U.S Department of the Interior, U.S. Geological Survey

Aerial image from Google Earth Development of New Information to Inform Fish Passage Decisions at the Yale and Merwin Hydro Projects on the Lewis River U.S Department of the Interior, U.S. Geological Survey Robert Al-Chokhachy (USGS)*, Dave Beauchamp (UW), Mark Sorel (UW), and Chris Clark (MSU) The data presented herein are published in: Al-Chokhachy, R., Clark, C.L., Sorel, M.H., and Beauchamp, D.A., 2018, Development of new information to inform fish passage decisions at the Yale and Merwin hydro projects on the Lewis River, Washington Final report, 2018: U.S. Geological Survey Open-File Report 2018 1190, 206 p., https://doi.org/10.3133/ofr20181190.

Outline 1. Project objectives 2. Task-by-task description of methods and results 3. Feasibility modeling

Scope of Work: project tasks 1. Review information regarding fish transport into Lake Merwin and Yale Lake 2. Habitat assessment of tributaries to Yale Lake and Lake Merwin 3. Assessment of adult potential for spawning success 4. Assess juvenile production potential and emigration success 5. Evaluation of Lake Merwin predator impacts 6. Assess anadromous/resident interactions

Scope of Work: project tasks 1. Acclimation facilities 2. Downstream collection 3. Adult upstream collection 4. Community interactions during reintroductions

Task 1-Downstream Collection, Efficiency Collection efficiency (%) 80 70 60 50 40 30 20 10 0 1996 1997 1998 1999 2000 2001 2002 2003 2004 Year 2005 2006 Chinook Coho O. mykiss 2007 2008 2009 2012 2013 2014 Cowlitz Falls Variability Annually Between species

Task 1-Downstream Collection, Efficiency/proportion of collected Collection effficiency (%) 100 80 60 40 20 0 Cowlitz Falls-Coho Cowlitz Falls-O. mykiss Cowlitz Falls-Chinook Mayfield-Coho Mayflied-O. mykiss Mayfield-Chinook PBR-O. mykiss Location PBR-Chinook Lower Baker-Early Lower Baker late Upper Baker Early Upper Baker Late Differences across locations and species Swift Reservoir Coho = 15.2% Chinook ~ 3% Steelhead = 19%

Task 1-Downstream Collection, Efficiency Swift Reservoir Coho = 15.2% Chinook ~ 3% Steelhead = 19% PacifiCorp and Cowlitz Public Utility District [PUD], 2017, Lewis River fish passage program 2016 annual report: Portland, Oreg., PacifiCorp and Cowlitz Public Utility District, 176 p.

Task 1-Downstream Collection, Survival and Injury River Facility Collector type Survival SD n Baker Upper Baker Forebay collector - Surface collector 1 0 4 Clackamas North Fork Forebay collector 0.92 0.07 8 Forebay collector - V-Screen Collector 0.99 0.01 3 River Mill Surface spill - Spillway weir 0.99 0.01 3 Columbia Bonneville Bonneville floating surface collector 0.86 0.15 21 Sampled from barge 0.89 0.12 33 Cowlitz Cowlitz Falls Forebay collector - retrofit baffle 0.99 0.02 45 Mayfield Louver system 0.96 0.02 32 Deschutes Pelton Round Butte Guidance net/skimmer 0.98 0.01 14 Willamette Willamette Falls Mixed 0.99 0.01 5 Swift FSC Average injury = 1.1% (range = 0 2.2%) Predominantly descaling (>70%) Average survival = 99.3% (range = 92 100%) Parr and smolts

Task 1-Downstream Collection, Survival and Injury River Facility Species Survival (%) SD n Cowlitz Cowlitz Falls Coastal cutthroat 99.6 0.3 13 Mayfield Coastal cutthroat 99.9-1 Deschutes Round Butte Bull Trout 98.8 0.3 5 Kokanee 93.5 1.5 5 Mt. Whitefish 99.9 0.02 5 Rainbow trout 99.2 1.2 5 Swift Survival (%) Species 2014 2015 Rainbow trout 100 100 Bull Trout 100 90.0 Goldendale 99.7 - Coastal cutthroat (smolt) 100 99.2 Coastal cutthroat (fry) 99.3 52.9

Task 1-Upstream Collection, Trap Efficiency Little reported information on upstream trap collection efficiency Lewis Recent study at Merwin trap (Caldwell et al. 2017) Trap efficiencies Steelhead = 61% Chinook = 38% Coho = 9% Mortality rates low Caldwell, L., D. Stroud, F. Carpenter, L. Belcher, M. Morasch, K. Denton, and K. Ross. 2017. Merwin Upstream Passage Adult Trap Efficiency: 2016 Final Report. Prepared by: Cramer Fish Sciences and K. Denton & Associates. Prepared for: Pacific Power (A Division of PacifiCorp).

Task 1: Summary Injury rates (upstream and downstream) appear to be relatively low for most years/species Proportion of emigrants collected at sites is highly variable-years, sites, species Efforts to improve collection are underway-pattern that has continued at other facilities (e.g., Cowlitz Falls)

Task 2: Habitat assessment of tributaries to Yale Lake, Lake Merwin, Swift Reservoir Study tributaries

Task 2: Habitat assessment of tributaries to Yale Lake, Lake Merwin, Swift Reservoir Objectives and methods Quantify the extent of habitat within the tributaries-yale and Merwin Quantify flow and thermal regimes in tributaries Assess tributary habitat and riparian conditions Rerun EDT model with quantitative field-bases measures of habitat

Photo: R. Al-Chokhachy, USGS Task 2: Habitat assessment of tributaries to Yale Lake and Lake Merwin Quantify flow and thermal regimes in tributaries Methods: Install pressure transducers at top and bottom of tributaries Quantify stage-discharge relationships

