIS-01 and MIS-17) in Misool, Raja Ampat. A total of 6693 benthic foraminiferal specimens, which belong to 34 species were recorded from 36 samples from both cores of the marine lakes. The species were characterized by a low diversity and dominated by hyaline perforated species of Ammonia sp, Brizalina semicarinata, Bolivina striatula, and Bolivina sp Four agglutinated species include Ammobaculites sp, Caronia exilis, Reophax irregularis, Textularia agglutinans and porcelanous imperforated species consist of Fissurina bispinata, Lagena sp, Quinqueloculina carinatastriata, Quinqueloculina sp and Quinqueloculina exsculpta. Downcore variation of the species indicates six major break along the cores which correlates to the six main cluster of the sample with a distinguish depth boundary. Comparison of the assemblages and species diversity shows that the foraminifera from Misool are similar to the ones from Palau. Assessment of individual species and assemblage environmental preferences suggest that oxygen level and salinity might have been the driving factors behind the changes in community assemblages. In comparison to the other community, the temporal partitioning along the cores fits with those based on the mollusk community, particularly at 200 cm depth where diversity was higher than the upper layer.

Marine lakes have been proposed as a unique ecosystem to assess the physical, chemical and biological interaction within a marine community. However, study on the dynamics of past community composition and biodiversity in marine lakes is still limited. Benthic foraminifera have been considered as important environmental indicators. This study investigated the diversity and distribution of foraminiferal assemblages from two marine lake sediment cores (MIS-01 and MIS-17) in Misool, Raja Ampat. A total of 6693 benthic foraminiferal specimens, which belong to 34 species were recorded from 36 samples from both cores of the marine lakes. The species were characterized by a low diversity and dominated by hyaline perforated species of Ammonia sp, Brizalina semicarinata, Bolivina striatula, and Bolivina sp Four agglutinated species include Ammobaculites sp, Caronia exilis, Reophax irregularis, Textularia agglutinans and porcelanous imperforated species consist of Fissurina bispinata, Lagena sp, Quinqueloculina carinatastriata, Quinqueloculina sp and Quinqueloculina exsculpta. Downcore variation of the species indicates six major break along the cores which correlates to the six main cluster of the sample with a distinguish depth boundary. Comparison of the assemblages and species diversity shows that the foraminifera from Misool are similar to the ones from Palau. Assessment of individual species and assemblage environmental preferences suggest that oxygen level and salinity might have been the driving factors behind the changes in community assemblages. In comparison to the other community, the temporal partitioning along the cores fits with those based on the mollusk community, particularly at 200 cm depth where diversity was higher than the upper layer.

The Antarctic Circumpolar Current is nowadays an important ocean current with the highest volume transport of all ocean currents and relatively many of its characteristics are known. However, the estimates on the onset time of the ACC vary widely. The aim of this thesis is therefore to establish a more comprehensive understanding of the onset and development of the ACC. A scientific literature search on the ACC was performed to research if the difference in the defined ages of the ACC is due to a difference in the definition of the ACC within earth scientific subdisciplines, due to a fundamental difference in definitions and descriptions used for the ACC per individual research or due to the fact that the ACC had multiple onsets. Interpretations of the results were later addressed in the discussion section and new hypotheses were established. The outcome of this thesis is that the difference in the estimated age of the ACC is due to a fundamental difference in definitions and descriptions that are used for it. The development of oceanic gateways that led to the current ACC has become generally clear. First, a westbound Antarctic Counter Current was in place at approximately 50-49 Ma. This current did not completely encircle Antarctica, as the Drake Passage was still closed. Between 49 and 41 Ma, but probably after 45 Ma, the first shallow eastward current encircled Antarctica. The first analogue of the modern ACC was established between 37 and 30 Ma. This current was of intermediate to deep depth and it had gained strength since the appearance of the first eastward current. The state of the ACC between 30 and 15 Ma is uncertain, although it is hypothesized that it weakened between 30 and 22 Ma, after which its strength remained approximately the same until about 15 Ma. The ACC gained strength in the period between 15 and 10 Ma, in which a full developed, strong and coherent ACC is reported. Lastly, the modern ACC exists of jet streams that each correspond to fronts

The Antarctic Circumpolar Current is nowadays an important ocean current with the highest volume transport of all ocean currents and relatively many of its characteristics are known. However, the estimates on the onset time of the ACC vary widely. The aim of this thesis is therefore to establish a more comprehensive understanding of the onset and development of the ACC. A scientific literature search on the ACC was performed to research if the difference in the defined ages of the ACC is due to a difference in the definition of the ACC within earth scientific subdisciplines, due to a fundamental difference in definitions and descriptions used for the ACC per individual research or due to the fact that the ACC had multiple onsets. Interpretations of the results were later addressed in the discussion section and new hypotheses were established. The outcome of this thesis is that the difference in the estimated age of the ACC is due to a fundamental difference in definitions and descriptions that are used for it. The development of oceanic gateways that led to the current ACC has become generally clear. First, a westbound Antarctic Counter Current was in place at approximately 50-49 Ma. This current did not completely encircle Antarctica, as the Drake Passage was still closed. Between 49 and 41 Ma, but probably after 45 Ma, the first shallow eastward current encircled Antarctica. The first analogue of the modern ACC was established between 37 and 30 Ma. This current was of intermediate to deep depth and it had gained strength since the appearance of the first eastward current. The state of the ACC between 30 and 15 Ma is uncertain, although it is hypothesized that it weakened between 30 and 22 Ma, after which its strength remained approximately the same until about 15 Ma. The ACC gained strength in the period between 15 and 10 Ma, in which a full developed, strong and coherent ACC is reported. Lastly, the modern ACC exists of jet streams that each correspond to fronts