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Tommasi, D, Stock CA, Hobday AJ, Methot R, Kaplan IC, Eveson JP, Holsman K, Miller TJ, Gaichas S, Gehlen M, Pershing A, Vecchi GA, Msadek R, Delworth T, Eakin CM, Haltuch MA, Seferian R, Spillman CM, Hartog JR, Siedlecki S, Samhouri JF, Muhling B, Asch RG, Pinsky ML, Saba VS, Kapnick SB, Gaitan CF, Rykaczewski RR, Alexander MA, Xue Y, Pegion KV, Lynch P, Payne MR, Kristiansen T, Lehodey P, Werner FE.  2017.  Managing living marine resources in a dynamic environment: The role of seasonal to decadal climate forecasts. Progress in Oceanography. 152:15-49.   10.1016/j.pocean.2016.12.011   AbstractWebsite

Recent developments in global dynamical climate prediction systems have allowed for skillful predictions of climate variables relevant to living marine resources (LMRs) at a scale useful to understanding and managing LMRs. Such predictions present opportunities for improved LMR management and industry operations, as well as new research avenues in fisheries science. LMRs respond to climate variability via changes in physiology and behavior. For species and systems where climate-fisheries links are well established, forecasted LMR responses can lead to anticipatory and more effective decisions, benefitting both managers and stakeholders. Here, we provide an overview of climate prediction systems and advances in seasonal to decadal prediction of marine-resource relevant environmental variables. We then describe a range of climate-sensitive LMR decisions that can be taken at lead-times of months to decades, before highlighting a range of pioneering case studies using climate predictions to inform LMR decisions. The success of these case studies suggests that many additional applications are possible. Progress, however, is limited by observational and modeling challenges. Priority developments include strengthening of the mechanistic linkages between climate and marine resource responses, development of LMR models able to explicitly represent such responses, integration of climate driven LMR dynamics in the multi-driver context within which marine resources exist, and improved prediction of ecosystem relevant variables at the fine regional scales at which most marine resource decisions are made. While there are fundamental limits to predictability, continued advances in these areas have considerable potential to make LMR managers and industry decision more resilient to climate variability and help sustain valuable resources. Concerted dialog between scientists, LMR managers and industry is essential to realizing this potential. (C) 2017 Elsevier Ltd. All rights reserved.

Collie, JS, Botsford LW, Hastings A, Kaplan IC, Largier JL, Livingston PA, Plaganyi E, Rose KA, Wells BK, Werner FE.  2016.  Ecosystem models for fisheries management: finding the sweet spot. Fish and Fisheries. 17:101-125.   10.1111/faf.12093   AbstractWebsite

The advent of an ecosystem-based approach dramatically expanded the scope of fisheries management, creating a critical need for new kinds of data and quantitative approaches that could be integrated into the management system. Ecosystem models are needed to codify the relationships among drivers, pressures and resulting states, and to quantify the trade-offs between conflicting objectives. Incorporating ecosystem considerations requires moving from the single-species models used in stock assessments, to more complex models that include species interactions, environmental drivers and human consequences. With this increasing model complexity, model fit can improve, but parameter uncertainty increases. At intermediate levels of complexity, there is a sweet spot' at which the uncertainty in policy indicators is at a minimum. Finding the sweet spot in models requires compromises: for example, to include additional component species, the models of each species have in some cases been simplified from age-structured to logistic or bioenergetic models. In this paper, we illuminate the characteristics, capabilities and short-comings of the various modelling approaches being proposed for ecosystem-based fisheries management. We identify key ecosystem needs in fisheries management and indicate which types of models can meet these needs. Ecosystem models have been playing strategic roles by providing an ecosystem context for single-species management decisions. However, conventional stock assessments are being increasingly challenged by changing natural mortality rates and environmentally driven changes in productivity that are observed in many fish stocks. Thus, there is a need for more tactical ecosystem models that can respond dynamically to changing ecological and environmental conditions.