Task 2: Habitat assessment of tributaries to Yale Lake, Lake Merwin, Swift Reservoir Assess tributary habitat and riparian conditions Methods: Utilize existing habitat protocols within the PNW (CHaMP) Continuous habitat surveys Given site-site variability in reach-based assessments

Channel unit attributes Habitat attributes Bankfull width, wetted width, depth Substrate Channel units Large woody debris Gradient Riparian condition All georeferenced Collected specifically for parameterizing EDT model Photo: R. Al-Chokhachy, USGS

Task 2: Habitat assessment-extent of Stream habitat in Merwin and Yale Length (km) Gradient (%) Lake Merwin Brooks Creek/B1 4.1 4.4 (2.4) Buncombe Hollow Creek 1.1 3.2 (1.8) Cape Horn Creek 0.5 5.2 (0.9) Indian George Creek 1.5 5.7 (1.8) Jim Creek 0.5 4.7 (1.1) Lower Speelyai 0.3 2.8 (0) Rock Creek 0.2 na Total 8.2 Yale Lake Cougar Creek 3.9 1.6 (0.9) Dog Creek 0.3 4.9 (0) North Siouxon Creek 0.7 7.0 (2.7) Ole Creek 1.7 2.0 (1.7) Panamaker Creek 0.4 - Siouxon Creek 6.1 2.1 (2.3) Speelyai Creek 6 6.2 (4.4) Swift Bypass Channel 6.5 0.7 (0.5) W. Fork Speelyai Creek 1.3 10.7 (2.5) W. Tributary Speelyai CK 1.1 9.0 (5.6) Total 28 Photo: R. Al-Chokhachy, USGS

Task 2: Habitat assessment Swift Stream Bedrock Boulder Cobble Gravel Fines Chickoon Creek 31.4 11.8 48.3 8 0.5 Clear Creek 0 4 60.4 28.1 5.7 Cussed Hollow Ck 24.9 12.7 45.2 10.4 2.1 Diamond Creek 0 36.4 46.3 17.2 0 Little Creek 0 0 24.5 21.7 53.7 P3 creek 0 50 22 16 12 P7 creek 0 18.4 53.5 24.2 2 Pepper Creek 6 9.2 52 28.3 3.2 Range Creek 2.5 49.3 28.9 14.5 0 S15 creek 7.8 60.9 28.6 2.7 0 S20 creek 0 23.7 73.8 1.8 0.7 Spencer Creek 5.9 30.6 56.5 7 0 Upper Lewis Creek 6.2 17.8 60.7 14.5 0.6 Lake Merwin Stream Bedrock Boulder Cobble Gravel Fines Brooks Ck 0.5 7.4 25.9 57.7 7.4 Buncombe Hollow Ck 38.2 0 22 33.1 6.6 Cape Horn Creek 27.4 15.4 31.1 19.8 6.4 Indian George Creek 5.1 5.9 43.7 42.4 1.8 Jim Creek 20.4 13.5 22.1 37.7 5.9 Lower Speelyai 0 6.4 15.5 53.6 15.5 Yale Lake Cougar Creek 0 0.9 34.4 52.7 3.5 Dog Creek 0 23.6 31.8 35.5 9.1 North Siouxon Creek 16.7 58.3 13.3 11.7 0 Ole Creek 0 14 52.7 32.3 1 Panamaker Creek 10 12.4 57.1 20 0 Siouxon Creek 13.3 46.1 33.3 7.2 0 Speelyai Creek 4.7 38 40.8 11.3 0.6 Bypass Channel 0.4 26.7 57 10.8 4.2 W. Fork Speelyai Ck 2 59.5 30.6 7.9 0 W. Tributary Speelyai 0.5 34.7 48.1 15.4 0.1

Task 2: Temperature in Merwin and Yale July August Reservoir Stream Avg. Range Avg. Range Lake Merwin Brooks Creek 13.8 12.4-19.4 13.8 12.8-14.8 Buncombe Hollow Creek 17.0 14.9-19.1 17.5 15.6-19.0 Cape Horn Creek 14.2 12.4-15.8 14.9 13.5-16.2 Indian George Creek 15.1 13.1-16.7 16.0 14.7-17.1 Jim Creek 14.9 13.1-16.4 15.6 14.3-16.6 Lower Speelyai - - - - Yale Lake Cougar Creek 7.3 7.1-7.7 7.4 7.1-7.6 Dog Creek 12.7 11.2-14.1 - - North Siouxon Creek 13.8 11.4-15.6 15.3 14.1-16.3 Ole Creek 13.4 11.5-14.7 14.7 13.6-15.4 Panamaker Creek 12.7 11.1-13.9 14.4 13.7-14.9 Siouxon Creek 15.4 12.4-17.7 16.9 14.9-18.6 Speelyai Creek 15.0 12.8-17.0 16.8 15.0-17.8 Swift Bypass Channel 12.3 11.0-13.1 13.4 12.4-14.3 W. Fork Speelyai Creek 13.6 11.6-15.3 15.0 13.4-15.9 W. Tributary Speelyai Ck 14.4 12.3-16.4 15.5 13.9-16.9

Task 2: Swift temperature

Task 2: Habitat Assessment Summary Empirical data used to parameterize EDT model including new data (USGS), USFS, and Meridian High quality habitat in tributaries The extent of habitat in Lake Merwin (8.2 km) is low suggesting limited capacity for reintroductions

Scope of Work: project tasks 1. Review information regarding fish transport into Lake Merwin and Yale Lake 2. Habitat assessment of tributaries to Yale Lake and Lake Merwin 3. Assessment of adult potential for spawning success in Yale and Merwin 4. Assess juvenile production potential and emigration success 5. Evaluation of Lake Merwin predator impacts 6. Assess anadromous/resident interactions

Task 3: Merwin adult potential for spawning success-methods Capacity for adults to access and successfully reproduce

Task 3: Merwin adult potential for spawning success-methods Capacity for adults to access and successfully reproduce 2014 only ~300 test adult Coho Identify locations of spawning Weekly redd surveys of all available habitat Juvenile surveys in tributaries with spawning activity in 2015

