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Index A Abandonment of spawning areas, 228-230 Adaptive Environmental Assessment and Management (AEAM) program, 296 Adaptive management, 333-335 definition of the problem, 333 determination of goals and objectives for management of ecosystems, 334 determination of the ecosystem baseline, 334 development of conceptual models, 334 evaluation of restoration efforts and proposals for remedial actions, 335 implementation of management actions 334-335 monitoring of the ecosystem response, 335 selection of future restoration actions, 334 Adaptive management for ecosystem restoration in the Klamath basin, 331-344 as an organizing framework, 332-337 ecosystem management and, 332-333 improvement of resource management, 340-343 385 key components of, 333-335 policy options and restoration activities, 337-339 status of, 335-337 Adequacy of nursery habitat for larvae and juveniles, 232-236 Adult endangered suckers in Upper Klamath Lake, 199-200, 237-240 entrainment, 237 loss of habitat, 240 mass mortality, 237-240 AEAM. See Adaptive Environmental Assessment and Management program Age distributions of suckers in Upper Klamath Lake, 205 Age structure, 204-207 of shortnose sucker sample from Copco Reservoir, 210 Agency Lake bathymetric map of, 98 Agriculture in the Klamath basin, 67-71 Ammonia, 116-117 Amory, Copley, 68 Aphanizomenon flos-aquae, 5-7, 13 explanations of dominance by, 108-110 Aquatic environments, 53-57 in the lower Klamath basin, 57 in the upper Klamath basin, 53-56

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386 B 13asinwide issues, 344-346 Bathymetric map of Upper Klamath Lake and Agency Lake, 98 PEA. See Bureau of Economic Analysis "pest available evidence" standard, 313- 314 Biological assessments and biological opinions of 2002, 37-45 endangered suckers, 38-41 overview of, 44-45 threatened coho salmon, 41-44 13luegreen (cyanobacterial) alga, 5 Bull trout, 184-185 Bureau of Economic Analysis (PEA), 74-75 C CALFED Sacramento-San Joaquin, 332 California Department of Fish and Game (CDFG), 9, 163, 263, 278-283 California Department of Water Resources (CDWR), 156, 339 Watermaster Service, 154 California State Water Resources Control Board (CSWRC13), 162 California Wild and Scenic Rivers Act, 172 Candlefish, 275 Captive propagation, 245 Cascadia volcanic arc, 47 Catostomidae, 184 Causal connections in suppression of populations of endangered suckers in Upper Klamath Lake diagram of, 221 Causes of decline and strategies for recovery of Klamath basin suckers, 214- 249 criteria for judging status and recovery of sucker populations, 214-217 lessons from comparative biology of suckers, 246-247 requirements for protection and recovery, 217-219 suppression of endangered suckers in Upper Klamath Lake, 219-246 CDFG. See California Department of Fish and Game Census of Agriculture, 83 INDEX Central Valley Project Improvement Act (1992), 306 Changes in cropping and water wells in the Scott Valley, 166 in numbers of cattle and cumulative acres of drained wetland in Klamath County, Oregon, 64 in operation of hatcheries, 303-304 Characteristics of farms and farm operators, 80, 90 of the lower Klamath basin, 1997, 90 of the upper Klamath basin, 1997, 80 Chasmistes brevirostris. See Shortnose suckers Chiloquin Dam removal of, 223 on the Sprague River, 3, 15 Chinook salmon, 8, 263-270 fall-run chinook salmon, 264-268 spring-run chinook salmon, 268-270 Chlorophyll changes over growing season, 111 relationship to water level in Upper Klamath Lake, 113 CH2M HILL, 223 Chum salmon, 274 Clean Water Act of 1972, 305 Clear Lake, 7, 13, 129-132 map of, 130 Clear Lake National Wildlife Refuge, 129 Climate and historical hydropattern of the Klamath River watershed, 51-53 Coast Range Geologic Province, 170 Coastal cutthroat trout, 274-275 Coho salmon, 252-263 findings about, 7-8 hatcheries, 262-263 life history, 254-261 pictured, 254 pools containing juvenile coho salmon, chinook salmon, and steelhead along main stem of Klamath River, 2001, as determined in snorkeling surveys, 257 population cycles in California, 261 status, 263 See also Threatened coho salmon Columnaris disease, 201, 238 Comparative biology of suckers lessons from, 246-247