Rose, KA, Fiechter J, Curchitser EN, Hedstrom K, Bernal M, Creekmore S, Haynie A, Ito S, Lluch-Cota S, Megrey BA, Edwards CA, Checkley D, Koslow T, McClatchie S, Werner F, MacCall A, Agostini V.  2015.  Demonstration of a fully-coupled end-to-end model for small pelagic fish using sardine and anchovy in the California Current. Progress in Oceanography. 138:348-380.   10.1016/j.pocean.2015.01.012   AbstractWebsite

We describe and document an end-to-end model of anchovy and sardine population dynamics in the California Current as a proof of principle that such coupled models can be developed and implemented. The end-to-end model is 3-dimensional, time-varying, and multispecies, and consists of four coupled sub-models: hydrodynamics, Eulerian nutrient-phytoplankton-zooplankton (NPZ), an individual-based full life cycle anchovy and sardine submodel, and an agent-based fishing fleet submodel. A predator roughly mimicking albacore was included as individuals that consumed anchovy and sardine. All submodels were coded within the ROMS open-source community model, and used the same resolution spatial grid and were all solved simultaneously to allow for possible feedbacks among the submodels. We used a super-individual approach and solved the coupled models on a distributed memory parallel computer, both of which created challenging but resolvable bookkeeping challenges. The anchovy and sardine growth, mortality, reproduction, and movement, and the fishing fleet submodel, were each calibrated using simplified grids before being inserted into the full end-to-end model. An historical simulation of 1959-2008 was performed, and the latter 45 years analyzed. Sea surface height (SSH) and sea surface temperature (SST) for the historical simulation showed strong horizontal gradients and multi-year scale temporal oscillations related to various climate indices (PDO, NPGO), and both showed responses to ENSO variability. Simulated total phytoplankton was lower during strong El Nino events and higher for the strong 1999 La Nina event. The three zooplankton groups generally corresponded to the spatial and temporal variation in simulated total phytoplankton. Simulated biomasses of anchovy and sardine were within the historical range of observed biomasses but predicted biomasses showed much less inter-annual variation. Anomalies of annual biomasses of anchovy and sardine showed a switch in the mid-1990s from anchovy to sardine dominance. Simulated averaged weights- and lengths-at-age did not vary much across decades, and movement patterns showed anchovy located close to the coast while sardine were more dispersed and farther offshore. Albacore predation on anchovy and sardine was concentrated near the coast in two pockets near the Monterey Bay area and equatorward of Cape Mendocino. Predation mortality from fishing boats was concentrated where sardine age-1 and older individuals were located close to one of the five ports. We demonstrated that it is feasible to perform multi-decadal simulations of a fully-coupled end-to-end model, and that this can be done for a model that follows individual fish and boats on the same 3-dimensional grid as the hydrodynamics. Our focus here was on proof of principle and our results showed that we solved the major technical, bookkeeping, and computational issues. We discuss the next steps to increase computational speed and to include important biological differences between anchovy and sardine. In a companion paper (Fiechter et al., 2015), we further analyze the historical simulation in the context of the various hypotheses that have been proposed to explain the sardine and anchovy cycles. (C) 2015 Elsevier Ltd. All rights reserved.

Levin, PS, Kelble CR, Shuford RL, Ainsworth C, deReynier Y, Dunsmore R, Fogarty MJ, Holsman K, Howell EA, Monaco ME, Oakes SA, Werner F.  2014.  Guidance for implementation of integrated ecosystem assessments: a US perspective. ICES Journal of Marine Science. 71:1198-1204.   10.1093/icesjms/fst112   AbstractWebsite

Ecosystem-based management (EBM) has emerged as a basic approach for managing human activities in marine ecosystems, with the aim of recovering and conserving marine ecosystems and the services they deliver. Integrated ecosystem assessments (IEAs) further the transition of EBM from principle to practice by providing an efficient, transparent means of summarizing the status of ecosystem components, screening and prioritizing potential risks, and evaluating alternative management strategies against a backdrop of environmental variability. In this paper, we draw upon lessons learned from the US National Oceanic and Atmospheric Administration's IEA programme to outline steps required for IEA implementation. We provide an overview of the conceptual framework for IEAs, the practical constraints that shape the structure of individual IEAs, and the uses and outcomes of IEAs in support of EBM.

Fogarty, MJ, Botsford LW, Werner FE.  2013.  Legacy of the US GLOBEC program: current and potential contributions to marine ecosystem-based management. Oceanography. 26:116-127.   10.5670/oceanog.2013.79   AbstractWebsite

