Model selection and multimodel inference for standardizing catch rates of bycatch species: A case study of oceanic whitetip shark in the Hawaii-based longline fishery

Canadian Journal of Fisheries and Aquatic Sciences

Volumn 70, Issue 12, 2013, Pages 1723-1740

  Brodziak, Jon ^a   Walsh, William A ^b  

^a PACIFIC ISLANDS FISHERIES SCIENCE CENTER   (United States)

^b UNIVERSITY OF HAWAII   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

BYCATCH; CATCH PER UNIT EFFORT; LONGLINING; MARICULTURE; MODEL VALIDATION; POISSON RATIO; SHARK;

HAWAII [UNITED STATES]; UNITED STATES;

EID: 84888378187     PISSN: 0706652X     EISSN: 12057533     Source Type: Journal    
DOI: 10.1139/cjfas-2013-0111     Document Type: Article

References (55)

1. Aires-da-Silva, A.M., Hoey, J.J., and Gallucci, V.F. 2008. A historical index of abundance for the blue shark (Prionace glauca) in the western North Atlantic. Fish. Res. 92: 41-52. doi:10.1016/j.fishres.2007.12.019.
2. Aitchison, J. 1955. On the distribution of a positive random variable having a discrete probability mass at the origin. J. Am. Stat. Assoc. 50: 901-908. doi: 10.1080/01621459.1955.10501976.
3. Au, D.W., Smith, S.E., and Show, C. 2008. Shark productivity and reproductive protection, and a comparison with teleosts. In Sharks of the open ocean: biology, fisheries, and conservation. Edited by M.D. Camhi, E.K. Pikitch, and E.A. Babcock. Blackwell Publishing Ltd., Oxford. pp. 298-308.
4. Baum, J.K., and Blanchard, W. 2010. Inferring shark population trends from generalized linear mixed models of pelagic longline catch and effort data. Fish. Res. 102: 229-239. doi:10.1016/j.fishres.2009.11.006.
5. Bigelow, K., Musyl, M.K., Poisson, F., and Kleiber, P. 2006. Pelagic longline gear depth and shoaling. Fish. Res. 77: 173-183. doi:10.1016/j.fishres.2005.10.010.
6. Bonfil, R., Clarke, S., and Nakano, H. 2008. The biology and ecology of the oceanic whitetip shark, Carcharhinus longimanus. In Sharks of the open ocean: biology, fisheries, and conservation. Edited by M.D. Camhi, E.K. Pikitch, and E.A. Babcock. Blackwell Publishing Ltd., Oxford. pp. 128-139.
7. Buckland, S.T., Burnham, K.P., and Augustin, N.H. 1997. Model selection: an integral part of inference. Biometrics, 53: 603-618. doi:10.2307/2533961.
8. Burnham, K.P., and Anderson, D.R. 2002. Model selection and multimodel inference: a practical information-theoretic approach. 2nd ed. Springer-Verlag, New York.
9. Camhi, M.D. 2008. Conservation status of pelagic elasmobranchs. In Sharks of the open ocean: biology, fisheries, and conservation. Edited by M.D. Camhi, E.K. Pikitch, and E.A. Babcock. Blackwell Publishing Ltd., Oxford. pp. 397-417.
10. Camhi, M.D., Pikitch, E.K., and Babcock, E.A. (Editors). 2008a. Trends in catches and abundance of pelagic sharks: Introduction. In Sharks of the open ocean: biology, fisheries, and conservation. Blackwell Publishing Ltd., Oxford. pp. 163-165.
11. Camhi, M.D., Lauck, E., Pikitch, E.K., and Babcock, E.A. 2008b. A global overview of commercial fisheries for open ocean sharks. In Sharks of the open ocean: biology, fisheries, and conservation. Edited by M.D. Camhi, E.K. Pikitch, and E.A. Babcock. Blackwell Publishing Ltd., Oxford. pp. 166-192.
12. Chambers, J., and Hastie, T. (Editors). 1993. Statistical models in S. Chapman and Hall, New York.
