Contrast of degraded and restored stream habitat using an individual-based salmon model

North American Journal of Fisheries Management

Volumn 33, Issue 2, 2013, Pages 384-399

  Railsback, Steven F ^a   Gard, Mark ^b   Harvey, Bret C ^c   White, Jason L ^c   Zimmerman, Julie K H ^b  

^a Railsback and Associates   (United States)

^b U S FISH AND WILDLIFE SERVICE   (United States)

^c PACIFIC SOUTHWEST RESEARCH STATION   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

EMERGENCE; FEEDING; FRESHWATER; GRAVEL; HABITAT RESTORATION; INDIVIDUAL-BASED MODEL; JUVENILE; PREDATION RISK; SALMONID; SALMONID FISHERY; SPAWNING; STREAM; SURVIVAL;

CALIFORNIA; UNITED STATES;

ONCORHYNCHUS TSHAWYTSCHA;

EID: 84876555644     PISSN: 02755947     EISSN: 15488675     Source Type: Journal    
DOI: 10.1080/02755947.2013.765527     Document Type: Article

References (40)

1. Beacham, T. D., and C. B. Murray. 1990. Temperature, egg size, and development of embryos and alevins of five species of Pacific salmon: a comparative analysis. Transactions of the American Fisheries Society 119:927-945.
2. Beechie, T. J., D. A. Sear, J. D. Olden, G. R. Pess, J. M. Buffington, H. Moir, P. Roni, and M. M. Pollock. 2010. Process-based principles for restoring river ecosystems. BioScience 60:209-222.
3. Bernhardt, E. S., and M. A. Palmer. 2011. River restoration: the fuzzy logic of repairing reaches to reverse catchment scale degradation. Ecological Applications 21:1926-1931.
4. Bernhardt, E. S., M. A. Palmer, J. D. Allan, G. Alexander, K. Barnas, S. Brooks, J. Carr, S. Clayton, C. Dahm, J. Follstad-Shah, D. Galat, S. Gloss, P. Goodwin, D. Hart, B. Hassett, R. Jenkinson, S. Katz, G. M. Kondolf, P. S. Lake, R. Lave, J. L. Meyer, T. K. O'Donnell, L. Pagano, B. Powell, and E. Sudduth. 2005. Synthesizing U.S. river restoration efforts. Science 308:636-637.
5. Booker, D. J., D. A. Sear, and A. J. Payne. 2001. Modelling three-dimensional flow structures and patterns of boundary shear stress in a natural pool-riffle sequence. Earth Surface Processes and Landforms 26:553-576.
6. Bovee, K. D. 1982. A guide to stream habitat analysis using the instream flow incremental methodology. U.S. Fish and Wildlife Service FWS/OBS-82/26.
7. Earley, J. T., D. J. Colby, and M. R. Brown. 2010. Juvenile salmonid monitoring in Clear Creek, California, from October 2008 through September 2009. U.S. Fish and Wildlife Service, Red Bluff Fish and Wildlife Office, Red Bluff, California. Available: www.fws.gov/redbluff/cvpia.aspx. (June 2012).
8. Gard, M. 2006. Modeling changes in salmon spawning and rearing habitat associated with river channel restoration. International Journal of River Basin Management 4:201-211.
9. Giovannetti, S. L., M. R. Brown, and L. A. Stafford. 2008. Fall Chinook Salmon spawning area mapping for the Clear Creek restoration program, 2007. U.S. Fish and Wildlife Service, Red Bluff Fish and Wildlife Office, Red Bluff, California. Available: www.fws.gov/redbluff/cvpia.aspx. (June 2012).
10. Grimm, V., and S. F. Railsback. 2005. Individual-based modeling and ecology. Princeton University Press, Princeton, New Jersey.
11. Harvey, B. C., and S. F. Railsback. 2007. Estimating multi-factor cumulative watershed effects on fish populations with an individual-based model. Fisheries 32:292-298.
12. Harvey, B. C., and S. F. Railsback. 2009. Exploring the persistence of streamdwelling trout populations under alternative real-world turbidity regimes with an individual-based model. Transactions of the American Fisheries Society 138:348-360.
13. Haschenburger, J. K. 1999. A probability model of scour and fill depths in gravel-bed channels. Water Resources Research 35:2857-2869.
14. Hayes, J. W., N. F. Hughes, and L. H. Kelly. 2007. Process-based modelling of invertebrate drift transport, net energy intake and reach carrying capacity for drift-feeding salmonids. Ecological Modelling 207:171-188.
15. Healey, M. C. 1991. Life history of Chinook Salmon (Oncorhynchus tshawytscha). Pages 311-394 in C. Groot and L. Margolis, editors. Pacific salmon life histories. University of British Columbia Press, Vancouver.
16. Healey, M. C., and W. R. Heard. 1984. Interand intra-population variation in the fecundity of Chinook Salmon (Oncorhynchus tshawytscha) and its relevance to life history theory. Canadian Journal of Fisheries and Aquatic Sciences 41:476-483.
17. Honea, J. M., J. C. Jorgensen, M. M. McClure, T. D. Cooney, K. Engie, D. Holzer, and R. Hilborn. 2009. Evaluating habitat effects on population status: influence of habitat restoration on spring-run Chinook Salmon. Freshwater Biology 54:1576-1592.
18. Jähnig, S. C., A. W. Lorenz, D. Hering, C. Antons, A. Sundermann, E. Jedicke, and P. Haase. 2011. River restoration success: a question of perception. Ecological Applications 21:2007-2015.