Task 3: Merwin adult potential for spawning success-methods Capacity for adults to access and successfully reproduce Identify locations of spawning Juvenile surveys in tributaries with spawning activity in 2015 Snorkel surveys and electrofishing surveys

Task 3: Merwin adult spawning (2014)

Task 3: Merwin-2015 juvenile surveys

Task 3: Merwin-2015 juvenile surveys 180 (a) 160 140 120 Clear Creek Count 100 80 60 40 20 0 18 16 14 12 (b) Brooks Creek Count 10 8 6 4 2 0 50 60 70 80 90 100 110 120 Fork length (mm)

Task 3: Merwin-2015 juvenile surveys Absence in others may be due to short habitat available Earlier migration-swift (Coho-20%) Longer reservoir residence

Task 3: Spawning patterns Swift

Task 3: Spawning habitat Lake Merwin Stream Bedrock Boulder Cobble Gravel Fines Brooks Ck 0.5 7.4 25.9 57.7 7.4 Buncombe Hollow Ck 38.2 0 22 33.1 6.6 Cape Horn Creek 27.4 15.4 31.1 19.8 6.4 Indian George Creek 5.1 5.9 43.7 42.4 1.8 Jim Creek 20.4 13.5 22.1 37.7 5.9 Lower Speelyai 0 6.4 15.5 53.6 15.5 Yale Lake Cougar Creek 0 0.9 34.4 52.7 3.5 Dog Creek 0 23.6 31.8 35.5 9.1 North Siouxon Creek 16.7 58.3 13.3 11.7 0 Ole Creek 0 14 52.7 32.3 1 Panamaker Creek 10 12.4 57.1 20 0 Siouxon Creek 13.3 46.1 33.3 7.2 0 Speelyai Creek 4.7 38 40.8 11.3 0.6 Bypass Channel 0.4 26.7 57 10.8 4.2 W. Fork Speelyai Ck 2 59.5 30.6 7.9 0 W. Tributary Speelyai 0.5 34.7 48.1 15.4 0.1 Photo: R. Al-Chokhachy, USGS

Task 3: Summary Test fish and empirical data from Swift suggest variety of habitats (spatially) will be utilized by reintroduced anadromous Salmon Habitat is generally in good condition-spawning gravel in some locations may be too large, but fines are not limiting Lack of YOY in tributaries with spawning may be due to early life-stage emigration, leading to increased reservoir rearing (capacity, Task 6)and potential predation effects (Task 5)

Task 4: Assess juvenile production potential and emigration success Objectives and methods 1. Determine emigration timing into Swift Reservoir 2. Quantify behavioral relationships with streamflow, temperature, and interannual differences 3. Quantify travel times and survival to collection facility 4. Evaluate reservoir behavior

Task 4: Methods-stream habitat Determine emigration timing into Swift Reservoir Wild Coho 20 reaches per year-5 km of habitat Marking fish with 12 mm PITtag 2013 = 357 fish 2014 = 883 fish 2015 = 800 fish

Task 4: Methods-stream habitat Determine emigration timing into Swift Reservoir Wild Coho Releases PIT-tagged acclimation Chinook Acclimation ponds Migration timing Year Species Clear Creek Crab Creek Muddy River 2013 Chinook 1,750 750 1,750 Coho 2,000 2014 Chinook 7,576 1 2015 Chinook 3,400 3,300 3,300

Task 4: methods Quantify travel times and survival to collection facility PIT-tagged fish Clear Creek Acclimation Chinook Screw trap PIT-tag antennae Swift Collection facility Screw trap

Task 4: methods Quantify travel times and survival to collection facility Integrate individual-specific data from PIT-tags, screw trap, and collection facility for estimates of travel times Overall downstream survival Swift Collection facility

Task 4: methods reservoir Evaluate travel behavior and near potential collection facilities Yale Lake Compliment PIT-tag data and previous radiotelemetry data for assessments of variability of travel times Depth use near dam~potential collection facility

Task 4: methods reservoir Evaluate travel behavior and near potential collection facilities 2014 test release of 5,000 Coho smolts Release at Yale Park

Task 4: methods reservoir Evaluate travel behavior and near potential collection facilities 2014 (5,000 Coho smolts) Hydroacoustic surveys (UW) Pre-release Day of release Near Yale Park to identify targets Post-release

Task 4: Results Photo: R. Al-Chokhachy, USGS

Number of coho emigrants Stage 20 18 16 14 12 10 8 6 4 2 0 2.5 2.0 1.5 1.0 0.5 0.0 Sep (a) (b) Jan May 2D Graph 1 Sep Date Stage Temperature Jan May Sep 2013 2014 2015 Task 4: Results-Coho 20 18 16 14 12 10 8 6 4 2 0 Emigration timing varied considerably across years Stream temperature ( o C) 2013-high flow event 2014-mixed results Association with high flow events similar to Pess et al. (2011) No summer emigration-mid- May-early August

Task 4: Results-Coho Year day 360 330 300 270 240 210 180 150 120 90 60 30 0 0 5 10 15 20 25 30 35 Sample reach (Upstream- ) No summer emigration Mid-May-early August No clear patterns of outmigration timing and tagging location

Task 4: Results-Coho Count 30 25 20 15 10 5 0 180 160 (a) (b) Wild Hatchery Timing to collector Similar for wild and hatchery Coho May 140 120 100 80 60 40 20 0 0 50 100 150 200 250 300 350 Year day

Task 4: Results-Coho Count 30 25 20 15 10 5 0 180 160 140 120 100 80 60 40 20 0 (a) (b) 0 50 100 150 200 250 300 350 Year day Wild Hatchery Timing to collector Coho smolt counts at FSC 16000 Similar for wild and 14000 hatchery Coho 12000 10000 May 8000 6000 4000 2000 0 January February March April May June July August September October November December Month Coho at FSC 2014 2015