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INDEX Conceptual models development of, 334 Conservation status, 212 Costs of remediation, 15-16, 352 Cottidae, 186-188 Criteria for judging status and recovery of sucker populations, 214-217 Critical habitat, 245-246 designation of, 318-320 CSWRC13. See California State Water Resources Control Board Cui-ui, 196, 247 Current status of aquatic ecosystems: lakes, 95-143 basic information on lakes of upper Klamath basin, 96 Clear Lake, 129-132 Gerber Reservoir, 132-133 Lower Klamath Lake, 133 reservoirs of the main stem, 134-141 Tule Lake, 133-134 Upper Klamath Lake, 97-129 Cyanobacterial alga, 5 Cyprinidae, 182-183 D Dams, 222-224 Degradation of spawning areas, 227-228 Deltistes luxatus. See Lost River suckers Discharge of the Klamath River and the Trinity River, 174 Dissolved oxygen, 117-122 Distribution of adult Lost River suckers and shortnose suckers in the Klamath basin, 192 DOI. See U.S. Department of the Interior Dominance by Aphanizomenon flos-aquae explanations of, 108-110 Dwinnell Dam, 8, 156 . . . . . . map depicting substantial water diversions from the Shasta River below, 155 E Economy of the Klamath basin, 74-93 characteristics of farms and farm operators, 80, 90 387 export based employment, 1998, 78, 87 farms in the Klamath Reclamation Project and in the upper Klamath basin, 83 fisheries characteristics of ports of Eureka and Crescent City, 92-93 lower basin, 82-93 output, value added, and employment, 1998, 77, 86 structural change, 1969-1999, 75, 85 upper basin, 74-82 value of agricultural production, 1998, 81, 91 Ecosystem baseline determination of, 334 Ecosystem management and adaptive management, 332-333 Ecosystem restoration adaptive management for the Klamath basin, 331-344 Ecosystem Restoration Office (ERO), 340- 341 Employment, 77, 86 in lower Klamath basin, 86 in upper Klamath basin, 77 Endangered Species Act of 1973 (ESA), 1, 4, 10, 17-19, 28, 146, 305 Endangered sucker species, 38-41, 346-349 commitments of the USER Biological Assessments of 2002 that are relevant to, 39 geographic subpopulations of in the upper Klamath basin, 216 needs for new information, 346-347 remedial actions, 347-349 the USER biological assessment, 38-40 the USFWS biological opinion, 40-41 Endangered suckers in other Klamath basin waters, 209-212 Endangered suckers of the Klamath River basin, 189-212, 190 age-class structure, 204-207 age distributions of suckers in Upper Klamath Lake based on fish kills, 205 age structure of a small sample of shortnose suckers taken from Copco Reservoir, 1987, 210 A ~ A conservation status, 212 current and former distribution of adult Lost River suckers and shortnose suckers in the Klamath basin, 192

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388 endangered suckers in other Klamath basin waters, 209-212 endangered suckers of the Klamath River basin, 190 generalized view of habitat of young suckers in Upper Klamath Lake, 197 juveniles (1-4 inches), 198-199 larvae, 196-198 locations of current and past populations of Lost River suckers and shortnose suckers, 193 perspective on age-class structure and strength, mortality, and reproductive output, 208-209 physiological tolerances, 200-203 population size, 203 spawning, 194-196 spawning-run abundances of lake suckers, lower Williamson River, 1995-2001, 206 subadults (4-10 inches) and adults, 199- 200 Entrainment of adults, 237 of larvae and juveniles, 231-232 Environmental impact statement (EIS), 25, 173 Environmental overview, 19-26 flow of the Williamson River, the largest water source for Upper Klamath Lake, and of the Klamath River main stem (at Iron Gate Dam) in a year of near-average water availability, 26 flows under conditions of average water availability in the upper Klamath basin, 22 mainstem dams on the Klamath River. 