13. Clarke, S. 2008. Use of shark fin trade data to estimate historic total shark removals in the Atlantic Ocean. Aquat. Living Resour. 21: 373-381. doi:10.1051/ alr:2008060.
14. Clarke, S., and Harley, S.J. 2010. Western and Central Pacific Fisheries Commission. Scientific Committee Sixth Regular Session, 10-19 August 2010. Nuku'alofa, Tonga. A proposal for a research plan to determine the status of the key shark species. WCPFC-SC6-2010/EB-WP-01.
15. Clarke, S.C., Magnussen, J.E., Abercrombie, D.L., McAllister, M.K., and Shivji, M.S. 2006a. Identification of shark species composition and proportion in the Hong Kong shark fin market based on molecular genetics and trade records. Conserv. Biol. 20: 201-211. doi:10.1111/j.1523-1739.2005.00247.x. PMID:16909673.
16. Clarke, S.C., McAllister, M.K., Milner-Gulland, E.J., Kirkwood, G.P., Michielsens, C.G.J., Agnew, D.J., Pikitch, E.K., Nakano, H., and Shivji, M.S. 2006b. Global estimates of shark catches using trade records from commercial markets. Ecol. Lett. 9: 1115-1126. doi:10.1111/j.1461-0248.2006.00968.x. PMID:16972875.
17. Clarke, S., Harley, S., Hoyle, S., and Rice, J. 2011. Western and Central Pacific Fisheries Commission. Scientific Committee Seventh Regular Session, 9-17 August 2011. Pohnpei, Federated States of Micronesia. An indicatorbased analysis of key shark species based on data held by SPC-OFP. WCPFCSC7-2011/EB-WP-01.
18. Clarke, S.C., Harley, S.J., Hoyle, S.D., and Rice, J.S. 2013. Population trends in Pacific Oceanic sharks and the utility of regulations on shark finning. Conserv. Biol. 27: 197-209. doi:10.1111/j.1523-1739.2012.01943.x. PMID:23110546.
19. Compagno, L.J.V. 1990. Shark exploitation and conservation. In Elasmobranchs as living resources: advances in the biology, ecology, systematics, and the status of the fisheries. Edited by H.L. Pratt, Jr., S.H. Gruber, and T. Taniuchi. NOAA Technical Report NMFS 90. pp. 391-414.
20. Crawley, M.J. 2007. The R book. John Wiley & Sons, Ltd., The Atrium, Southern Gate, Chichester, England.
21. Curran, D., and Bigelow, K. 2011. Effects of circle hooks on pelagic catches in the Hawaii-based tuna longline fishery. Fish. Res. 109: 265-275. doi:10.1016/j. fishres.2011.02.013.
22. Department of Commerce. 2004. Fisheries off West Coast states and in the western Pacific; highly migratory species fisheries. National Marine Fisheries Service, National Oceanic and Atmospheric Administration, Federal Register 69(67): 50 CFR Parts 223, 224, and 660.
23. Dulvy, N.K., Baum, J.K., Clarke, S., Compagno, L.J.V., Cortés, E., Domingo, A., Fordham, S., Fowler, S., Francis, M.P., Gibson, C., Martínez, J., Musick, J.A., Soldo, A., Stevens, J.D., and Valenti, S. 2008. You can swim but you can't hide: the global status and conservation of oceanic pelagic sharks and rays. Aquat. Conserv. Mar. Freshw. Ecosyst. 18: 459-482. doi:10.1002/aqc.975.
24. Faunce, C.H., and Barbeaux, S.J. 2011. The frequency and quantity of Alaskan groundfish catcher-vessel landings made with and without an observer. ICES J. Mar. Sci. 68: 1757-1763. doi:10.1093/icesjms/fsr090.
25. Fry, F.E.J. 1971. The effect of environmental factors on the physiology of fish. In Fish physiology. Vol. VI. Environmental relations and behavior. Edited by W.S. Hoar and D.J. Randall. Academic Press, New York. pp. 1-98.