Management of living marine resources is undergoing a profound transition toward a more holistic, ecosystem-based paradigm. The interplay of climate and environmental forcing, ecosystem structure and function, and human influences and requirements shape the dynamics of these systems in complex ways. The US Global Ocean Ecosystem Dynamics (GLOBEC) program was designed to unravel the elements of this complexity and to forge the tools needed to explore the scope for predictability of ecosystem change in a rapidly changing ocean. As a basic science program, US GLOBEC established new standards in ecological monitoring, technological development, and coupled bio-physical modeling of marine systems. Its legacy goes beyond these fundamental achievements, however, through the realized and potential importance of the GLOBEC approach and findings in resource management. Development of the US GLOBEC program considerably predated the formal adoption of strategies for ecosystem-based management of coastal and marine systems in the United States under the aegis of the National Ocean Policy. The GLOBEC strategy and its resulting products and tools have nonetheless proven extremely valuable in moving toward the goal of operational marine ecosystem-based management. The GLOBEC selection of target species of direct relevance to management (including economically important species and those with special conservation status) underscored the recognized need to provide results of the highest scientific caliber while also meeting broader societal needs and objectives for sustainable resource management. Here, we trace some of the current applications of GLOBEC science in resource management (including the extension of single species management strategies to incorporate climate forcing and the use of broader ecosystem models) and point to its potential to further shape the evolution of marine ecosystem-based management.

Stock, CA, Alexander MA, Bond NA, Brander KM, Cheung WWL, Curchitser EN, Delworth TL, Dunne JP, Griffies SM, Haltuch MA, Hare JA, Hollowed AB, Lehodey P, Levin SA, Link JS, Rose KA, Rykaczewski RR, Sarmiento JL, Stouffer RJ, Schwing FB, Vecchi GA, Werner FE.  2011.  On the use of IPCC-class models to assess the impact of climate on Living Marine Resources. Progress in Oceanography. 88:1-27.   10.1016/j.pocean.2010.09.001   AbstractWebsite

The study of climate impacts on Living Marine Resources (LMRs) has increased rapidly in recent years with the availability of climate model simulations contributed to the assessment reports of the Intergovernmental Panel on Climate Change (IPCC). Collaboration between climate and LMR scientists and shared understanding of critical challenges for such applications are essential for developing robust projections of climate impacts on LMRs. This paper assesses present approaches for generating projections of climate impacts on LMRs using IPCC-class climate models, recommends practices that should be followed for these applications, and identifies priority developments that could improve current projections. Understanding of the climate system and its representation within climate models has progressed to a point where many climate model outputs can now be used effectively to make LMR projections. However, uncertainty in climate model projections (particularly biases and inter-model spread at regional to local scales), coarse climate model resolution, and the uncertainty and potential complexity of the mechanisms underlying the response of LMRs to climate limit the robustness and precision of LMR projections. A variety of techniques including the analysis of multi-model ensembles, bias corrections, and statistical and dynamical downscaling can ameliorate some limitations, though the assumptions underlying these approaches and the sensitivity of results to their application must be assessed for each application. Developments in LMR science that could improve current projections of climate impacts on LMRs include improved understanding of the multi-scale mechanisms that link climate and LMRs and better representations of these mechanisms within more holistic LMR models. These developments require a strong baseline of field and laboratory observations including long time series and measurements over the broad range of spatial and temporal scales over which LMRs and climate interact. Priority developments for IPCC-class climate models include improved model accuracy (particularly at regional and local scales), inter-annual to decadal-scale predictions, and the continued development of earth system models capable of simulating the evolution of both the physical climate system and biosphere. Efforts to address these issues should occur in parallel and be informed by the continued application of existing climate and LMR models. Published by Elsevier Ltd.

Kishi, MJ, Ito S-I, Megrey BA, Rose KA, Werner FE.  2011.  A review of the NEMURO and NEMURO.FISH models and their application to marine ecosystem investigations. Journal of Oceanography. 67:3-16.   10.1007/s10872-011-0009-4   AbstractWebsite

The evolution of the North Pacific Ecosystem Model for Understanding Regional Oceanography (NEMURO) family of models to study marine ecosystems is reviewed. Applications throughout the North Pacific have shown the models to be robust and to be able to reproduce 1D, 2D and 3D components of nutrient, carbon cycle and biogeochemical cycles as well as aspects of the lower trophic levels ecosystem (phyto- and zooplankton). NEMURO For Including Saury and Herring, an extension that includes higher trophic levels, can be run uncoupled or coupled to NEMURO. In the uncoupled mode, the growth and weight of an individual fish is computed using plankton densities simulated by NEMURO but with no feedback between fish consumption and plankton mortality. In the coupled mode, the feeding, growth and weight of a representative fish are computed, and prey removals due to feeding by fish appear as mortality terms on the prey. The NEMURO family of models continues to evolve, including effects of the microbial loop and iron limitation at lower trophic levels, and full life cycle, multi-species and multi-generational simulations at higher trophic levels. We outline perspectives for future end-to-end modeling efforts that can be used to study marine ecosystems in response to global environmental change.

