Reef fishes and other marine species occur in patchily distributed benthic populations that are interlinked by a larval stage where individuals disperse throughout the pelagic environment. This larval connectivity will play a critical role in determining whether marine protected area (MPA) networks can effectively promote the persistence of increasingly exploited reef fish populations. However, the amount, direction and variation of this connectivity are unknown for most species in most reef ecosystems of conservation concern. Furthermore, connectivity data are difficult to obtain and expensive to measure. Here, we demonstrate that if MPA locations are chosen according to certain easily measurable reef characteristics-'connectivity surrogates'-the resulting MPA networks can maintain reef fish populations and allow fishery harvests superior to random expectation. Surrogates offer managers an opportunity to cheaply consider connectivity into MPA network design while data collection on connectivity is ongoing. We use a high-resolution biophysical model of reef fish larval connectivity on the Great Barrier Reef (GBR) to assess the effectiveness of 5 connectivity surrogates: 2 based on the reef's physical dimensions, 2 based on spawning biomass and 1 based on the efficient representation of conservation features. Biomass attributes generally perform best; however, the appropriate choice depends on the size of the proposed MPA network and the relative value placed on conservation outcomes and fisheries performance. Our results are relatively insensitive to the parameters used in the model and the morphology of the reef system. This robustness suggests that insights from the GBR could provide useful guidance to the management of other reef systems.

The coexistence of multiple species on a smaller number of limiting resources is an enduring ecological paradox. The mechanisms that maintain such biodiversity are of great interest to ecology and of central importance to conservation. We describe and prove a unique and robust mechanism for coexistence: Species that differ only in their dispersal abilities can coexist, if habitat patches are distributed at irregular distances. This mechanism is straightforward and ecologically intuitive, but can nevertheless create complex coexistence patterns that are robust to substantial environmental stochasticity. The Great Barrier Reef (GBR) is noted for its diversity of reef fish species and its complex arrangement of reef habitat. We demonstrate that this mechanism can allow fish species with different pelagic larval durations to stably coexist in the GBR. Further, coexisting species on the GBR often dominate different subregions, defined primarily by cross-shelf position. Interspecific differences in dispersal ability generate similar coexistence patterns when dispersal is influenced by larval behavior and variable oceanographic conditions. Many marine and terrestrial ecosystems are characterized by patchy habitat distributions and contain coexisting species that have different dispersal abilities. This coexistence mechanism is therefore likely to have ecological relevance beyond reef fish.

The global biodiversity crisis has made a priority of understanding biodiversity maintenance in ecological communities. It is increasingly apparent that dispersal patterns can have important effects on such maintenance processes. Nevertheless, most competition theory has focused on a small subset of the possible dispersal patterns in nature. Here, we show that spatially asymmetric dispersal, i.e. the disproportionate transport of propagules towards or away from particular habitat patches in a metacommunity, when it differs between species, can promote the coexistence of competing species even in the absence of environmental heterogeneity among habitat patches. Moreover, when asymmetric dispersal is present, changes in the self-recruitment of competitive dominants and subordinates have important, but fundamentally different, effects on species coexistence. Our results underscore the importance of the interplay between species interactions and dispersal patterns for understanding the effects of habitat fragmentation and for designing regional-scale conservation strategies, such as networks of protected areas.

Any numerical solution of the convective transport equation in an Eulerian framework will exhibit inherent numerical dispersion and solution oscillations. The magnitude of such numerical errors is often so severe as to destroy the value of many computed solutions. A successful and economical algorithm for the convective transport equation in one spatial dimension has been published recently by one of the authors (RJS), in which an exact solution is achieved by means of a moving coordinate system. The present study describes the extension of this work to the more important and challenging two-dimensional case.

Marine Protected Areas (MPAs) are an emerging tool for managing marine resources. Many of the benefits associated with MPAs have been widely investigated and the field is an active area of research in theoretical ecology. One benefit of MPAs that has remained largely overlooked is their value as a tool for learning about the population dynamics of a fishery. We investigate the economic optimality of implementing an MPA, purely for the purpose of obtaining more informative data about a fish population, thereby allowing a better management strategy. A stochastic dynamic programming framework for finding optimal management strategies in this scenario is developed. A simple example is investigated using this framework, with the results illustrating that in some situations the knowledge gained from MPAs can be sufficient to make their creation economically optimal. This establishes an additional benefit of MPAs that should be considered further by fishery managers.

