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NOAA Technical Memorandum NMFS-NWFSC-110. Atlantis Model NOAA Technical Memorandum NMFS-NWFSC-110 Atlantis Model Development for the Northern Gulf of California May 2011 U.S. DEPARTMENT OF COMMERCE National Oceanic and Atmospheric Administration National Marine Fisheries Service NOAA Technical Memorandum NMFS-NWFSC Series The Northwest Fisheries Science Center of the National Marine Fisheries Service, NOAA, uses the NOAA Technical Memorandum NMFS-NWFSC series to issue scientific and technical publications. Manuscripts have been peer reviewed and edited. Documents published in this series may be cited in the scientific and technical literature. The NMFS-NWFSC Technical Memorandum series of the Northwest Fisheries Science Center continues the NMFS- F/NWC series established in 1970 by the Northwest & Alaska Fisheries Science Center, which has since been split into the Northwest Fisheries Science Center and the Alaska Fisheries Science Center. The NMFS-AFSC Technical Memorandum series is now used by the Alaska Fisheries Science Center. Reference throughout this document to trade names does not imply endorsement by the National Marine Fisheries Service, NOAA. This document should be referenced as follows: Ainsworth, C.H., I.C. Kaplan, P.S. Levin, R. Cudney-Bueno, E.A. Fulton, M. Mangel, P. Turk-Boyer, J. Torre, A. Pares- Sierra, and H.N. Morzaria Luna. 2011. Atlantis model development for the northern Gulf of California. U.S. Dept. Commer., NOAA Tech. Memo. NMFS-NWFSC-110, 293 p. NOAA Technical Memorandum NMFS-NWFSC-110 Atlantis Model Development for the Northern Gulf of California Cameron H. Ainsworth,1 Isaac C. Kaplan, Phillip S. Levin, Richard Cudney-Bueno,2 Elizabeth A. Fulton,3 Marc Mangel,4 Peggy Turk-Boyer,5 Jorge Torre,6 Alejandro Pares-Sierra,7 and Hem Nalini Morzaria Luna Northwest Fisheries Science Center 2725 Montlake Boulevard East Seattle, Washington 98112 1Northwest Fisheries Science Center Present affiliation: University of South Florida College of Marine Science 140 7th Avenue South St. Petersburg, Florida 33701 2The David and Lucile Packard Foundation 300 Second Street Los Altos, California 94022 3Commonwealth Scientific and Industrial Research Organization Castray Esplanade Hobart, Tasmania 7000, Australia 4University of California Santa Cruz Jack Baskin School of Engineering Center for Stock Assessment Research 1156 High Street Santa Cruz, California 95064 5Intercultural Center for the Study of Deserts and Oceans Inc. Apartado Postal Number 53 Puerto Peñasco, Sonora 83550, Mexico 6Comunidad y Biodiversidad Boulevard Agua Marina Number 297, entre Jaiba y Tiburon Colonia Delicias Guaymas, Sonora 85420, Mexico 7Centro de Investigación Científica y de Educación Superior de Ensenada Carretera Ensenada-Tijuana Number 3918, Zona Playitas Ensenada, Baja California 22860, Mexico May 2011 U.S. DEPARTMENT OF COMMERCE National Oceanic and Atmospheric Administration National Marine Fisheries Service Most NOAA Technical Memorandums NMFS-NWFSC are available online at the Northwest Fisheries Science Center Web site (http://www.nwfsc.noaa.gov) Copies are also available from: National Technical Information Service 5285 Port Royal Road Springfield, VA 22161 phone orders (1-800-553-6847) e-mail orders ([email protected]) ii Table of Contents List of Figures.........................................................................................................................................v List of Tables .........................................................................................................................................ix Executive Summary...............................................................................................................................xi Acknowledgments............................................................................................................................... xiii Abbreviations and Acronyms ...............................................................................................................xv Introduction.............................................................................................................................................1 Ecosystem-based Fisheries Management ...........................................................................................1 PANGAS ............................................................................................................................................2 Atlantis Model....................................................................................................................................2 Objective of this Technical Memorandum .........................................................................................3 Northern Gulf of California................................................................................................................3 Fisheries..............................................................................................................................................9 Methods ................................................................................................................................................12 Atlantis .............................................................................................................................................12 Northern Gulf of California Model ..................................................................................................15 Functional Groups ............................................................................................................................15 Functional Group Descriptions.........................................................................................................41 Catch Reconstruction........................................................................................................................71 Initial Conditions File (CDF) ...........................................................................................................74 Dynamics File (PRM).......................................................................................................................76 Box Geometry Model File................................................................................................................79 Oceanographic Forcing Using ROMS Model ..................................................................................81 1985 Historical Model......................................................................................................................83 Model Tuning and Diagnostics.........................................................................................................84 Results...................................................................................................................................................86 No Fishing Scenario (1985 to 2008).................................................................................................86 Historical Reconstruction (1985 to 2008) ........................................................................................87 Forward Projections from 2008........................................................................................................89 Discussion.............................................................................................................................................96 iii Beyond Single-species Methods.......................................................................................................96 Status of the Models .........................................................................................................................97 Future Applications ..........................................................................................................................98 References.............................................................................................................................................99 Appendix A: Functional Group Information ......................................................................................121 Appendix B: Basic Parameterization ..................................................................................................225 Appendix C: Field Work Protocols.....................................................................................................251 Trawl and Longline Sampling Protocol for Atlantis Gulf of California EBFM Modeling Project. PANGAS Training Protocol Version 2.0 (February 2008)..............................................251 Fish Stomach Sampling Protocol for Atlantis Gulf of California EBFM Modeling Project. PANGAS Training Protocol Version 1.0 (December 2007) ..........................................................262 Community Interview Questionnaire for Fishers in Support of Atlantis Gulf of California EBFM Modeling Project ................................................................................................................270 Appendix D: Model Dynamics ...........................................................................................................273 iv List of Figures Figure 1. Northern Gulf of California, Mexico, with major fishing communities.......................................4 Figure 2. Spawning and recruitment schedule...........................................................................................19 Figure 3. Food web diagram showing complete connectance present in availabilities matrix ..................23 Figure 4. Biomass determined using observational columns versus linear
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