26. Goodyear, C.P. 2003. Test of the robustness of habitat-standardized abundance indices using simulated blue marlin catch-effort data. Mar. Freshw. Res. 54: 369-381. doi:10.1071/MF01253.
27. Heithaus, M.R., Frid, A., Vaudo, J.V., Worm, B., and Wirsing, A.J. 2010. Unraveling the ecological importance of elasmobranchs. In Sharks and their relatives II: Biodiversity, adaptive physiology, and conservation. Edited by J.C. Carrier, J.A. Musick, and M.R. Heithaus. CRC Press. Boca Raton, Fla. pp. 611-637.
28. Hinton, M., and Nakano, H. 1996. Standardizing catch and effort statistics using physiological, ecological, or behavioral constraints and environmental data, with application to blue marlin (Makaira nigricans) catch and effort data from Japanese longline fisheries in the Pacific. Int.-Am. Trop. Tuna Comm. Bull. 21: 171-200.
29. Hurvich, C., and Tsai, C.-L. 1989. Regression and time series model selection in small samples. Biometrika, 76: 297-307. doi:10.1093/biomet/76.2.297.
30. Kitchell, J.F., Essington, T.E., Boggs, C.H., Schindler, D.E., and Walters, C.J. 2002. The role of sharks and longline fisheries in a pelagic ecosystem of the Central Pacific. Ecosystems, 5: 202-216. doi:10.1007/s10021-001-0065-5.
31. Lawson, T. 2011. Estimation of catch rates and catches of key shark species in tuna fisheries of the Western and Central Pacific Ocean using observer data. Scientific Committee Seventh Regular Session, 9-17 August 2011. Pohnpei, Federated States of Micronesia. A progress report on the shark work plan. WCPFC-SC7-2011/EB-IP-02.
32. Lynch, P.D., Shertzer, K.W., and Latour, R.J. 2012. Performance of methods used to estimate indices of abundance for highly migratory species. Fish. Res. 125-126: 27-39. doi:10.1016/j.fishres.2012.02.005.
33. Martin, T.G., Wintle, B.A., Rhodes, J.R., Kuhnert, P.M., Field, S.A., Low-Choy, S.J., Tyre, A.J., and Possingham, H.P. 2005. Zero tolerance ecology: improving ecological inference by modeling the source of zero observations. Ecol. Lett. 8: 1235-1246. doi:10.1111/j.1461-0248.2005.00826.x. PMID:21352447.
34. Maunder, M.N., and Punt, A.E. 2004. Standardizing catch and effort data: a review of recent approaches. Fish. Res. 70: 141-159. doi:10.1016/j.fishres.2004. 08.002.
35. Maunder, M., Hinton, M., Bigelow, K., and Langley, A. 2006. Developing indices of abundance using habitat data in a statistical framework. Bull. Mar. Sci. 79: 545-559.
36. Minami, M., Lennert-Cody, C.E., Gao, W., and Román-Verdesoto, M. 2007. Modeling shark bycatch: the zero-inflated negative binomial regression model with smoothing. Fish. Res. 84: 210-221. doi:10.1016/j.fishres.2006.10.019.
37. Musyl, M.K., Brill, R.W., Curran, D.S., Fragoso, N.M., McNaughton, L.M., Nielsen, A., Kikkawa, B.S., and Moyes, C.D. 2011. Postrelease survival, vertical and horizontal movements, and thermal habitats of five species of pelagic sharks in the central Pacific Ocean. Fish. Bull. 109: 349-368.
38. Nakano, H., and Clarke, S. 2006. Filtering method for obtaining stock indices by shark species from species-combined logbook data in tuna longline fisheries. Fish. Sci. 72: 322-332. doi:10.1111/j.1444-2906.2006.01153.x.
39. Pacific Islands Regional Office. 2011. Hawaii Longline Observer Program Field Manual. Version LM. 09.11. Honolulu.
