Ivonne Ortiz^1,2, and Kerim Aydin^2
1UW School of Aquatic & Fishery Sciences
²Alaska Fisheries Science Center
April 19, 2011

The Bering Sea Integrated Research Program (BSIERP) is a 5 year program designed to test hypotheses regarding the ecosystem’s response to climate change. Both historical and BSIERP field data are used to put together a vertically integrated model that includes 5 modules: i) Climate (specific to the Bering Sea), ii) ROMS (Regional Ocean Modeling System) , iii) NPZ-benthos (Nutrient-Phytoplankton-Zooplankton-benthos), iv) FEAST (Forage/Euphausiid Abundance in Space and Time), and v) Economics (fleet movement model). The vertically integrated model in turn, will be used as the “real world” model in a Management Strategy Evaluation for the Bering Sea pollock, and Pacific cod fisheries. We will start with a presentation of the vertically integrated model structure and feedbacks, summarizing some of the challenges of working across multiple scales, units and objectives. We will then discuss the development, ongoing tuning and validation of the fish module FEAST, highlighting transitions from original to current formulations of bioenergetics, movement and reproduction through several rounds of meetings with field biologists. Finally, we’ll detail what processes in the model are expected to respond to climate change, where we expect them to be buffered, and where they are non-sensitive. FEAST runs on a grid of ~10 km resolution and models size-based, two way interactions between 13 fish species (walleye pollock, Pacific cod, arrowtooth flounder, salmon, capelin, herring, eulachon, sandlance, myctophids, squids, shrimp, crabs and other), and the 7 zooplankton groups in the NPZ model (small/large microzooplankton, small/large copepods, euphausiids, jellyfish, and benthic infauna). Both temperature and advection from ROMS are used in the bioenergetics and movement components. The operating hypothesis in FEAST is that forage fish and macrozooplankton are tightly coupled in a two-way interaction, and the dynamics of this interaction under different climate scenarios is a strong structuring element for the ecosystem as a whole.

Melissa Haltuch
Northwest Fisheries Science Center
March 14, 2011

Petrale sole are a commercially important flatfish that migrate seasonally between feeding and spawning grounds, and have recently been declared overfished. The summer trawl survey shows a decline in petrale sole abundance since 2005 similar to the unstandardized summer catch-per-unit-effort (CPUE) from the fishery. However, many stakeholders disagree that petrale sole abundance has been declining, instead choosing to focus on the unstandardized winter CPUE that shows a strong increase beginning in 2000. The assessment attributes the increasing trend in winter CPUE to management actions that forced the fleet to 1) increase fishing effort during the winter, and 2) conduct winter fishing in locations with high historical catch rates. Standardized fishery CPUE was not used in the assessment due to changing management regulations beginning in the late 1990s and the high likelihood of a winter CPUE index showing hyper-stability due to the fishery focusing on the aggregated spawning stock. Given the potential discrepancy between the assessment results and the experience of the groundfish fleet, particularly during the winter fishing season, and the limited conclusions that can be drawn from unstandardized CPUE, this work explores the utility of the summer and winter fishery CPUE series as indices of abundance for the petrale sole stock assessment. The ultimate goals are to determine if an adequate index of abundance can be created using fishery CPUE, and to address the uncertainty due to the discrepancy between the fishery independent and fishery dependent data sources and therefore the perceived stock assessment uncertainty.

Charlotte Boyd and Mathieu Woillez
UW School of Aquatic & Fishery Sciences
February 28, 2011

Geostatistical conditional simulations are a useful tool for capturing the full range of variability in spatial data. The distribution of schooling fish is inherently patchy – this patchiness may be lost in kriging which presents a best local estimate at each point and tends to smooth over local variability. In contrast, stochastic geostatistical simulations reproduce the variability of a variogram model. Simulations can be conditioned on the observed data values, and, on average, reproduce the statistical properties and spatial pattern of the sample data. Multiple simulations can therefore be used as the basis for estimating uncertainty at given locations. Geostatistical simulation is thus relevant to analyses of spatial sample data in which measurement error, local variability, or sampling uncertainty are important (such as risk assessment and decision analysis). In the Gaussian case, geostatistical conditional simulation can be achieved relatively easily by adding a simulated error term to the kriging. However, in the case of acoustic surveys of schooling fish, where the acoustic backscatter is often characterized by a high proportion of zeroes and skewed positive values, some transformations are necessary. Here, we present and discuss two contrasting approaches to perform geostatistical conditional simulation in this context – one based on transformed Gaussian simulations and on a Gibbs sampler to handle the numerous zero acoustic values within a classical geostatistical framework, and the other based on a binomial/ lognormal hurdle model within a generalized linear mixed modeling framework.

