Fishery Stock Assessment Models for the 21St Century, October 8-11, 1997, Anchorage, Alaska

Edited by F. Funk, T.J. Quinn II, J. Heifetz, J.N. Ianelli, J.E. Powers, J.F. Schweigert, P.J. Sullivan, and C.-I. Zhang

Proceedings of the International Symposium on Fishery Stock Assessment Models for the 21st Century, October 8-11, 1997, Anchorage, Alaska

Lowell Wakefield Fisheries Symposium

University of Alaska Sea Grant College Program AK-SG-98-01 1998 Price $40.00 Elmer E. Rasmuson Library Cataloging-in-Publication Data

International Symposium on Fishery Stock Assessment Models for the 21st Century (1997 : Anchorage, Alaska). Fishery stock assessment models : proceedings of the International Symposium on Fishery Stock Assessment Models for the 21st Century, October 8-11, 1997, Anchorage, Alaska.

(Lowell Wakefield Fisheries Symposium) (University of Alaska Sea Grant College Program ; AK-SG-98-01)

1. Fish stock assessment—Alaska—Congresses. 2. Fishery management—Alaska— Congresses. I. Alaska Sea Grant College Program. II. Title. III. Series: Lowell Wakefield fisheries symposium series. 15th. IV. Series: Alaska Sea Grant College Program report : 98-01.

SH329.F56F57 1997

ISBN 1-56612-057-8

Citation for this volume is Fishery Stock Assessment Models, edited by F. Funk, T.J. Quinn II, J. Heifetz, J.N. Ianelli, J.E. Powers, J.F. Schweigert, P.J. Sullivan, and C.-I. Zhang, Alaska Sea Grant College Program Report No. AK-SG-98-01, University of Alaska Fairbanks, 1998.

Acknowledgments This book is the result of work sponsored by the University of Alaska Sea Grant College Program, which is cooperatively supported by the U.S. Department of Com- merce, NOAA National Sea Grant Office, under grant no. NA86RG-0050, project A/75-01; and by the University of Alaska with state funds. The University of Alaska is an affirmative action/equal opportunity institution. Sea Grant is a unique partnership with public and private sectors combining research, education, and technology transfer for public service. This national net- work of universities meets changing environmental and economic needs of people in our coastal, ocean, and Great Lakes regions.

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ii Contents

About the Symposium ...... ix About This Proceedings ...... ix The Lowell Wakefield Symposium Series ...... x Review of the Symposium ...... xii

Keynote Address Living Marine Resource Assessment for the 21st Century: What Will Be Needed and How Will It Be Provided? Keith Sainsbury ...... 1

Data Issues and Model Specification Evaluation of the Status of Fisheries Data Collection and Stock Assessment Problems in São Paulo, Southeastern Brazil Maria de los Angeles Gasalla and Acácio Ribeiro Gomes Tomás ...... 41

Evaluation of CPUE Estimates for the 1995 Crab Fisheries of the Bering Sea and Aleutian Islands Based on Observer Data Laurence C. Byrne and Douglas Pengilly ...... 61

Catch and Effort Analysis with Uncertain Stock and Effort Dynamics: Southern Bluefin Tuna Longline Robert Campbell ...... 75

Stock Production Models of Blue Marlin and White Marlin in the Atlantic Ocean: A Case History Christopher D. Jones, Eric D. Prince, Gerald P. Scott, and Mark I. Farber ...... 99

Evaluation of Multiple Survey Indices in Assessment of Black Sea Bass from the U.S. South Atlantic Coast Douglas S. Vaughan, Boxian Zhao, Mark R. Collins, John C. McGovern, and H. Scott Meister ...... 121

iii An Index for Weighting Results in Catch-at-Age Models Based on Diagnostic Tests for Lack of Fit T. Polacheck, K.A. Haskard, N. Klaer, A. Betlehem, and A. Preece ...... 137

An Integrated Assessment of Southern Blue Whiting (Micromesistius australis) from New Zealand Using Separable Sequential Population Analysis Stuart Hanchet, Vivian Haist, and Dave Fournier ...... 155