40. Pennington, M. 1983. Efficient estimators of abundance for fish and plankton surveys. Biometrics, 39: 281-286. doi:10.2307/2530830.
41. R Development Core Team. 2008. R: a language and environment for statistical computing. R Foundation for Statistical Computing, Vienna.
42. Rice, J., and Harley, S. 2012. Stock assessment of oceanic whitetip sharks in the western and central Pacific Ocean. WCPFC-SC8-2012/SA-WP-06 Rev 1.
43. Searle, S. 1987. Linear models for unbalanced data. John Wiley and Sons, New York.
44. Smith, S.E., Au, D.W., and Show, C. 1998. Intrinsic rebound potentials of 26 species of Pacific sharks. Mar. Freshw. Res. 49: 663-678. doi:10.1071/MF97135.
45. Stefánsson, G. 1996. Analysis of groundfish survey abundance data: combining the GLM and delta approaches. ICES. J. Mar. Sci. 53: 577-588. doi:10.1006/ jmsc.1996.0079.
46. Stevens, J.D. 2010. Epipelagic oceanic elasmobranchs. In Sharks and their relatives. II: Biodiversity, adaptive physiology, and conservation. Edited by J.C. Carrier, J.A. Musick, and M.R. Heithaus. CRC Press, Boca Raton, Fla. pp. 3-35.
47. Stevens, J.D., Bonfil, R., Dulvy, N.K., and Walker, P.A. 2000. The effects of fishing on sharks, rays, and chimaeras (chondrichthyans), and the implications for marine ecosystems. ICES. J. Mar. Sci. 57: 476-494. doi:10.1006/jmsc.2000. 0724.
48. Tavares, R., Ortiz, M., and Arocha, F. 2012. Population structure, distribution and relative abundance of the blue shark (Prionace glauca) in the Caribbean Sea and adjacent waters of the North Atlantic. Fish. Res. 129-130: 137-152. doi: 10.1016/j.fishres.2012.06.018.
49. Walsh, W.A., and Clarke, S.C. 2011. Analysis of catch data for oceanic whitetip and silky sharks reported by fishery observers in the Hawaii-based longline fishery in 1995-2010. Pacific Islands Fisheries Science Center Admin. Rep. H-11-10.
50. Walsh, W.A., Kleiber, P., and McCracken, M. 2002. Comparison of logbook reports of incidental blue shark catch rates by Hawaii-based longline vessels to fishery observer data by application of a generalized additive model. Fish. Res. 58: 79-94. doi:10.1016/S0165-7836(01)00361-7.
51. Walsh, W.A., Ito, R.Y., Kawamoto, K.E., and McCracken, M. 2005. Analysis of logbook accuracy for blue marlin (Makaira nigricans) in the Hawaii-based longline fishery with a generalized additive model and commercial sales data. Fish. Res. 75: 175-192. doi:10.1016/j.fishres.2004.11.007.
52. Walsh, W.A., Bigelow, K.A., and Ito, R.Y. 2007. Corrected catch histories and logbook accuracy for billfishes (Istiophoridae) in the Hawaii-based longline fishery. NOAA Tech. Memo. NMFS-PIFSC-13.
53. Walsh, W.A., Bigelow, K.A., and Sender, K.L. 2009. Decreases in shark catches and mortality in the Hawaii-based longline fishery as documented by fishery observers. Mar. Coast. Fish. Dyn. Manage. Ecosyst. Sci. 1: 270-282. doi:10.1577/ C09-003.1.
54. Zeileis, A., Klieber, C., and Jackman, S. 2008. Regression models for count data in R. J. Stat. Softw. 27(8): 1-25.
55. Zuur, A.E., Ieno, E.N., Walker, N.J., Saveliev, A.A., and Smith, G.M. 2009. Zerotruncated and zero-inflated models for count data. In Mixed effects models and extensions in ecology with R. Springer Science + Business Media, LLC, New York. pp. 261-293.