Bill Clark¹, and Rick Methot^2
1International Pacific Halibut Commission and UW School of Aquatic & Fishery Sciences
²Northwest Fisheries Science Center
February 7, 2011

Current efforts to conserve Pacific salmon (Oncorhynchus spp.) rely on a variety of information sources including empirical observations, expert opinion, and models. I will outline a framework for incorporating detailed information on density-dependent population growth, habitat attributes, hatchery operations, and harvest management into conservation planning in a time-varying, spatially explicit manner. The model relies on a multi-stage Beverton-Holt model to describe the production of salmon from one life stage to the next. We used information from the literature to construct relationships between the physical environment and the necessary productivity and capacity parameters for the model. As an example of how policy makers can use the model in recovery planning, we applied the model to a threatened population of Chinook salmon (O. tshawytscha) in the Snohomish River basin in Puget Sound, Washington, USA. By incorporating additional data on hatchery operations and harvest management for Snohomish River basin stocks, we show how proposed actions to improve physical habitat throughout the basin translate into projected improvements in four important population attributes: abundance, productivity, spatial structure, and life history diversity. I will also describe how to adapt the model to a variety of other management applications.

Judith E. Zeh
UW Department of Statistics
October 05, 2005

The International Whaling Commission (IWC) was established in 1946 by the International Convention for the Regulation of Whaling, signed by 14 whaling nations, “to provide for the proper conservation of whale stocks and thus make possible the orderly development of the whaling industry”. Part of the Convention is a Schedule that contains the actual regulations regarding species and numbers of great whales that can be caught, times and places in which whaling is allowed, etc. Amendments to the Schedule, which require a 3/4 majority vote for adoption, must be “based on scientific findings”. Thus, since its inception, the intent of the IWC has been to base management on science, and one of its standing committees has been the Scientific Committee (SC). The SC meets annually, just before the Commission meets, and the Chair of the SC presents SC findings to the Commission. I will talk about successes and failures of this management process before, during, and since my 1999-2002 term as SC Chair. Successes have come when the Commission obtained and followed good scientific advice. Failures have sometimes occurred because of inadequate scientific advice, but more often because economics or politics got in the way of following good advice. Both successes and failures occurred in the 1960s, when a committee of three scientists appointed by the Commission recommended immediate protection of Antarctic humpback and blue whales from whaling and drastic reductions in fin whale catches. The Commission did protect humpback and blue whales, but delayed reductions in fin whale catches because of pressure from whaling nations. Eventually greater reductions in fin whale catches had to be made to allow the stock to recover. The management procedure developed by the SC during the 1970s proved unworkable because it required classifying whale stocks on the basis of quantities that were difficult to estimate. Meanwhile, some whaling nations stopped whaling and other nations joined the IWC. It now has 66 members, the majority of which are non-whaling nations and many of which could be characterized as anti-whaling nations. This adds a complicating dimension to the “science and policy interface”. During the 1980s, the Commission imposed a moratorium on commercial whaling that is still in effect. However, the Convention allows whaling in spite of the moratorium by nations that objected to its adoption and by any nation under Special Permits for scientific research. Meanwhile, the SC has developed a revised management procedure (RMP) that requires only regular estimates of abundance of a stock and the known catch history. The RMP was tested by simulations of 100 years of catches using it. These simulations took into account uncertainties in a wide range of factors. In my view, whales and whalers would be better protected by use of the RMP to manage whaling than by the moratorium. The SC currently provides advice on aboriginal subsistence catch limits for bowhead whales using a similar management procedure.