Statistics, Software, and Fish Stock Assessment Jon T. Schnute, Laura J. Richards, and Norm Olsen ...... 171

A Statistical Framework for Analysis of Limit Reference Points Laura J. Richards, Jon T. Schnute, and Norm Olsen ...... 185

Joint Time Series Analysis of Catch-at-Age and CPUE Data Gudmundur Gudmundsson ...... 199

Dynamics of a Migratory Fish Population with Applications to the Management of Sablefish Jonathan Heifetz and Terrance J. Quinn II ...... 219

Stock Assessment of Gemfish (Rexea solandri) in Eastern Australia Using Maximum Likelihood and Bayesian Methods Anthony D.M. Smith and André E. Punt ...... 245

Forecast Methods for Inseason Management of the Southeast Alaska Chinook Salmon Troll Fishery Jerome J. Pella, Michele M. Masuda, and D.G. Chen ...... 287

A Monte Carlo Evaluation of the Stock Synthesis Assessment Program David B. Sampson and Yanshui Yin ...... 315

Fuzzy Regression in Fisheries Science: Some Methods and Applications Saul B. Saila and Scott Ferson ...... 339

Evaluation of Assumed Error Structure in Stock Assessment Models That Use Sample Estimates of Age Composition Paul R. Crone and David B. Sampson ...... 355

A Parametric Bootstrap of Catch-Age Compositions Using the Dirichlet Distribution Erik H. Williams and Terrance J. Quinn II ...... 371

Some Intrinsic Limitations of Sample Variances in Stock Assessment Models Clay E. Porch ...... 385

iv Diagnosing Systematic Errors in Reported Fishery Catch Stratis Gavaris and Lutgarde Van Eeckhaute ...... 399

Model Misspecification or Data Bias: The Assessment of Prince Rupert Herring Jacob F. Schweigert ...... 413

A Stochastic Implementation of an Age-Structured Production Model Victor R. Restrepo and Christopher M. Legault ...... 435

When Lengths Are Better Than Ages: The Complex Case of Bocaccio Stephen Ralston and James N. Ianelli ...... 451

Integrated Catch-Age Mark-Recapture Model: Application to B.C. Sablefish Stocks Vivian Haist ...... 469

Integrating Ecosystem Studies: A Bayesian Comparison of Hypotheses Milo D. Adkison, Brenda Ballachey, James Bodkin, and Leslie Holland-Bartels ...... 495

Assessment of Southeast Alaska Pink Salmon Abundance Based on Commercial Catch and Effort and Sex Ratio Data Jie Zheng and Ole A. Mathisen ...... 511

Stage-Structured and Size-Based Applications Progress and Problems in the Application of Management Procedures to South Africa’s Major Fisheries José A.A. De Oliveira, Douglas S. Butterworth, and Susan J. Johnston ...... 513

A Length-Based Population Model for Hard-to-Age Invertebrate Populations Terrance J. Quinn II, Clive T. Turnbull, and Caihong Fu ...... 531

Coping with a Challenging Stock Assessment Situation: The Kamishak Bay Sac-Roe Herring Fishery Edward O. Otis, William R. Bechtol, and Wesley A. Bucher ...... 557

Abundance Estimation of St. Matthew Island Blue King Crabs Using Survey and Commercial Catch and Effort Data J. Zheng, M.C. Murphy, and G.H. Kruse ...... 575

Using Multiple Data Sets to Assess Red King Crab in Norton Sound, Alaska: Length-Based Stock Synthesis Jie Zheng, Gordon H. Kruse, and Lowell Fair ...... 591

v Treatment of Data and Model Uncertainties in the Assessment of Southern Bluefin Tuna Stocks Tom Polacheck, Ann Preece, Andrew Betlehem, and Neil Klaer ...... 613

Virtual Population Analysis with the Adjoint Method M.J. Huiskes ...... 639

Examination of a Length-Based Population Analysis Takashi Matsuishi ...... 659

Ocean Ecosystems Incorporation of Predation into a Population Assessment Model of Eastern Bering Sea Walleye Pollock Patricia A. Livingston and Richard D. Methot ...... 663

