Biological Opinions - Bureau of Reclamation

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Esleroad, A. 2004. Williamson River delta restoration program vegetation technical report. The Nature Conservancy, Portland, Oregon. 22 p. FERC [Federal Energy Regulatory Commission]. 2007. Final Environmental Impact Statement for Hydropower License, Klamath Hydropower Project, FERC Project No. 2082-027, FERC/EIS-0201F, Oregon and California. Washington D.C., FERC, Office of Energy Projects, Division of Hydropower Licensing. November 2007. 1148 p. Ferguson JA, W. Koketsu, I. Ninomiya, P.A. Rossignol, K.C. Jacobson, and M.L. Kent. 2011. Mortality of coho salmon (Oncorhynchus kisutch) associated with burdens of multiple parasite species. International Journal for Parasitology 41:1197–1205. Flint, L.E., and Flint, A.L., 2012. Estimation of stream temperature in support of fish production modeling under future climates in the Klamath River Basin: USGS Scientific Investigations Report 2011–5171. 31 p. Flosi, G., S. Downie, J. Hopelain, M. Bird, R. Coey and B. Collins. 2010. California Salmonid Stream Habitat Restoration Manual. Fourth edition. California Department of Fish and Game. Wildlife and Fisheries Division. Foott, J.S. 2004. Health monitoring of adult Lost River sucker (Deltistes luxatus) and shortnose sucker (Chasmistes brevirostris) in Upper Klamath Lake, Oregon, April-September 2003. Joint U.S. Fish and Wildlife Service and U.S. Geological Survey project. 37 p. Foott, J.S., R. Stone, and R. Fogerty. 2007. Lack of disease response in juvenile Upper Klamath Lake suckers (age 0+) to adverse water quality conditions – Pilot study August 2007. U.S. Fish and Wildlife Service California-Nevada Fish Health Center, Anderson, CA. 12 p. Foott, J. S., R. Stone, and R. Fogerty. 2010. FY2009 Technical Report: Health and energy evaluation of juvenile fish from Link R. trap and haul project and J-canal salvage. Anderson, California. Foster, K., and D. Bennetts. 2006. Entrainment monitoring report for the Lost River Diversion Channel in 2005. Final Report. U.S. Bureau of Reclamation, Klamath Falls, Oregon. 12 p. Freitas, S.E., D.M. Mauser, and J. Beckstrand. 2007. Ecology of Shortnose and Lost River Suckers in Tile Lake national Wildlife Refuge, California, Progress Report April through September 2007. Klamath Basin Refuge Complex. 69 p. Gannett, M.W., K.E. Lite Jr., J.L. LaMarche, B.J. Fisher, and D.J. Polette. 2007. Ground-water hydrology of the Upper Klamath Basin, Oregon and California. USGS Scientific Investigations Report 2007-5050. 98 p. 417
Garen, D. 2011, Upper Klamath Basin water supply forecasting: status, issues, and outlook. Issue and discussion paper. U.S. Department of Agriculture-Natural Resources Conservation Service, Portland, Oregon. Gilroy, D.J. K.W. Kauffman, R.A. Hall, X. Huang, and F.S. Chu. 2000. Assessing Potential Health Risks from Microcystin Toxins in Blue-Green Algae Dietary Supplements. Environmental Health Perspectives 108 (51): 435-439. Grabowski, T.B. and C.A. Jenkins. 2009. Post-release movements and habitat use of robust redhorse transplanted to the Ocmulgee River, Georgia. Aquatic Conservation of Marine and Freshwater Ecosystems 19: 170-177. Guillen, G. 2003. Klamath River fish die-off, September 2002: Causative factors of mortality. Report number AFWO-F-02-03. U.S. Fish and Wildlife Service, Arcata Fish and Wildlife Office. Arcata, CA. 128 pp. Gutermuth, B., E. Pinkston, and D. Vogel. 2000a. A-Canal fish entrainment during 1997 and 1998, with emphasis on endangered suckers. Completion Report. New Earth/Cell Tech, Klamath Falls, Oregon and Natural Resource Scientists, Inc., Red Bluff, California. Gutermuth, B., C. Watson, and J. Kelly. 2000b. Link River hydroelectric project (eastside and westside powerhouses) final entrainment study report. Cell Tech, Klamath Falls, Oregon and PacifiCorp Environmental Services, Portland, Oregon. Hamlet, A.F., P.W. Mote, N. Mantua, and D.P. Lettenmaier. 