Barange, M, Allen I, Allison EC, Badjeck M-C, Blanchard J, Drakeford B, Dulvy NK, Harle J, Holmes RC, Holt JW, Jennings S, Lowe J, Merino G, Mullon C, Pilling G, Rodwell L, Tompkins E, Werner F.  2011.  Predicting the impacts and socio-economic consequences of climate change on global marine exosystems and fisheries: the QUEST_Fish Framework. World fisheries : a social-ecological analysis. ( Ommer R, Ed.).:31-59., Ames, Iowa Chichester, West Sussex, UK: Wiley-Blackwell Abstract
McGillicuddy, Dennis J., J, deYoung B, Doney SC, Glibert PM, Stammer D, Werner FE.  2010.  Models: Tools for synthesis in international oceanographic research programs. Oceanography. 23:126-139.   10.5670/oceanog.2010.28   AbstractWebsite
Perry, IR, Ommer RE, Barange M, Werner F.  2010.  The challenge of adapting marine social-ecological systems to the additional stress of climate change. Current Opinion in Environmental Sustainability. 2:356-363.   10.1016/j.cosust.2010.10.004   AbstractWebsite

A broad marine policy goal is to maintain healthy marine social-ecological systems that sustain desirable ecosystem services and support human livelihoods. Marine social-ecological systems are already stressed by a number of environmental factors and the impacts of globalisation. Climate change is an additional stress that may push marine social-ecological systems beyond the ranges of past variability to which they have become adapted. Human social systems have well-developed strategies for dealing with variability within their normal ranges of experience, although these capacities are not distributed homogeneously around the globe. This paper addresses the additional impacts of climate change on marine social-ecological systems that are focussed around fishing. For example, human social fishing systems dealing with high variability upwelling systems with rapidly reproducing fish species may have greater capacities to adjust to the additional stress of climate change than human social fishing systems focussed on longer-lived and generally less variable species. The details of local impacts of climate change and its interactions with existing stresses on marine social-ecological systems are difficult to predict but will lead to more extreme events and increased uncertainty. Management must strive to enhance the adaptive capacities of these systems to uncertainty and change. Primary challenges are to address non-climate change stresses such as overfishing and how they may interact with climate change to produce surprises, and to recognise that multiple interacting time, space and organisational scales make identification and resolution of impacts difficult. Additional challenges are to develop integrated observing and modelling systems for the full social-ecological system so as to quickly recognise changes, to enhance communications with stakeholders, and to develop flexible institutions that can adjust rapidly to new circumstances.

deYoung, B, Werner FE, Batchelder H, Carlotti F, Fiksen O, Hofmann EE, Kim S, Kishi MJ, Yamazaki H.  2010.  Dynamics of marine ecosystems: integration through models of physical-biological interactions. Marine Ecosystems and Global Change. ( Barange M, Field JG, Harris RP, Hofmann EE, Perry RI, Werner FE, Eds.).:89-128., New York: Oxford University Press AbstractWebsite
Hofmann, EE, Barange M, Field JG, Harris RP, Perry IR, Werner FE.  2010.  Marine ecosystems and global change: a synthesis. Marine Ecosystems and Global Change. ( Barange M, Field JG, Harris RP, Hofmann EE, Perry RI, Werner FE, Eds.).:323-336., New York: Oxford University Press AbstractWebsite
Chassignet, EP, Hurlburt HE, Metzger JE, Smedstad OM, Cummings JA, Halliwell GR, Bleck R, Baraille R, Wallcraft AJ, Lozano C, Tolman HL, Srinivasan A, Hankin S, Cornillon P, Weisberg R, Barth A, He R, Werner F, Wilkin J.  2009.  US GODAE Global Ocean Prediction with the HYbrid Coordinate Ocean Model (HYCOM). Oceanography. 22:64-75.   10.5670/oceanog.2009   AbstractWebsite

During the past five to ten years, a broad partnership of institutions under NOPP sponsorship has collaborated in developing and demonstrating the performance and application of eddy-resolving, real-time global- and basin-scale ocean prediction systems using the HYbrid Coordinate Ocean Model (HYCOM). The partnership represents a broad spectrum of the oceanographic community, bringing together academia, federal agencies, and industry/commercial entities, and spanning modeling, data assimilation, data management and serving, observational capabilities, and application of HYCOM prediction system outputs. In addition to providing real-time, eddy-resolving global- and basin-scale ocean prediction systems for the US Navy and NOAA, this project also offered an outstanding opportunity for NOAA-Navy collaboration and cooperation, ranging from research to the operational level. This paper provides an overview of the global HYCOM ocean prediction system and highlights some of its achievements. An important outcome of this effort is the capability of the global system to provide boundary conditions to even higher-resolution regional and coastal models.

