Modeling larval connectivity of coral reef organisms in the Kenya-Tanzania region

Most coral reef organisms have a bipartite life-cycle; they are site attached to reefs as adults but have pelagic larval stages that allow them to disperse to other reefs. Connectivity among coral reef patches is critical to the survival of local populations of reef organisms, and requires movement across gaps that are not suitable habitat for recruitment. 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 by direct observation alone. An approach that couples ocean circulation models with individual based models (IBMs) of larvae with different degrees of life-history complexity has been previously used to assess connectivity patterns in several coral reef regions (e.g., the Great Barrier Reef (GBR) and the Caribbean). We applied the IBM particle tracking approach to the Kenya-Tanzania region, which exhibits strong seasonality in the alongshore currents due to the influence of the monsoon. A 3-dimensional (3D) ocean circulation model with 2 km horizontal resolution was coupled to IBMs that track virtual larvae released from each of 661 reef habitats, associated with 15 distinct regions. Given that reefs provide homes to numerous species, each with distinctive, and in aggregate very diverse life-histories, several life-history scenarios were modeled to examine the variety of dispersal and connectivity patterns possible. We characterize virtual larvae of Acropora corals and Acanthurus surgeonfish, two coral reef inhabitants with greatly differing pelagic life-histories, to examine the effects of short (50 days) pelagic larval durations (PLD), differences in swimming abilities (implemented as reef perception distances), and active depth keeping in reef connectivity. Acropora virtual larvae were modeled as 3D passive particles with a precompetency period of 4 days, a total PLD of 12 days and a perception distance of 10 m. Acanthurus virtual larvae were characterized by 50 days precompetency period, a total PLD of 72 days and a perception distance of 4 km. Acanthurus virtual larvae were modeled in two ways — as 3D passive particles and including an idealized ontogenetic vertical migration behavior. A range of distances within which larvae were able to perceive reefs and directionally swim to settle on them during the competency period were evaluated. The influence of interannual environmental variations was assessed for two years (2000, 2005) of contrasting physics. The spatial scale of connectivity is much smaller for the short PLD coral, with successful connections restricted to a 1° radius (~100 km) around source reefs. In contrast, long distance connections from the southern to the northernmost reefs (~950 km) are common for virtual Acanthurids. Successful settlement for virtual Acropora larvae was 20% overall, with cross-region recruitment much increased compared to the coral larvae. Approximately 8% of Acropora larvae that successfully settled, recruited to their source reef (self-recruitment), an important proportion compared to only 1-2 % self-recruitment for Acanthurus. These rates and dispersal distances are similar to previous modelling studies of similar species in other coral reef regions and agree well with the few observational studies within the Kenya-Tanzania region

Spatiotemporal scales of larval dispersal and connectivity among oil and gas structures in the North Sea

The ecological role of offshore man-made infrastructure is of growing international interest. By 2030, globally more than 7500 oil and gas platforms could be removed, many of which now host mature hard substrate ecosystems formed by sessile benthic species including sponges, corals and mussels. We investigated the spatiotemporal scales of generalised species dispersal and connectivity among oil and gas structures in the North Sea using strategically designed 3D advective passive particle tracking experiments forced by high resolution (1.8 km, hourly) velocity fields including tide-, density- and wind-driven currents. Trajectories from 2 seasonal releases during mixed winter (February) and stratified summer (July) conditions of 2010 were analysed for a variety of pelagic larval durations (PLDs) spanning 2 to 28 d. Particles dispersed on average 32 km away from their origins after just 5 d, 67 km after 15 d, and 109 km after 28 d, with considerable spatial variability and limited seasonal variations. Short (2 d) PLDs generated highly connected networks over smaller spatial scales, while longer PLDs (28 d) generated less fragmented networks covering a much larger area but with fewer connections. Tidally driven dispersal was isolated using a new method based on the harmonic analysis of the velocity fields: the resulting maximum linear dispersal distances varied from ~4 km in the northern North Sea to ~8 km in the southern North Sea. The present study provides baseline spatiotemporal scales of dispersal and connectivity patterns and optimized relocatable methods to assess connectivity in tidally active shelf seas

