Relative magnitude of cohort, age, and year effects on size at age of exploited marine fishes

Fisheries Research

Volumn 180, Issue , 2016, Pages 45-53

  Thorson, James T ^a   Minte Vera, Carolina V ^b,c  

^a NORTHWEST FISHERIES SCIENCE CENTER   (United States)

^b STATE UNIVERSITY OF MARINGÁ   (Brazil)

^c INTER AMERICAN TROPICAL TUNA COMMISSION   (United States)

Author keywords

Bayesian hierarchical model; Condition factor; Growth rate; Time varying growth; Von Bertlanffy growth function; Weight at age

Indexed keywords

EID: 84964334502     PISSN: 01657836     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.fishres.2014.11.016     Document Type: Article

References (50)

1. Alós J., Palmer M., Balle S., Grau A.M., Morales-Nin B. Individual growth pattern and variability in Serranus scriba: a Bayesian analysis. ICES J. Mar. Sci. (J. Cons.) 2010, 67:502-512. 10.1093/icesjms/fsp265.
2. Black B.A. Climate-driven synchrony across tree, bivalve, and rockfish growth-increment chronologies of the northeast Pacific. Mar. Ecol. Prog. Ser. 2009, 378:37-46. 10.3354/meps07854.
3. Black B.A., Schroeder I.D., Sydeman W.J., Bograd S.J., Lawson P.W. Wintertime ocean conditions synchronize rockfish growth and seabird reproduction in the central California current ecosystem. Can. J. Fish. Aquat. Sci. 2010, 67:1149-1158.
4. Brander K.M. The role of growth changes in the decline and recovery of North Atlantic cod stocks since 1970. ICES J. Mar. Sci. (J. Cons.) 2007, 64:211-217.
5. Browne W.J., Draper D. Implementation and performance issues in the Bayesian and likelihood fitting of multilevel models. Comput. Stat. 2000, 15:391-420.
6. Browne W.J., Draper D. A comparison of Bayesian and likelihood-based methods for fitting multilevel models. Bayesian Anal. 2006, 1:473-514.
7. Charnov E.L., Gislason H., Pope J.G. Evolutionary assembly rules for fish life histories. Fish Fish. 2013, 14:213-224.
8. Clark W.G., Hare S.R. Effects of climate and stock size on recruitment and growth of Pacific Halibut. North Am. J. Fish. Manage. 2002, 22:852-862. 10.1577/1548-8675(2002)022<0852:EOCASS>2.0.CO;2.
9. Daan N., Bromley P.J., Hislop J.R.G., Nielsen N.A. Ecology of North Sea fish. Neth. J. Sea Res. 1990, 26:343-386.
10. Denwood M.J. Runjags: Run Bayesian MCMC Models in the BUGS syntax from Within R 2011.
11. Froese R. Cube law, condition factor and weight-length relationships: history, meta-analysis and recommendations. J. Appl. Ichthyol. 2006, 22:241-253. 10.1111/j. 1439-0426.2006.00805.x.
12. Froese R., Thorson J.T., Reyes R.B. A Bayesian approach for estimating length-weight relationships in fishes. J. Appl. Ichthyol. 2014, 30:78-85. 10.1111/jai.12299.
13. Gelman A. Prior distributions for variance parameters in hierarchical models. Bayesian Anal. 2006, 1:515-533.
14. Gelman A., Carlin J.B., Stern H.S., Rubin D.B. Bayesian Data Analysis 2003, Chapman & Hall, Boca Raton, FL. second ed.
15. Gelman A., Rubin D.B. Inference from iterative simulation using multiple sequences. Stat. Sci. 1992, 7:457-472.
16. Helser T.E., Brodziak J.K. Impacts of density-dependent growth and maturation on assessment advice to rebuild depleted US silver hake (Merluccius bilinearis) stocks. Can. J. Fish. Aquat. Sci. 1998, 55:882-892.
17. Hilborn R., Mangel M. The Ecological Detective: Confronting Models with Data 1997, Princeton University Press, Princeton, NJ. first ed.
18. Hilborn R., Minte-Vera C.V. Fisheries-induced changes in growth rates in marine fisheries: are they significant?. Bull. Mar. Sci. 2008, 83:95-105.
19. Ianelli J.N., Honkalehto T., Barbeaux S., Kotwicki S., Aydin K., Williamson N. Assessment of the Walleye Pollock Stock in the Eastern Bering Sea, NPFMC Bering Sea and Aluetian Islands Stock Assessment and Fishery Evaluation Reports 2012, Alaska Fisheries Science Center, National Marine Fisheries Service, Seattle, WA.
20. Knaus J. Snowfall: Easier Cluster Computing (based on snow) 2010, Available at: http://cran.r-project.org/web/packages/snowfall/index.html.
21. Mangel M. The Theoretical Biologist's Toolbox: Quantitative Methods for Ecology and Evolutionary Biology 2006, Cambridge University Press.
22. Marshall C.T., Frank K.T. Implications of density-dependent juvenile growth for compensatory recruitment regulation of haddock. Can. J. Fish. Aquat. Sci. 1999, 56:356-363. 10.1139/f99-018.
23. Martell S., Stewart I. Towards defining good practices for modeling time-varying selectivity. Fish. Res. 2014, 158:84-95.
24. Mehl S., Sunnana K. Changes in growth of Northeast Arctic cod in relation to food consumption in 1984-1988. ICES Mar. Sci. Symp. 1991, 193:109-112.
