NOAA Technical Memorandum NMFS-NWFSC-110. Atlantis Model

313 Pages·2011·5.49 MB·Spanish

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])
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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
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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

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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 transects.................................29
Figure 5. Trawl and longline survey design...............................................................................................31
Figure 6. Seasonal fish biomass estimates from PANGAS sampling and literature values......................33
Figure 7. Grid points used for transect biomass allocation algorithm.......................................................34
Figure 8. Substrate map supporting transect biomass allocation algorithm...............................................36
Figure 9. Fishery utilization areas: shallow reef species and deep reef species.........................................37
Figure 10. Biogeographic regions of the northern gulf, based on principle components analysis of
pigment concentration time series at 33 locations......................................................................................68
Figure 11. Fish gape size versus length from sampling.............................................................................78
Figure 12. Atlantis polygons with box numbers........................................................................................80
Figure 13. Bathymetry with Atlantis polygons overlayed.........................................................................80
Figure 14. Spatial domain and grid resolution of the Gulf of California ROMS model............................82
Figure 15. Sea surface temperature example for northern Gulf of California ROMS model....................83
Figure 16. Annual mean water transport, temperature, and salinity example for the northern Gulf of
California ROMS model.............................................................................................................................83
Figure 17. Unexploited biomass predicted by the tuned 1985 model........................................................87
Figure 18. Reserve nitrogen and structural nitrogen at the end of the no-fishing scenario relative to
initial conditions in the 1985 model............................................................................................................88
Figure 19. Predicted versus observed biomass in 2008.............................................................................90
Figure 20. Predicted reef fish distribution in 2028....................................................................................91
Figure 21. Predicted demersdal fish distribution in 2028..........................................................................91
Figure 22. Predicted invertebrate distribution in 2028...............................................................................92
Figure 23. Predicted mammal distribution in 2028....................................................................................92
Figure 24. Predicted chemical distribution in 2028...................................................................................92
Figure B-1. Length-weight relationships determined from sampling for 12 functional groups..............226
Figure B-2. Length-weight relationships determined from sampling for eight functional groups..........227
Figure B-3. Biomass by sediment type predicted by biomass allocation algorithm for 20 functional
groups........................................................................................................................................................228
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Figure B-4. Biomass by sediment type predicted by biomass allocation algorithm for 15 functional
groups........................................................................................................................................................229
Figure B-5. Spatial biomass distributions of 12 functional groups by polygon for 2008 model.............230
Figure B-6. Spatial biomass distributions of 12 functional groups by polygon for 2008 model.............231
Figure B-7. Spatial biomass distributions of 12 functional groups by polygon for 2008 model.............232
Figure B-8. Spatial biomass distributions of 12 functional groups by polygon for 2008 model.............233
Figure B-9. Spatial biomass distributions of seven functional groups by polygon for 2008 model........234
Figure B-10. Relative biomass time series...............................................................................................235
Figure B-11. Catch reconstruction for 18 northern Gulf of California functional groups.......................236
Figure B-12. Catch reconstruction for 15 northern Gulf of California functional groups.......................237
Figure C-1. Randomly selected work sites..............................................................................................253
Figure C-2. Trawl and longline survey design at site level west of Puerto Peñasco...............................255
Figure C-3. Trawl and longline survey design at site level east of Puerto Peñasco.................................256
Figure C-4. Data entry form (page 1 of 2)...............................................................................................257
Figure C-5. Data entry form (page 2 of 2)...............................................................................................258
Figure C-6. Trawl and longline survey design.........................................................................................259
Figure C-7. Trawl depth should not exceed 12 m....................................................................................260
Figure C-8. Specimen collection form.....................................................................................................263
Figure C-9. Fork length and total length for fish specimen.....................................................................264
Figure C-10. Gape size of fish specimen.................................................................................................265
Figure C-11. Laboratory analysis form....................................................................................................266
Figure C-12. Example of completed laboratory analysis form................................................................269
Figure D-1. Biomass dynamics 1985–2008 for 15 functional groups.....................................................274
Figure D-2. Biomass dynamics 1985–2008 for 15 functional groups.....................................................275
Figure D-3. Biomass dynamics 1985–2008 for 15 functional groups.....................................................276
Figure D-4. Biomass dynamics 1985–2008 for 14 functional groups.....................................................277
Figure D-5. Numbers dynamics by age-class 1985–2008 for 15 functional groups................................278
Figure D-6. Numbers dynamics by age-class 1985–2008 for 15 functional groups................................279
Figure D-7. Numbers dynamics by age-class 1985–2008 for five functional groups..............................280
Figure D-8. Reserve nitrogen dynamics by age-class 1985–2008 for 15 functional groups...................281
Figure D-9. Reserve nitrogen dynamics by age-class 1985–2008 for 15 functional groups...................282
Figure D-10. Reserve nitrogen dynamics by age-class 1985–2008 for five functional groups...............283
Figure D-11. Structural nitrogen dynamics by age-class 1985–2008 for 15 functional groups..............284
Figure D-12. Structural nitrogen dynamics by age-class 1985–2008 for 15 functional groups..............285
Figure D-13. Structural nitrogen dynamics by age-class 1985–2008 for five functional groups............286
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Figure D-14. Annual values of catch and biomass in simulation 1985–2008 for 24 functional groups..287
Figure D-15. Annual values of catch and biomass in simulation 1985–2008 for 24 functional groups..288
Figure D-16. Annual values of biomass in simulation 1985–2008 for 24 functional groups..................289
Figure D-17. Annual values of biomass in simulation 1985–2008 for 24 functional groups..................290
Figure D-18. Multispecies catch and biomass equilibrium plots for 20 functional groups.....................291
Figure D-19. Multispecies catch and biomass equilibrium plots for 20 functional groups.....................292
Figure D-20. Multispecies catch and biomass equilibrium plots for 19 functional groups.....................293

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