Problems with an Environmental-Based Recruitment Index: Examples from a New Zealand Snapper Assessment (Pagrus auratus) Mark N. Maunder ...... 679

Cross-Validation of Trophic Level Estimates from a Mass-Balance Model of Prince William Sound Using 15N/14N Data Thomas C. Kline Jr. and Daniel Pauly ...... 693

Calculating Capelin Consumption by Icelandic Cod Using a Spatially Disaggregated Simulation Model Höskuldur Björnsson ...... 703

Spatial Analysis of Fish Distribution and Abundance Patterns: A GIS Approach Anthony J. Booth ...... 719

Comparing Different Information Sources in a Multispecies Context Gunnar Stefánsson ...... 741

Rapid Appraisal of the Status of Fisheries for Small Pelagics Using Multivariate, Multidisciplinary Ordination Tony Pitcher, Steven Mackinson, Marcelo Vasconcellos, Leif Nøttestad, and David Preikshot ...... 759

Development of a Simple Biomass Analysis Model Rex Baleña ...... 783

Multivariate Interdisciplinary Assessment of Small-Scale Tropical Fisheries David Preikshot and Daniel Pauly ...... 803

vi Mass-Balance Food Web Ecosystem Models as an Alternative Approach for Combining Multiple Information Sources in Fisheries Daniel Pauly, Johanne Dalsgaard, Thomas A. Okey, Robert Powell, and Stuart Pimm ...... 815

Harvest Policy Estimates of Shrimp Trawl Bycatch of Red Snapper (Lutjanus campechanus) in the Gulf of Mexico B.J. Gallaway, M. Longnecker, J.G. Cole, and R.M. Meyer ...... 817

A Summary of Assessment Information for Managing Alaska Groundfish Stocks Jane DiCosimo ...... 841

Harvest Control for Schooling Fish Stocks under Cyclic Oceanographic Regimes: A Case for Precaution and Gathering Auxiliary Information Marcelo Vasconcellos and Tony Pitcher ...... 853

Implications of a Bayesian Approach for Simulating Salmon Population Dynamics Ryan A. Hill and Brian J. Pyper ...... 873

In Search of a New Approach to Fisheries Management in the Middle Amazon Region Victoria J. Isaac, Mauro L. Ruffino, and David McGrath ...... 889

From Fisheries Assessment Uncertainty to Risk Analysis for Immediate Management Actions Stratis Gavaris and Alan Sinclair ...... 903

Consistency of Stock Assessment and Evaluation of Fisheries Management for European Fish Stocks, 1983-1995 D. Gascuel, G. Fontenelle, C. Maguer, and A. Biseau ...... 917

A General Approach for Making Short-Term Stochastic Projections from an Age-Structured Fisheries Assessment Model Jon Brodziak, Paul Rago, and Ramon Conser ...... 933

A Simulation Study of the Effects of Aging Error and Sample Size on Sustained Yield Estimates Lewis G. Coggins Jr. and Terrance J. Quinn II ...... 955

vii The Effects of Artisanal Fisheries on Penaeid Shrimp Stocks in the Gulf of Mexico Adolfo Gracia and Ana Rosa Vázquez Bader ...... 977

Fisheries Management Based on Reproductive Potential: An Example for Chub Mackerel Toshio Katsukawa and Yoshiharu Matsumiya ...... 999