24 map of the upper Klamath basin, 23 water routing diagram for the Klamath Project, 21 Environmental Protection Agency Index of Watershed Indicators, 64 ERO. See Ecosystem Restoration Office ESA. See Endangered Species Act of 1973 ESU. See Evolutionarily significant unit Eulachon, 275 Evolutionarily significant unit (ESU), 262 Explanations summarized, 282-283 INDEX Export based employment, 1998, 78, 87 lower Klamath basin, 87 upper Klamath basin, 78 Extent of mortality, 278-279 F Facilitating recovery of coho salmon and other anadromous fishes of the Klamath River, 287-310 changes in operation of hatcheries, 303- 304 creation of a framework for fish management, 305-307 land-management practices, 304 lowermost Klamath and ocean conditions, 301-302 main-stem Klamath River, 298-301 possible future effects of climate change, 307-308 removal of dams, 302-303 restoration of tributaries, 287-298 Factors likely to limit production of coho and other salmonids in the Shasta, Scott, Salmon, and Trinity Rivers and their tributaries, 288 Factors relevant to all life-history stages, 240-244 hybridization and introgression, 242- 244 nonindigenous species as predators and competitors, 242 water quality, 241-242 Fall-run chinook salmon, 264-268 hatcheries, 267 life history of fall-run chinook salmon 264-267 status, 267-268 Farms in the Klamath Reclamation Project and in the upper Klamath basin, 83 Fathead minnow, 188 Federal agency conservation duty, 321-323 Federal Energy Regulatory Commission (FERC), 42, 136 FERC. See Federal Energy Regulatory Commission Findings, 3-10 about coho salmon, 7-8 about Lost River and shortnose suckers, 3-7

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INDEX about the Klamath River fish kill of 2002, 8-9 legal, regulatory, and administrative context of recovery actions, 9-10 Finley, William, 68 Fish and Wildlife Coordination Act of 1934, 305 "Fish kills," 5 age distributions of suckers in Upper Klamath Lake based on, 205 Fisheries characteristics of ports of Eureka (Humboldt County) and Crescent City (Del Norte Fry, 5 County), 92-93 Fishes, 26-28 "mass mortality" of, 6, 202, 219 Fishes of the lower Klamath basin, 250-286 chinook salmon, 263-270 chum salmon, 274 coastal cutthroat trout, 274-275 coho salmon, 252-263 eulachon, 275 green sturgeon, 276 mass mortality of fish in the Lower Klamath River in 2002, 278-283 native fishes of the Lower Klamath River and its tributaries, 251-252 nonnative fishes of the Lower Klamath and Trinity Rivers, 253 nonnative nonanadromous species, 277 nonnative species, 277-278 Pacific lamprey, 276-277 pink salmon, 274 steelhead, 270-274 Fishes of the upper Klamath basin, 179-213 endangered suckers of the Klamath basin, 189-212 native fishes, 180-188 nonnative fishes, 188-189 Fishing and attempts to regulate loss of fish, 71 Flavobacterium columnare, 201 Flows under conditions of average water availability in the upper Klamath basin, 22 Framework for fish management, 305-307 Central Valley Project Improvement Act, 306 Clean Water Act of 1972, 305 Endangered Species Act of 1973, 305 389 Fish and Wildlife Coordination Act of 1934, 305 National Environmental Policy Act of 1970, 305 National Forest Management Act of 1976, 305 Sustainable Fisheries Act of 1996, 305 Trinity River Basin Fish and Wildlife Management Act, 305-306 Trinity River Stream Rectification Act, 305 Wild and Scenic Rivers Act of 1968, 305 Fur trapping in the Klamath basin, 59 G Gabrielson, Ira, 69 Geologic setting of the Klamath River watershed, 46-51 Gerber Reservoir, 7, 132-133 Global circulation models (GCM), 307 Gold-bearing placer deposits, 60 Gorda Plates, 46 Gordon Report, 63 Grab-sample data for surface waters in the main-stem reservoir system, 2001, 140 Green sturgeon, 276 H Habitat loss of adults, 240 Hardy Phase II draft report, 298 Hatcheries of coho salmon, 262-263 of fall-run chinook salmon, 267 of winter steelhead, 272-273 History of land use in the Klamath basin, 57-71 agriculture, 67-71 changes in numbers of cattle and cumulative acres of drained wetland in Klamath County, Oregon, 64 fur trapping, 59 mining, 59-63 ranching, 63-65 timber, 65-67

