Incorporating Spatial Structure in Stock Assessment: Movement Modeling in Marine Fish Population Dynamics

REFERENCES

• Adam , M. S. and Sibert , J. R. 2002 . Population dynamics and movements of skipjack tuna (Katsuwonus pelamis) in the Maldivian fishery: Analysis of tagging data from an advection-diffusion-reaction model. . Aquat. Living Resour , 15 : 13 – 23 .
   Web of Science ®Google Scholar
• Aires-da-Silva , A. M. , Maunder , M. N. , Gallucci , V. F. , Kohler , N. E. and Hoey , J. J. 2009 . A spatially-structured tagging model to estimate movement and fishing mortality rates for the blue shark (Prionace glauca) in the North Atlantic Ocean. . Mar. Freshwater Res , 60 : 1029 – 1043 .
   Web of Science ®Google Scholar
• Aldenberg , T. 1975 . Virtual population analysis and migration, a theoretical treatment , : 14 ICES C.M. 1975/F:32 (mimeo)
   Google Scholar
• Anganuzzi , A. , Hilborn , R. and Skalski , J. R. 1994 . Estimation of size selectivity and movement rates from mark-recovery data. . Can. J. Fish. Aquat. Sci. , 51 : 734 – 742 .
   Web of Science ®Google Scholar
• Bentley , N. , Davies , N. M. and McNeill , S. E. 2004 . A spatially explicit model of the snapper (Pagrus auratus) fishery in SNA1. . N.Z. Min. of Fish. , 2004/26 : 64
   Google Scholar
• Beverton , R. J. H. and Holt , S. J. 1957 . “ On the dynamics of exploited fish populations. ” . In Fisheries Investment Series 2 , London : Chapman and Hall . 19. U.K. Min. of Agr. and Fish
   Google Scholar
• Brown , C. A. , Porch , C. E. and Scott , G. P. 2005 . Gulf of Mexico greater amberjack virtual population assessment , S.E.F.S.C., Sustainable Fisheries Division. SEDAR9-AW-10
   Google Scholar
• Butterworth , D. S. and Punt , A. E. 1994 . The robustness of estimates of stock status for the western North Atlantic bluefin tuna population to violations of the assumptions underlying the associated assessment models. . Col. Vol. Sci. Pap. ICCAT , 42 : 192 – 210 .
   Google Scholar
• Cadrin , S. and Secor , D. 2009 . “ Accounting for spatial population structure in stock assessment: Past, present, and future ” . In The Future of Fisheries Science in North America , Edited by: Beamish , R. and Rothschild , B. 752 New York : Springer .
   Google Scholar
• Caswell , H. 2000 . Matrix Population Models, , 2nd ed. , Sunderland , MA : Sinauer Associates .
   Google Scholar
• Coggins , L. G. , Pine , W. E. , Walters , C. J. and Martell , S. J. 2006 . Age-structured mark-recapture analysis: A virtual-population-analysis-based model for analyzing age-structured capture-recapture data. . N. Am. J. Fish. Manage. , 26 : 201 – 205 .
   Web of Science ®Google Scholar
• Cooch , E. and White , G. C. 2010 . Program mark—a gentle introduction . Available from http://www.phidot.org/software/mark/docs/book/
   Google Scholar
• Deriso , R. B. , Punsley , R. G. and Bayliff , W. H. 1991 . A Markov movement model of yellowfin tuna in the Eastern Pacific Ocean and some analyses for international management. . Fish. Res , 11 : 375 – 395 .
   Web of Science ®Google Scholar
• Faugeras , B. and Maury , O. 2005 . An advection-diffusion-reaction size-structured fish population dynamics model combined with a statistical parameter estimation procedure: Application to the Indian Ocean skipjack tuna fishery. . Math. Biosci. Eng , 2 : 719 – 741 .
   PubMed Web of Science ®Google Scholar
• Fournier , D. A. , Hampton , J. and Sibert , J. R. 1998 . MULTIFAN-CL: A length-based, age-structured model for fisheries stock assessment, with application to South Pacific albacore, Thunnus alalunga. . Can. J. Fish. Aquat. Sci , 55 : 2105 – 2116 .
   Web of Science ®Google Scholar
• Fu , C. and Fanning , L. P. 2004 . Spatial considerations in the management of Atlantic cod off Nova Scotia, Canada. . N. Amer. J. Fish. Man , 24 : 775 – 784 .
   Web of Science ®Google Scholar
• Getz , W. M. and Haight , R. G. 1989 . Population Harvesting: Demographic Models of Fish, Forest, and Animal Resources , Princeton , NJ : Princeton University Press .