Participants ...... 1013

Index ...... 1025

viii About the Symposium The International Symposium on Fishery Stock Assessment Models for the 21st Century: Combining Multiple Information Sources is the fifteenth Lowell Wakefield symposium. The program concept was suggested by Fritz Funk of the Alaska Department of Fish and Game. The meeting was held October 8-11, 1997, in Anchorage, Alaska. Eighty-five presentations were made, with a keynote address by Keith Sainsbury, CSIRO (Commonwealth Scientific and Industrial Research Organisation) Division of Marine Re- search, Hobart, Australia. The symposium was organized and coordinated by Brenda Baxter, Alaska Sea Grant College Program, with the assistance of the organizing and program committees. Organizing committee members are: Fritz Funk, co-chair, Alaska Department of Fish and Game; Terrance J. Quinn II, co- chair, Fisheries Division, University of Alaska Fairbanks; Jane DiCosimo, North Pacific Fishery Management Council; James N. Ianelli, U.S. National Marine Fisheries Service; and Patrick J. Sullivan, International Pacific Hal- ibut Commission. Program planning committee members are: Alajandro Anganuzzi, Inter-American Tropical Tuna Commission; Rick Deriso, Inter- American Tropical Tuna Commission; Stratis Gavaris, Department of Fish- eries and Oceans Canada; John Hampton, South Pacific Commission; Tore Jakobsen, Institute of Marine Research, Norway; Peggy Merritt, Alaska De- partment of Fish and Game; Rick Methot, U.S. National Marine Fisheries Service; Steven A. Murawski, U.S. National Marine Fisheries Service; Peggy Murphy, Alaska Department of Fish and Game; Tony J. Pitcher, University of British Columbia, Canada; Joseph Powers, U.S. National Marine Fisher- ies Service; Jacob F. Schweigert, Department of Fisheries and Oceans Can- ada; John Sibert, University of Hawaii; Stephen J. Smith, Department of Fisheries and Oceans Canada; Tony Smith, Division of Fisheries, CSIRO, Australia; Gunnar Stefansson, Marine Research Institute, Iceland; and Chang-Ik Zhang, National Fisheries University of Pusan, Korea. Symposium sponsors are: Alaska Department of Fish and Game; Inter- national Pacific Halibut Commission; North Pacific Fishery Management Council; U.S. National Marine Fisheries Service, Alaska Fisheries Science Center; and Alaska Sea Grant College Program, University of Alaska Fair- banks.

About This Proceedings This publication has 55 symposium papers. Each paper has been reviewed by two peer reviewers. Peer reviewers are: Milo Adkison, Jim Anderson, John Anderson, Man- uela Azevedo, Timothy Baker, Rex Baleña, Bill Bechtol, Dave Bernard, Andrew Betlehem, Höskuldur Björnsson, Tony Booth, Barry Bracken, Jon Brodziak, Joan Browder, Robert Campbell, David Carlile, Lew Coggins, Keith Criddle, Paul Crone, Nancie Cummings, Nick Davies, José De Oliveira,

ix Richard Deriso, Martin Dorn, Emmanis Dorval, Lowell Fair, Chris Francis, Steven Fried, Caihong Fu, Jeff Fujioka, Fritz Funk, Maria Gasalla, Stratis Gavaris, Harold Geiger, Gudmundur Gudmundsson, Vivian Haist, John Hampton, Stuart Hanchet, David Hankin, Jonathan Heifetz, Ray Hilborn, Ryan Hill, Mark Huiskes, Victoria Isaac, Larry Jacobson, Tore Jakobsen, Christopher Jones, Dan Kimura, Tom Kline, Cliff Kraft, Gordon Kruse, Han- lin Lai, Patricia Livingston, Chris Lunsford, Alec MacCall, Bob Marshall, Michele Masuda, Ole Mathisen, Mark Maunder, Sandy McFarlane, Peggy Merritt, Rick Methot, Steven Murawski, Peggy Murphy, Ken Newman, Jorge Flores Olivares, Ted Otis, William Overholtz, Ana Parma, A.J. Paul, Daniel Pauly, Jerry Pella, Ian Perry, Tony Pitcher, Tom Polacheck, Clay Porch, Ann Preece, Andre Punt, Terry Quinn, Steve Ralston, Victor Restrepo, Jake Rice, Laura Richards, Gregg Rosenkranz, Saul Saila, David Sampson, Mark Saun- ders, Jon Schnute, Jake Schweigert, John Sibert, Michael Sigler, Alan Sin- clair, Stephen Smith, Tony Smith, Kevin Stokesbury, Zhenming Su, Jack Tagart, Joe Terry, Grant Thompson, Sachiko Tsuji, Clive Turnbull, Jack Turnock, Douglas Vaughan, Jay Ver Hoef, Erik Williams, George Winters, Dave Witherell, Chris Wood, Douglas Woodby, and Jie Zheng. Editing, layout, format, and proofing are by Carol Kaynor, Sue Keller, and Brenda Baxter of University of Alaska Sea Grant. Cover design is by Susan Gibson and David Brenner.