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390 Hudson Bay Company, 59 Hybridization and introgression, 242-244 Hydraulic placer mining, 61 Hydrography for the lower Shasta River, 153 for the Salmon River, 169 for the Scott River, 160 I Iakish, J. R., 69 IMPLAN modeling process, 74 Implementation of management actions, 334-335 Improvement of resource management in the Klamath basin, 340-343 Index map of the Trinity River watershed, 170 Index of Watershed Indicators, 64 Indirect causes of mortality, 279-282 Interested parties, 30-37 judging the degree of scientific support for proposed actions pursuant to the goals of the ESA, 35 Iron Gate Dam, 1, 8-9,283 Iron Gate Hatchery, 272 Iron Gate Reservoir, 8-9 Juan de Fuca Plate, 46 Juveniles (1-4 inches), 198-199 adequacy of nursery habitat for, 232-236 mortality among, 5 overview of production of, 236-237 K Klamath basin agriculture in, 67-71 aquatic environments in, 53-57 Klamath Basin Ecosystem Restoration Office (ERO), 340-341 Klamath Drainage District, 69 Klamath largescale sucker, 184 Klamath Mountains, 48 Klamath Mountains Geologic Province, 51 Klamath Project, 1-2,4,10,32-33, 55, 82 Lost River system regulation from, 7 water routing diagram for, 21 INDEX Klamath River findings about the fish kill of 2002,8-9 Klamath River Basin Restoration Task Force (KR13RTF), 342 Klamath River lamprey, 182 Klamath River watershed, 46-53 climate and historical hydropattern, 51- 53 geologic setting, 46-51 runoff, yield, and basin areas for, 52 Klamath smallscale sucker, 184 Klamath Strait Drain, 135 Klamath Straits, 54 Klamath Tribes Native Fish Hatchery, 245 Klamath tui chub, 182 KR13RTF. See Klamath River Basin Restoration Task Force L Lake of the Woods, 13,218 Lampreys, 181-182 Land-management practices, 304 Land use and water management, 46-94 aquatic environments, 53-57 description of the Klamath River watershed, 46-53 economy of the Klamath basin, 74-93 fishing and attempts to regulate loss of fish, 71 history of land use in the Klamath basin, 57-71 overview, 93-94 wetland transformations, 71-74 Larvae, 196-198 adequacy of nursery habitat for, 232-236 hydraulic transport of, 12 overview of production of, 236-237 Larval habitat availability calculated as percentage of lakeshore inundated to a depth of at least 1 ft for lake edge and marsh regions, 233 Legal, regulatory, and administrative context of recovery actions, 9-10 Life history of fishes coho salmon, 254-261 fall-run chinook salmon, 264-267 spring-run chinook salmon, 268-269 summer steelhead, 273-274 winter steelhead, 270-272

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INDEX Link River entrainment from, 7 Link River Dam, 7, 97 Listing of endangered and threatened species, 317 Longitudinal transect data on Keno Reservoir (Lake Ewauna), 2001, 139 Lost River suckers, 146-147 Klamath Indian name for, 58 locations of current and past populations of, 193 Lost River system regulation from the Klamath Project, 7 reservoirs on, 1 status of, 146-147 Lower Klamath basin, 57, 82-93 agriculture in, 70-71 aquatic environments in, 57 characteristics of farms and farm operators of, 90 export based employment in, 87 output, value added, and employment in, 86 structural change in economy of, 85 value of agricultural production in, 91 -I --- --- -- r - ------ - 7 - Lower Klamath Basin Input-Output Model, 91 Lower Klamath Lake, 7, 133 Lower Klamath Lake National Wildlife Refuge, 68 Lower Klamath main stem status of minor tributaries to, 175-176 Lowermost Klamath and ocean conditions, 301-302 M Main-stem Klamath River, 298-301 dams on, 24 management of flow at Iron Gate Dam, 299-301 modeling of habitat availability in relation to flow, 298-299 to the Pacific, 176-177 water temperature of the Klamath River at Orleans, 177 to the Pacific, status of, 176-177 reservoirs of, 134-141 status of Iron Gate Dam to Orleans, 147-153 391 Main-stem Klamath River, from Iron Gate Dam to Orleans, 147-153 annual hydrograph for the lower Shasta River, 153 mean annual concentrations of total nitrogen (TN) and total phosphorus (TP), nitrate (NO3- expressed as N), and soluble reactive phosphorus (SRP), 152 mean monthly flows at