Assessing the influence of behavioural parameterisation on the dispersal of larvae in marine systems

Predicting dispersal and quantifying ecological connectivity are increasingly referenced as fundamental to understanding how biodiversity is structured across space and time. Dispersal models can provide insight, but their predictions are influenced by our capacity to simulate the biology and physics known to influence dispersal. In a marine context, vertical swimming behaviour is considered important in influencing the spatial organisation of species across seascapes, but the mechanisms underpinning these movements remain unresolved, making it unclear how best to incorporate behaviour within models. Here, using a 3-D hydrodynamic model coupled with a Lagrangian particle tracker, we show how different modelled larval behaviours, alongside spatial and temporal hydrodynamic changes, influence larval dispersal predictions. Additionally, we compare the application of a novel approach of reverse-engineered larval swimming behaviour against two commonly modelled behaviours: passive dispersal and tidal vertical migration (TVM). We used statistical models (LME and GAM) to test the effects of change in tidal state conditions, season, and planktonic larval duration in conjunction with behavioural parameters on dispersal. For shorter PLDs (i.e., 1 day), we find that passive models match ‘behaving’ model outputs, but for longer PLDs, excluding behaviour leads to overestimates of dispersal; an effect that increases with time. Our results highlight the sensitivity of biophysical models to behavioural inputs, specifically how vertical migration behaviour can significantly reduce dispersal distance - especially for species with longer planktonic durations. This study demonstrates the disproportionate effects that even a single behaviour - vertical swimming - can have on model predictions, our understanding of ecosystem functioning, and ultimately, the ecological coherence of marine systems

On the dynamics of the Zanzibar Channel

Author Posting. © American Geophysical Union, 2015. This article is posted here by permission of American Geophysical Union for personal use, not for redistribution. The definitive version was published in Journal of Geophysical Research: Oceans 120 (2015): 6091–6113, doi:10.1002/2015JC010879.The Zanzibar Channel lies between the mainland of Tanzania and Zanzibar Island in the tropical western Indian Ocean, is about 100 km long, 40 km wide, and 40 m deep, and is essential to local socioeconomic activities. This paper presents a model of the seasonal and tidal dynamics of the Zanzibar Channel based on the Regional Ocean Modeling System (ROMS) and a comparison of the model and observations. The seasonal dynamics of the channel is forced by remote processes and the local wind. Remote forcing creates the East African Coastal Current, a portion of which flows through the channel northward with a seasonally varying magnitude. The local wind enhances this seasonality in the surface Ekman layer, resulting in a stronger northward flow during the southwest monsoon season and a weak northward or occasionally southward flow during the northeast monsoon season. The tidal flows converge and diverge in the center of the channel and reduce the transport in the channel. The remotely forced, wind-forced, and tidal dynamics contain 5%, 3%, and 92% of the total kinetic energy, respectively. Despite their low kinetic energy, the remotely forced and wind-forced flows are most relevant in advecting channel water to the open ocean, which occurs in 19 days at the peak of the southwest monsoon season. The channel is well mixed, except during brief periods in the two rainy seasons, and temporarily cools between December and February. The dispersion of passive tracers is presented as an example of potential model applications.National Science Foundation Grant Numbers: OISE-0827059 , OCE-0550658 , OCE-0851493 , OCE-09274722016-03-1

AMM15: a new high-resolution NEMO configuration for operational simulation of the European north-west shelf