   Google Scholar
• Grant , W. E. , Matis , J. H. and Miller , T. H. 1991 . A stochastic compartmental model for migration of marine shrimp. . Ecol. Model , 54 : 1 – 15 .
   Web of Science ®Google Scholar
• Haist , V. , Fournier , D. A. and Saunders , M. W. 1999 . Reconstruction of B.C. sablefish stocks, 1966–1998, and catch projections for 1999, using an integrated catch-age mark-recapture model with area and depth movement. DFO Canada , Can. Stock Ass. Secr. Res. Doc., 99/79
   Google Scholar
• Hampton , J. 1991 . Estimation of southern bluefin tuna, Thunnus maccoyii, natural mortality and movement rates from tagging experiments . Fish. Bull. , 89 : 591 – 610 .
   Google Scholar
• Hampton , J. and Fournier , D. A. 2001 . A spatially disaggregated, length-based, age-structured population model of yellowfin tuna (Thunnus albacares) in the western and central Pacific Ocean. . Mar. Fresh. Res , 52 : 937 – 963 .
   Web of Science ®Google Scholar
• Hart , D. R. 2001 . Individual-based yield-per-recruit analysis, with an application to the Atlantic sea scallop, Placopecten magellanicus . Can. J. Fish. Aquat. Sci , 58 : 2351 – 2358 .
   Web of Science ®Google Scholar
• Hart , D. R. and Cadrin , S. 2004 . “ Yellowtail flounder (Limanda ferruginea) off the Northeastern United States: Implications of movement among stocks ” . In Applications in RAMAS , Edited by: Akçakaya , Resit and et al , H. 230 – 243 . New York : Oxford University Press .
   Google Scholar
• Heifetz , J. 1996 . Dynamics of a migratory fish population with applications to management of sablefish in the NE Pacific Ocean , PhD. Dissertation, University of Alaska Fairbanks, Juneau, AK
   Google Scholar
• Heifetz , J. and Fujioka , J. T. 1991 . Movement dynamics of tagged sablefish in the northeastern Pacific. . Fisheries Res , 11 : 355 – 374 .
   Web of Science ®Google Scholar
• Heifetz , J. and Quinn , T. J. II . 1998 . “ Dynamics of an age by region fish population model ” . In Proceedings of the Symposium on Fishery Stock Assessment Models in the 21st Century , 219 – 244 . Fairbanks , AK : Alaska Sea Grant College Program .
   Google Scholar
• Hewitt , D. A. , Janney , E. C. , Hayes , B. S. and Shively , R. S. 2010 . Improving inferences from fisheries capture-recapture studies through remote detection of PIT tags. . Fisheries , 35 : 217 – 231 .
   Web of Science ®Google Scholar
• Hightower , J. E. , Jackson , J. R. and Pollock , K. H. 2001 . Use of telemetry models to estimate natural and fishing mortality of striped bass in Lake Gaston, North Carolina. . T. Am. Fish. Soc. , 130 : 557 – 567 .
   Web of Science ®Google Scholar
• Hilborn , R. 1990 . Determination of fish movement patterns from tag recoveries using maximum likelihood estimators . Can. J. Fish. Aquat. Sci , 47 : 635 – 643 .
   Web of Science ®Google Scholar
• Ishii , T. 1979 . Attempt to estimate migration of fish population with survival parameters from tagging experiment data by the simulation method . Inv. Pesq , 43 : 301 – 317 .
   Google Scholar
• Jones , R. 1959 . A method of analysis of some tagged haddock returns. . ICES J. Mar. Sci. , 25 : 58 – 72 .
   Google Scholar
• Kritzer , J. P. and Sale , P. F. 2004 . Metapopulation ecology in the sea: from Levins' model to marine ecology and fisheries science. . Fish and Fish , 5 : 131 – 140 .
   Web of Science ®Google Scholar
• MacCall , A. D. 1990 . Dynamic Geography of Marine Fish Populations , Seattle , WA : University of Washington Press .
   Google Scholar
• Maunder , M. 1998 . Integration of tagging and population dynamics models in fisheries stock assessment , 306 Seattle : University of Washington . Ph.D. dissertation
   Google Scholar
• Maunder , M. 2000 . Software review: AD model builder. . AFS Comp. User Sect. News , XIV : 10 – 14 .
