The Columbia River (CR) estuary is characterized by high river discharge and strong tides that generate high velocity flows and sharp density gradients. Its dynamics strongly affects the coastal ocean circulation. Tidal straining in turn modulates the stratification in the estuary. Simulating the hydrodynamics of the CR estuary and plume therefore requires a multi-scale model as both shelf and estuarine circulations are coupled. Such a model has to keep numerical dissipation as low as possible in order to correctly represent the plume propagation and the salinity intrusion in the estuary. Here, we show that the 3D baroclinic discontinuous Galerkin finite element model SLIM 3D is able to reproduce the main features of the CR estuary-to-ocean continuum. We introduce new vertical discretization and mode splitting that allow us to model a region characterized by complex bathymetry and sharp density and velocity gradients. Our model takes into account the major forcings, i.e. tides, surface wind stress and river discharge, on a single multi-scale grid. The simulation period covers the end of spring-early summer of 2006, a period of high river flow and strong changes in the wind regime. SLIM 3D is validated with in-situ data on the shelf and at multiple locations in the estuary and compared with an operational implementation of SELFE. The model skill in the estuary and on the shelf indicate that SLIM 3D is able to reproduce the key processes driving the river plume dynamics, such as the occurrence of bidirectional plumes or reversals of the inner shelf coastal currents.

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The containment of genetically modified (GM) pollen is an issue of significant concern for many countries. For crops that are bee-pollinated, model predictions of outcrossing rates depend on the movement hypothesis used for the pollinators. Previous work studying pollen spread by honeybees, the most important pollinator worldwide, was based on the assumption that honeybee movement can be well approximated by Brownian motion. A number of recent studies, however, suggest that pollinating insects such as bees perform Lévy flights in their search for food. Such flight patterns yield much larger rates of spread, and so the Brownian motion assumption might significantly underestimate the risk associated with GM pollen outcrossing in conventional crops. In this work, we propose a mechanistic model for pollen dispersal in which the bees perform truncated Lévy flights. This assumption leads to a fractional-order diffusion model for pollen that can be tuned to model motion ranging from pure Brownian to pure Lévy. We parametrize our new model by taking the same pollen dispersal dataset used in Brownian motion modelling studies. By numerically solving the model equations, we show that the isolation distances required to keep outcrossing levels below a certain threshold are substantially increased by comparison with the original predictions, suggesting that isolation distances may need to be much larger than originally thought.@en

With the second largest outflow in the world and one of the widest hydrological basins, the Congo River is of a major importance both locally and globally. However, relatively few studies have been conducted on its hydrology, as compared to other great rivers such as the Amazon, Nile, Yangtze, or Mississippi. The goal of this study is therefore to help fill this gap and provide the first high-resolution simulation of the Congo river-estuary-coastal sea continuum. To this end, we are using a discontinuous-Galerkin finite element marine model that solves the two-dimensional depth-averaged shallow water equations on an unstructured mesh. To ensure a smooth transition from river to coastal sea, we have considered a model that encompasses both hydrological and coastal ocean processes. An important difficulty in setting up this model was to find data to parameterize and validate it, as it is a rather remote and understudied area. Therefore, an important effort in this study has been to establish a methodology to take advantage of all the data sources available including nautical charts that had to be digitalized. The model surface elevation has then been validated with respect to an altimetric database. Model results suggest the existence of gyres in the vicinity of the river mouth that have never been documented before. The effect of those gyres on the Congo River dynamics has been further investigated by simulating the transport of Lagrangian particles and computing the water age.@en

Aim Connectivity is a key determinant of coral reef resilience. However, connectivity models rarely account for deep or submerged reefs, despite their widespread occurrence in many coral reef provinces. Here, we model coral larval connectivity among submerged and near-sea-surface (NSS) reefs, investigate differences in dispersal potential for coral larvae from these differing reef morphologies and estimate the potential for deeper reef habitats (> 10 m) to provide a source of larvae to shallower reef habitats (< 10 m). Location Great Barrier Reef, Australia. Methods We used two newly developed, high-resolution models to identify the location and spatial extent of submerged and NSS reefs and to simulate oceanographic currents (‘SLIM’) affecting larval dispersal. Dispersal patterns for five depth-generalist coral species with differing life histories and dispersal potential were modelled using an individual-based model (IBM). Results Near-sea-surface reefs were the largest source of larvae successfully settling, but submerged reefs exported a greater proportion of larvae per unit area to other reefs. Larvae originating from submerged reefs also dispersed greater distances. Recruits on shallow-water reef habitats primarily originated from other shallow areas, but two-way connectivity did occur between deep and shallow habitats. Empirical data indicate that long-term coral cover has declined most steeply on the shallow habitats predicted by our model to be highly dependent on other shallow habitats for recruits. Main conclusions Submerged reefs may contribute significantly to larval production and should therefore be considered in connectivity analyses. The hydrodynamic environment on submerged reefs results in larvae dispersing greater distances, potentially increasing their importance as source reefs following disturbances. Deep reef habitats are generally less exposed to disturbances and could therefore constitute an important larval source to some shallow habitats following disturbances. Given the importance of connectivity to coral reef resilience, greater attention should be afforded to identifying and protecting submerged reefs and other deeper habitats.@en