2005. Effects of Climate change on the Columbia River Basin’s water resources. JISAO Center for Science in the Earth System. Climate Impacts Group and Department of Civil and Environmental Engineering, University of Washington. November 2005. Hamilton, A., R. Piaskoski, and S. Snedaker. 2003. 2003 Progress Report: Evaluation of fish entrainment and fish habitat use along Miller Creek, Lost River Basin, Oregon. Bureau of Land Management, Klamath Falls Area Office. 6 p. Helsel, D.R. and R.M. Hirsch. 2002. Statistical methods in water resources. Techniques of Water-Resources Investigations of the United States Geological Survey, Book 4, Hydrologic Analysis and Interpretation, Chapter A3. U.S. Geological Survey, Reston, Virginia. Helsel, D.R., D.K. Mueller, and J.R. Slack. 2005. Computer program for the Kendall family of trend tests. U.S. Geological Survey Scientific Investigations Report 2005-5275. Hendrixson, H.A., S.M. Burdick, B.L. Herring, and S.P. VanderKooi. 2007a. Differential habitat use by juvenile suckers in Upper Klamath Lake, Oregon. In: "Nearshore and offshore habitat use by endangered, juvenile Lost River and shortnose suckers in Upper Klamath Lake, Oregon: Annual Report 2004."U.S. Geological Survey, Western Fisheries Research Center, Klamath Falls Field Station. 57 p. 418
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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
Page 383 and 384: Boulder faces in the deflector stru
Page 385 and 386: conditions may fail if those condit
Page 387 and 388: Adverse effects of the proposed act
Page 389 and 390: Potential Stressor Habitat Reductio
Page 391 and 392: Potential Stressor Elevated water t
Page 393 and 394: 12.6.2 Effects of fitness consequen
Page 395 and 396: 13 INCIDENTAL TAKE STATEMENT Sectio
Page 397 and 398: Table 13.1 Summary of maximum annua
Page 399 and 400: in fewer larvae and juveniles, and
Page 401 and 402: Table 13.2 Estimated annual maximum
Page 403 and 404: 1.2.1.8. Incidental Take Caused by
Page 405 and 406: characteristics of aquatic species,
Page 407 and 408: Table 13.5 Expected annual Environm
Page 409 and 410: Cause of Incidental Take Habitat Re
Page 411 and 412: Clear Lake, Gerber Reservoir, and T
Page 413 and 414: This term and condition is requirin
Page 415 and 416: 13.4 Mandatory Monitoring and Repor
Page 417 and 418: Required hydrologic monitoring incl
Page 419 and 420: Table 13.7. Summary of LRS and SNS
Page 421 and 422: T&C or Mandatory Monitoring Mandato
Page 423 and 424: Table 13.9 Summary of reporting and
Page 425 and 426: Table 13.10 Summary of meetings req
Page 427 and 428: the above QA/QC procedures describe
Page 429 and 430: Barry, P.M., E.C. Janney, D.A. Hewi
Page 431 and 432: Burdick, S.M. and J. Rasmussen. 201
Page 433: Dunsmoor, L., L. Basdekas, B. Wood,
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
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Sommer, T. R., M. L. Nobriga, W. C.
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Taylor, R. 1991. A review of local
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USFWS [U. S. Fish and Wildlife Serv
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Ward G, and Armstrong N. 2010. Asse
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Winker, K., J. H. Rappole, and M. A
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77 FR 476. National Marine Fisherie
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UKL Elevation (feet) Active Storage
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16.2 Appendix B: Elevation Flow Dat
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490
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Week of Water Year 1981 1982 1983 1
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Water Year October November Decembe
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16.3 Appendix C: Description of Res
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4. Removal of Small Dams (permanent
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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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