Biological Opinions - Bureau of Reclamation

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Strange, J. S. 2011. Salmonid use of thermal refuges in the Klamath River: 2010 annual monitoring study. Final Technical Report. Yurok Tribal Fisheries Program. Hoopa, CA. May. Stone, R., J.S. Foott, and R. Fogerty. 2008. Comparative susceptibility to infection and disease from Ceratomyxa shasta and Parvicapsula minibicornis in Klamath River basin juvenile Chinook, Coho and Steelhead populations. US Fish and Wildlife Service California- Nevada Fish Health Center. Anderson, CA. http://www.fws.gov/canvfhc/reports.asp. Stutzer, G. M., J. Ogawa, N. J. Hetrick, and T. Shaw. 2006. An initial assessment of radio telemetry for estimating juvenile coho salmon survival, migration behavior, and habitat use in response to Iron Gate Dam discharge on the Klamath River, California. U. S. Fish and Wildlife Service, Arcata Fish and Wildlife Office, Arcata Fisheries Technical Report Number TR2006-05, Arcata, California. Sullivan, K., D.J. Martin, R.D. Cardwell, J. E. Toll, and S. Duke. 2000. An analysis of the effects of temperature on salmonids of the Pacific Northwest with implications for selecting temperature criteria. Sustainable Ecosystems Institute. Portland, Oregon. Sutton, R., M. Deas, R. Faux, R. A. Corum, T. Soto, M. Belchik, J. E. Holt, B. W. McCovey Jr., and F. J. Myers. 2004. Klamath River Thermal Refugia Study, Summer 2003. Prepared for the Klamath Area Office, Bureau of Reclamation, Klamath Fall, Oregon. 147 p. Sutton, R. J., M. L. Deas, S. K. Tanaka, T. Soto, R. A. Corum. 2007. Salmonid Observations at a Klamath River Thermal Refuge Under Various Hydrological and Meteorological Conditions. River Research and Applications. Available at: http://www3.interscience.wiley.com/cgi-bin/fulltext/114228897/PDFSTART Sutton, R. and T. Soto. 2010. Juvenile coho salmon behavior characteristics in Klamath River summer thermal refugia. River Res. Applic. doi:10.1002/rra.1459 Swan, G. A. 1989. Chinook salmon spawning surveys in deep waters of a large, regulated river. Regulated Rivers: Research and Management 4:355-370. Swanston, D. N. 1991. Natural processes. pp. 139-179. In W. R. Meehan, editor. Influences of forest and rangeland management on salmonid fishes and their habitats. Amer. Fish. Soc. Spec. Publ. 19. 751 p. Sweeting, R. M., R. J. Beamish, D. J. Noakes and C. M. Neville. 2003. Replacement of wild coho salmon by hatchery-reared coho salmon in the Strait of Georgia over the past three decades. Trans. Am. Fish. Soc. 23: 492-502. Tanaka, S. K. 2007. Modeling to Improve Environmental System Management: Klamath River Thermal Refugia and the Sacramento-San Joaquin Delta. Ph.D Dissertation. University of California at Davis. 471
Taylor, R. 1991. A review of local adaptation in Salmonidae, with particular reference to Atlantic and Pacific salmon. Aquaculture 11: 185–207. Tharme, R. E. 2003. A global perspective on environmental flow assessment: emerging trends in the development and application of environmental flow methodologies for rivers. River Research and Applications 19:397–442. Thomas, C.D., A. Cameron, R.E. Green, M. Bakkenes, L.J. Beaumont, Y.C. Collingham, B.F.N. Erasmus, M.F. de Siqueira, A. Grainger, L. Hannah, L. Hughes, B. Huntley, A.S. van Jaarsveld, G.F. Midgley, L. Miles, M.A. Ortega-Huerta, A. Townsend Peterson, O.L. Phillips, and S.E. Williams. 2004. Extinction risk from climate change. Nature 427. Thomas, J. W., M. G. Raphael, R. G. Anthony, E. D. Forsman, A. G. Gunderson, R. S. Holthausen, B. G. Marcot, G. H. Reeves, J. R. Sedell, and D. M. Solis. 1993. Viability assessments and management considerations for species associated with late-successional and old-growth forest of the Pacific Northwest. Research Report of the Scientific Analysis Team. U.S. Forest Service, Washington, D.C. 530 pp Thomas, V.G. 1985. Experimentally determined impacts of a small, suction gold dredge on a Montana stream. North American Journal of Fisheries Management 5: 480-488. Trihey and Associates. 1996. Instream Flow Requirements for Tribal Trust Species in the Klamath River. Prepared on behalf of the Yurok Tribe. March. True, K, A. Bolick and JS Foott. 2012. FY2008 Investigational Study: Prognosis of Ceratomyxa shasta and Parvicapsula minibicornis infections in Klamath River coho and Trinity River Chinook. U.S. Fish & Wildlife Service California – Nevada Fish Health Center, Anderson, CA. True, K., A. Bolick, and J.S. Foott. 2013. FY 2012 Investigational Report: Myxosporean Parasite (Ceratomyxa shasta and Parvicapsula minibicornis) Annual Prevalence of Infection in Klamath River Basin Juvenile Chinook Salmon, April-August 2012. U.S. Fish & Wildlife Service California – Nevada Fish Health Center, Anderson, CA. True, K., Foott J.S., Bolick A., Benson S., Fogerty R. 2010. Myxosporean parasite (Ceratomyxa shasta and Parvicapsula minibicornis) incidence and severity in Klamath Basin juvenile Chinook salmon, April-August 2009. FY 2009 Investigational Report. U.S. Fish and Wildlife Service, California–Nevada Fish Health Center, Anderson, California. Trush, B. 2007. Commentary on the Klamath River Settlement Agreement. McBain and Trush. Arcata, CA. November 9. Tschaplinski, P. J. 1988. The use of estuaries as rearing habitats by juvenile coho salmon. In Proceedings of a Workshop: Applying 15 Years of Carnation Creek Results. Edited by T.W. Chamberlin. Carnation Creek Steering Committee, Nanaimo, B.C. pp. 123–142. 472
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National Marine Fisheries Service U
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7.4.5 LRS and SNS Population Dynami
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11.1.5 Critical Assumptions .......
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16 APPENDICIES ....................
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Table 8.2 UKL end-of-month elevatio
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LIST OF FIGURES Figure 3.1. The act
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Figure 11.17. Coho salmon fry habit
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ABBREVIATIONS AND ACRONYMS Abbrevia
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Abbreviation/Acronym YTEP WDFW WRIM
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In 2001, the Services issued BiOps
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Findings of Fact and Order of Deter
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proposed changes to the vegetation
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Figure 3.1. The action area for Rec
