COORDINATION:

The Nez Perce Tribal Hatchery (NPTH) Monitoring and Evaluation (M&E) Program and Chinook salmon supplementation research activities have been developed in coordination with the Bonneville Power Administration, Idaho Department of Fish and Game, U.S. Fish and Wildlife Service, National Marine Fisheries Service, and the U.S. Forest Service.  The project is in cooperation with the B-Run Steelhead Supplementation Effectiveness Research project BPA # 2010-057-00.  The M&E Action Plan, describing the goals, objectives, tasks and activities of the NPTH M&E Program has been reviewed and approved by the Independent Scientific Review Panel, and calls for continued coordination with regional co-managers.  Beginning in 2013, Project 1998-010-04, "Monitor and Evaluate (M&E) Performance of Juvenile Snake River Fall Chinook Salmon from Fall Chinook Acclimation Project (FCAP)" was incorporated into this NPTH M&E Project.  This project evaluates the success of Lyons Ferry Hatchery fall Chinook salmon supplementation above Lower Granite Dam at acclimation sites on the Snake and Clearwater rivers, coordinates with the Technical Advisory Committee of US v Oregon on the yearly Snake River Fall Chinook Run Reconstruction, and facilitates management decisions for future conservation and perpetuation of naturally spawning fall Chinook populations above Lower Granite Dam specifically addressing RPA184 in the FCRPS 2000 Biological Opinion and as recommended in the FWP, Snake Hell's Canyon and Clearwater Subbasin Summaries, and Wy-Kan-Ush-Mi Wa-Kish-Wit.  Since 2015, this project also PIT tags a substantial number of subyearling fall Chinook salmon released from FCAP facilities on the Snake River as part of the Comparative Survival Studies (CSS) in cooperation with the Fish Passage Center.  The NPTH M&E Project desires to increase PIT tags proportionally across all fall Chinook release groups, especially in the Clearwater River Subbasin, for the CSS in the future.

PROJECT SUMMARY:

In June of 2000 the Northwest Power Planning Council approved the construction of the Nez Perce Tribal Hatchery.  The NPTH was scheduled to begin rearing and releasing spring, fall and early-fall stocks of Chinook salmon starting in 2003 as part of the Nez Perce Tribe's overall goal to restore self-sustaining Chinook salmon to their ancestral habitats in Clearwater River Subbasin.  In June of 2011, the Independent Scientific Review Panel recommended funding this project.  In October of 2011, the Northwest Power and Conservation Council's final recommendations for funding 2012 through 2014 projects included this project as well as the FCAP M&E project.

The Monitoring and Evaluation Program for NPTH is designed to provide adaptive management guidance at multiple life stages for both hatchery and natural fish segments as outlined in the M&E Action Plan (Hesse and Cramer 2000).  Supplementation benefits to be evaluated under the M&E program include increases in the distribution, abundance, and harvest of hatchery and natural Chinook salmon (Oncorhynchus tshawytcsha) populations in the Clearwater River subbasin. To measure these benefits, changes in the abundance of Chinook salmon in the mainstem Clearwater River and its tributaries will be monitored over the next 15 to 20 years.  In addition to measuring project related benefits, the M&E Program is designed to provide information on the capacity of the natural environment to support Chinook salmon production, give early warning of adverse impacts caused by the project on resident biota, and track trends in environmental quality, management, and policy that may affect the project's success.  

Changes in fish populations in the mainstem Clearwater River and its tributaries over the next 15 to 20 years will be used to determine whether desired results are being achieved, and to enable adaptive management. The M&E program examines the performance and status of hatchery and natural fish, species interactions and impacts to non-targeted fish populations, sustainability of harvest, and will communicate its findings to enable adaptive management of NPTH.  The action plan covers multiple aspects of Chinook salmon life history in all treatment streams.  Treatment streams are Meadow Creek (Selway River), Lolo Creek, and Newsome Creek for spring Chinook salmon, the lower reaches of the South Fork Clearwater and Selway rivers for early-fall Chinook salmon, and the mainstem Clearwater and Snake rivers for fall Chinook salmon.  Outcomes in these treatment streams will also be compared to those in similar non-treatment (reference) streams and other hatchery programs to help distinguish treatment effects from the effects of environmental variation between years.

The M&E Program assesses which supplementation strategies are best for supplementing natural, depleted, or non-existent spring, early fall, and fall Chinook salmon populations and what effect supplementation has on these and resident fish populations.  The program will identify which of the supplementation strategies employed are beneficial in terms of increasing adult returns (to harvest and spawning streams) and the level of supplementation necessary to sustain specific levels of adult returns.  Biological evaluation points include parr density, summer and winter survival to stream mouth, survival to Lower Granite Dam and other downstream dams, adult returns to weirs, spawning escapement, and pre-smolt and smolt yield from both treatment and control streams.  Genetic monitoring of the treatment and reference populations will also occur.  

Although NPTH did not start releasing fish until 2003, the NPTH Program has actively been involved in supplementing a number of streams in the basin since 1993.  The M&E Program has been actively assessing the effects of trial supplementation efforts in order to:
  
1) evaluate the effectiveness of supplementation,
2) monitor changes in the environment that are causally linked to supplementation,
3) provide information on the capacity of the natural environment to assimilate and support supplemented salmon populations, and
4) to detect early warning of changes in environmental quality and management policy that may affect the project's success.