We analysed simulated connectivity patterns for reef fish larvae in the Cairns section of the Great Barrier Reef, and identified 2 key subregions that exhibit regional scale source-sink dynamics. The source and sink were separated latitudinally by a boundary at 16.1 degrees S, with the source subregion lying to the north. Larval transport between the 2 subregions was predominantly unidirectional, from north to south. Only a few local populations, described here as 'gateway reefs', were able to transport larvae from the sink subregion to the source subregion and thus maintain the connectedness of the metapopulation. The northern subregion was able to persist without external larval supply, but when conditions were recruitment limited, the southern Subregion depended on larval supply from the north to persist. The relative autonomy of the northern subregion, and its importance in sustaining the Southern subregion, will influence the effectiveness of conservation efforts.

Modelling ocean circulation in regions of high topographic complexity, notably around groups of reefs and islands, makes large demands on spatial resolution. This problem has largely been overcome by a parametrisation scheme in which the dynamics associated with flow around unresolved reefs and islands are represented by modified momentum equations on a relatively coarse grid. However, the performance of this scheme deteriorates at high velocities, due to the increasing importance of flow separation and eddy formation, processes that are excluded in the original scheme. We extend the earlier model to include a parametrisation of the nonlinear advective terms, and test the performance of the modified scheme in the case of steady flow.

In steady hill-slope seepage problems, the advection diffusion equation can be conformally transformed to a semi-regular solution domain using (?,?) coordinates. Uniform flow in the (?,?) domain reduces the advection diffusion equation to a simpler version with constant coefficients. The solutions depend on finding the eigenvalues (or natural frequencies ) of an (elliptic) Helmholtz equation. In the absence of natural frequencies, this equation can be solved for nonzero boundary conditions using analytic series methods. In this paper, we present a pseudo-spectral approach to solve for the series coefficients. At the natural frequencies, the determinant of the coefficient matrix becomes zero, thus marking the natural frequencies. We present some preliminary results and identify natural frequencies for a set of test problems.

A marina was constructed in the Great Barrier Reef World Heritage Area in close proximity to coral reefs that could be damaged by excess turbidity generated during construction. Since there was uncertainty about both the fate of suspended sediments and their effect on corals, initial water quality constraints were set very conservatively. In order to better understand the movement of suspended sediment during construction, a numerical model study was commissioned using three-dimensional, numerical, hydrodynamic, and Lagrangian particle tracking models. The study was successful in: (1) increasing the understanding of and reducing the uncertainty of sediment dispersal patterns under a range of common forcing conditions; (2) testing the variation in suspended sediment concentrations over sensitive areas for two different outfall locations; (3) offering evidence that a good choice in outfall locations will reduce the threat to corals; and importantly (4) presenting the results in a way that enhanced understanding by nontechnical reef managers. This final result was achieved by creating movies of sediment movement that clearly demonstrated the complex hydrodynamic processes involved with near-coastal water currents. Specific model results showed: (1) that a more seaward outfall increases effluent dispersal away from sensitive areas; (2) the highest concentrations of effluent over sensitive sites occur during no wind and neap tide conditions; and (3) prevailing southeast winds advect effluent offshore, away from sensitive sites.

The well‐known capability of TOPEX/Poseidon altimetry to map sea levels precisely in the deep oceans motivates its application to the topographically complex Coral Sea and NE Australian continental margin. We assess several global tidal models for correcting TOPEX altimetry in the Coral Sea and find CSR3.0 offers good overall performance, based on comparisons of model‐predicted and tide gauge harmonic constituents. Using CSR3.0 tidal corrections, we evaluate residual Sea Surface Height (SSH) Root Mean Square (RMS) variability and residual M2 tidal alias errors. Away from large reefs and islands, CSR3.0 amplitude and phase errors for M2 are typically less than 5 cm and 8 deg, respectively, with RMS tidal errors of 5 cm or less and RMS SSH residuals approximating 10 cm. Since model deficiencies appear in the macro‐tidal region of the Southern Great Barrier Reef Lagoon, near Broad Sound, we employ a high‐resolution hydrodynamic model in this area to compute the tidal corrections. Predicted M2 amplitude and phase in this region are within 3 cm and 5 deg of observations, RMS errors are mostly under 4 cm and coastal RMS SSH residuals are as low as 15 cm, in spite of coastal trapped waves and submesocale eddies in the Lagoon. Daily and monthly smoothed SSH residual time series, respectively, yield optimal lagged correlations with in situ sea level data in the range 0.3–0.9 and 0.6–0.9 for locations spanning the Coral Sea and in the Lagoon. Lag correlations of monthly smoothed Geostrophic Current Anomalies derived from TOPEX SSH gradients with long‐term currents from the continental slope yield optimal correlations of 0.5 and 0.8, respectively, near Jewell (lat 14 deg S) and Myrmidon Reef (19 deg S). Our results demonstrate that low‐frequency sea level and geostrophic current variations can be reliably observed using altimetry over the Coral Sea and NE Australian continental slope, and for selected locations on the continental shelf, if appropriate tide correction models are employed.