Iron Gate Dam in 1961-1996 compared with reconstructed flows for 1905- 1912, 148 simulated and measured temperature in the Klamath River below Iron Gate Dam, 149 simulated daily maximum, mean, and . . minimum water temperatures on the Klamath River from Iron Gate Dam to Seiad Valley for Iron Gate Dam releases of 1,000 cfs (A) and 3,000 cfs (13) under meteorological conditions of August 14, 1996, 150 Management of ecosystems determination of goals and objectives for, 334 Management of flow at Iron Gate Dam' 299-301 Maps of Clear Lake, 130 depicting substantial water diversions from the Shasta River below Dwinnell Dam, 155 of the Klamath River basin showing surface waters and landmarks, 2 of the upper Klamath basin, 23 of the upper Klamath River basin showing surface waters and landmarks, 18 Marbled sculpins, 187-188 Marbut, C. F., 68-69 Mass mortality of adults, 6, 237-240 Mass mortality of fish in the Lower Klamath River in 2002, 278-283 direct causes of mortality, 279 extent of mortality, 278-279 indirect causes of mortality, 279-282 summary of explanations, 282-283 Maximum weekly average temperature (MWAT), 166

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392 Mean water levels proposed by USER for Net loss, through drainage, of wetland years of varying water availability water level in Upper Klamath Lake and, 100 Miller Lake lamprey, 182 Mining in the Klamath basin, 59-63 Minnesota IMPLAN Group, Inc., 83-84 Minnows, 182-183 fathead, 188 Minor tributaries to the lower Klamath main stem, 175- 176 Modeling of habitat availability in relation to flow, 298-299 Modoc Point Irrigation District (MPID), 223 Monitoring of the ecosystem response, 335 Morphological anomalies in young fish, 230-231 Mortality direct causes of, 279 Mount Mazama, 47, 97 Mount Shasta, 47 MPID. See Modoc Point Irrigation District MWAT. See Maximum weekly average temperature N National Environmental Policy Act of 1970, 305 National Forest Management Act of 1976 (NFMA), 30s National Marine Fisheries Service (NMFS), 1, 3, 28, 263, 298-299, 312-330 biological opinion on threatened coho salmon, 43-44 Native species, 180-188 Catostomidae suckers, 184 Cottidae sculpins, 186-188 Cyprinidae minnows, 182-183 of the Lower Klamath River and its tributaries, 251-252 native fishes of the upper Klamath basin, 181 and the paradox of persistent endemics, 244 Petromyzontidae lampreys, 181-182 Salmonidae salmon and trout, 184-186 of the upper Klamath basin, 181 Nature Conservancy, The, 33, 73, 234 INDEX connected to Upper Klamath Lake, 72 New information needs about the endangered Lost River and shortnose suckers, 346-347 about threatened coho salmon, 14-15, 349-350 NFMA. See National Forest Management Act of 1976 NFMS. See National Marine Fisheries ~ . service Nitrogen-fixing by bluegreen alga, 5 Nitrogen in Upper Klamath Lake, 108 Nonindigenous species, 188-189, 277-278 of the Lower Klamath and Trinity Rivers, 253 nonanadromous, 277 as predators and competitors, 242 Nursery habitat adequacy for larvae and juveniles, 232- 236 Nutrients of Upper Klamath Lake, 102-103 o ODFW. See Oregon Department of Fish and Wildlife OECD. See Organization for Economic Co- Operation and Development Ogden, Peter Skene, 59 Oncorhynchus kisutch. See Coho salmon Oregon Department of Fish and Wildlife (ODFW), 185 Oregon State Water Resources 13oard, 66 Organization for Economic Co-Operation and Development (OECD), 104 Organizing framework adaptive management as, 332-337 Overview of larvae and juvenile production, 236-237 Overview of the ESA in the Klamath context, 312-316 the "best available evidence" standard, 313-314 the decision-making burden of proof, 314-316 the species-specific orientation of the ESA, 316

