Contrast of Degraded and Restored Stream Habitat Using an Individual-Based Salmon Model

REFERENCES

• Beacham , T. D. and Murray , C. B. 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 .
   Web of Science ®Google Scholar
• Beechie , T. J. , Sear , D. A. , Olden , J. D. , Pess , G. R. , Buffington , J. M. , Moir , H. , Roni , P. and Pollock , M. M. 2010 . Process-based principles for restoring river ecosystems . BioScience , 60 : 209 – 222 .
   Web of Science ®Google Scholar
• Bernhardt , E. S. and Palmer , M. A. 2011 . River restoration: the fuzzy logic of repairing reaches to reverse catchment scale degradation . Ecological Applications , 21 : 1926 – 1931 .
   PubMed Web of Science ®Google Scholar
• Bernhardt , E. S. , Palmer , M. A. , Allan , J. D. , Alexander , G. , Barnas , K. , Brooks , S. , Carr , J. , Clayton , S. , Dahm , C. , Follstad-Shah , J. , Galat , D. , Gloss , S. , Goodwin , P. , Hart , D. , Hassett , B. , Jenkinson , R. , Katz , S. , Kondolf , G. M. , Lake , P. S. , Lave , R. , Meyer , J. L. , O’Donnell , T. K. , Pagano , L. , Powell , B. and Sudduth , E. 2005 . Synthesizing U.S. river restoration efforts . Science , 308 : 636 – 637 .
   PubMed Web of Science ®Google Scholar
• Booker , D. J. , Sear , D. A. and Payne , A. J. 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 .
   Web of Science ®Google Scholar
• 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
   Google Scholar
• Earley , J. T. , Colby , D. J. and Brown , M. R. 2010 . Juvenile salmonid monitoring in Clear Creek, California, from October 2008 through September 2009 , Red Bluff , California : U.S. Fish and Wildlife Service, Red Bluff Fish and Wildlife Office . Available: www.fws.gov/redbluff/cvpia.aspx. (June 2012)
   Google Scholar
• 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 .
   Google Scholar
• Giovannetti , S. L. , Brown , M. R. and Stafford , L. A. 2008 . Fall Chinook Salmon spawning area mapping for the Clear Creek restoration program, 2007 , Red Bluff , California : U.S. Fish and Wildlife Service, Red Bluff Fish and Wildlife Office . Available: www.fws.gov/redbluff/cvpia.aspx. (June 2012)
   Google Scholar
• Grimm , V. and Railsback , S. F. 2005 . Individual-based modeling and ecology , Princeton , New Jersey : Princeton University Press .
   Google Scholar
• Harvey , B. C. and Railsback , S. F. 2007 . Estimating multi-factor cumulative watershed effects on fish populations with an individual-based model . Fisheries , 32 : 292 – 298 .
   Web of Science ®Google Scholar
• Harvey , B. C. and Railsback , S. F. 2009 . Exploring the persistence of stream-dwelling trout populations under alternative real-world turbidity regimes with an individual-based model . Transactions of the American Fisheries Society , 138 : 348 – 360 .
   Web of Science ®Google Scholar
• Haschenburger , J. K. 1999 . A probability model of scour and fill depths in gravel-bed channels . Water Resources Research , 35 : 2857 – 2869 .
   Web of Science ®Google Scholar
• Hayes , J. W. , Hughes , N. F. and Kelly , L. H. 2007 . Process-based modelling of invertebrate drift transport, net energy intake and reach carrying capacity for drift-feeding salmonids . Ecological Modelling , 207 : 171 – 188 .
   Web of Science ®Google Scholar
• Healey , M. C. 1991 . “ Life history of Chinook Salmon (Oncorhynchus tshawytscha) ” . In Pacific salmon life histories , Edited by: Groot , C. and Margolis , L. 311 – 394 . Vancouver : University of British Columbia Press .
   Google Scholar
• Healey , M. C. and Heard , W. R. 1984 . Inter- and 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 .
   Web of Science ®Google Scholar
• Honea , J. M. , Jorgensen , J. C. , McClure , M. M. , Cooney , T. D. , Engie , K. , Holzer , D. and Hilborn , R. 2009 . Evaluating habitat effects on population status: influence of habitat restoration on spring-run Chinook Salmon . Freshwater Biology , 54 : 1576 – 1592 .
   Web of Science ®Google Scholar
• Jähnig , S. C. , Lorenz , A. W. , Hering , D. , Antons , C. , Sundermann , A. , Jedicke , E. and Haase , P. 2011 . River restoration success: a question of perception . Ecological Applications , 21 : 2007 – 2015 .
   PubMed Web of Science ®Google Scholar
• Jeffres , C. and Moyle , P. 2012 . When good fish make bad decisions: Coho Salmon in an ecological trap . North American Journal of Fisheries Management , 32 : 87 – 92 .
   Web of Science ®Google Scholar
• Korman , J. , Martell , S. J. D. and Walters , C. 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 .
   Web of Science ®Google Scholar
• Mesa , M. G. and Magie , C. D. 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 .
