Reproducible and relocatable regional ocean modelling: Fundamentals and practices

In response to an increasing demand for bespoke or tailored regional ocean modelling configurations, we outline fundamental principles and practices that can expedite the process to generate new configurations. The paper develops the principle of Reproducibility and advocates adherence by presenting benefits to the community and user. The elements to this principle are reproducible workflows and standardised assessment, with additional effort over existing working practices being balanced against the added value generated. The paper then decomposes the complex build process, for a new regional ocean configuration, into stages and presents guidance, advice and insight on each component. This advice is compiled from across the user community, is presented in the context of NEMOv4, though aims to transcend NEMO version. Detail and region specific worked examples are linked in companion repositories and DOIs. The aim is to broaden the user community skill base, and to accelerate development of new configurations in order to increase available time exploiting the configurations

Lagrangian ocean analysis: fundamentals and practices

Lagrangian analysis is a powerful way to analyse the output of ocean circulation models and other ocean velocity data such as from altimetry. In the Lagrangian approach, large sets of virtual particles are integrated within the three-dimensional, time-evolving velocity fields. Over several decades, a variety of tools and methods for this purpose have emerged. Here, we review the state of the art in the field of Lagrangian analysis of ocean velocity data, starting from a fundamental kinematic framework and with a focus on large-scale open ocean applications. Beyond the use of explicit velocity fields, we consider the influence of unresolved physics and dynamics on particle trajectories. We comprehensively list and discuss the tools currently available for tracking virtual particles. We then showcase some of the innovative applications of trajectory data, and conclude with some open questions and an outlook. The overall goal of this review paper is to reconcile some of the different techniques and methods in Lagrangian ocean analysis, while recognising the rich diversity of codes that have and continue to emerge, and the challenges of the coming age of petascale computing

Modeled Larval Connectivity Patterns in two Coral Reef Regions : the Western Caribbean and the Kenyan-Tanzanian Shelf

Tropical coral reef ecosystems are very important from both the ecological and economical points of view. However, they are also particularly fragile, and have been declining in recent years in most regions of the world, since they are highly susceptible to anthropogenic stressors operating at global scales (e.g., global warming and ocean acidification) and local scales (e.g., pollution/eutrophication, fishing, overcommercialization for recreation). Coral reef ecosystems are complex communities with very high species diversity. Most reef species have a bipartite life history with a planktonic larval stage and a benthic associated adult life. Therefore most adult reef organisms are distributed in metapopulations connected by pelagic larvae that disperse subject to the ocean currents. Knowledge of population connectivity among individual reef habitats within a broader geographic region of coral reefs has been identified as key to developing efficient spatial management strategies to protect marine ecosystems. The study of larval connectivity of marine organisms is a complex multidisciplinary challenge that is difficult to address with direct observations. This research examines the temporal and spatial, physical and ecological processes influencing connectivity of two important coral reef genera among isolated reef habitats within two regions: the Kenyan-Tanzanian and the Western Caribbean coasts. High resolution ocean circulation models were developed for each region and coupled to individual based models (IBM) that track particles (virtual larvae) released from each reef habitat. The connectivity patterns for two coral reef species groups having contrasting larval behavior and development duration where characterized in the two study regions: Acropora, a genus of branching corals with passive larvae and fast development (pelagic larval duration (PLD)<12 days), and Acanthurus, a genus of highly mobile, herbivorous fish, with long PLD (>50 days). Additional simulations were done to represent better the complexity of the Acanthurus larval life: one experiment included an idealized ontogenetic vertical migration behavior; another experiment examined how temperature-determined larval duration influenced trajectories and settlement patterns. The more complicated behavioral and development models were evaluated by comparing connectivity matrices to the passively transported case. To investigate interannual variations in connectivity patterns and percentage of successful settlement experiments were done for two contrasting years 2000 and 2005. Environmental seasonal and interannual variability in the ocean circulation models was analyzed to detect the mechanisms controlling connectivity in the two regions. The connectivity patterns and the mechanisms causing them were compared among the two study regions. Results are interpreted in the context of marine spatial management, describing the implications of the modeled connectivity patterns for currently established Marine Protected Areas. The connectivity patterns, and the processes controlling connectivity for different taxa, provide policy relevant scientific information that enables managers and decision-makers to make more informed choices regarding the size, spacing and optimal spatial design of marine protected networks

Mayorga-AdameCharacterizingCirculationKenyan.pdf

The Kenyan-Tanzanian coastal region in the western Indian Ocean faces several environmental challenges including coral reef conservation, fisheries management, coastal erosion, and nearshore pollution. The region lacks hydrodynamic records and oceanographic studies at adequate spatial and temporal scales to provide information relevant to the local environmental issues. We have developed a 4 km horizontal resolution ocean circulation model of the region: the Kenyan-Tanzanian Coastal Model (KTCM) that provides coastal circulation and hydrography with higher resolution than previous models and observational studies of this region. Comparisons to temperature profiles, satellite-derived sea surface temperature and sea surface height anomaly fields, indicate that the model reproduces the main features of the regional circulation, while greatly increasing the details of the nearshore circulation. We describe the seasonal ocean circulation and hydrography of the Kenyan-Tanzanian coastal region based on a climatology of 8 years (2000–2007) of the KTCM simulations. The regional monsoon seasonality produces two distinct coastal circulation regimes: (1) during December–March, there are relatively sluggish shelf flows and (2) during April–November, there are strong northward transports. Simulations from the model will be useful for examining dispersal of pollutants and spatial connectivity of coral reef species.Keywords: coastal ocean circulation model, monsoon seasonality, Kenya Tanzania coastal circulation, western Indian Ocea