Freon, P, Werner F, Chavez FP.  2009.  Conjectures on future climate effects on marine ecosystems dominated by small pelagic fish. Climate Change and Small Pelagic Fish. :312-343. AbstractWebsite

Direct effects of humans on the environment (agricultural practices, fishing) have been evident for hundreds of years. Some of these direct effects (increased carbon dioxide in the atmosphere) are now spilling over into the climate system creating uncertainty regarding the future of marine ecosystems. Here, we review possible scenarios of climate change (CC) and physical oceanography in the SPACC context. Three predicted avenues of ecological change are discussed: (1) changes in productivity and composition of lower trophic levels; (2) distributional changes of marine organisms; and (3) changes in circulation and their effects on recruitment processes. Research gaps are identified with special attention to current limitations of available data, models, and projected scenarios. We identify significant gaps in the knowledge of processes and interactions between changes in climate and other ecosystem stressors. These other stressors, such as ocean acidification, eutrophication, and overfishing, constitute additional anthropogenically induced components of global change but are not the focus of this review. The main conclusion is that, although more information is needed before the scientific community is able to make reliable predictions regarding the future state of marine ecosystems, there is already evidence of sensitivity of pelagic species and pelagic ecosystems to CC and of decreased resilience of natural ecosystems caused by overexploitation.

Kristiansen, T, Lough GR, Werner FE, Broughton EA, Buckley LJ.  2009.  Individual-based modeling of feeding ecology and prey selection of larval cod on Georges Bank. Marine Ecology Progress Series. 376:227-243.   10.3354/meps07796   AbstractWebsite

Understanding larval fish survival dynamics is essential to determining variability in future adult population structure. Realistic modeling of larval fish feeding ecology depends on incorporating both the biotic and abiotic conditions that affect predator-prey interactions. We used an individual-based model (IBM) to test which variables drive Atlantic larval cod Gadus morhua feeding preferences. The IBM included a bioenergetics component that incorporated metabolic parameters and growth and a mechanistic prey selection component that depended on larval development and behavior, prey size and behavior, depth, light, and physical oceanographic conditions. We applied our model to Georges Bank and incorporated high-resolution field data on environmental conditions and prey abundance to analyze larval cod feeding ecology. Based on simulated selectivity indices, we found that cod prey selection was determined by differential encounter of prey due to the abundance of suitably sized prey, their visibility, and larval cod ability to capture these prey items. The model suggested that Pseudocalanus spp. were the dominant prey species for larval cod because of their abundance in the water column and their large image area. Centropages spp. were also modeled to be an important part of larval diet, but no copepodite stages of this taxon were found in gut samples. Lack of Centropages spp. in the gut samples indicated that they are more elusive in their behavior than Pseudocalanus spp. Overall our results suggest larval cod feeding ecology on Georges Bank is a consequence of the physical and biological conditions rather than active prey selection.

deYoung, B, Barange M, Beaugrand G, Harris R, Perry IR, Scheffer M, Werner F.  2008.  Regime shifts in marine ecosystems: detection, prediction and management. Trends in Ecology & Evolution. 23:402-409.   10.1016/j.tree.2008.03.008   AbstractWebsite

Regime shifts are abrupt changes between contrasting, persistent states of any complex system. The potential for their prediction in the ocean and possible management depends upon the characteristics of the regime shifts: their drivers (from anthropogenic to natural), scale (from the local to the basin) and potential for management action (from adaptation to mitigation). We present a conceptual framework that will enhance our ability to detect, predict and manage regime shifts in the ocean, illustrating our approach with three well-documented examples: the North Pacific, the North Sea and Caribbean coral reefs. We conclude that the ability to adapt to, or manage, regime shifts depends upon their uniqueness, our understanding of their causes and linkages among ecosystem components and our observational capabilities.