19. Jeffres, C., and P. Moyle. 2012. When good fish make bad decisions: Coho Salmon in an ecological trap. North American Journal of Fisheries Management 32:87-92.
20. Korman, J., S. J. D. Martell, and C. Walters. 2011. Describing population dynamics for early life stages of Rainbow Trout (Oncorhynchus mykiss) using a stock synthesis model. Canadian Journal of Fisheries and Aquatic Sciences 68:1110-1123.
21. Mesa, M. G., and C. D. Magie. 2006. Evaluation of energy expenditure in adult spring Chinook Salmon migrating upstream in the Columbia River basin: an assessment based on sequential proximate analysis. River Research and Applications 22:1085-1095.
22. Miller, J. A., A. Gray, and J. Merz. 2010. Quantifying the contribution of juvenile migratory phenotypes in a population of Chinook Salmon Oncorhynchus tshawytscha. Marine Ecology Progress Series 408:227-240.
23. NSR (North State Resources), McBain and Trush, and Matthews and Associates. 2000. Lower Clear Creek floodway rehabilitation project: channel reconstruction, riparian vegetation, and wetland creation design document. Report to the Clear Creek Restoration Team, NSR, Redding, California, McBain and Trush, Arcata, California, and Matthews and Associates, Weaverville, California. Available: www.srwp.org/documents/watershed/lowerclearcreek/restfish/LwrClearCreekFloodwayRehabProject08-30-00.pdf. (June 2012).
24. Railsback, S. F., and B. C. Harvey. 2001. Individual-based model formulation for Cutthroat Trout, Little Jones Creek, California. U.S. Forest Service General Technical Report PSW-GTR-182.
25. Railsback, S. F., and B. C. Harvey. 2002. Analysis of habitat-selection rules using an individual-based model. Ecology 83:1817-1830.
26. Railsback, S. F., and B. C. Harvey. 2011. Importance of fish behaviour in modelling conservation problems: food limitation as an example. Journal of Fish Biology 79:1648-1662.
27. Railsback, S. F., B. C. Harvey, S. K. Jackson, and R. H. Lamberson. 2009. InSTREAM: the individual-based stream trout research and environmental assessment model. U.S. Forest Service General Technical Report PSW-GTR218.
28. Railsback, S. F., B. C. Harvey, and J. L. White. 2012. InSALMO version 1.0: model improvements and demonstration application to Chinook Salmon spawning, incubation, and rearing in Clear Creek, California. Final Report to U.S. Bureau of Reclamation, Lang, Railsback and Associates, and U.S. Forest Service, Redwood Sciences Laboratory, Arcata, California. Available: www.fws.gov/sacramento/Fisheries/Instream-Flow/fisheriesinstreamflowinSalmo.htm. (June 2012).
29. Railsback, S. F., R. H. Lamberson, B. C. Harvey, and W. E. Duffy. 1999. Movement rules for individual-based models of stream fish. Ecological Modelling 123:73-89.
30. Railsback, S. F., H. B. Stauffer, and B. C. Harvey. 2003. What can habitat preference models tell us? tests using a virtual trout population. Ecological Applications 13:1580-1594.
31. Roni, P., K. Hanson, and T. Beechie. 2008. Global review of the physical and biological effectiveness of stream habitat rehabilitation techniques. North American Journal of Fisheries Management 28:856-890.
32. Steffler, P., and J. Blackburn. 2002. River2D-two-dimensional depth averaged model of river hydrodynamics and fish habitat: introduction to depth averaged modeling and user's manual. University of Alberta, Edmonton. Available: www.river2d.ualberta.ca/download.htm. (June 2012).
33. Stewart-Koster, B., S. E. Bunn, S. J. MacKay, N. L. Poff, R. J. Naiman, and P. S. Lake. 2010. The use of Bayesian networks to guide investments in flow and catchment restoration for impaired river ecosystems. Freshwater Biology 55:243-260.
34. USFWS (U.S. Fish and Wildlife Service). 2005. Monitoring of restoration projects in Clear Creek using 2-dimensional modeling methodology. USFWS, Sacramento Fish and Wildlife Office, Sacramento, California.
35. USFWS (U.S. Fish and Wildlife Service). 2006. Phase 3A Clear Creek restoration: 2-d modeling. USFWS, Final Report, Sacramento Fish and Wildlife Office, Sacramento, California. Available: www.fws.gov/sacramento/Fisheries/Instream-Flow/fisheriesinstream-flowreports.htm. (June 2012).
36. Walters, C. J. 1986. Adaptive management of renewable resources. Macmillan, New York.
37. Walters, C. J., and C. S. Holling. 1990. Large-scale management experiments and learning by doing. Ecology 71:2060-2068.
38. Walters, C. J., J. Korman, L. E. Stevens, and B. Gold. 2000. Ecosystem modeling for evaluation of adaptive management policies in the Grand Canyon. Conservation Ecology [online serial] 4(2):article 1.
39. Wheaton, J. M., G. B. Pasternack, and J. E. Merz. 2004. Spawning habitat rehabilitation: I. conceptual approach and methods. International Journal of River Basin Management 2:3-20.
40. Yoshiyama, R. M., E. R. Gerstung, F. W. Fisher, and P. B. Moyle. 2000. Chinook Salmon in the California Central Valley: an assessment. Fisheries 25(2):6-20.