Biological Opinions - Bureau of Reclamation

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The variability of early life history behavior of coho salmon observed by Chesney et al. (2007) and by the Yurok and Karuk tribes mentioned in the sections above is not unprecedented; coho salmon have been shown to spend up to two years in freshwater (Bell and Duffy 2007), migrate to estuaries within a week of emerging from the gravels (Tschaplinski 1988), enter the ocean at less than one year of age at a length of 60 to 70 mm (Godfrey et al. 1975), and redistribute into riverine ponds following fall rains (Peterson 1982; Soto et al. 2008; Hillemeier et al. 2009). Taken together, the research by the Yurok and Karuk tribes, plus the research from outside the Klamath Basin, indicate that coho salmon in the Klamath River exhibit a diversity of early life history strategies, utilizing the mainstem Klamath River throughout various parts of the year as both a migration corridor and a rearing zone. 12.3.2 Risk of Extinction of Klamath Populations While the Status of the Species section discussed the viability of the SONCC coho salmon ESU, this section provides a more in-depth discussion of the extinction risk of the Klamath River basin populations affected by the proposed action, which consist of the Upper Klamath, Middle Klamath, Shasta, Scott, and Salmon River populations. Within the California portion of the SONCC coho salmon ESU, estimating the risk of extinction of a given coho salmon population is difficult since longstanding monitoring and abundance trends are largely unavailable. Williams et al. (2008) proposed biological viability criteria, including population abundance thresholds. The viability criteria developed by Williams et al. (2008) address and incorporate the underlying viability concepts (i.e., abundance, productivity, diversity and spatial structure) outlined within McElhany et al. (2000), and are intended to provide a means by which population and ESU viability can be evaluated in the future when more population data become available. Comparing population estimates against population viability thresholds proposed by Williams et al. (2008) allow NMFS to make conservative assumptions concerning the current risk of extinction of Klamath River mainstem and tributary populations. Generally speaking, none of the five populations of coho salmon affected by the proposed action are considered viable. Even the most optimistic estimates from Ackerman et al. (2006) indicate each population falls well short of abundance thresholds for the proposed viability criteria that, if met, would suggest that the populations were at low risk of extinction for this specific criterion. In some years, populations have fallen below the high risk abundance threshold, such as the Shasta River population. A population is considered at low risk of extinction if all criteria are met, therefore failure to meet any one specific criterion would result in the population being at an elevated risk of extinction (i.e., not viable). The annual adult run size estimate between 2009 and 2012 has been fewer than 116, with a low of nine adults for the Shasta River, all of which were males. Similarly, the Scott River coho salmon population fell well below the high risk abundance threshold in three of the most recent four years (Table 12.3). For both of these populations, abundance is low and they are likely experiencing depensation pressures. With regard to spatial structure and diversity, Williams et al. (2008) abundance thresholds were based upon estimated historical distribution and abundance of spawning coho salmon, and thus capture the essence of these two viability parameters. By not meeting the low risk annual abundance 325
threshold, all Klamath River coho salmon populations are likewise failing to meet spatial structure and diversity conditions consistent with viable populations. Several of these populations have also recently failed to meet the high risk abundance thresholds, underscoring the critical nature of recent low adult returns. Below, the populations that may be affected by the proposed action are discussed in more detail. Run size approximations compiled by CDFW were used to gage whether specific populations had met the low extinction risk threshold at any time during the period 2009 to 2012 (Table 12.3). Populations in the Shasta, Scott, and Salmon rivers do not spawn in the action area, but use the action area for migration, rearing, and holding. Effects of the proposed action, such as hydrologic changes, are the highest in the reach between IGD and Orleans. Therefore, the Upper Klamath, Shasta and Scott River populations are affected by the proposed action to a greater degree than other populations located downstream. Table 12.3. Estimated naturally spawning coho salmon abundance for populations in the action area. Stratum Population 2009 2010 2011 2012 High Risk Annual Abundance Threshold a Low Risk Annual Abundance Threshold b Interior – Klamath River Upper Klamath d < 200
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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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Page 293 and 294: The proposed action results in agri
Page 295 and 296: Figure 11.21. Monthly mean of daily
Page 297 and 298: Riparian restoration projects will
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Page 301 and 302: Table 11.13. Annual percent of proj
Page 303 and 304: esource needs as they grow, and 3)
Page 305 and 306: 11.5.2 Klamath River Basin Adjudica
Page 307 and 308: coho salmon within the Klamath Rive
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Page 311 and 312: element of coho salmon critical hab
Page 313 and 314: 12.1.1.1 Risk Analyses for Endanger
Page 315 and 316: ESU DIVERSITY STRATA POPULATIONS IN
Page 317 and 318: eproduction, and distribution. The
Page 319 and 320: Figure 12.2. Historic population st
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Page 323 and 324: Although long-term data on coho sal
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Page 327 and 328: maintain viable abundances in many
Page 329 and 330: 12.2.5.5 Viability Summary Though p
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Page 333 and 334: 12.2.6.2 Marine Derived Nutrients M
Page 335 and 336: fisheries south of Cape Falcon, Ore
Page 337 and 338: 12.3 Environmental Baseline of Coho
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Page 345 and 346: abundance threshold (Table 12.3). T
Page 347 and 348: mainstem Klamath and Trinity rivers
Page 349 and 350: Although there are risks to Klamath
Page 351 and 352: activities are generally beneficial
Page 353 and 354: 12.4 Effects to Individuals The pro
Page 355 and 356: 12.4.1.2 Response 12.4.1.2.1 Adults
Page 357 and 358: (2012) believes is representative o
Page 359 and 360: genotype II density of 5 spores/L w
Page 361 and 362: flows provide a limit to the increa
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Page 367 and 368: etween Trees of Heaven (RM 172) and
Page 369 and 370: action. Reclamation estimated that
Page 371 and 372: Based on literature, increased comp
Page 373 and 374: Table 12.6. Summary of risks result
Page 375 and 376: most juveniles. Stream flow diversi
Page 377 and 378: at most fish relocation sites, base
Page 379 and 380: 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
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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
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Janney, E.C., B.S. Hayes, D.A. Hewi
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Laenen, A., and A.P. LeTourneau. 19
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Miller, R.R., and G.R. Smith. 1981.
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Perkins, D.L., and G.G. Scoppettone
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(Deltistes luxatus) in Tule and Cle
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Terwilliger, M. 2006. Physical habi
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USBR [U.S. Bureau of Reclamation].
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Williams, J.E. 2000. Chapter 13. Th
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Arthington, A.H., S.E. Bunn, N.L. P
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Beeman, J., S. Juhnke, G. Stutzer a
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Brommer, J.E. 2000. The evolution o
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Department of the Army Regional Gen
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Chilcote, M. W. 2003. Relationship
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Dunsmoor LK, and Huntington CW. 200
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Foott, J.S., R. Stone, E. Wiseman,
Page 467 and 468:
Habera, J.W., R.J. Strange, B.D. Ca
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Hemstreet, T. 2013. Electronic mail
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Jordan, M. S. 2012. Hydraulic predi
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Kostow, K. E., A. R. Marshall and S
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MacFarlane, R. B., S. Hayes, and B.
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Moyle, P. B. 2002. Inland Fishes of
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PacifiCorp Klamath Hydroelectric Pr
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Oregon Department of Environmental
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Puckridge, J. T., F. Sheldon, K. F.
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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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