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INDEX Overview of water quality in Upper Klamath Lake, 122-125 Oxygenation as a management tool, 128- 129 p Pacific Fisheries Management Council, 306 Pacific Flyway, 54 Pacific lamprey, 276-277 PacifiCorp, 24, 41-43, 139 Perch, 188-189 Perspective on age-class structure and strength, mortality, and reproductive output, 208-209 Petromyzontidae, 181-182 pH, 113-116 Phosphorus in Upper Klamath Lake, 5, 103-108 Physiological tolerances, 200-203 Pink salmon, 274 Planning and external review recommendation, 345-346 Policy options and restoration activities, 337-339 Population cycles of coho salmon in California, 261 Production and viability of eggs, 222-230 abandonment of spawning areas, 228- 230 dams, 222-224 degradation of spawning areas, 227-228 water level in Upper Klamath Lake, 224-227 Prohibition against jeopardy and adverse modification caused by federal agencies, 323-325 of take and incidental take, 325-329 R Ranching in the Klamath basin, 63-65 Razorback suckers, 246 Recommendations, 10-15, 344-352 on basinwide issues, 344-346 costs of remediation, 15-16, 352 endangered Lost River and shortnose Requirements suckers, 346-349 393 new Information needed on coho salmon, 14-15 planning and external review, 345-346 planning and organization of research and monitoring for listed species, 11-12 priority of recovery actions based on current knowledge of endangered suckers, 13-14 remediation measures justified from current knowledge, 15 research and monitoring on endangered suckers, 12-13 scope of ESA actions by NMFS and USFWS, 11, 344-345 threatened coho salmon, 349-352 Record of Decision (ROD), 25, 296-297 Recovery issues, 244-246 captive propagation, 245 critical habitat, 245-246 legal, regulatory, and administrative context of, 9-10 other natives and the paradox of persistent endemics, 244 planning, 320-321 Redband trout, 185-186 Regulatory consequences, 321-329 authorities prohibiting take and incidental take, 325-329 federal agency conservation duty, 321- 323 prohibition against jeopardy and adverse modification caused by federal agency, 323-325 Regulatory context of the Endangered Species Act, 311-331 overview of the ESA in the Klamath context, 312-316 regulatory consequences, 321-329 species listing and designation of critical habitat, 316-321 Remediation of the endangered Lost River and shortnose suckers, 347-349 measures justified from current knowledge, 15 proposals for, 335 of threatened coho salmon, 350-351 Removal of dams, 223, 302-303 1 - _ _ of the Endangered Species Act, 28-30 for protection and recovery, 217-219

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394 Research and monitoring on endangered suckers, 12-13 Reservoirs of the main stem, 134-141 longitudinal transect data on Keno Reservoir (Lake Ewauna), 13-14 August 2001, 139 summary of grab-sample data for surface waters in the mains stem reservoir system, 2001, 140 water temperature and dissolved oxygen (DO), 137-138 in all main-stem reservoirs, July 2000, 138 in Copco and Iron Gate Reservoirs, January 2000, 137 Residualization, 303 Restoration evaluation of efforts, 335 selection of future actions, 334 Restoration of tributaries, 287-298 factors likely to limit production of coho and other salmonids in the Shasta, Scott, Salmon, and Trinity Rivers and their tributaries, 288 Salmon River, 292-294 Scott River, 291-292 Shasta River, 289-290 small main-stem tributaries, 298 Trinity River, 294-298 1992 Rio Declaration, 314 Robust redhorse suckers, 247 ROD. See Record of Decision Roosevelt, Franklin, 68 Runoff, yield, and basin areas for the Klamath Watershed, 52 S Sacramento perch, 188 Salmon, 184-186 Salmon River, 67, 168, 292-294 status of, 168 Salmonidae, 184-186 San Andreas-Coast Range Fault system, 48 Science and the Endangered Species Act, 315 Scope of ESA actions by NMFS and USFWS expanded, 11 recommendation, 344-345 Scott River, 159-168, 291-292 annual hydrograph of Scott River at Fort Jones, California, 160 INDEX changes in cropping and water wells in the Scott Valley, 166 declines in late summer and early fall flows on, 164 declines in late summer and early fall flows on the Scott River, 164 plot of downstream changes in maximum weekly average water temperature on the main stem of the Scott River during summer, 167 status of, 159-168 Sculpins, 186-188 marbled, 187-188 slender, 187 Seasonal development of algal biomass, 110-113 SEA. See Sustainable Fisheries Act of 1996 Shasta River, 