16000 Coho smolt counts at FSC 14000 12000 10000 8000 6000 4000 2000 0 30 (a) 25 20 15 10 January February March April May June July Month August September October November December 2014 2015 Wild Task 4: Results-Coho Travel time to FSC Leaving Clear Creek Median = 121 days Range = 21-347 Screw trap Median = 37 Range = 8 391 days Count 5 0 180 160 140 120 100 (b) Hatchery Difference a result of when emigrating from tributaries Also variability in reservoir rearing 80 60 40 20 0 0 50 100 150 200 250 300 350 Year day

Task 4: Results-Chinook Acclimation Chinook in Clear Creek Direct and acclimation pond releases (2014 2015) ~60% emigrate within a week 98% within 60 days

Task 4: Results Count 50 40 30 20 10 0 1.0 (a) (b) Acclimation Chinook (Clear Creek) time in Swift after passing antenna Median days = 69 Range = 5 320 days Cumulative frequency 0.8 0.6 0.4 0.2 0.0 0 50 100 150 200 250 300 350 Days between emigration and FSC

Task 4: Results 250 Days between release and FSC Count 200 150 100 50 0 700 600 500 400 300 200 100 0 0 100 200 300 400 500 600 700 * 2013 2015 Crab Creek Travel time (days) Muddy River 2013 2014 2015 Clear Creek Release location/year * All acclimation Chinook From release Crab Creek, Muddy River, Clear Creek Bimodal Apparent differences across sites and years

20 (a) 2013 15 Task 4: Results 10 5 All acclimation Chinook 0 50 (b) 2014 Considerable differences across years Count 40 30 2013 and 2015 vs. 2014 20 10 0 100 (c) 2015 80 60 * 40 20 0 0 50 100 150 200 250 300 350 Year day

Task 4: Results Fish reaching the FSC in Swift Reservoir As December 31, 2015 focusing specifically on PIT-tagged fish reaching the FSC: Coho 14% of hatchery Coho (2013) 3.4% of wild Coho PIT-tagged 2013-2015 15.2 % from screw trap (2013, 2014) Difference from Clear Creek data due to overwinter and migration mortality Steelhead 18.7% of fish marked at screw trap (2013-2014) Photo: R. Al-Chokhachy, USGS

Task 4: Results Fish reaching the FSC in Swift Reservoir Coho 14% of hatchery Coho (2013-spring release) 3.4% of wild Coho PIT-tagged 2013-2015 15.2 % from screw trap (2013, 2014) Steelhead 18.7% of fish marked at screw trap (2013-2014) Acclimation Chinook 1.4-2.0% of PIT-tagged fish (2013-2015) 3.7% of the 202,666 released fish Photo: R. Al-Chokhachy, USGS

Task 4: methods reservoir Hydroacoustic survey Pre-release Day of release Post-release Zones Paths

Task 4: Reservoir Results Hydroacoustic results Smolts relatively rapidly movements to collector Use of upper water column (<20 m) Side-looker data

Task 4: Summary Proportion of fish collected (remains low)

Collection 8% 0% 15% Fish reaching the FSC in Swift Reservoir Coho 14% of hatchery Coho (2013-spring release) 3.4% of Coho PIT-tagged 2013-2015 15.2 % from screw trap (2013, 2014) Steelhead 18.7% of fish marked at screw trap (2013-2014) Acclimation Chinook 1.4-2.0% of PIT-tagged fish (2013-2015) 3.7% of the 202,666 released fish 6% 0% 6% PacifiCorp and Cowlitz Public Utility District [PUD], 2017, Lewis River fish passage program 2016 annual report: Portland, Oreg., PacifiCorp and Cowlitz Public Utility District, 176 p. Photo: R. Al-Chokhachy, USGS

Task 4: Summary Proportion of fish collected (remains low) Emigration time Juvenile Coho is ~ 5 weeks (highly variable) Spring Chinook = > 2 months Test release data suggest relatively rapid migrations Radiotelemetry data = 5.2 km/day travel rate Hydroacoustics, Yale Yale Park Dam (2014) = ~7 km Together results suggest difficulties of fish finding collector Consistent with results from Cramer Fish Sciences (90%) within 140 m of collector

Task 5: Evaluation of Lake Merwin Objectives and methods predator impacts 1. Estimate abundance and size structure of predators 2. Quantify predator-prey interactions and evaluate if predation will be a limiting factor for anadromous populations 3. Quantify spatial and temporal distributions of predators, which may provide information for potential control efforts, if needed

Task 5: Evaluation of Lake Merwin predator impacts: methods Estimate abundance and size structure of predators Gill netting Mark-recapture study to estimate abundance (2013 2014) External floy tags Photo: R. Al-Chokhachy, USGS Chapman estimator

Task 5: Evaluation of Lake Merwin predator impacts: methods Estimate abundance and size structure of predators Tiger Muskie Predation on Northern Pikeminnow Stocking records Average 1,340/year Survival estimated via catch curves Photo: M. Sorel, U. Washington

Task 5: Thermal experiences Catch information by depth and season Limnological and thermal data collected

Task 5: Biological and diet data Biological data Size, age, growth, diet, energetic, trophic & reproductive status Gut contents -Diet Muscle tissue: -Stable isotopes Photo: D. Beauchamp, USGS Scales & Otoliths: -Age & Back-calculate size-at-age

Task 5: Lake Merwin predation potential Length frequency Temporal Diet Composition Thermal Experience 120 100 80 60 40 20 Consumer Growth Bioenergetics Model Predator Energy Density Prey Energy Density 0 200 300 400 500 600 Consumer Size Structure & Abundance Fork length (mm) Biomass of Exploitable prey Consumption Estimate Population Consumption Consumption as % of Prey Biomass or Production

