Spatial variations in the distribution of yearling spring Chinook salmon off Washington and Oregon using COZIGAM analysis

Marine Ecology Progress Series

Volumn 465, Issue , 2012, Pages 253-265

  Yu, Hao ^a   Bi, Hongsheng ^a   Burke, Brian ^b   Lamb, Jesse ^c   Peterson, William ^c  

^a UNIVERSITY OF MARYLAND CENTER FOR ENVIRONMENTAL SCIENCE   (United States)

^b NORTHWEST FISHERIES SCIENCE CENTER   (United States)

^c NOAA EARTH SYSTEM RESEARCH LABORATORY   (United States)

Author keywords

Alongshore ocean current; Chlorophyll; Juvenile salmon; Yearling Chinook; Zero inflated generalized additive model

Indexed keywords

ABUNDANCE; BIOMASS; CHLOROPHYLL; COASTAL CURRENT; ENVIRONMENTAL FACTOR; SALMONID; SPATIAL DISTRIBUTION; SPATIAL VARIATION; SPATIOTEMPORAL ANALYSIS;

OREGON; UNITED STATES; WASHINGTON [UNITED STATES];

COPEPODA; ONCORHYNCHUS TSHAWYTSCHA;

EID: 84866975192     PISSN: 01718630     EISSN: None     Source Type: Journal    
DOI: 10.3354/meps09909     Document Type: Article

References (51)