   Web of Science ®Google Scholar
• Miller , J. A. , Gray , A. and Merz , J. 2010 . Quantifying the contribution of juvenile migratory phenotypes in a population of Chinook Salmon Oncorhynchus tshawytscha . Marine Ecology Progress Series , 408 : 227 – 240 .
   Web of Science ®Google Scholar
• 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 , Weaverville , California : Report to the Clear Creek Restoration Team, NSR, Redding, California, McBain and Trush, Arcata, California, and Matthews and Associates . Available: www.srwp.org/documents/watershed/lowerclearcreek/restfish/LwrClearCreek_FloodwayRehabProject08-30-00.pdf. (June 2012)
   Google Scholar
• Railsback , S. F. and Harvey , B. C. 2001 . Individual-based model formulation for Cutthroat Trout, Little Jones Creek, California . U.S. Forest Service General Technical Report PSW-GTR-182
   Google Scholar
• Railsback , S. F. and Harvey , B. C. 2002 . Analysis of habitat-selection rules using an individual-based model . Ecology , 83 : 1817 – 1830 .
   Web of Science ®Google Scholar
• Railsback , S. F. and Harvey , B. C. 2011 . Importance of fish behaviour in modelling conservation problems: food limitation as an example . Journal of Fish Biology , 79 : 1648 – 1662 .
   PubMed Web of Science ®Google Scholar
• Railsback , S. F. , Harvey , B. C. , Jackson , S. K. and Lamberson , R. H. 2009 . InSTREAM: the individual-based stream trout research and environmental assessment model . U.S. Forest Service General Technical Report PSW-GTR-218
   Google Scholar
• Railsback , S. F. , Harvey , B. C. and White , J. L. 2012 . InSALMO version 1.0: model improvements and demonstration application to Chinook Salmon spawning, incubation, and rearing in Clear Creek, California , Arcata , California : Final Report to U.S. Bureau of Reclamation, Lang, Railsback and Associates, and U.S. Forest Service, Redwood Sciences Laboratory . Available: www.fws.gov/sacramento/Fisheries/Instream-Flow/fisheries_instream-flow_inSalmo.htm. (June 2012)
   Google Scholar
• Railsback , S. F. , Lamberson , R. H. , Harvey , B. C. and Duffy , W. E. 1999 . Movement rules for individual-based models of stream fish . Ecological Modelling , 123 : 73 – 89 .
   Web of Science ®Google Scholar
• Railsback , S. F. , Stauffer , H. B. and Harvey , B. C. 2003 . What can habitat preference models tell us? tests using a virtual trout population . Ecological Applications , 13 : 1580 – 1594 .
   Web of Science ®Google Scholar
• Roni , P. , Hanson , K. and Beechie , T. 2008 . Global review of the physical and biological effectiveness of stream habitat rehabilitation techniques . North American Journal of Fisheries Management , 28 : 856 – 890 .
   Web of Science ®Google Scholar
• Steffler , P. and Blackburn , J. 2002 . River2D—two-dimensional depth averaged model of river hydrodynamics and fish habitat: introduction to depth averaged modeling and user's manual , Edmonton : University of Alberta . Available: www.river2d.ualberta.ca/download.htm. (June 2012)
   Google Scholar
• Stewart-Koster , B. , Bunn , S. E. , MacKay , S. J. , Poff , N. L. , Naiman , R. J. and Lake , P. S. 2010 . The use of Bayesian networks to guide investments in flow and catchment restoration for impaired river ecosystems . Freshwater Biology , 55 : 243 – 260 .
   Web of Science ®Google Scholar
• USFWS (U.S. Fish and Wildlife Service) . 2005 . Monitoring of restoration projects in Clear Creek using 2-dimensional modeling methodology , Sacramento , California : USFWS, Sacramento Fish and Wildlife Office .
   Google Scholar
• USFWS (U.S. Fish and Wildlife Service) . 2006 . Phase 3A Clear Creek restoration: 2-d modeling , Sacramento , California : USFWS, Final Report, Sacramento Fish and Wildlife Office . Available: www.fws.gov/sacramento/Fisheries/Instream-Flow/fisheries_instream-flow_reports.htm. (June 2012)
   Google Scholar
• Walters , C. J. 1986 . Adaptive management of renewable resources , New York : Macmillan .
   Google Scholar
• Walters , C. J. and Holling , C. S. 1990 . Large-scale management experiments and learning by doing . Ecology , 71 : 2060 – 2068 .
   Web of Science ®Google Scholar
• Walters , C. J. , Korman , J. , Stevens , L. E. and Gold , B. 2000 . Ecosystem modeling for evaluation of adaptive management policies in the Grand Canyon . Conservation Ecology [online serial] , 4 ( 2 ) article 1
   Google Scholar
• Wheaton , J. M. , Pasternack , G. B. and Merz , J. E. 2004 . Spawning habitat rehabilitation: I. conceptual approach and methods . International Journal of River Basin Management , 2 : 3 – 20 .
   Google Scholar
• Yoshiyama , R. M. , Gerstung , E. R. , Fisher , F. W. and Moyle , P. B. 2000 . Chinook Salmon in the California Central Valley: an assessment . Fisheries , 25 ( 2 ) : 6 – 20 .
   Web of Science ®Google Scholar