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4 PROPOSED ACTION Reclamation propo
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4.2 Element Two Operate the Project
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October 1 and March 1. The proposed
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Reclamation incorporated the 1981 t
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Provide Project irrigation deliveri
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Table 4.3. UKL fill rate adjustment
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Table 4.5. Calculation of fall/wint
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Flows below IGD are ultimately the
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The EWA, Project Supply, and UKL Re
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Table 4.8. Environmental Water Acco
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eleases somewhat on the ascending l
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fish disease, die off, entrainment,
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acre-feet when the Project Supply c
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Table 4.11. Monthly maximum Lower K
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4.2.4 Ramp-Down Rates at Iron Gate
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progresses and EWA volumes are upda
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O&M activities are carried out eith
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1. The A Canal has six headgates th
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Therefore, Reclamation proposes to
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coordinate with the NMFS to develop
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the confluence with Omogar Creek at
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though several major improvements t
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Sucker larvae transform into age-0
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units: (1) Clear Lake; (2) Tule Lak
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Figure 7.2. Adult spawning populati
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Table 7.1. Estimated LRS and SNS ad
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1905, Ch. 567, 33 Stat. 714). The P
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Figure 7.4 Modeled April through No
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7.9.2 Klamath Basin The Oregon Clim
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A change in mean precipitation rang
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Table 7.2 Impaired water bodies wit
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Table 7.3 Seasonal comparisons of p
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ammonia that is lethal to 50 percen
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Table 7.4 Estimated external phosph
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examination of juvenile suckers fro
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Evaluation of baseline hydrology in
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2012 1931 through 2012 12.6% 0.24 5
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The overall water year trend (Table
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Figure 7.7 Sprague River trends, wa
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Figure 7.9 Sprague River trends, wa
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Figure 7.12 Williamson River trends
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Figure 7.14 UKL trends, water years
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Figure 7.17 UKL: net inflow departu
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7.10.3.3 Competition and Predation
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By late July, surviving larval suck
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Threat Nature of Threat Life Stage
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2011) and increased adult spawning
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Based on the best available informa
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contrast, water levels began 1.5 ft
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evaporation and seepage estimated a
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prolonged low oxygen conditions if
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The April through September 4,034.6
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8 EFFECTS OF THE ACTION ON LOST RIV
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Although the volume of Project wate
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than 1 m), and fitting one or more
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Figure 8.3. UKL elevations at the e
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Services and Reclamation will deter
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For cumulative net inflow values be
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Figure 8.8. UKL elevations at the e
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Figure 8.10. UKL elevations at the
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Figure 8.12. UKL elevations at the
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natural and man-caused changes in i
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Table 8.1 UKL end-of-month surface
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UKL. Based on best available inform
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larvae in UKL. Annual production of
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Table 8.5 UKL end-of-month elevatio
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Based on our review of the literatu
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into the Pelican Bay water quality
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We assume that UKL surface elevatio
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vary by several orders of magnitude
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survival rates, we know that some o
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populations, and contains the large
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8.3.5.1 Effects to Adult Sucker Spa
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Table 8.8 Clear Lake surface elevat
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occur, especially in the west lobe.