1. Arab A, Wildhaber ML, Wikle CK, Gentry CN (2008) Zeroinflated modeling of fish catch per unit area resulting from multiple gears: application to channel catfish and shovelnose sturgeon in the Missouri River. N Am J Fish Manag 28: 1044-1058
2. Beale CM, Lennon JJ, Yearsley JM, Brewer MJ, Elston DA (2010) Regression analysis of spatial data. Ecol Lett 13: 246-264
3. Bi H, Ruppel RE, Peterson WT (2007) Modeling the pelagic habitat of salmon off the Pacific Northwest (USA) coast using logistic regression. Mar Ecol Prog Ser 336: 249-265
4. Bi H, Ruppel RE, Peterson WT, Casillas E (2008) Spatial distribution of ocean habitat of yearling Chinook (Oncorhynchus tshawytscha) and coho (Oncorhynchus kisutch) salmon off Washington and Oregon, USA. Fish Oceanogr 17: 463-476
5. Bi H, PetersonWT, Lamb J, Casillas E (2011a) Copepods and salmon: characterizing the spatial distribution of juvenile salmon along the Washington and Oregon coast, USA. Fish Oceanogr 20: 125-138
6. Bi H, Peterson WT, Strub PT (2011b) Transport and coastal zooplankton communities in the northern California Current system. Geophys Res Lett 38: L12607, doi: 10.1029/2011GL047927
7. Brodeur RD, Fisher JP, Teel DJ, Emmett RL, Casillas E, Miller TW (2004) Distribution, growth, condition, origin, and associations of juvenile salmonids in the northern California Current. Fish Bull 102: 25-46
8. Chhak KC, Lorenzo ED (2007) Decadal variations in the Cali fornia Current upwelling cells. Geophys Res Lett 34: L14604, doi: 10.1029/2007GL030203
9. Chhak KC, Lorenzo ED, Schneider N, Cummins PF (2009) Forcing of low-frequency ocean variability in the northeast Pacific. J Clim 22: 1255-1276
10. Ciannelli L, Fauchald P, Chan KS, Agostini VN, Dingsor GE (2008) Spatial fisheries ecology: recent progress and future prospects. J Mar Syst 71: 223-236
11. Cunningham RB, Lindenmayer DB (2005) Modeling count data of rare species: some statistical issues. Ecology 86: 1135-1142
12. Dahl J, Dannewitz J, Karlsson L, Petersson E, Löf A, Ragnarsson B (2004) The timing of spawning migration: implications of environmental variation, life history, and sex. Can J Fish Aquat Sci 82: 1864-1870
13. Friedland KD (1998) Ocean climate influences on critical Atlantic salmon (Salmo salar) life history events. Can J Fish Aquat Sci 55(Suppl 1): 119-130
14. Hall DB (2000) Zero-inflated Poisson and binomial regression with random effects: a case study. Biometrics 56: 1030-1039
15. Hickey BM (1995) Coastal submarine canyons. In: Muller P, Henderson D (eds) Proceedings of the University of Hawaii 'Aha Huliko'a Workshop on flow topography interactions. SOEST Special Publication, University of Hawaii, Honolulu, HI, p 95-110
16. Hickey BM, Banas NS (2008) Why is the northern end of the California Current system so productive? Oceanography (Wash DC) 21: 90-107
17. Hinch SG, Healey MC, Diewert RE, Thomson KA, Hourston R, Henderson MA, Juanes F (1995) Potential effects of climate change on marine growth and survival of Fraser River sockeye salmon. Can J Fish Aquat Sci 52: 2651-2659
18. Hinke JT, Foley DG, Wilson C, Watters GM(2005) Persistent habitat use by Chinook salmon Oncorhynchus tsha wytscha in the coastal ocean. Mar Ecol Prog Ser 304: 207-220
19. Hooff RC, Peterson WT (2006) Copepod biodiversity as an indicator of changes in ocean and climate conditions of the northern California Current ecosystem. Limnol Oceanogr 51: 2607-2620
20. Jonsson B, Jonsson N (2004) Factors affecting marine production of Atlantic salmon (Salmo salar). Can J Fish Aquat Sci 61: 2369-2383
21. Keister JE, Lorenzo EDI, Morgan CA, Combes V, Peterson WT (2011) Zooplankton species composition is linked to ocean transport in the northern California Current. Glob Change Biol 17: 2498-2511
22. Kendall NW, Dittman AH, Quinn TP (2010) Comparative maturation schedules of two Columbia River sockeye salmon Oncorhynchus nerka populations. Endang Species Res 13: 51-61
23. Kosro PM, Peterson WT, Hickey BM, Shearman RK, Pierce SD (2006) Physical vs. the biological spring transition: 2005. Geophys Res Lett 33: L22S03, doi: 10.1029/2006GL027072
24. Lambert D (1992) Zero-inflated Poisson regression, with an application to detects in manufacturing. Technometrics 34: 1-14
25. Latimer AM, Wu S, Gelfand AE, Silander JA (2006) Building statistical models to analyze species distribution. Ecol Appl 16: 33-50
26. Lee RF, Hagen W, Kattner G (2006) Lipid storage in marine zooplankton. Mar Ecol Prog Ser 307: 273-306
27. Liu H, Chan KS (2010) Introducing COZIGAM: an R package for unconstrained and constrained zero-inflated generalized additive model analysis. J Stat Softw 35: 1-26
28. Logerwell EA, Mantua N, Lawson PW, Francis RC, Agostini VN (2003) Tracking environmental processes in the coastal zone for understanding and predicating Oregon coho (Oncorhynchus kisutch) marine survival. Fish Oceanogr 12: 554-568
29. Mackas DL, Peterson WT, Ohman MD, Lavaniegos BE (2006) Zooplankton anomalies in the California Current system before and during the warm ocean conditions of 2005. Geophys Res Lett 33: L22S07, doi: 10.1029/2006GL027930
30. Mantua NJ, Hare SR, Zhang Y, Wallace JM, Francis RC (1997) A Pacific interdecadal climate oscillation with impacts on salmon production. Bull Am Meteorol Soc 78: 1069-1079
31. Maunder MN, Punt AE (2004) Standardizing catch and effort data: a review of recent approaches. Fish Res 70: 141-159
32. Metcalfe NB (1998) The interaction between behavior and physiology in determining life history patterns in Atlantic salmon (Salmo salar). Can J Fish Aquat Sci 55(Suppl 1): 93-103
33. Minami M, Lennert-Cody CE, Gao W, Roman-Verdesoto M (2007) Modeling shark bycatch: the zero-inflated negative binomial regression model with smoothing. Fish Res 84: 210-221
34. Moran PAP (1950) Notes on continuous stochastic phenomena. Biometrika 37: 17-23
35. Nickelson TE (1986) Influences of upwelling, ocean temperature, and smolt abundance on marine survival of coho salmon (Oncorhynchus kisutch) in the Oregon Production Area. Can J Fish Aquat Sci 43: 527-535
36. Pearcy WG (1992) Ocean ecology of North Pacific salmonids. University of Washington Press, Seattle, WA
37. Pearcy WG, Fisher JP (1990) Distribution and abundance of juvenile salmonids off Oregon and Washington, 1981-1985. NOAA Tech Rep 93: 1-83, WA
38. Peterson WT, Schwing FB (2003) A new climate regime in northeast Pacific ecosystems. Geophys Res Lett 30, doi: 10.1029/2003GL017528
39. Peterson WT, Morgan CA, Fisher JP, Casillas E (2010) Ocean distribution and habitat associations of yearling coho (Oncorhynchus kisutch) and Chinook (O. tsha wytscha) salmon in the northern California Current. Fish Oceanogr 19: 508-525
40. Pool S, Reese D, Brodeur R (2012) Defining marine habitat of juvenile Chinook salmon, Oncorhynchus tshawytscha, and coho salmon, O. kisutch, in the northern California Current system. Environ Biol Fishes 93: 233-243
41. Richards SA (2008) Dealing with overdispersed count data in applied ecology. J Appl Ecol 45: 218-227
42. Rupp DE, Wainwright TC, Lawson PW, Peterson WT (2012) Marine environment-based forecasting of coho salmon (Oncorhynchus kisutch) adult recruitment. Fish Oceanogr 21: 1-19
43. Saraceno M, Strub PT, Kosro PM(2008) Estimates of sea surface height and near-surface alongshore coastal currents from combinations of altimeters and tide gauges. J Geophys Res 113: C11013, doi: 10.1029/2008JC004756
44. Stoner A, Manderson J, Pessutti J (2001) Spatially explicit analysis of estuarine habitat for juvenile winter flounder: combining generalized additive models and geographic information systems. Mar Ecol Prog Ser 213: 253-271
45. Swartzman G, Huang C, Kaluzny S (1992) Spatial analysis of Bering Sea groundfish survey data using generalized additive models. Can J Fish Aquat Sci 49: 1366-1378
46. Trudel M, Fisher J, Orsi JA, Morris JFT and others (2009) Distribution and migration of juvenile Chinook salmon derived from coded wire tag recoveries along the continental shelf of western North America. Trans Am Fish Soc 138: 1369-1391
47. Tucker S, Trudel M, Welch DW, Candy JR and others (2011) Life history and seasonal stock-specific ocean migration of juvenile Chinook salmon. Trans Am Fish Soc 140: 1101-1119
48. Ware DM, Thomson RE (2005) Bottom-up ecosystem tropic dynamics determine fish production in the Northeast Pacific. Science 308: 1280-1284
49. Welsh AH, Cunningham RB, Donnelly CF, Lindenmayer DB (1996) Modelling the abundance of rare species: statistical models for counts with extra zeros. Ecol Model 88: 297-308
50. Wood SN (2006) Generalized additive models: an introduction with R. Chapman & Hall/CRC, Boca Raton, FL
51. Yu H, Jiao Y, Winter A (2011) Catch-rate standardization for yellow perch in Lake Erie: a comparison of the spatial generalized linear model and the generalized additive model. Trans Am Fish Soc 140: 905-918