Task 5: Results Photo: R. Al-Chokhachy, USGS

Task 5: Results Abundance Northern Pikeminnow Tagged > 2,000 fish Abundance 200-300 mm = 544,259, (95% CI 190,609-1,554,062) Abundance >300 mm = 11,240 (95% CI = 3,370 39,880) Tiger Muskellunge 5,488 (based on survival analysis and stocking)

Task 5: Results June (Spring) July-September (Summer) November (Fall) Gill Net Depth (m) 0-15 16-30 >30 200-299 mm 300+ mm N = 4 L, 1 S No Data N = 2 L, 3 S No Data N = 2 L, 5 S N = 13 L, 57 S N = 2 L, 1 S N = 4 L, 7 S N = 2 L, 2 S 0 10 20 30 0 10 20 30 0 10 20 30 Northern Pikeminnow Caught / Set Distribution Majority of NPM in upper 15 m during stratification High predation potential during all seasons, but particularly during spring/summer

Task 5: Results 0.6 2013-2014 1958-1963 0.4 Size distribution Proportional Frequency 0.2 0.0 0.6 0.4 Males Females Northern Pikeminnow Tiger Muskie controls Fewer >250mm fish (P<0.10) 0.2 0.0 200 250 300 350 400 450 500 550 600 Fork Length (mm)

Task 5: Results-NPM diets 1.0 200-300 mm 0.8 200 300 mm Proportion 0.6 0.4 Zooplankton, inverts, vegetation 0.2 0.0 1.0 >300 mm >300 mm Crayfish, NPM, Kokanee Proportion 0.8 0.6 0.4 0.2 Zooplankton Terrestrial inverts Aquatic inverts Kokanee Sculpin NPM Crayfish Vegetation Shift with increasing abundance of salmon? 0.0 Spring Summer Fall Season

Task 5: Results-Tiger Muskie diets 1.0 Diets Diet proportion 0.8 0.6 0.4 0.2 NPM LSS PKS Kokanee Inverts Largest proportion of diets Year-round predation on NPM 0.0 Spring Summer Fall Season Very few Kokanee Shift under anadromous reintroductions?

Task 5: Results Stable isotope data Substantial differences in trophic level and forage NPM >300 mm <300mm Tiger Muskie

Task 5: Isotope results -22 Size relationships -24 13 C -26-28 -30 Northern Pikeminnow Tiger Muskellunge 11 10 9 8 7 6 5 NPM 15 N Shift in carbon source (more pelagic) Shift to piscivory Tiger-Muskie Consistent carbon Increasing trophic level 0 200 400 600 800 1000 4 FL (mm)

Task 5: Results-NPM piscivory Prey FL (mm) 350 300 250 200 150 100 Kokanee N. pikeminnow Sculpin 50% Pred. FL 40 % Pred. FL Primarily sculpin <300 mm Shift to salmonids and cannibalism >300 mm 50 0 200 300 400 500 600 Predator FL (mm)

Task 5: Results-NPM piscivory # spring Chinook Salmon consumed 10000 8000 6000 4000 2000 0 Larger Chinook consumption SmallerChinook consumption Larger Chinook Salmon Smaller Chinook Salm Apr May Jun Jul Aug Sep Oct Nov Dec Jan Feb Mar 50 40 30 20 10 0 spring Chinook Salmon mass (g) Bioenergetics results Per 1,000 NPM Annual estimates 18 g juvenile Chinook 39,250 45 g juvenile chinook 16,022

Task 5: Results-NPM piscivory Per 1,000 NPM # spring Chinook Salmon consumed 10000 8000 6000 4000 2000 0 Larger Chinook consumption SmallerChinook consumption Larger Chinook Salmon Smaller Chinook Salm Apr May Jun Jul Aug Sep Oct Nov Dec Jan Feb Mar 50 40 30 20 10 0 spring Chinook Salmon mass (g) Abundance estimates ~11,000 NPM > 300 mm Annual consumption at the population level 18 g >431,000 45 g 176,242 Rearing time 2-3 months? 40,000 110,000 Fry

Conclusions-Task 5 Tiger Muskellunge appear to have significant effect on size structure of NPM NPM population of piscivorous fish remains relatively large Estimates of juvenile Salmon predation, even seasonal appears to be high

Objectives 1. Potential influences of anadromous salmon reintroductions on bull trout populations 1. Evidence of competition/overlap in resources 1. Food resources 2. Habitat 2. Reservoir and tributaries

Study area: bull trout Adfluvial life-history Tributary rearing (1-3 years) Reservoir-growth and maturity Photo: R. Al-Chokhachy, USGS Photo: C. Muhlfeld, USGS

Methods Interactions across life-stages Quantify distributional overlap in key bull trout spawning and rearing areas Foodweb analyses to evaluate potential bull trout shifts in diet after reintroduction Superimposition of coho on existing bull trout redds Reservoir capacity

Methods: distributional overlap in tributaries Systematic snorkel surveys Pine Creek and P8, Rush Creek Spatial and temporal extent Photo: R. Al-Chokhachy, USGS

Study area: bull trout Adfluvial life-history Tributary rearing (1-3 years) Reservoir-growth and maturity Photo: R. Al-Chokhachy, USGS Photo: C. Muhlfeld, USGS

Methods: distributional overlap in tributaries Systematic snorkel surveys Pine Creek and P8, Rush Creek Spatial and temporal extent Photo: R. Al-Chokhachy, USGS

Methods: tributaries Tributaries Shifts since reintroduction Summer, fall Coho and bull trout diet overlap Fin clips and macroinvert. Stable isotopes Gastric lavage for diet data Photos: R. Al-Chokhachy, USGS

Methods: diet overlap, foodweb, and trophic position in Swift Reservoir Trawl and gillnet data Diets and stable isotopes Trophic shifts Photo: D. Beauchamp, USGS