Field activities for the NPTH M&E Program in 1993 began with the outplanting of approximately 100,000 fingerling spring Chinook in Meadow Creek.  Habitat use and species interactions were monitored using snorkeling to evaluate the effectiveness of various release strategies and impact on resident fish.  Fish migration out of Meadow Creek was also measured to assess survival, growth in the natural environment, and emigration timing using a rotary screw trap.  The FCAP began with the supplementation of Lyons Ferry Hatchery fall Chinook at three acclimation sites above Lower Granite Dam.  The Pittsburg Landing site on the Snake River began releasing yearling fall Chinook in 1996, followed by Big Canyon Creek on the Clearwater River in 1997, and a second site on the Snake at Captain John Rapids in 1998.  During 2003, NPTH began releasing fall Chinook subyearlings from Lyons Ferry Hatchery into the Clearwater River and began trapping fall Chinook adults at the NPTH fish ladder for 2004 juvenile releases.

Plans for 2017 include the monitoring and evaluation of hatchery and natural fish.  Adult monitoring of the Meadow Creek fish has been very problematic, little to no adult information has been collected over the past 10 years.  Spawning ground surveys have not occurred for the past 4 years due to forest fires and smoke.  It is our desire to have a PIT tag Array in the lower Selway River to monitor the adult retruns from our Meadow Creek outplants and from the Fall Chinook outplants at the Lukes Gulch acclimatnion facility.  We would like to start purchasing the equipment over a number of years without new BPA dollars.  In 2015 the majority of the equipment was purchased for the first Array from a No Cost-Line Item Transfer and in 2016 we have identified the purchase of 6 antennas at $5,000  each.      

Primary monitoring activities to be conducted under the Nez Perce Tribal Hatchery Monitoring and Evaluation Program with associated evaluation products.

PIT Tagging • Ongoing • All Stocks (Hatchery & Natural)
1. Estimate and 95% confidence interval of survival from release (or natural parr) to emigration.
2. Estimate and 95% confidence interval of survival (egg-to-smolt and release -to-smolt) to LGR or other mainstem dams.
3. Estimate the percentage of fish barged from LGR and other mainstem dams from each treatment group.
4. Estimate of difference in survival to Lower Granite Dam between spring Chinook salmon presmolts that overwinter in the treatment stream and presmolts that overwinter in the Clearwater or Snake rivers.
5. Population estimates and 95% confidence intervals of hatchery and wild juvenile Chinook salmon passing the trap as fry, parr, presmolts, and smolts.
6. Estimate and 95% confidence interval for the number of smolts produced from each stream.
Median, 20th percentile, and 80th percentile travel times (days) and arrival at detector dams in the Snake and Columbia rivers.
7. Estimated and 95 % confidence interval of survival during mainstem passage from LGR to JDD for each treatment group.

Weir Operation and/or Spawning Ground Surveys • Ongoing • All Stocks
1. Hatchery and natural escapement at weirs.
2. Counts of hatchery and  natural Chinook, by age, taken for brood stock.
3. Percentage that each age composes of the returns, by sex, to each stream.
4. Time-frequency of arrival at brood collection points.
5. Differential survival rate between subyearling and yearling smolts for early-fall Chinook in South Fork Clearwater River.
6. Estimates of the minimum percentage of spawners that strayed from their home stream for each release strategy in each stream.
7. Percentage that NPTH strays compose of spawners in non-target streams
8. Total redds in each reach surveyed
9. Time frequency of redd construction in each reach surveyed.
10. Percentage of total redds contained in discrete stream sections.  
11. Estimated number of hatchery and natural spawners in each reach surveyed (Mark-recapture of fish from weirs).
12. Estimates of age and sex-specific maturity rates for each race, and possibly each treatment stream
13. Annual estimates of the percentage of carcasses that are less than 80% spawned in each stream.
14. Differential survival rate between subyearling and yearling smolts for fall Chinook.
15. Estimates of the minimum percentage of spawners that strayed from their home stream for each release strategy in each stream.
16. Percentage that NPTH strays compose of spawners in non-target streams
17. Change in spawning time and age at maturity across generations of natural Chinook in stream where NPTH strays constitute at least 10% of all spawners.

Screw Trapping • Ongoing • Spring Chinook
1. Time-frequency distribution of emigration.
2. Mean and 95% confidence interval, regression of mean length for each life stage and Julian day.
3. Estimate of the ratio of spring Chinook salmon presmolt (fall) to smolt (spring)  migrants passing the rotary-screw trap from each brood.
4. Difference in fall presmolt passage at the upper and lower traps in Lolo Creek.
5. Estimate of parr abundance, based on marked-to-unmarked ratio of fish arriving at the screw trap.
6. Estimate of survival from parr to smolting in each treatment stream.
7. Estimate of survival from emigration to Lower Granite Dam (McNary).

Habitat Surveys • 12 years • Spring Chinook
1. Comparison of weekly water temperatures and flows within and between streams.
2. Weekly water temperatures at the time and location of spawning and egg incubation within each stream.

Genetic Analysis • Ongoing • All stocks and Hatcheries
1. Annual gene frequencies for populations of natural spawners in each study stream.
2. Difference in gene frequencies between natural juveniles and natural adults of the same brood in each study stream.
3. Annual gene frequencies for populations of Chinook salmon in each NPTH treatment, including Lyons Ferry Hatchery.
                4. Parentage Base Tagging (PBT) on all NPTH broodstock (fall Chinook) beginning 2011 and NPTH broodstock (spring Chinook) in Meadow Creek beginning 2011.

Harvest Monitoring • Ongoing • All Stocks
1. Estimated fraction of Chinook salmon harvested by age and race each year (1) in the ocean and (2) within the Columbia River
2. Estimated number of Chinook salmon harvested by age and race each year within the Clearwater River subbasin.
3. Estimated difference in hatchery :natural ratios in the catch for specific times, locations or gears within the Clearwater Basin.
4. Estimated mortality rate prior to spawning on fish that are caught and released by fisheries in the Clearwater Basin.