Biological Opinions - Bureau of Reclamation

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Coots, M. 1965. Occurrences of the Lost River sucker, Deltistes luxatus (Cope), and shortnose sucker, Chasmistes brevirostris (Cope), in northern California. California Department of Fish and Game 51: 68-73. Courter, I., J. Vaughan, and S. Duery. 2010. 2010 Tule Lake Sucker Relocation Report: Project Summary. Cramer Fish Sciences. Report to the U.S. Bureau of Reclamation, Klamath Basin Area Office, Klamath Falls, Oregon. 11 p. Crandall, J.D., L.B. Bach, N. Rudd, M. Stern, and M. Barry. 2008. Response of larval Lost River and shortnose suckers to wetland restoration at the Williamson River Delta, Oregon: Transactions of the American Fisheries Society 137: 402-416. Deas, M., and J. Vaughn. 2006. Characterization of organic matter fate and transport in the Klamath River below Link Dam to assess treatment/reduction potential: Completion Report. Watercourse Engineering Inc., Davis, California. Prepared for the U.S. Bureau of Reclamation, Klamath Basin Area Office. 152 p. DeLonay, A.J., and E.E. Little. 1997. Swimming performance of juvenile shortnose suckers (Chasmistes brevirostris Cope) and Lost River suckers (Deltistes luxatus Cope). Prepared for U.S. Bureau of Reclamation, Klamath Area Office, Klamath Falls, OR. Prepared by U.S. Geological Survey, Biological Resources Division, Midwest Science Center, Columbia, Missouri. 11p. Densmore, C.L., C.A. Ottinger, K.R. Echols, T.M. Wood, S.P. VanderKooi, B.H. Rosen, and S.M. Burdick. 2011. Algal Toxins in Upper Klamath Lake, Oregon: Histopathology of Age-0 Lost River and Shortnose Suckers in 2007 and 2008. In: Thorsteinson, VanderKooi, and Duffy editors. Proceedings of the Klamath Basin Science Conference, Medford, Oregon, February 1–5, 2010. USGS Open File Report 2011-1196. Page 240. Desjardins, M., and D.F. Markle. 2000. Distribution and biology of suckers in Lower Klamath Reservoirs. 1999 Final Report. Submitted to PacifiCorp, Portland, Oregon. Dileanis, P.D., S.E. Schwarzbach, J. Bennett, and others. 1996. Detailed study of water quality, bottom sediment, and biota associated with irrigation drainage in the Klamath Basin, California and Oregon, 1990-92. U.S. Geological Survey. Water-Resources Investigations Report 95-4232. 172p. Dowling, T. 2005. Conservation genetics of endangered Lost River and shortnose suckers. Unpublished report for the U.S. Fish and Wildlife Service, Klamath Falls, Oregon. 14 p. Dowling, T.E., and C.L. Secor. 1997.The role of hybridization in the evolutionary diversification of animals. Annual Reviews in Ecology and Systematics 28: 593-619. Doyle, M.C., and D.D. Lynch. 2005. Sediment oxygen demand in Lake Ewauna and the Klamath River, Oregon, June 2003. U.S. Geological Survey Scientific Investigations Report 2005-5228. 14 p. 415
Dunsmoor, L., L. Basdekas, B. Wood, and B. Peck. 2000. Quality, composition, and distribution of emergent vegetation along the Lower River and Upper Klamath Lake shorelines of the Williamson River delta, Oregon. Completion report. Klamath Tribes, Chiloquin, Oregon, and the U.S. Bureau of Reclamation, Klamath Basin Area Office, Klamath Falls, Oregon. 27 pp. Eilers, J.M., J. Kann, J. Cornett, K. Moser, and A. St. Amand. 2004. Paleolimnological evidence of a change in a shallow, hypereutrophic lake: Upper Klamath Lake, Oregon. Hydrobiologia 520: 7-18. Eilers, J.M. and B.J. Eilers. 2005. Fish habitat analysis of Upper Klamath Lake and Agency Lake, Oregon. Completion report to U.S. Bureau of Reclamation. J.C. Headwaters, Inc., Bend, Oregon. 37 p. Eldridge, S.L.C., T.M. Wood, and K.R. Echols. 2012. Spatial and Temporal Dynamics of Cyanotoxins and Their Relation to Other Water Quality Variables in Upper Klamath Lake, Oregon, 2007–09. USGS Scientific Investigations Report 2012–5069. Ellsworth, C.M., and Martin, B.A., 2012, Patterns of larval sucker emigration from the Sprague and Lower Williamson Rivers of the Upper Klamath Basin, Oregon, after the removal of Chiloquin Dam—2009–10 annual report: U.S. Geological Survey Open-File Report 2012-1037, 42 p. (Also available at http://pubs.usgs.gov/of/2012/1037/.) Ellsworth, C.M., T.J. Tyler, C.D. Luton, S.P. VanderKooi, and R. S. Shively. 2007. Spawning migration movements of Klamath largescale, Lost River, shortnose suckers in the Williamson and Sprague Rivers, Oregon, prior to the removal of the Chiloquin Dam: Annual report 2005. U.S. Geological Survey, Western Fisheries Research Center, Klamath Falls Field Station. 42 p. Ellsworth, C. M., T. J. Tyler, and S. P. Vanderkooi. 2010. Using spatial, seasonal, and diel drift patterns of larval Lost River suckers Deltistes luxatus (Cypriniformes: Catostomidae) and shortnose suckers Chasmistes brevirostris (Cypriniformes: Catostomidae) to help identify a site for a water with-drawl structure on the Williamson River, Oregon. Environmental Biology of Fishes 89:47-57. Erdman, C.S., and H.A. Hendrixson. 2010. Larval Lost River and Shortnose Sucker Response to Large Scale Wetland Restoration of the Williamson River Delta Preserve. 2009 Annual Data Summary, 11/2/2010. The Nature Conservancy, Klamath Falls, Oregon. 40 p. Erdman, C.S., and H.A. Hendrixson. 2011. Larval Lost River and Shortnose Sucker Response to Large Scale Wetland Restoration of the Williamson River Delta Preserve. 2010 Annual Data Summary, October 2011. The Nature Conservancy, Klamath Falls, Oregon. 29 p. Erdman, C.S., H.A. Hendrixson, and N.T. Rudd. 2011. Larval sucker distribution and condition before and after large-scale restoration at the Williamson River Delta, Upper Klamath Lake, Oregon. Western North American Naturalist 71(4): 472–480. 416
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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
Page 381 and 382: 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: Burdick, S.M. and J. Rasmussen. 201
Page 435 and 436: 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 and 488:
Sommer, T. R., M. L. Nobriga, W. C.
Page 489 and 490:
Taylor, R. 1991. A review of local
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
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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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