153-159, 289-290 map depicting substantial water diversions from below Dwinnell Dam, 155 map depicting substantial water diversions from the Shasta River below Dwinnell Dam, 155 simulation of daily mean water temperatures in the Shasta River at three flows for August 2001 conditions, 159 status of, 153-159 temperature (thin line) and daily average temperature (wide line) within the Shasta River below Dwinnell Dam during the summer of 2001, 158 Shortnose suckers, 3-7 findings about, 3-7 Klamath Indian name for, 58 locations of current and past populations of, 193 other locations in the Klamath basin, 7 Upper Klamath Lake, 3-7 Sierra Nevada block, 48 Simpson, George, 59 Siskiyou County Resource Conservation District (SRCD), 70, 162 Slender sculpins, 187 Small main-stem tributaries, 298 Smolts, 7-8 Snake River suckers, 246 SONCC. See Southern Oregon/northern California coasts

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INDEX South Fork Trinity River, 296 Southern Oregon/Northern California coasts (SONCC), 17, 20, 28, 263, 312 Spawning, 194-196 ~ . pawnmg areas abandonment of, 228-230 Spawning-run abundances of lake suckers, lower Williamson River, 1995- 2001, 206 Species listing and designation of critical habitat, 316-321 designation of critical habitat, 318-320 listing of endangered and threatened species, 317 recovery planning, 320-321 ~pecies-specific orientation of the ESA, 316 Speckled dace, 183 Sprague River Chiloquin Dam on, 3 Spring-run chinook salmon, 268-270 life history, 268-269 status, 269-270 SRCD. See Siskiyou County Resource Conservation District Status findings of adaptive management in the Klamath basin, 335-337 of coho salmon, 263 of fall-run chinook salmon, 267-268 of spring-run chinook salmon, 269-270 of summer steelhead, 274 of various hypotheses related to water quality of Upper Klamath Lake 123 of winter steelhead, 273 Status of river and stream ecosystems, 144- 178 Lost River, 146-147 main-stem Klamath, from Iron Gate Dam to Orleans, 147-153 main-stem Klamath to the Pacific, 176- 177 minor tributaries to the lower Klamath main stem, 175-176 Salmon River, 168 Scott River, 159-168 Shasta River, 153-159 tributaries to Upper Klamath Lake, 144- 146 Trinity River, 168-175 395 Steelhead, 270-274 summer steelhead, 273-274 winter steelhead, 270-273 Stress in suckers of Upper Klamath Lake incidence indicators of, 239 Structural change, 1969-1999, 75, 85 in the lower Klamath basin economy, 85 in the upper Klamath basin economy, 75 Subadults (4-10 inches), 199-200 Suckers, 184 razorback, 246 robust redhorse, 247 shortnose, 3-7 Snake River, 246 Utah, 246 Summer steelhead, 273-274 life history, 273-274 status, 274 Suppression of endangered suckers in Upper Klamath Lake, 219-246 adults, 237-240 April water level and larval abundance (mean catch per unit effort [CPUE]) in Upper Klamath Lake, 225 diagram of causal connections in suppression of populations of endangered suckers in Upper Klamath Lake, 221 factors relevant to all life-history stages, 240-244 incidence (%) of various indicators of stress in suckers of Upper Klamath Lake based on visual inspection, 239 other issues relevant to recovery, 244- 246 production and viability of eggs, 222- 230 survival of larvae and juveniles, 230-237 Survival of larvae and juveniles, 230-237 adequacy of nursery habitat for larvae and juveniles, 232-236 entrainment of larvae and juveniles, 231-232 morphological anomalies in young fish, 230-231 overview of larvae and juvenile production, 236-237 Sustainable Fisheries Act of 1996 (SFA), 305