Methods: coho superimposition and Tributaries potential population effects Quantify distributional overlap in key bull trout spawning and rearing areas Do juvenile bull trout and coho diets overlap and is there evidence of potential bull trout shifts in diet after reintroduction? Superimposition of coho on existing bull trout redds Reservoir capacity

Methods: superimposition Tributaries Redd Counts All existing bull trout and coho redd data Identify extent of temporal overlap of coho redds Photo: R. Al-Chokhachy, USGS

Methods: superimposition Redd Counts Superimposition Identified bull trout redds minimize sampling error Superimposition of coho on existing bull trout redds Photo: R. Al-Chokhachy, USGS

Methods: superimposition Redd Counts Photo: R. Al-Chokhachy, USGS

Reservoir carrying capacity Estimate juvenile Salmon capacity Add to information from habitat, predation, collection Interactions with resident salmonids

Reservoir carrying capacity Depth-distributions of fishes across seasons Gill nets Hydroacoustics Depth-thermal profiles and thermal experience

Reservoir carrying capacity Depth-distributions of fishes across seasons Depth-thermal profiles and thermal experience Zooplankton-seasonally Clarke-Bumpus sampler Forage by depth Biomass Production-egg development Photo: P. Budy, USGS

Reservoir carrying capacity Depth-distributions of fishes across seasons Depth-thermal profiles and thermal experience Zooplankton-seasonally Diets, stable isotopes, growth Bioenergetics modeling consumption demand Reservoir environment Seasonally Thermally excluded from epilimnion (summer) Swift Rainbow trout: (biomass + production) - demand Forage to support juvenile Salmon Photo: P. Budy, USGS

Photo: R. Al-Chokhachy, USGS Task 6: Results

Snorkel surveys 2013-2014 0 0 Few coho observed during each year 1 0 2013, n = 2 2014, n = 40 0 0 1 7 3 11 7 10

Snorkel surveys 2013-2014 Number of bull trout observed in snorkel surveys 1200 1000 800 600 400 200 0 0 0 1 0 0 0-50 50-100 100-150 150-200 200-250 250-300 300-350 350-400 400-450 450-500 Size class (mm) Coast cutthroat trout 500-550 0 550-600 600-650 650-700 1 7 Few coho observed during each year Relatively low abundance compared to coastal cutthroat trout (10-100x higher) 3 11 7 10

Snorkel surveys 2015: expanded surveys Spring-early summer Rush Creek Pine, P8, P3

Snorkel surveys 2015: expanded surveys Mid-late summer Rush Creek Pine, P8, P3

Snorkel surveys 2013-2014 Proportion of fish 1.4 (a) Bull Trout Coastal Cutthroat Trout 1.2 Coho Mountain Whitefish YOY Oncorhynchus spp. 1.0 0.8 0.6 0.4 0.2 0.0 Pine Creek P8 2013 Coho Relatively low abundance Coastal cutthroat trout Proportion of fish 1.4 (b) Bull Trout Coastal Cutthroat Trout 1.2 Coho Mountain Whitefish YOY Oncorhynchus spp. 1.0 0.8 0.6 0.4 2014 0.2 0.0 Pine Creek Sample stream P8

Snorkel surveys 2013-2015 Proportion of fish 1.4 (a) Bull Trout Coastal Cutthroat Trout 1.2 Coho Mountain Whitefish YOY Oncorhynchus spp. 1.0 0.8 0.6 0.4 0.2 2013 Proportion of fish 1.4 (a) Bull Trout Coastal Cutthroat Trout 1.2 Coho Mountain Whitefish YOY Oncorhynchus spp. 1.0 0.8 0.6 0.4 0.2 Early 0.0 Pine Creek P8 0.0 Pine Creek P8 Proportion of fish 1.4 (b) Bull Trout Coastal Cutthroat Trout 1.2 Coho Mountain Whitefish YOY Oncorhynchus spp. 1.0 0.8 0.6 0.4 0.2 2014 Proportion of fish (b) 1.4 Bull Trout Coastal Cutthroat Trout Coho 1.2 Mountain Whitefish YOY Oncorhynchus spp. 1.0 0.8 0.6 0.4 0.2 Late 0.0 Pine Creek P8 0.0 Pine Creek P8 Sample stream Sample stream

Snorkel surveys 2013-2015 Proportion of fish 1.4 (a) Bull Trout Coastal Cutthroat Trout 1.2 Coho Mountain Whitefish YOY Oncorhynchus spp. 1.0 0.8 0.6 0.4 Early Proportion of fish 1.4 (a) Bull Trout Coastal Cutthroat Trout 1.2 Coho Mountain Whitefish YOY Oncorhynchus spp. 1.0 0.8 0.6 0.4 Early 0.2 0.2 0.0 Pine Creek P8 0.0 P3 Rush Creek Proportion of fish (b) 1.4 Bull Trout Coastal Cutthroat Trout Coho 1.2 Mountain Whitefish YOY Oncorhynchus spp. 1.0 0.8 0.6 0.4 0.2 Late Proportion of fish (b) 1.4 Bull Trout Coastal Cutthroat Trout Coho 1.2 Mountain Whitefish YOY Oncorhynchus spp. 1.0 0.8 0.6 0.4 0.2 Late 0.0 Pine Creek P8 0.0 P3 Rush Creek Sample stream Sample stream

Snorkel surveys: Coho Growth (g/d/d) 0.04 0.03 0.02 0.01 0.00-0.01-0.02 7.2 0 5 10 15 20 25 Temperature (C) Outmigration due to thermal limitations for growth? Habitat Photo: R. Al-Chokhachy, USGS Temperature (C) 7.0 6.8 6.6 6.4 Jul Jul Jul Aug Aug Sep Date