   Google Scholar
• Maunder , M. 2001 . “ Integrated tagging and catch-at-age analysis (ITCAAN): Model development and simulation testing ” . In Spatial Processes and Management of Marine Populations , Edited by: Kruse , G. H. , Bez , N. , Booth , A. , Dorn , M. W. , Hills , S. , Lipcius , R. N. , Pelletier , D. , Roy , C. , Smith , S. J. and Witherell , D. Fairbanks , AK : University of Alaska Sea Grant . AK-SG-01–02
   Google Scholar
• Maunder , M. N. 2005 . IATTC Workshop on Stock Assessment Methods La Jolla , CA November 7–11, 2005
   Google Scholar
• Methot , R. D. 2009 . Stock synthesis (ver. 3.02C) . NOAA Fish. Tool. , NOAA Fisheries
   Google Scholar
• Miller , S. E. , Quinn , T. J. and Ianelli , J. N. 2008 . “ Estimation of age-specific migration in an age-structured model ” . In Resiliency of Gadid Stocks to Fishing and Climate Change , Edited by: Kruse , G. H. , Drinkwater , K. , Ianelli , J. N. , Link , J. S. , Stram , D. L. , Wespestad , V. and Woodby , D. Fairbanks , AK : University of Alaska Sea Grant . AK-SG-08–01
   Google Scholar
• Nolan , C. P. , ed. 1999 . Proceedings of the International Conference on Integrated Fisheries Monitoring Sydney , Australia 1–5 February
   Google Scholar
• National Research Council (NRC) . 1994 . An Assessment of Atlantic Bluefin Tuna , 148 Washington , DC : National Academy Press .
   Google Scholar
• Ortiz , M. 2006 . Preliminary status of gag grouper in the Gulf of Mexico: Continuity run VPA , : 30 S.E.F.S.C., Sustainable Fisheries Division, SEDAR10-AW-03
   Google Scholar
• Palmer , M. C. , Wigley , S. E. , Hoey , J. J. and Palmer , J. E. 2007 . An evaluation of the Northeast Region's study fleet pilot program and electronic logbook system: Phases I and II , NOAA Tech. Mem., NMFS-NE-204
   Google Scholar
• Pine , W. E. , Pollock , K. H. , Hightower , J. E. , Kwak , T. J. and Rice , J. A. 2003 . A review of tagging methods for estimating fish population size and components of mortality. . Fisheries , 28 : 10 – 23 .
   Web of Science ®Google Scholar
• Pollock , K. H. , Hoenig , J. M. , Hearn , W. S. and Calingaert , B. 2001 . Tag reporting rate estimation: 1. An evaluation of the high-reward tagging method. . N. Amer. J. Fish. Man , 21 : 521 – 532 .
   Web of Science ®Google Scholar
• Porch , C. E. 1995 . Trajectory-based approaches to estimating velocity and diffusion from tagging data. . Fish. Bull , 93 : 694 – 709 .
   Google Scholar
• Porch , C. 2003 . VPA-2Box (ver. 3.01) , Ass. Prog. Doc., ICCAT
   Google Scholar
• Porch , C. E. 2004 . An age-structured assessment model for red snapper that allows for multiple stocks, fleets and habitats , S.E.F.S.C., Sustainable Fisheries Division, SEDAR7-DW-50
   Google Scholar
• Porch , C. E. and Diaz , G. A. 2004 . Virtual population analyses of Atlantic and Gulf king mackerel using tag-recapture data and alternative models of migration , : 10 S.E.F.S.C., Sustainable Fisheries Division
   Google Scholar
• Porch , C. , Kleiber , P. , Turner , S. , Sibert , J. , Bailey , R. and Cort , J. L. 1998 . The efficacy of VPA models in the presence of complicated movement patterns. . Col. Vol. Sci. Pap. ICCAT , 50 : 591 – 622 .
   Google Scholar
• Porch , C. , Turner , S. C. and Powers , J. E. 2001 . Virtual population analyses of Atlantic bluefin tuna with alternative models of transatlantic migration: 1970–1997. . Col. Vol. Sci. Pap. ICCAT , 52 : 1022 – 1045 .
   Google Scholar
• Punt , A. E. and Butterworth , D. S. 1995 . Use of tagging data within a VPA formalism to estimate migration rates of bluefin tuna across the North Atlantic. . Col. Vol. Sci. Pap. ICCAT. , 44 : 166 – 182 .
   Google Scholar
• Punt , A. E. , Pribac , F. , Walker , T. I. , Taylor , B. L. and Prince , J. D. 2000 . Stock assessment of school shark, Galeorhinus galeus, based on a spatially explicit population dynamics model. . Mar. Freshwater Res , 51 : 205 – 220 .