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Table 8.9 End of the month surface
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8.3.7.4 Effects of Entrainment Loss
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The source of the sediment is unkno
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period when they migrate upstream t
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limited LRS and SNS persistence in
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term and localized and because fish
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8.5.1 Canal Salvage Reclamation pro
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high predation rates and failure of
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include the Klamath Basin Rangeland
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Figure 9.1 Designated CHUs for the
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These are discussed in greater deta
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The proposed action will have no ef
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No other spawning habitat exists be
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consulted on. Current monitoring da
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proposed action and this PCE suppor
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Because of a multi-decade lack of r
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Adverse effects of the proposed act
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that juvenile survival is most like
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elocation effort in Lake Ewauna to
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LRS and SNS population resiliency o
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stratum 4 (Interior Klamath) in whi
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Pacific salmonids Oncorhynchus spp.
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scenario, actions and elements of t
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flow prescriptions should mimic pro
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11.2.1 Current Condition of Critica
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11.2.2 Factors Affecting SONCC Coho
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e disoriented or displaced downstre
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enhancement, and rehabilitative act
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Water Temperature Sedimentation Org
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Figure 11.1 Longitudinal and season
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functioning floodplains that fail t
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downstream of IGD, (2) enhance coho
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few local ranchers and water distri
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in some tributaries, access to and
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11.3.7 Summary of Critical Habitat
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these two time periods, the effects
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consists of approximately 29,000 ac
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The PacifiCorp habitat conservation
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IGD, or used in constructed habitat
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estoration, watershed planning, sal
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Table 11.4. Modeled suspended sedim
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parasites Ceratomyxa shasta (causes
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that become infected is estimated t
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where snow water equivalent is proj
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minimizing disease risks, the detai
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Figure 11.4. Proposed action, histo
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Figure 11.6. Proposed action weekly
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Figure 11.9. Regression between EWA
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Figure 11.11. Proposed action and o
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Figure 11.12. Number of days per wa
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Figure 11.14. Monthly coefficient o
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IGD. The proposed action modeled da
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The results from Table 11.7 indicat
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likely to increase the quantity of
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habitat decreases between the Shast
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Table 11.9. Daily average mainstem
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Table 11.10. Daily average mainstem
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5% 3336 13176 27664 26168 30946 237
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The proposed action results in agri
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Figure 11.21. Monthly mean of daily
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Riparian restoration projects will
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expected to be typical riparian spe
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Table 11.13. Annual percent of proj
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esource needs as they grow, and 3)
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11.5.2 Klamath River Basin Adjudica
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coho salmon within the Klamath Rive
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aspects of a natural flow regime th
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element of coho salmon critical hab
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12.1.1.1 Risk Analyses for Endanger
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ESU DIVERSITY STRATA POPULATIONS IN
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eproduction, and distribution. The
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Figure 12.2. Historic population st
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the average ratio of IP-km to total
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Although long-term data on coho sal
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1980 1981 1982 1983 1984 1985 1986
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maintain viable abundances in many
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12.2.5.5 Viability Summary Though p
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coastal currents and upwelling, kno
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12.2.6.2 Marine Derived Nutrients M
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fisheries south of Cape Falcon, Ore
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12.3 Environmental Baseline of Coho
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water temperatures up to 19 ºC in
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some coho salmon smolts may stop mi
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threshold, all Klamath River coho s
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abundance threshold (Table 12.3). T