The Lowell Wakefield Symposium Series The University of Alaska Sea Grant College Program has been sponsoring and coordinating the Lowell Wakefield Fisheries Symposium series since 1982. These meetings are a forum for information exchange in biology, management, economics, and processing of fish species and complexes, as well as an opportunity for scientists from high latitude countries to meet and discuss their work. The symposium series had its origin in the Americanization of the fisheries off Alaska in the late 1970s. At that time a lack of information on target species impeded the ability to make good management decisions. In 1979 the North Pacific Fishery Management Council Scientific and Sta- tistical Committee (SSC) recommended that scientists meet to look at the pandalid shrimp resource, in circumpolar countries where the shrimp was commercially important. The meeting was held that year and a proceedings with 42 papers was published by Alaska Sea Grant. In 1980 the SSC suggested a meeting to provide information on herring. The meetings evolved into a series named in honor of Lowell Wakefield, who founded the Alaska king crab industry. Wakefield recognized the two major ingredients necessary for the fishery to survive were ensuring that a quality product was available to the consumer, and that a viable fishery could be maintained only through sound management practices based on the best scientific data available. Lowell

x Wakefield and Wakefield Seafoods played important roles in the development and implementation of quality control legislation, in the preparation of fishing regulations for Alaska waters, and in drafting international agree- ments for the high seas. Toward the end of his career, Lowell Wakefield joined the faculty of the University of Alaska as an adjunct professor of fisheries, where he influenced the early directions of the university’s Sea Grant Program. Four Wakefield symposia are planned for 1999-2001.

xi Review of the Symposium Reviews in Fish Biology and Fisheries 8:113-115, 1998. Reprinted by per- mission of the editorial team of Reviews in Fish Biology and Fisheries.

Conference Report 15th Lowell Wakefield Fisheries Symposium Fishery Stock Assessment Models for the 21st Century: Combining Information from Multiple Sources. Having worked with fish stock assessment models for more than 20 years, I often ponder the limitations of current techniques for resolving the real problems of fishery management. Frequent reports of declining fish stocks do not inspire confidence. Obviously mindful of these problems, colleagues in Alaska organized the 15th Lowell Wakefield Fisheries Symposium on the topic: “Fishery stock assessment models for the 21st century: combining information from multiple sources.” During four sunny October days in Anchorage, 167 participants from 19 countries debated the merits of a wide spectrum of assessment techniques. The Lowell Wakefield symposia have a distinguished history of gathering fishery expertise on specialized topics. Proceedings have been published for each meeting, and the 1992 symposium on “Management strategies for exploited fish populations” went through a second printing to meet the demand. Brenda Baxter, at the University of Alaska Fairbanks, deserves particular credit for coordinating this run of 15 successful meetings. She explained to me that her approach stems from an innate Alaskan sense of hospitality. Living in splendid isolation among mountains and glaciers, Alaskans seek perspective by inviting outsiders to visit and share their knowledge. She’s right. The Alaskans make great hosts, and the isolation stimulates an intense scientific exchange. This symposium was organized into four theme sessions: data con- flicts and model specification, stage structured populations, ocean ecosystems, and harvest policy. Talks never ran concurrently. Thus, the opportunity to hear them all was limited only by a participant’s mental energy and preoccupation with interesting hallway conversations. Central issues came up repeatedly in each of the four sessions. Is stock assessment really possible; that is, do the available data really allow us to infer stock abundance and potential yield? Do ancillary data add or detract from the assessment results? In particular, can the influence of climate data be detected convincingly in modern assessment models? Recogniz- ing that ecosystems are complex, do simple or complex models lead to better understanding? Above all, what aspects of the analysis contribute to sound, useful advice for managers and stakeholders? How can this advice be communicated in ways that draw attention to risk and the need for risk management?