This paper describes the next-generation ocean forecast model for the European north-west shelf, which will become the basis of operational forecasts in 2018. This new system will provide a step change in resolution and therefore our ability to represent small-scale processes. The new model has a resolution of 1.5 km compared with a grid spacing of 7 km in the current operational system. AMM15 (Atlantic Margin Model, 1.5 km) is introduced as a new regional configuration of NEMO v3.6. Here we describe the technical details behind this configuration, with modifications appropriate for the new high-resolution domain. Results from a 30-year non-assimilative run using the AMM15 domain demonstrate the ability of this model to represent the mean state and variability of the region. Overall, there is an improvement in the representation of the mean state across the region, suggesting similar improvements may be seen in the future operational system. However, the reduction in seasonal bias is greater off-shelf than on-shelf. In the North Sea, biases are largely unchanged. Since there has been no change to the vertical resolution or parameterization schemes, performance improvements are not expected in regions where stratification is dominated by vertical processes rather than advection. This highlights the fact that increased horizontal resolution will not lead to domain-wide improvements. Further work is needed to target bias reduction across the north-west shelf region

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

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 of 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 for each component. This advice is compiled from across the NEMO (Nucleus for European Modelling of the Ocean) user community and sets out principles and practises that encompass regional ocean modelling with any model. With detailed and region-specific worked examples in Sects. 3 and 4, the linked companion repositories and DOIs all target NEMOv4. The aim of this review and perspective paper is to broaden the user community skill base and to accelerate development of new configurations in order to increase the time available for exploiting the configurations

Conversion of forest to agriculture increases colored dissolved organic matter in a subtropical catchment and adjacent coastal environment

Land-ocean dissolved organic matter (DOM) transport is a significant and changing term in global biogeochemical cycles which is increasing as a result of human perturbation, including land-use change. Knowledge of the behavior and fate of transported DOM is lacking, particularly in the tropics and subtropics where land-use change is occurring rapidly. We used Parallel Factor (PARAFAC) Analysis to investigate how land-use influenced the composition of the DOM pool along a subtropical land-use gradient (from near-pristine broadleaf forest to agri-urban settings) in Belize, Central America. Three humic-like and two protein-like components were identified, each of which was present across land uses and environments. Land-use mapping identified a strong (R2 = 0.81) negative correlation between broadleaf forest and agri-urban land. All PARAFAC components were positively associated with agri-urban land-use classes (cropland, grassland, and/or urban land), indicating that land-use change from forested to agri-urban exerts influence on the composition of the DOM pool. Humic-like DOM exhibited linear accumulation with distance downstream and behaved conservatively in the coastal zone whilst protein-like DOM exhibited nonlinear accumulation within the main river and nonconservative mixing in coastal waters, indicative of differences in reactivity. We used a hydrodynamic model to explore the potential of conservative humics to reach the region's environmentally and economically valuable coral reefs. We find that offshore corals experience short exposures (10 ± 11 days yr−1) to large (∼120%) terrigenous DOM increases, whilst nearshore corals experience prolonged exposure (113 ± 24 days yr−1) to relatively small (∼30%) terrigenous DOM increases

The small pelagic fishery of the Pemba Channel, Tanzania: what we know and what we need to know for management under climate change

Small pelagic fish, including anchovies, sardines and sardinellas, mackerels, capelin, hilsa, sprats and herrings, are distributed widely, from the tropics to the far north Atlantic Ocean and to the southern oceans off Chile and South Africa. They are most abundant in the highly productive major eastern boundary upwelling systems and are characterised by significant natural variations in biomass. Overall, small pelagic fisheries represent about one third of global fish landings although a large proportion of the catch is processed into animal feeds. Nonetheless, in some developing countries in addition to their economic value, small pelagic fisheries also make an important contribution to human diets and the food security of many low-income households. Such is the case for many communities in the Zanzibar Archipelago and on mainland Tanzania in the Western Indian Ocean. Of great concern in this region, as elsewhere, is the potential impact of climate change on marine and coastal ecosystems in general, and on small pelagic fisheries in particular. This paper describes data and information available on Tanzania's small pelagic fisheries, including catch and effort, management protocols and socio-economic significance

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