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mainstem Klamath and Trinity rivers
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Although there are risks to Klamath
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activities are generally beneficial
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12.4 Effects to Individuals The pro
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12.4.1.2 Response 12.4.1.2.1 Adults
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(2012) believes is representative o
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genotype II density of 5 spores/L w
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flows provide a limit to the increa
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polychaete and sediment disturbance
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which will likely result in a relat
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etween Trees of Heaven (RM 172) and
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action. Reclamation estimated that
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Based on literature, increased comp
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Table 12.6. Summary of risks result
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most juveniles. Stream flow diversi
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at most fish relocation sites, base
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higher, the minimally increased sed
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Small pulses of moderately turbid w
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Boulder faces in the deflector stru
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conditions may fail if those condit
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Adverse effects of the proposed act
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Potential Stressor Habitat Reductio
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Potential Stressor Elevated water t
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12.6.2 Effects of fitness consequen
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13 INCIDENTAL TAKE STATEMENT Sectio
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Table 13.1 Summary of maximum annua
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in fewer larvae and juveniles, and
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Table 13.2 Estimated annual maximum
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1.2.1.8. Incidental Take Caused by
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characteristics of aquatic species,
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Table 13.5 Expected annual Environm
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Cause of Incidental Take Habitat Re
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Clear Lake, Gerber Reservoir, and T
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This term and condition is requirin
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13.4 Mandatory Monitoring and Repor
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Required hydrologic monitoring incl
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Table 13.7. Summary of LRS and SNS
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T&C or Mandatory Monitoring Mandato
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Table 13.9 Summary of reporting and
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Table 13.10 Summary of meetings req
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the above QA/QC procedures describe
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Barry, P.M., E.C. Janney, D.A. Hewi
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Burdick, S.M. and J. Rasmussen. 201
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Dunsmoor, L., L. Basdekas, B. Wood,
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Garen, D. 2011, Upper Klamath Basin
Page 437 and 438: Janney, E.C., B.S. Hayes, D.A. Hewi
Page 439 and 440: Laenen, A., and A.P. LeTourneau. 19
Page 441 and 442: Miller, R.R., and G.R. Smith. 1981.
Page 443 and 444: Perkins, D.L., and G.G. Scoppettone
Page 445 and 446: (Deltistes luxatus) in Tule and Cle
Page 447 and 448: Terwilliger, M. 2006. Physical habi
Page 449 and 450: USBR [U.S. Bureau of Reclamation].
Page 451 and 452: Williams, J.E. 2000. Chapter 13. Th
Page 453 and 454: Arthington, A.H., S.E. Bunn, N.L. P
Page 455 and 456: Beeman, J., S. Juhnke, G. Stutzer a
Page 457 and 458: Brommer, J.E. 2000. The evolution o
Page 459 and 460: Department of the Army Regional Gen
Page 461 and 462: Chilcote, M. W. 2003. Relationship
Page 463 and 464: Dunsmoor LK, and Huntington CW. 200
Page 465 and 466: Foott, J.S., R. Stone, E. Wiseman,
Page 467 and 468: Habera, J.W., R.J. Strange, B.D. Ca
Page 469 and 470: Hemstreet, T. 2013. Electronic mail
Page 471 and 472: Jordan, M. S. 2012. Hydraulic predi
Page 473 and 474: Kostow, K. E., A. R. Marshall and S
Page 475 and 476: MacFarlane, R. B., S. Hayes, and B.
Page 477 and 478: Moyle, P. B. 2002. Inland Fishes of
Page 479 and 480: PacifiCorp Klamath Hydroelectric Pr
Page 481 and 482: Oregon Department of Environmental
Page 483 and 484: Puckridge, J. T., F. Sheldon, K. F.
Page 485 and 486: Ring, T.E. and B. Watson. 1999. Eff
Page 487: Sommer, T. R., M. L. Nobriga, W. C.
Page 491 and 492: USFWS [U. S. Fish and Wildlife Serv
Page 493 and 494: Ward G, and Armstrong N. 2010. Asse
Page 495 and 496: Winker, K., J. H. Rappole, and M. A
Page 497 and 498: 77 FR 476. National Marine Fisherie
Page 499 and 500: UKL Elevation (feet) Active Storage
Page 505 and 506: 16.2 Appendix B: Elevation Flow Dat
Page 507 and 508: 490
Page 509 and 510: Week of Water Year 1981 1982 1983 1
Page 527 and 528: Water Year October November Decembe
Page 533 and 534: 16.3 Appendix C: Description of Res
Page 535 and 536: 4. Removal of Small Dams (permanent
Page 537 and 538: Information regarding consideration
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9. Piping Ditches a. Project Descri
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. Site-Specific Restrictions Restri
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6. Protection Measures The followin
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to enter or be placed where they co
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shall be distributed throughout the
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weed free straw, silt fences) are i
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the project is located, and compris
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2. Post Construction Monitoring and
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Median Seasonal Flow (acre-feet) Me
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Median Seasonal Net Inflow (acre-fe
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16.5 Appendix E: Observed and Model
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Observed and modeled proposed actio
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Observed and modeled proposed actio
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16.6 Appendix F: Analyzing the rela
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Table 1. Paired comparison of the c
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Table 3. The difference in the mean
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