   Web of Science ®Google Scholar
• Punt , A. E. and Restrepo , V. R. 1995 . Some effects of ignoring mixing when managing fish populations subject to limited mixing , : 30 ICES Long-Term Management Measures Working Group, WP1
   Google Scholar
• Quinn , T. J. II and Deriso , R. B. 1999 . Quantitative Fish Dynamics , 542 New York : Oxford University Press .
   Google Scholar
• Quinn , T. J. II , Deriso , R. B. and Neal , P. R. 1990 . Migratory catch-age analysis. . Can. J. Fish. Aquat. Sci. , 47 : 2315 – 2327 .
   Web of Science ®Google Scholar
• Salvadó , C. A. M. 1993 . Population field theory with applications to tag analysis and fishery modeling: The empirical Green function. . Can. J. Fish. Aquat. Sci , 50 : 2491 – 2512 .
   Web of Science ®Google Scholar
• Schwarz , C. J. 2005 . “ Estimation of movement from tagging data ” . In Stock Identification Methods , Edited by: Cadrin , S. X , Friedland , K. D. and Waldman , J. R. San Diego : Elsevier Academic Press .
   Google Scholar
• Schnute , J. T. , Richards , L. J. and Olsen , N. 1998 . “ Statistics, software, and fish stock assessment ” . In Fishery Stock Assessment Models , Edited by: Funk , F. , Quinn , T. J. IIM , Heifetz , J. , Ianelli , J. N. , Powers , J. E. , Schweigert , J. F. , Sullivan , P. J. and Zhang , C. I. 171 – 184 . Fairbanks , AK : University of Alaska Sea Grant . AK-SG-98–01
   Google Scholar
• Seber , G. A. F. 1982 . Estimation of Animal Abundance, , 2nd ed. , London : Griffin .
   Google Scholar
• Secor , D. 2002 . Is Atlantic bluefin tuna a metapopulation? . Col. Vol. Sci. Pap. ICCAT , 54 : 390 – 399 .
   Google Scholar
• Sibert , J. R. 1984 . A two-fishery tag attrition model for the analysis of mortality, recruitment and fishery interaction , : 27 Tuna and Billfish Ass. Prog., Nuomea, New Caledonia, South Pacific Commission
   Google Scholar
• Sibert , J. R. and Fournier , D. A. 1994 . “ Evaluation of advection-diffusion equations for estimation of movement patterns from tag recovery data ” . In Proceedings of the First FAO Expert Consultation on Interactions of Pacific Ocean Tuna Fisheries Edited by: Shomura , R. , Majkowski , J. and Langi , S. Vol. 336 , 108 – 121 . Noumea , New Caledonia FAO Fish. Tech. Paper
   Google Scholar
• Sibert , J. R. , Hampton , J. , Fournier , D. A. and Bills , P. J. 1999 . An advection-diffusion-reaction model for the estimation of fish movement parameters from tagging data, with application to skipjack tuna (Katsuwonus pelamis). . Can. J. Fish. Aquat. Sci , 56 : 925 – 938 .
   Web of Science ®Google Scholar
• Sibert , J. R. , Musyl , M. K. and Brill , R. W. 2003 . Horizontal movements of bigeye tuna (Thunnus obesus) near Hawaii determined by Kalman filter analysis of archival tagging data. . Fish. Oceanogr , 12 : 141 – 151 .
   Web of Science ®Google Scholar
• Skellam , J. G. 1951 . Random dispersal in theoretical populations. . Biometrika , 38 : 196 – 218 .
   PubMed Web of Science ®Google Scholar
• Smedbol , R. K. and Stephenson , R. L. 2001 . The importance of managing within-species diversity in cod and herring fisheries of the North-Western Atlantic. . J. Fish Bio. , 59 ( Suppl. A ) : 109 – 128 .
   Google Scholar
• Stephenson , R. L. 1999 . Stock complexity in fisheries management: A perspective of emerging issues related to population sub-units . Fish. Res , 43 : 247 – 249 .
   Web of Science ®Google Scholar
• Taylor , N. , McAllister , M. K. , Block , B. and Lawson , G. 2009 . A multi stock age structured tag integrated model (MAST) for the assessment of Atlantic bluefin tuna. . Col. Vol. Sci. Pap. ICCAT. , 64 : 513 – 531 . (SCRS/2008/097)
   Google Scholar
• Williams , B. K. , Nichols , J. D. and Conroy , M. J. 2002 . Analysis and Management of Animal Populations , San Diego : Academic Press .
   Google Scholar