25. Minte-Vera, C.V., 2004. Meta-analysis of density-dependent growth. Ph. D. Thesis, University of Washington, Seattle, 1-204.
26. Nash R.D., Valencia A.H., Geffen A.J. The origin of Fulton's condition factor-setting the record straight. Fisheries 2006, 31:236-238.
27. Plummer M. JAGS: a program for analysis of Bayesian graphical models using Gibbs sampling. Proceedings of the 3rd International Workshop on Distributed Statistical Computing (DSC 2003) 2003, (Presented at the 3rd International Workshop on Distributed Statistical Computing (DSC 2003)).
28. Punt A.E. Refocusing stock assessment in support of policy evaluation. Fisheries for Global Welfare and Environment 2008, 139-152. TerraPub, Tokyo. K. Tsukamoto, T. Kawamura, T. Takeuchi, T.D. Beard, M.J. Kaiser (Eds.).
29. Quince C., Abrams P.A., Shuter B.J., Lester N.P. Biphasic growth in fish I: theoretical foundations. J. Theor. Biol. 2008, 254:197-206.
30. Quince C., Shuter B.J., Abrams P.A., Lester N.P. Biphasic growth in fish II: empirical assessment. J. Theor. Biol. 2008, 254:207-214.
31. Quinn T.J., Deriso R.B. Quantitative Fish Dynamics 1999, Oxford University Press, Oxford, UK. first ed.
32. Ratkowsky D.A. Statistical properties of alternative parameterizations of the von Bertalanffy growth curve. Can. J. Fish. Aquat. Sci. 1986, 43:742-747.
33. R Core Development Team R: A Language and Environment for Statistical Computing 2012, R Core Development Team, Vienna, Austria.
34. Rijnsdorp A.D. Population-regulating processes during the adult phase in flatfish. Neth. J. Sea Res. 1994, 32:207-223.
35. Ruggerone G.T., Farley E., Nielsen J., Hagen P. Seasonal marine growth of Bristol Bay sockeye salmon (Oncorhynchus nerka) in relation to competition with Asian pink salmon (O. gorbuscha) and the 1977 ocean regime shift. Fish. Bull. 2005, 103:355-370.
36. Ruggerone G.T., Nielsen J.L., Bumgarner J. Linkages between Alaskan sockeye salmon abundance, growth at sea, and climate, 1955-2002. Deep Sea Res., II: Top. Stud. Oceanogr. 2007, 54:2776-2793. 10.1016/j.dsr2.2007.08.016.
37. Sainsbury K.J., Punt A.E., Smith A.D. Design of operational management strategies for achieving fishery ecosystem objectives. ICES J. Mar. Sci. (J. Cons.) 2000, 57:731-741.
38. Schindler D.E., Hilborn R., Chasco B., Boatright C.P., Quinn T.P., Rogers L.A., Webster M.S. Population diversity and the portfolio effect in an exploited species. Nature 2010, 465:609-612.
39. Shelton A.O., Munch S.B., Keith D., Mangel M. Maternal age, fecundity, egg quality, and recruitment: linking stock structure to recruitment using an age-structured Ricker model. Can. J. Fish. Aquat. Sci. 2012, 69:1631-1641.
40. Sinclair A.F., Swain D.P., Hanson J.M. Disentangling the effects of size-selective mortality, density, and temperature on length-at-age. Can. J. Fish. Aquat. Sci. 2002, 59:372-382.
41. Spiegelhalter D.J., Best N.G., Carlin B.P., Linde, van der A. Bayesian measures of model complexity and fit. J. R. Stat. Soc. Ser. B Stat. Methodol. 2002, 64:583-639.
42. Stewart I.J., Leaman B., Martell S., Webster R.A. Assessment of the Pacific halibut stock at the end of 2012. International Pacific Halibut Commission Eighty-Ninth Annual Meeting 2012.
43. Su Y.-S., Yajima M. R2jags: A Package for Running jags from R 2012, http://cran.r-project.org/web/packages/R2jags/index.html.
44. Thorson, J.T., Hicks, A.C., Methot, R., In press. Random effect estimation of time-varying factors in Stock Synthesis. ICES J. Mar. Sci. , . http://icesjms.oxfordjournals.org/content/early/2014/01/09/icesjms.fst211.abstract.
45. Thorson, J.T., Minto, C., In press. Mixed effects: a unifying framework for statistical modelling in fisheries biology. ICES J. Mar. Sci. , . http://icesjms.oxfordjournals.org/content/early/2014/12/03/icesjms.fsu213.full.
46. Thorson J.T., Scheuerell M.D., Buhle E.R., Copeland T. Spatial variation buffers temporal fluctuations in early juvenile survival for an endangered Pacific salmon. J. Anim. Ecol. 2014, 83:157-167. 10.1111/1365-2656.12117.
47. Von Bertalanffy L. Quantitative laws in metabolism and growth. Q. Rev. Biol. 1957, 32:217-231.
48. Walters C.J., Post J.R. Density-dependent growth and competitive asymmetries in size-structured fish populations: a theoretical model and recommendations for field experiments. Trans. Am. Fish. Soc. 1993, 122:34-45.
49. Whitten A.R., Klaer N.L., Tuck G.N., Day R.W. Accounting for cohort-specific variable growth in fisheries stock assessments: a case study from south-eastern Australia. Fish. Res. 2013, 142:27-36.
50. Yee E.H., Murray S.N. Effects of temperature on activity, food consumption rates, and gut passage times of seaweed-eating Tegula species (Trochidae) from California. Mar. Biol. 2004, 145:895-903.