10 8 6 (a) Coastal Cutthroat (<150 mm) 2009 Coastal Cutthroat (>150 mm) Tributary trophic interactions N 4 2 Bull Trout (<150 mm) Sculpin Bull Trout (~150 mm) δ 15 N and δ 13 C 0-2 P8 10 (b) 2014 N 8 6 4 2 0-2 Plecoptera (larvae) Coastal Cutthroat (<150 mm) Bull Trout (<150 mm) Ephemeroptera Coho Diptera (larvae) Lepidoptera Trichoptera (adult) Vegetation Trichoptera (larvae) Coleoptera carabidae Coastal Cutthroat (>150 mm) Plecoptera (adult) Terrestrial Coleoptera (larvae) Diptera (adult) Bull trout and coho Similar trophic level ~similar food resources -36-34 -32-30 -28-26 -24 13 C

10 2009 Tributary trophic 8 CCT (>150) interactions N 6 CCT (<150) Bull trout (<150) Sculpin (lg) Rush Creek 4 Sculpin (sm) 2 2014 Consistent pattern with P8 8 CCT (<150) Bull trout and coho N 6 Sculpin (lg) Coho Similar trophic level 4 Bull trout (<150) ~similar food resources 2-34 -32-30 -28-26 -24-22 13 C

Tributary trophic interactions 1.0 Summer diet data Proportion 0.8 0.6 0.4 0.2 0.0 Bull Trout Coho CCT/RBT (<150) CCT/RBT (>150) Sculpin Stoneflies Mayflies Caddisflies True flies Beetles True bugs Ants/beetles Mites Other aquatic Terrestrial Other Consistent results with isotope data High overlap Mayflies True flies Species Caddisflies

Tributary trophic interactions 1.0 Fall diet data Proportion 0.8 0.6 0.4 0.2 Stoneflies Mayflies Caddisflies True flies Beetles True bugs Ants/beetles Mites Other aquatic Terrestrial Other Shifts in fall 0.0 Bull Trout Coho CCT/RBT (<150) CCT/RBT (>150) Sculpin Species

Redd superimposition: Coho redds 2012-2014

Temporal overlap: superimposition Cumulative distribution 1.0 0.8 0.6 0.4 0.2 0.0 240 260 280 300 320 340 September 1 October 1 Year Day November 1 Coho Bull trout Bull trout redds 2012 current Pine/P8 Coho redds 2012 present All tributaries above swift 80% of coho spawning occurs after bull trout Hatchery individuals

Coho redds (2012-2014) Superimposition found on 3 of the 23 bull trout redds during 2014 No data for 2015

N 14 12 10 8 6 4 2 0-2 -32-30 -28-26 -24-22 -20 8.0 7.5 7.0 (a) (b) SB (< 100mm) Summer copepods BT pre (100-399 mm) COT (75-174 mm) Summer daphnia BT pre (400-699 mm) COT (<75 mm) LSS (350-449 mm) Crayfish Snails Trichoptera larva CCT (200-399 mm) BT post (400-699 mm) BT post (100-399 mm) MW (250-449 mm) LSS (50-349 mm) RBT h (200-349 mm) Reservoir trophic interactions Bull trout >400mm top predator Slightly higher trophic position Slight shift in sources N 6.5 COT (75-174 mm) RBT (100-349 mm) 6.0 COHO (50-299mm) 5.5 CHK (100-299 mm) LSS (350-449 mm) 5.0-27 -26-25 -24-23 13 C

N 14 12 10 8 6 4 2 0-2 -32-30 -28-26 -24-22 -20 8.0 7.5 7.0 (a) (b) SB (< 100mm) Summer copepods BT pre (100-399 mm) COT (75-174 mm) Summer daphnia BT pre (400-699 mm) COT (<75 mm) LSS (350-449 mm) Crayfish Snails Trichoptera larva CCT (200-399 mm) BT post (400-699 mm) BT post (100-399 mm) MW (250-449 mm) LSS (50-349 mm) RBT h (200-349 mm) Reservoir trophic interactions Bull trout <400mm High trophic position Consistent across periods Substantial shift in forage sources N 6.5 COT (75-174 mm) RBT (100-349 mm) 6.0 COHO (50-299mm) 5.5 CHK (100-299 mm) LSS (350-449 mm) 5.0-27 -26-25 -24-23 13 C

Bull trout gape limitations/foraging patterns Lowery and Beauchamp 2015 Length-foraging patterns Finding prey Shift with increasing prey and size classes?

Reservoir carrying capacity Population consumption (MT) Daphnia (MT) Daphnia (MT) 40 30 20 10 0 400 300 200 100 0 400 300 200 100 Apr May Jun Jul Aug Sep Oct Nov Hatchery Rainbow Trout Standing stock biomass (B) Production (P) Epilimnion (<10 m) Meta- and hypolimnion (>10 m) Apr May Jun Jul Aug Sep Oct Nov (a) (b) (c) Swift RBT demand Biomass + production Consumption/(B+P) Support ~150,000 spring Chinook Consumption / Biomass 0 1.0 C/B >10 m Jul-Sep C/B all depths 0.8 C/(B+P) >10 m Jul-Sep C/(B+P) all depths 0.6 0.4 0.2 0.0 Apr May Jun Jul Aug Sep Oct Nov Apr May Jun Jul Aug Sep Oct Nov (d)

Reservoir carrying capacity Population consumption (MT) Daphnia (MT) Daphnia (MT) Consumption / Biomass 40 30 20 10 0 400 300 200 100 0 400 300 200 100 0 Apr May Jun Jul Aug Sep Oct Nov Hatchery Rainbow Trout Standing stock biomass (B) Production (P) Epilimnion (<10 m) Meta- and hypolimnion (>10 m) Apr May Jun Jul Aug Sep Oct Nov 1.0 C/B >10 m Jul-Sep C/B all depths 0.8 C/(B+P) >10 m Jul-Sep C/(B+P) all depths 0.6 0.4 0.2 0.0 Apr May Jun Jul Aug Sep Oct Nov Apr May Jun Jul Aug Sep Oct Nov (a) (b) (c) (d) Swift RBT demand Biomass + production Consumption/(B+P) Support ~150,000 spring Chinook Other fishes? Coho Fry ~6 months to year Parr/smolts Residualized salmon Low collection rates