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396 T Task statement, 4, 379-380 Tectonic setting for Northern California and Southern Oregon illustrating the Cascadia subduction zone, the Cascade volcanic arc, the Basin and Range Province, and the Oregon fore-arc and Sierra Nevada blocks, 47 Threatened coho salmon, 41-44, 349-352 needs for new information, 349-350 the NMFS biological opinion, 43-44 remediation, 350-351 the USER biological assessment, 41-43 ' Timber in the Klamath basin, 65-67 TMDL. See Total-maximum-daily-load Total-maximum-daily-load (TMDL), 108, 127, 172 Tributaries to Upper Klamath Lake, 144- 146 relative external phosphorus loading from tributaries and other sources to Upper Klamath Lake, 145 Trinity Alps, 51 Trinity Management Council, 301 Trinity River, 8, 168-175, 294-298 index map of the Trinity River watershed, 170 reservoirs, 9 status of, 168-175 Trinity River Basin Fish and Wildlife Management Act (1984), 305- 306 Trinity River Diversion (TRD) project, 8, 25, 169 Trinity River Flow Evaluation Study, 306 Trinity River Hatchery, 14, 270 Trinity River Mainstream Fishery Restoration program, 175 Trinity River Restoration Project, 9 Trophic status of Upper Klamath Lake, 102-103 Trout, 184-186 Tui chub, 182 Tule Lake, 7, 133-134 Tule Lake National Wildlife Refuge, 55, 68-69 Tule Lake Sump, 69, 134 INDEX U United Nations Conference on Environment and Development, 314 Upper Klamath basin, 1, 10, 74-82 agriculture in, 67-70 aquatic environments in, s3-s6 basic information on the lakes of, 96 characteristics of farms and farm operators of, 80 export based employment in, 78 output, value added, and employment in, 77 structural change in economy of, 75 value ot agricultural production in, 81 Upper Klamath Lake, 97-129 adult endangered suckers in, 237-240 age distributions of suckers in, 205 ammonia, 116-117 April water level and larval abundance in, 225 bathymetric map of, 98 change in chlorophyll over growing season, 111 connections between human activity and high abundances of phytoplankton in, 124 description, 97-102 dissolved oxygen, 117-122 explanations of dominance by A phanizomenon flos-aquae, 108- 110 hypertrophicity of, 5 Lost River and shortnose suckers in, 3-7 nitrogen in, 108 nutrients and trophic status of, 102-103 overview of water quality in, 122-125 oxygenation as a management tool, 128-129 pH, 113-116 phosphorus in, 103-108 potential (?) and demonstrated (,/) causal connections between high abundance of phytoplankton and harm to fish through poor water- quality conditions, 125 potential for improvement of water quality in, 126-128 probable cause of low dissolved oxygen throughout the water column of, 120-121

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INDEX relationship between water level and dissolved oxygen in the water column of, 120 relationship between water level and pH in, 115 relationship of mean chlorophyll and peak chlorophyll to water level, 113 seasonal development of algal biomass in, 110-113 status of tributaries to, 144-146 status of various hypotheses related to water quality of, 123 water level in, 100-101 U.S. Bureau of Reclamation (US13R), 1, 3, 10,14,20-21,65,99,219,311, 335 biological assessment of endangered suckers, 38-40 biological assessment of the threatened coho salmon, 41-43 U.S. Department of Agriculture, 2,19 U.S. Department of Commerce, 2,19 U.S. Department of the Interior (DOI), 2, 19,173 U.S. Fish and Wildlife Service (USFWS), 1, 3,10,56,99,128,214,312-330 biological opinion of endangered suckers, 40-41 U.S. Forest Service (USES), 11 U.S. Geological Survey (USGS), 9,148,278 US13R. See U.S. Bureau of Reclamation USES. See U.S. Forest Service USFWS. See U.S. Fish and Wildlife Service USGS. See U.S. Geological Survey Utah suckers, 246 397 V Value of agricultural production, 1998,81, 91 in lower Klamath basin, 91 in upper Klamath basin, 81 W Wanger, Oliver, 173 Water level in Upper Klamath Lake, 100- 101,224-227 fluctuations in, 101 and mean water levels proposed by US13R, 100 Water quality, 241-242 harming large fish, 5 Water routing diagram for the Klamath Project, 21 Water temperature and dissolved oxygen (DO), 137-138 in all main-stem reservoirs, 2000,138 in Copco and Iron Gate Reservoirs, 2000,137 Water temperature of the Klamath River at Orleans, 177 Wetland transformations, 71-74 net loss, through drainage, of wetland connected to Upper Klamath Lake, 72 Wild and Scenic Rivers Act of 1968,305 Williamson River system, 12-13,53,101 Winter steelhead, 270-273 hatcheries, 272-273 life history, 270-272 status, 273 Wood River, 54,101

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