xii The opening keynote talk by Keith Sainsbury (Hobart, Tasmania) focused particularly on management issues, challenging many of the classi- cal approaches to assessment. For example, fishery scientists need to examine broader control options than mere quota recommendations. In a later talk, Chris Francis (Wellington, New Zealand) reviewed the concept of risk. He observed that fisheries management objectives are often conflict- ing. Thus, the measure of risk varies with the objective. Chris also provided summary comments at the close of the meeting, after an exhausting four days. Even then, had it not been for flight departures and other per- sonal reasons, I’m sure that participants would have peppered him with questions. Such was the enthusiasm and intensity of the meeting. Not surprisingly, the discussion often focused on statistical methods. Bayesian inference clearly dominates the modern analyses, in contrast with typical analyses 20 (or even 10) years ago. Furthermore, Bayes poste- rior sampling methods, such as the Markov Chain Monte Carlo (MCMC), have captured some people’s attention. At one point in the discussion, I mentioned a very readable book on MCMC methods (Gilks et al. 1996). To my surprise, Ken Newman (University of Idaho, Moscow, Idaho) actually had a copy in hand at that moment. The book’s cover, with distinct shades of red, yellow, and green, could easily be recognized across the room. This small example illustrates the common thread of new analytical techniques being pursued independently by fishery scientists worldwide. On the other hand, Saul Saila (University of Rhode Island, Narragansett, Rhode Island) demonstrated his usual flair for complete originality by present- ing analyses based on fuzzy logic and fuzzy regressions. Who can say what statistical methods will dominate analyses 20 years in the future? I take a particular interest in statistical theory, and an encounter at the meeting shed some light on its practical consequences. During a talk I presented, I cited an example in which frequentist and Bayes approaches give different interpretations of the risk of a low stock biomass. Later, at an evening gathering for wine and pizza, Kevin Sullivan (Wellington, New Zealand) pointed out that this seeming anomaly actually motivates two schools of thought in managing New Zealand fisheries. Computer software came up repeatedly in the talks. Several speakers reported positively on the use of AD Model Builder, a generic model development tool available from Otter Research Ltd. The author of this software, David Fournier (Nanaimo, British Columbia), attended the meeting and appeared as coauthor on three of the presentations. Other speakers had used Stock Synthesis, a software package designed explicitly for catch- age analyses with auxiliary data. Richard Methot, the author of Stock Syn- thesis, also attended the meeting and appeared as coauthor on one of the talks. Still other speakers preferred relatively simple analyses that could be implemented in spreadsheets. It wasn’t difficult to get involved in pas- sionate discussions about software preferences, which correlate to some extent with views about model complexity.

xiii Numerous talks described modern complex models designed to cap- ture the information from multiple data sources. Examples included: (1) eastern Bering Sea walleye pollock data linked with oceanographic data, (2) nine data sources for California bocaccio, in which the age composition data are ultimately rejected, and (3) British Columbia sablefish catch- age data linked with tag recovery data. One speaker (David Sampson, Newport, Oregon) conducted an experiment on the Stock Synthesis model itself, using simulated data to test the model’s sensitivity to various sources of error. Not everyone, however, proposed models with high complexity. For example, Daniel Pauly (University of British Columbia, Vancouver) discussed a mass balance approach to food web ecosystems. Based on data from various species, the mass balance concept implies a relatively straightfor- ward calculation of biomass requirements to sustain the web. Participants were certainly sympathetic to “back of the envelope” calculations. In fact, a few fishermen attended the meeting and made serious efforts to follow the bookkeeping in complex catch-age models. In this brief report, I’ve only sampled topics that were discussed. In- terested readers can consult the full published proceedings planned for the fall of 1998. Perhaps a final story can portray the candid spirit that characterized the meeting. Patrick Sullivan (Seattle, Washington) gave a thought-provoking talk describing recent changes in the model for Pacific halibut. These have resulted in substantially revised estimates of stock status. His analysis illustrated the variety of interpretations possible for most fishery data. He closed with a quotation from Edmund Burke, “No- body makes a greater mistake than he who does nothing because he could only do a little.” Not surprisingly, I found participants ready to debate even that point.

References Gilks, W.R., S. Richardson, and D.J. Spiegelhalter. (1996) Markov Chain Monte Carlo in Practice. London, UK, Chapman & Hall, 486 pp.

—Jon Schnute Pacific Biological Station, Nanaimo, British Columbia

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