There is growing interest in models of marine ecosystems that deal with the effects of climate change through the higher trophic levels. Such end-to-end models combine physicochemical oceanographic descriptors and organisms ranging from microbes to higher-trophic-level (HTL) organisms, including humans, in a single modeling framework. The demand for such approaches arises from the need for quantitative tools for ecosystem-based management, particularly models that can deal with bottom-up and top-down controls that operate simultaneously and vary in time and space and that are capable of handling the multiple impacts expected under climate change. End-to-end models are now feasible because of improvements in the component submodels and the availability of sufficient computing power. We discuss nine issues related to the development of end-to-end models. These issues relate to formulation of the zooplankton submodel, melding of multiple temporal and spatial scales, acclimation and adaptation, behavioral movement, software and technology, model coupling, skill assessment, and interdisciplinary challenges. We urge restraint in using end-to-end models in a true forecasting mode until we know more about their performance. End-to-end models will challenge the available data and our ability to analyze and interpret complicated models that generate complex behavior. End-to-end modeling is in its early developmental stages and thus presents an opportunity to establish an open-access, community-based approach supported by a suite of true interdisciplinary efforts

A new operational ocean forecast system, the Atlantic Margin Model implementation of the Forecast Ocean Assimilation Model (FOAM-AMM), has been developed for the European North West Shelf (NWS). An overview of the system is presented including shelf specific developments of the physical model, the Nucleus for European Modeling of the Ocean (NEMO), and the Sea Surface Temperature (SST) data assimilation scheme. Initial validation is presented of the tides and model SST. The SST skill of the system is significantly improved by the data assimilation scheme. Finally, an analysis of the seasonal tidal mixing fronts shows that these in general agree well with observation, but data assimilation does not significantly alter their positions. Lead Author's Biography In 2004, after completing a PhD. in computational fluid dynamics, Enda O'Dea joined the Met Office to work in ocean modelling. He now develops ocean forecast models in the Ocean Forecasting Research and Development (OFRD) group. Recently, the group has overseen the transition from a POLCOMS based forecast system to a NEMO based forecast system for the shelf seas around the U.K. Enda's principal research area is in shelf seas forecasting and interests include the dynamics of tides, seasonal stratification, shelf slope currents and regions of fresh water influence.

Many factors have been implicated in the decline of Delta Smelt Hypomesus transpacificus in the upper SanFrancisco Estuary, and the importance of each factor is difficult to determine using field data alone. We describe a spatially explicit, individual-based population model of Delta Smelt configured for the upper estuary. The model followed the reproduction, growth, mortality, and movement of individuals over their entire life cycle on the same spatial grid of cells as the Delta Simulation Model (DSM2) hydrodynamics model. Daily values of water temperature, salinity, and densities of six zooplankton prey types were represented on the spatial grid. Reproduction was evaluated daily, and new individuals were introduced into the model as yolk sac larvae. Growth of feeding individuals was based on bioenergetics and zooplankton densities. Mortality sources included natural mortality, starvation, and entrainment in water diversion facilities. Movement of larvae was determined using a particle tracking model, while movement of juveniles and adults was based on salinity. Simulations were performed for 1995-2005. The baseline simulation was generally consistent with the available data. Predicted daily fractions of larvae entrained and annual fractions of adults entrained were similar in magnitude to data-based estimates but showed less interannual variation. Interannual differences in mean length at age 1 had large effects on maturity and subsequent egg production. Predicted and observed spatial distributions in the fall showed moderately good agreement for extremely low-and high-outflow years. As indicated by the population growth rate, 1998 was the best year and 2001 was the worst year. Water year 1998 (i.e., October 1997-September 1998) was characterized by fast growth in fall 1997, low entrainment, and high stage-specific survival rates, whereas water year 2001 had opposite conditions. Our analysis further shows how multiple factors can operate simultaneously to result in the decline in abundance of Delta Smelt.

Field-derived growth rates (RNA-DNA based) of cod (Gadus morhua) larvae collected on the southern flank of Georges Bank were higher on average in May 1993 than May 1994, despite the apparent higher abundance of potential prey in 1994. A biophysical modeling study is presented here in which factors are examined that may have led to the difference in population mean growth. A one-dimensional physical model, forced by winds and tides, was used to simulate the vertical structure (of currents, temperature field, and turbulent kinetic energy dissipation rate) following a column of water in a Lagrangian sense at a site on the southern flank of Georges Bank over 5-day periods in late May of 1993 and 1994. The biophysical model and observed zooplankton abundance allowed us to explore the vertical structure and temporal (hourly) evolution of feeding and growth for cod larvae in relation to environmental conditions. Our trophodynamic model is improved over previous versions and now includes the effect of light on larval feeding response, as well as the effect of temperature on larval metabolic costs, ingestion, and digestion. Larval prey profiles, comprising four copepod species, were used from a time series of 1/4-m 2 MOCNESS tows to define the prey field. Data from a collateral time-series of larval gut contents (1-m 2 MOCNESS tows) was used to define maximum ingestion (satiation level) and prey selection. Model outputs provide depth-dependent estimates of growth, prey biomass ingested, larval length, and larval weight. Watercolumn growth-rate profiles were made for four size classes of larvae (5, 6, 7 and 9 mm) under the environmental conditions observed in May 1993 and 1994. A weighted-mean growth rate based on the mean vertical distribution of larvae was estimated for each size class. In all cases, when using all available potential prey, the model-derived 1994 growth rates were higher (by 3-6% day )1 ) than those for 1993. However, simulations in which 7-mm larvae followed the field-derived weighted mean depth over the sampling period, and were limited to their preferred Pseudocalanus prey, resulted in average growth of 12.2% day )1 for 1993 and 9.7% day )1 for 1994. These compared closely to the field growth means of 11.3% day )1 in 1993 and 9.8% day )1 in 1994. Thus, the lower observed growth in May 1994 may have resulted from depth-dependent food limitation and prey-selectivity coupled with the greater metabolic costs induced by the higher temperature that year.

Marine legislation is becoming more complex and marine ecosystem-based management is specified in national and regional legislative frameworks. Shelf-seas community and ecosystem models (hereafter termed ecosystem models) are central to the delivery of ecosystem-based management, but there is limited uptake and use of model products by decision makers in Europe and the UK in comparison with other countries. In this study, the challenges to the uptake and use of ecosystem models in support of marine environmental management are assessed using the UK capability as an example. The UK has a broad capability in marine ecosystem modelling, with at least 14 different models that support management, but few examples exist of ecosystem modelling that underpin policy or management decisions. To improve understanding of policy and management issues that can be addressed using ecosystem models, a workshop was convened that brought together advisors, assessors, biologists, social scientists, economists, modellers, statisticians, policy makers, and funders. Some policy requirements were identified that can be addressed without further model development including: attribution of environmental change to underlying drivers, integration of models and observations to develop more efficient monitoring programmes, assessment of indicator performance for different management goals, and the costs and benefit of legislation. Multi-model ensembles are being developed in cases where many models exist, but model structures are very diverse making a standardised approach of combining outputs a significant challenge, and there is a need for new methodologies for describing, analysing, and visualising uncertainties. A stronger link to social and economic systems is needed to increase the range of policy-related questions that can be addressed. It is also important to improve communication between policy and modelling communities so that there is a shared understanding of the strengths and limitations of ecosystem models