Arni Magnusson
UW School of Aquatic & Fishery Sciences
April 27, 2005

Uncertainty is a fundamental part of fisheries stock assessment, that needs to be quantified to successfully manage the resource. Among the statistical methods that are used to measure uncertainty are Markov chain Monte Carlo (MCMC) simulations, bootstrap, and Hessian delta-method approximation. In this study, a large number of stochastic datasets is generated, where the true parameter values are known. Confidence bounds are then estimated using the different methods, and the claimed uncertainty is compared with how often they contain the true value. The findings from this simulation study are reviewed, as well as theoretical and practical differences between the methods.

Tom Helser
NOAA Northwest Fisheries Science Center
April 13, 2005

A generalized linear mixed model (GLMM) that treats year and spatial cell as fixed effects while treating vessel as a random effect is used to estimate biomass and variances for 11 slope species in the NMFS bottom trawl surveys on the upper continental slope of U.S. West coast. A Bernoulli distribution is used to model the probability of a non-zero haul and we examine alternative error distributions from the exponential family using AIC to model the non-zero catch rates.

André E. Punt
UW School of Aquatic & Fishery Sciences
February 9, 2005

The Pacific Fishery Management Council adopted rebuilding plans for eight groundfish species in 2004 in the form of Amendments 16-2 and 16-3 to the groundfish FMP. Each of these eight stocks will be re-assessed during 2005 and, as a consequence, there will be an opportunity to determine whether or not they have responded to recovery efforts and are on track to rebuild as previously projected. It is to be expected that the results of the 2005 groundfish assessments with not conform exactly with the results expected based on the previous assessments. The question that arises then is whether the fishing mortality rate used to set harvest guidelines specified as part of the rebuilding plan should be changed, and if so how. A further consideration is that data now available may show that the original basis for the rebuilding plan is no longer valid (e.g. because the values assumed for natural mortality or stock recruitment steepness have changed markedly). Although guidelines exist regarding how rebuilding analyses are to be conducted, there no guidelines to determine whether (and to what extent) rebuilding plans are to be updated given new information. The objectives of this presentation are to outline: a) a set of possible “rebuilding revision rules” which could be used to measure progress towards rebuilding (and make appropriate adjustments to rebuilding plans as needed), and b) a framework which uses simulation to provide a quantitative means to compare alternative rebuilding revision rules in terms of their effectiveness at correctly (and adequately) making adjustments to rebuilding plans.

Trevor Branch,
UW School of Aquatic & Fishery Sciences
November 3, 2004

Can we devise a set of regulations for multispecies fisheries so that productive species are not undercaught (resulting in economic loss) while preventing overfishing of unproductive species? The groundfish fisheries of British Columbia and the U.S. West Coast offer some insights. They were managed by individual trip limits (with all their associated problems) until 1996, but thereafter diverged. The B.C. fishery implemented a 100% on-board observer system, permitting individual accountability of catch and discard mortality, followed in 1997 by the introduction of Individual Transferable Quotas (ITQs). The West Coast fishery, forbidden to consider ITQs by the Sustainable Fisheries Act, continued on the path of increasingly restrictive retention limits, and ever-increasing regulatory-induced discarding, as additional species were declared overfished. By almost any measure, the B.C. fishery is now in a better state of health: ITQs have resulted in greater flexibility, increased profitability, reduced overcapitalization, compliance with TACs, and the reduction of marketable discards to near zero. The reduction in discards alone provides additional income sufficient to cover the costs of observer coverage. A model of fishermen’s location choice highlights the benefits of accounting for catches and discards under 100% observer coverage and the benefits of increased flexibility under ITQs.

Ray Hilborn
UW School of Aquatic & Fishery Sciences
November 3, 2004

Many of Alaska’s salmon fisheries are models of biological success, with management structures that have maintained biomass, stock diversity and biological yield. At the same time the fisheries face severe challenges due to low price for the product, and the fisheries have been declared formal “economic” disasters by state and federal agencies in recent years. From many perspectives these fisheries are in crisis. I explore how the governance system for Alaskan salmon has led to biological success and economic failure. I review a range of alternative governance structures that are in place or being considered that might provide for social and economic sustainability. I also demonstrate that the basic biological principal that has guided management, Maximum Sustainable Yield, is a serious impediment to social and economic sustainability.