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Section 7(A)(2) Biological Opinion and Magnuson-Stevens Fishery Conservation and Management Act Essential Fish Habitat (EFH) Consultation

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Section 7(A)(2) Biological Opinion and Magnuson-Stevens Fishery Conservation and Management Act Essential Fish Habitat (EFH) Consultation Endangered Species Act (ESA) Section 7(a)(2) Biological Opinion and Magnuson-Stevens Fishery Conservation and Management Act Essential Fish Habitat (EFH) Consultation Four Summer/Fall Chinook Salmon and Two Fall Chinook Salmon Hatchery Programs in the Upper Columbia River Basin NMFS Consultation Number: WCR-2015-3607 Action Agencies: National Marine Fisheries Service (NMFS) U.S. Army Corps of Engineers (USACE) Affected Species and Determinations: ESA-Listed Species Status Is the Action Is the Action Is the Action Likely to Adversely Likely To Likely To Affect Species or Jeopardize the Destroy or Critical Habitat? Species? Adversely Modify Critical Habitat? Chinook salmon (Oncorhynchus tshawytscha) Upper Columbia River Spring Endangered Yes No No Snake River Spring/Summer Threatened Yes No No Snake River Fall Threatened Yes No No Lower Columbia River Threatened Yes No No Upper Willamette River Spring Threatened Yes No No Steelhead (O. mykiss) Upper Columbia River Threatened Yes No No Snake River Threatened Yes No No Middle Columbia River Threatened Yes No No Lower Columbia River Threatened Yes No No Upper Willamette River Threatened Yes No No Sockeye salmon (O. nerka) Snake River Endangered Yes No No Chum salmon (O. keta) Columbia River Threatened Yes No No Coho salmon (O. kisutch) Lower Columbia River Threatened Yes No No Killer whales (Orcinus orca) Southern Resident Endangered No No No Green sturgeon (Acipenser medirostris) Southern Distinct Population No No No Threatened Segment Southern Distinct Population No No No Threatened Se ment Pacific Coast Salmon No Consultation Conducted By: National Marine Fisheries Service, West Coast Region, Sustainable Fisheries Division Issued By: Barry A. T Regional Date: UCR-Ringold summer/fall Chinook hatcheries opinion 11 TABLE OF CONTENTS INTRODUCTION ........................................................................................................................ 1 Background ....................................................................................................................... 2 Consultation History ......................................................................................................... 2 Proposed Federal Action .................................................................................................. 5 1.1.1. Chelan, Douglas, and Grant PUD Activities ............................................................... 6 1.1.2. USACE Activities ........................................................................................................ 7 1.1.3. Hatchery Operator Activities ....................................................................................... 7 1.1.3.1. Broodstock Collection and Mating ....................................................................... 9 1.1.3.2. Juvenile Rearing and Release ............................................................................. 10 1.1.3.3. Adult Management ............................................................................................. 12 1.1.3.4. Facility Operations ............................................................................................. 13 1.1.3.5. Research, Monitoring, and Evaluation (RM&E) ................................................ 15 1.1.4. Changes in Proposed Programs Since Last Biological Opinion ................................ 15 Interrelated and Interdependent Actions ........................................................................ 16 ENDANGERED SPECIES ACT: BIOLOGICAL OPINION AND INCIDENTAL TAKE STATEMENT ..... 16 Analytical Approach ....................................................................................................... 16 Range-wide Status of the Species and Critical Habitat .................................................. 18 Status of Listed Species ............................................................................................. 20 Upper Columbia River Spring Chinook Salmon ESU ....................................... 21 Snake River Spring/summer Chinook Salmon ESU .......................................... 23 Snake River Fall Chinook Salmon ESU ............................................................. 25 Lower Columbia River Chinook Salmon ESU .................................................. 27 Upper Willamette River Spring Chinook Salmon ESU ..................................... 32 Upper Columbia River Steelhead DPS ............................................................... 37 Snake River Steelhead DPS ................................................................................ 39 Mid-Columbia River Steelhead DPS .................................................................. 40 Lower Columbia River Steelhead DPS .............................................................. 44 Upper Willamette River Steelhead DPS ............................................................. 47 Snake River Sockeye Salmon ESU .................................................................... 54 Columbia River Chum Salmon ESU .................................................................. 54 Lower Columbia River Coho Salmon ESU ........................................................ 60 Range-wide Status of Critical Habitat ....................................................................... 65 UCR-Ringold summer/fall Chinook hatcheries opinion iii Climate Change ......................................................................................................... 68 Action Area .................................................................................................................... 68 Environmental Baseline .................................................................................................. 68 Habitat and Hydropower (NMFS 2012a) .................................................................. 68 Climate Change ......................................................................................................... 70 Hatcheries .................................................................................................................. 72 Harvest ....................................................................................................................... 73 Effects on ESA Protected Species and on Designated Critical Habitat ......................... 80 Factors That Are Considered When Analyzing Hatchery Effects ............................. 80 Effects of the Proposed Action .................................................................................. 82 Factor 1. The hatchery program does or does not remove fish from the natural population and use them for broodstock ............................................................ 82 Factor 2. Hatchery fish and the progeny of naturally spawning hatchery fish on spawning grounds and encounters with natural-origin and hatchery fish at adult collection facilities .............................................................................................. 82 Factor 3. Hatchery fish and the progeny of naturally spawning hatchery fish in juvenile rearing areas, the migratory corridor, estuary, and ocean .................... 89 Factor 4. Research, monitoring, and evaluation that exists because of the hatchery program .............................................................................................. 105 Factor 5. Construction, operation, and maintenance of facilities that exist because of the hatchery program ...................................................................... 106 Factor 6. Fisheries that exist because of the hatchery programs ...................... 109 Cumulative Effects ....................................................................................................... 109 Integration and Synthesis ............................................................................................. 111 UCR Spring Chinook Salmon ESU ......................................................................... 111 UCR Steelhead DPS ................................................................................................ 113 Snake River ESUs/DPS, Mid-Columbia River Steelhead DPS, Columbia River Chum Salmon ESU, Lower Columbia River ESUs/DPS, and Upper Willamette River ESU/DPS............................................................................................................................. 114 Critical Habitat ......................................................................................................... 116 Conclusion .................................................................................................................... 116 Incidental Take Statement ............................................................................................ 117 Amount or Extent of Take ....................................................................................... 118 Effect of the Take .................................................................................................... 120 Reasonable and Prudent Measures .......................................................................... 120 Terms and Conditions .............................................................................................. 120 UCR-Ringold summer/fall Chinook hatcheries opinion iv Conservation Recommendations .................................................................................. 122 Re-initiation of Consultation ........................................................................................ 122 “Not Likely to Adversely
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