Reservoir carrying capacity Population consumption (MT) Daphnia (MT) Daphnia (MT) Consumption / Biomass 40 30 20 10 0 400 300 200 100 0 400 300 200 100 0 0.6 0.4 0.2 0.0 N N 14 12 10 8 6 Apr May Jun Jul Aug Sep Oct Nov (a) Hatchery Rainbow Trout 4 Standing stock biomass (B) Summer copepods Production (P) 2 0 Epilimnion (<10 m) -2-32 -30-28 -26-24 -22-20 8.0 Meta- and hypolimnion (>10 m) Apr May Jun Jul Aug Sep Oct Nov (b) 7.5 7.0 COT (75-174 mm) 6.5 RBT (100-349 mm) Apr May Jun Jul Aug Sep Oct Nov 1.0 C/B >10 m Jul-Sep 0.8 C/B all depths C/(B+P) >10 m Jul-Sep C/(B+P) all depths 6.0 5.5 SB (< 100mm) BT pre (100-399 mm) COT (75-174 mm) Summer daphnia COHO (50-299mm) CHK (100-299 mm) BT pre (400-699 mm) COT (<75 mm) LSS (350-449 mm) LSS (350-449 mm) Crayfish Snails Trichoptera larva CCT (200-399 mm) BT post (400-699 mm) BT post (100-399 mm) MW (250-449 mm) LSS (50-349 mm) RBT h (200-349 mm) 5.0 Apr -27 May Jun -26 Jul Aug -25 Sep Oct -24 Nov -23 13 C (a) (b) (c) (d) Swift RBT demand Biomass + production Consumption/(B+P) Support ~150,000 spring Chinook Other fishes? Coho Fry ~6 months to year Parr/smolts Residualized salmon Low collection rates

Integrating field data: potential effects on bull trout Field data into a modeling framework Integrate results with local data from WDFW, USFS, PacifiCorp Photo: R. Al-Chokhachy, USGS

Individual-based model Small population in Swift/Yale Enables tracking of individuals Averages for small populations not applicable (e.g., matrix models) Local, empirical data Mature bull trout Egg 1 2 3 4 5 6 7 8... 12 Reservoir Al-Chokhachy et al. 2015 Transactions of the American Fisheries Society

Individual-based model Small population in Swift/Yale -Negative effects of superimposition Mature bull trout Egg 1 2 3 4 5 6 7 8... 12 Competitive interactions -Competitive interactions -Growth, fecundity Reservoir Al-Chokhachy et al. 2015 Transactions of the American Fisheries Society

Bull trout adfluvial life history Adfluvial life-history 8 2013 Majority of emigration occurs at age-2 6 Sexual maturity Literature-ages 4-6 Number of bull trout observed in snorkel surveys 4 2 0 40 30 20 2014 10 0 0-50 50-100 100-150 150-200 200-250 250-300 300-350 350-400 400-450 450-500 500-550 550-600 600-650 650-700 Size class (mm)

Bull trout adfluvial life history Adfluvial life-history Majority of emigration occurs at age-2 Sexual maturity Literature-ages 4-6 Growth information PIT-tag data (J. Doyle, J. Byrne) Growth (mm/yr) 350 300 250 200 150 100 50 0 200 300 400 500 600 700 800 Tag length

Bull trout adfluvial life history Adfluvial life-history Majority of emigration occurs at age-2 Sexual maturity Literature-ages 4-6 Growth information PIT-tag data (J. Doyle, J. Byrne) Survival Literature values-early life stages Stillwater Sciences Adult survival estimates

Individual-based model Likely risk to populations Egg 1 2 3 4 5 6 7 8... 12 Reservoir Al-Chokhachy et al. 2015 Transactions of the American Fisheries Society

Individual-based model Likely risk to populations Scenarios 1. Reductions in rearing carrying capacity 1. Distributional overlap 2. Diet overlap 2. Redd superimposition 1. Field data-timing, superimposition 2. Literature-habitat similarities, similar body sizes 3. Hatchery stock and natal homing and historical changes in the Lewis 3. Reductions in reservoir carrying capacity 1. Task 4-collection efficiencies 2. Literature and regional evidence of landlocked populations 3. Density-dependent effects on bull trout growth, survival (Johnston and Post 2009)

Risk assessment results Number of adult bull trout 500 400 300 200 100 Baseline population model Absolute abundance not critical 5 10 15 20 Year

Risk assessment results Number of adults 400 350 300 250 200 150 100 Perturbations Superimposition and reservoir growth No real effect 50 0 Baseline Coho superimposition (20% loss) 20% reduction in reservoir growth 20% reduction in growth and survival 20% reduction in K

Risk assessment results Number of adults 400 350 300 250 200 150 100 Perturbations Superimposition and reservoir growth No real effect Reductions in reservoir survival Largest effect on bull trout 50 0 Baseline Coho superimposition (20% loss) 20% reduction in reservoir growth 20% reduction in growth and survival 20% reduction in K

Survival Number of adults 400 350 300 250 200 150 100 50 Risk assessment results Perturbations Superimposition and reservoir growth No real effect Reductions in reservoir survival Largest effect on bull trout 0 Baseline Coho superimposition (20% loss) 20% reduction in reservoir growth 20% reduction in growth and survival 20% reduction in K Abundance Johnston and Post 2009

Risk assessment results Number of adults 400 350 300 250 200 150 100 50 0 Baseline Coho superimposition (20% loss) 20% reduction in reservoir growth 20% reduction in growth and survival 20% reduction in K Perturbations Superimposition and reservoir growth No real effect Reductions in reservoir survival Largest effect on bull trout Reductions in carrying capacity Negatively effect on bull trout

Aerial image: Google Earth Conclusions

Photo: R. Al-Chokhachy, USGS Questions