In Gulf St Vincent, Australia, the salinity of the head waters can exceed 42 in summer when evaporation is maximum and the rainfall is minimal. A depth-integrated implicit finite difference model is extended to simulate the summer–autumn evolution of salinity, temperature, and density distributions, with climatological evaporation, rainfall, air temperature, and wind stress as inputs. Advection of salt and heat by the density- and wind-driven circulation is modelled by the Quick scheme, whereas horizontal mixing by tidal circulation is parameterised by a dispersion coefficient related to the oscillatory vertical shear. Simulated distributions and seasonal variations compare well with available observations, which feature the flow of highly saline water along the eastern side of the gulf, while the western side is bathed by less saline shelf water. Model results show that, despite the increasing salinity gradients in summer, opposing temperature gradients can stifle the shelfward density currents in the southern parts of the region. Autumn cooling intensifies these density currents so that at the end of the season the flushing of highly saline water, accumulated in the gulf throughout the summer, is enhanced. It was found that the variability in the general circulation brought about by the directional variability in the prevailing winds is an important factor in maintaining the observed salinity distributions in the region.

An improved understanding of the dispersal patterns of marine organisms is a prerequisite for successful marine resource management. For species with dispersing larvae, regional-scale hydrodynamic models provide a means of obtaining results over relevant spatial and temporal scales. In an effort to better understand the role of the physical environment in dispersal, we simulated the transport of reef fish larvae among 321 reefs in and around the Cairns Section of the Great Barrier Reef Marine Park over a period of 20 years. Based on regional-scale hydrodynamics, our models predict the spatial and temporal frequency of significant self-recruitment of the larvae of certain species. Furthermore, the results suggest the importance of a select few local populations in ensuring the persistence of reef fish metapopulations over regional scales.

Events that occur during the pelagic larval stage are thought to be important determinants of reef fish population dynamics. Recent research contradicts the early paradigm of larvae being advected as passive propagules and indicates that many late stage larvae have well-developed sensory and locomotory capabilities. Whether and how larvae use these capabilities to influence their dispersal is unknown. We compare alternative hypotheses regarding larval behavior. Contrary to the trend in dispersal modeling, we focus on larval biology rather than physical oceanographic considerations. Specifically, we present two streams of models: one that describes a return-based strategy and one in which dispersal is a central component. The models depend on different sets of behavioral assumptions for a pomacentrid species and for acanthurids, two groups with contrasting early life histories. Whether dispersal or return-based strategies are favored depends on the efficiency and sustainability of larval swimming methods and the environmental conditions experienced during dispersal. We argue that dispersal models should consider a variety of behavioral hypotheses and that the sensitivity of results to the behavioral assumptions made should be quantified.

A. R. Robinson has proposed a method for studying population growth and advection in the sea. The assumption made by Robinson of a non–divergent velocity field for the biological tracer may not be valid for many situations. When the assumption is valid the biological dynamics of an advected patch are no different from those of a stationary patch, unless a greater degree of spatial structure is incorporated than he considers. The generality and applicability of the model are increased if the assumption of non–divergence can be relaxed. If the velocity field associated with a patch is convergent, as can occur for many biological tracers, then new dynamics arise, both in a Lagrangian sense and when working at the whole–patch level. These new dynamics are explored for four fundamental examples, which could provide new paradigms for spatially explicit models in mathematical ecology.

The goal of our TOPEX/POSEIDON Extended Mission (TPEM) project is to investigate applications of TOPEX radar altimetry to studies of regional and coastal circulation in northern Australian marginal seas. To this end we are developing regional tidal models for computing accurate tidal corrections in coastal settings. The residual low frequency sea level variations and associated currents are compared with in situ observations. These residuals will ultimately be assimilated into regional hydrodynamic models, to serve chiefly as an input to ecological studies.

The field of storm surge modeling has developed and matured considerably over the past 30 years. Several operational surge models have been implemented in Europe over the past decade. These operational advances have been accompanied by research into new areas, chiefly coupled surge-wave models and data assimilation, both of which are covered in this review. Surge-wave models attempt to provide more realistic model physics for the crucial area of air-sea interaction. Assimilation techniques use available data to generate improved numerical solutions, despite model inadequacies. The current activity in surge modeling and related areas is highlighted by the large proportion of recent papers cited in this work. Despite this activity, there is a general recognition that inadequate meteorological inputs remain the weak link in surge modeling. In addition, the advances in midlatitude modeling are not mirrored in the tropics. This is largely due to difficulties in predicting the paths and properties of tropical storms, but it also serves to emphasize the importance that has been attached to storm surge modeling in Europe.