Rose, KA, Megrey BA, Hay D, Werner F, Schweigert J.  2008.  Climate regime effects on Pacific herring growth using coupled nutrient-phytoplankton-zooplankton and bioenergetics models. Transactions of the American Fisheries Society. 137:278-297.   10.1577/t05-152.1   AbstractWebsite

We used a nutrient-phytoplankton-zooplankton (NPZ) model coupled to a fish bioenergetics model to simulate the weight-at-age responses of Pacific herring Clupea pallasii to climate regimes. The NPZ model represents the daily dynamics of the lower trophic levels by simulating the uptake and recycling dynamics of nitrogen and silicon and the photosynthesis and grazing interactions of multiple functional groups of phytoplankton and zooplankton. The bioenergetics model simulates the number and mean weight of Pacific herring for each of 10 age-classes. Three zooplankton groups simulated in the NPZ model provide estimates of the prey used to determine the consumption component of the herring bioenergetics model. We used a spawner-recruit relationship to estimate the number of new age-1 individuals joining the herring population every year. The coupled models were applied to the coastal upwelling area off the west coast of Vancouver Island. Model simulations were performed to isolate the effects of each of four documented climate regimes on Pacific herring weights at age. The climate regimes differed in the environmental variables used in the spawner-recruit relationship as well as in the water temperature, mixed-layer depth, and nutrient influxing rate used by the NPZ model. In agreement with general opinion and with the Pacific herring data from the west coast of Vancouver Island, the model-predicted estimates of weight at age, recruitment, and spawning stock biomass were highest in regime 1 (1962-1976), intermediate in regime 2 (1977-1988), and lowest in regime 3 (1989-1999). Insufficient time has passed to adequately document the conditions and herring responses in regime 4 (1998-2002). The overall regime effect on weights at age was a mix of recruitment effects and lower trophic level effects that varied in direction and magnitude among the four regimes. Coupling bioenergetics models to physics and food web models is the next challenge in understanding and forecasting how climate change will affect fish growth and population dynamics.

Edwards, KP, Hare JA, Werner FE.  2008.  Dispersal of black sea bass (Centropristis striata) larvae on the southeast US continental shelf: results of a coupled vertical larval behavior - 3D circulation model. Fisheries Oceanography. 17:299-315.   10.1111/j.1365-2419.2008.00480.x   AbstractWebsite

In the marine environment, pelagic dispersal is important for determining the distribution and abundance of populations, as well as providing connections among populations. Estimates of larval dispersal from spawning grounds are important to determining temporal and spatial patterns in recruitment that may have significant influences on the dynamics of the population. We present a case study of the dispersal of Centropristis striata (black sea bass) larvae on the southeast U.S. continental shelf. We use a coupled larval behavior - 3D circulation model to compare the effects of the timing and location of spawning against that of larval vertical migration on larval dispersal. Using the results of field data on larval vertical distributions, we compare the dispersal of virtual 'larvae' which have ontogenetic changes in vertical behavior with that of particles fixed near the surface and near the bottom. Larvae were released at potential spawning sites four times throughout the spawning season (February through May) for 3 yr (2002-04) and tracked for the assumed larval duration (from 27 to 37 days including the egg stage). Results indicate that adult behavior, in the form of spawning time and location, may be more important than larval vertical behavior in determining larval dispersal on the inner- and mid-continental shelves of this region.

Edwards, KP, Hare JA, Werner FE, Seim H.  2008.  Using 2-dimensional dispersal kernels to identify the dominant influences on larval dispersal on continental shelves. Marine Ecology Progress Series. 352:77-87.   10.3354/meps07169   AbstractWebsite

Pelagic larval dispersal is thought to be the main mechanism connecting many marine populations and is an important determinant both of an individual's success and a population's distribution and spatial structure. Thus, quantitative estimates of the retention or dispersion of larvae from spawning grounds is important for the determination of recruitment success in fisheries. Models can be used to study connectivity through a dispersal curve or dispersal kernel: the probability that a larva will settle at a given distance from its release location. We applied a 3-dimensional circulation model and a Lagrangian particle tracking model to the southeast US continental shelf to describe dispersal kernels in 2 dimensions. We used a fully orthogonal design to assess the importance of factors that influence the dispersal kernel, including spawning time, spawning location, larval behavior (vertical position in the water column), larval duration, and turbulent dispersal. Our results indicate that adult behavior, in the form of spawning time and location, may be more important than larval behavior in determining larval dispersal on the inner- and mid-shelves in this region.

Werner, FE, Cowen RK, Paris CB.  2007.  Coupled biological and physical models present capabilities and necessary developments for future studies of population connectivity. Oceanography. 20:54-69.   10.5670/oceanog.2007.29   AbstractWebsite

The combination of wide-ranging spatial and temporal scales associated with the oceanic environment, together with processes intrinsic to the biology of marine organisms, makes the quantitative study of population connectivity a formidable challenge. Sampling over all scales, except for targeted field efforts that focus on selected processes of life stages in limited domains, is presently not possible (Gawarkiewicz et al., this issue). As such, modeling approaches that simultaneously include key physical dynamics and biological traits provide a way forward to investigate general ecological questions as well as provide qualitative assessments regarding connectivity of specific regions and populations (Cowen et al., 2000, 2006; Werner et al., 2001a). In some instances, model results have provided information of relevance to decision-makers in determining marine protected areas and other management strategies (Fogarty and Botsford, this issue). At a minimum, models can be used to generate hypotheses for empirical studies. Overall, coupled biological-physical models are critical tools for addressing the complex processes driving population connectivity in marine systems.

Cowen, RK, Gawarkiewic G, Pineda J, Thorrold SR, Werner FE.  2007.  Population connectivity in marine systems an overview. Oceanography. 20:14-21.   10.5670/oceanog.2007.26   AbstractWebsite

There is growing consensus that life within the world’s ocean is under considerable and increasing stress from human activities (Hutchings, 2000; Jackson et al., 2001). This unprecedented strain on both the structure and function of marine ecosystems has led to calls for new management approaches to counter anthropogenic impacts in the coastal ocean (Botsford et al., 1997; Browman and Stergiou, 2004: Pikitch et al., 2004). Spatial management, including Marine Protected Areas (MPAs), has been touted as a method for both conserving biodiversity and managing fisheries (Agardy, 1997). Continuing debates on the efficacy of MPAs have identified the need for models that capture the spatial dynamics of marine populations, especially with respect to larval dispersal (Willis et al., 2003; Sale et al., 2005). Theoretical studies suggest that population connectivity plays a fundamental role in local and metapopulation dynamics, community dynamics and structure, genetic diversity, and the resiliency of populations to human exploitation (Hastings and Harrison, 1994; Botsford et al., 2001). Modeling efforts have been hindered, however, by the paucity of empirical estimates of, and knowledge of the processes controlling, population connectivity in ocean ecosystems. While progress has been made with older life stages, the larval-dispersal component of connectivity remains unresolved for most marine populations. This lack of knowledge represents a fundamental obstacle to obtaining a comprehensive understanding of the population dynamics of marine organisms. Furthermore, a lack of spatial context that such information would provide has limited the ability of ecologists to evaluate the design and potential benefits of novel conservation and resource-management strategies.

Greenberg, DA, Dupont F, Lyard FH, Lynch DR, Werner FE.  2007.  Resolution issues in numerical models of oceanic and coastal circulation. Continental Shelf Research. 27:1317-1343.   10.1016/j.csr.2007.01.023   AbstractWebsite

The baroclinic and barotropic properties of ocean processes vary on many scales. These scales are determined by various factors such as the variations in coastline and bottom topography, the forcing meteorology, the latitudinal dependence of the Coriolis force, and the Rossby radius of deformation among others. In this paper we attempt to qualify and quantify scales of these processes, with particular attention to the horizontal resolution necessary to accurately reproduce physical processes in numerical ocean models. We also discuss approaches taken in nesting or down-scaling from global /basin- scale models to regional-scale or shelf-scale models. Finally we offer comments on how vertical resolution affects the representation of stratification in these numerical models. (c) 2007 Elsevier Ltd. All rights reserved.

Aretxabaleta, A, Blanton BO, Seim HE, Werner FE, Nelson JR, Chassignet EP.  2007.  Cold event in the South Atlantic Bight during summer of 2003: Model simulations and implications. Journal of Geophysical Research-Oceans. 112   10.1029/2006jc003903   AbstractWebsite

A set of model simulations are used to determine the principal forcing mechanisms that resulted in anomalously cold water in the South Atlantic Bight ( SAB) in the summer of 2003. Updated mass field and elevation boundary conditions from basin-scale Hybrid Coordinate Ocean Model ( HYCOM) simulations are compared to climatological forcing to provide offshore and upstream influences in a one-way nesting sense. Model skill is evaluated by comparing model results with observations of velocity, water level, and surface and bottom temperature. Inclusion of realistic atmospheric forcing, river discharge, and improved model dynamics produced good skill on the inner shelf and midshelf. The intrusion of cold water onto the shelf occurred predominantly along the shelf-break associated with onshore flow in the southern part of the domain north of Cape Canaveral ( 29 degrees to 31.5 degrees). The atmospheric forcing ( anomalously strong and persistent upwelling-favorable winds) was the principal mechanism driving the cold event. Elevated river discharge increased the level of stratification across the inner shelf and midshelf and contributed to additional input of cold water into the shelf. The resulting pool of anomalously cold water constituted more than 50% of the water on the shelf in late July and early August. The excess nutrient flux onto the shelf associated with the upwelling was approximated using published nitrate-temperature proxies, suggesting increased primary production during the summer over most of the SAB shelf.

Megrey, BA, Rose KA, Klumb RA, Hay DE, Werner FE, Eslinger DL, Smith LS.  2007.  A bioenergetlics-based population dynamics model of Pacific herring (Clupea harengus pallasi) coupled to a lower trophic level nutrient-phytoplankton-zooplankton model: Description, calibration, and sensitivity analysis. Ecological Modelling. 202:144-164.   10.1016/j.ecolmodel.2006.08.020   AbstractWebsite

We describe an approach to dynamically couple a fish bioenergetics-based population dynamics model to the NEMURO lower trophic level nutrient-phytoplankton-zooplankton model. The coupled models, denoted NEMURO.FISH and configured for Pacific herring (Clupea harengus pallasii) on the west coast of Vancouver island, are capable of simulating the daily dynamics of the lower trophic levels and the daily average weight and numbers of individual herring in each of 10 age classes over multiple years. New recruits to the herring population are added each June based on either constant recruitment or dynamic recruitment generated from an environmental Ricker spawner-recruitment relationship. The dynamics of the three zooplankton groups in the NEMURO model determine the consumption rate of the herring; herring consumption affects the zooplankton, and egestion and excretion contribute to the nitrogen dynamics. NEMURO was previously calibrated to field data for the West Coast Vancouver Island. Thirty-year simulations of herring growth and population dynamics were performed that used repeated environmental conditions for the lower trophic levels of NEMURO and historical environmental variables for the herring spawner-recruit relationship. Herring dynamics were calibrated to the west coast of Vancouver Island such that the coupled models reasonably duplicated observed herring weights-at-age and total herring biomass. Additional 30-year simulations under constant recruitment with herring coupled and uncoupled from NEMURO clearly showed the effects of the feedback mechanism between the two models and also showed that herring have small to moderate effects on their prey. Monte Carlo uncertainty analysis showed the importance of feeding- and respiration-related parameters to predicted individual and population herring growth. The utility of the NEMURO.FISH framework for improving our understanding of climate change effects on marine ecosystem dynamics is discussed. (c) 2006 Elsevier B.V. All rights reserved.

Rose, KA, Megrey BA, Werner FE, Ware DM.  2007.  Calibration of the NEMURO nutrient-phytoplankton-zooplankton food web model to a coastal ecosystem: Evaluation of an automated calibration approach. Ecological Modelling. 202:38-51.   10.1016/j.ecolmodel.2006.08.016   AbstractWebsite

A one spatial-box version of the NEMURO oceanic lower trophic food web model was applied to a coastal upwelling environment typified by West Coast Vancouver Island. We used both ad hoc calibration and the automatic calibration program PEST. NEMURO was first calibrated to I year of monthly field data using the usual ad hoc approach of trial and error changes to 18 candidate parameters. Four PEST calibrations were then performed. The first three PEST calibrations used model predictions in year 10 from the ad hoc calibration as data in a twin experiment design; the fourth PEST calibration repeated the ad hoc procedure by having PEST calibrate NEMURO to the field data. When provided with ad hoc calibration model predictions as data, PEST accurately recovered the known 18 parameter values, even when small and large phytoplankton were lumped into total phytoplankton. When 57 parameters were allowed to vary PEST-estimated-reasonable values for all 57 parameters, but they differed from the ad hoc calibrated values. However, when applied to the field data, PEST-estimated parameter values that differed greatly from the ad hoc values. The PEST calibration fitted some of the field data better than the ad hoc calibration but at the cost of unequal small and large phytoplankton concentrations. Thus, with proper and careful implementation, PEST offers a viable approach for objective calibration of NEMURO to site-specific monitoring data. We recommend that automatic calibration methods, such as PEST, be used for application of the NEMURO model to new locations. When the field data allow for specification of time series for each phytoplankton and zooplankton state variable, PEST will provide an objective, defensible, and repeatable way to calibrate the many parameters of the NEMURO model. If the available data are insufficient for specification of each state variable, then ad hoc calibration will likely be needed to allow for inclusion of qualitative decisions about model fit. Use of PEST in this situation will provide better understanding of the data-model mis-matches and will provide an alternative calibration to the necessary, but subjective, ad hoc calibration. Comparison of the ad hoc and PEST calibrations (even if unsuccessful) will help in the interpretation of the ad hoc calibration. Robust parameter estimation by any method depends on the quality and consistency of the calibration dataset. (c) 2006 Elsevier B.V. All rights reserved.