The purpose of the Idaho Supplementation Study (ISS) is to help determine the utility of supplementation as a potential recovery tool for imperiled stocks of spring and summer Chinook salmon in Idaho.  Our goals are to assess the use of hatchery Chinook salmon to restore or augment natural populations, and to evaluate the effects of supplementation on the survival and fitness of existing natural populations.  The program operates in both the Clearwater and Salmon sub-basins, and encompasses 30 streams throughout Idaho. Sixteen streams have received supplementation treatments and 14 are non-supplemented controls.  Data collection responsibility is partitioned among the Idaho Department of Fish and Game, Nez Perce Tribe, Shoshone-Bannock Tribe, and the U.S. Fish and Wildlife Service.  
Our experimental design utilizes three main approaches.  The first and main level of evaluation is large-scale population production and productivity studies designed to provide relatively generic inferences state wide.  The second level uses the same study streams as individual “case histories” to evaluate specific supplementation programs (i.e., individual hatchery programs), although inferences at this level are limited to only descriptive assessments.  The third level represents small-scale studies designed to address specific hypotheses concerning the mechanism of supplementation.

The long-term design tests the response of populations to treatments (supplemented) over time compared to controls (non-supplemented).  To evaluate these effects, we monitor a number of production and productivity response variables.  Production variables measure the effects of supplementation on fish numbers.  Productivity variables measure the effect of supplementation on the overall replacement ability of the naturally spawning populations.  Our general hypothesis is that supplementation can increase natural production but not productivity.  However, we hypothesize that reductions in natural productivity can be minimized through the use of locally derived broodstocks (where available) so that enhanced production more than compensates for reduced productivity.  

The ISS study design uses a multi-phased approach to evaluate supplementation. In Phase I, local adult returns were collected to develop supplementation broodstock. Phase II (treatment phase) used the returning supplementation adults to augment natural reproduction in treatment streams. In Phase III, or evaluation phase, supplementation treatments will be terminated, but we will continue to monitor production and productivity in both treatment and control populations for one Chinook salmon generation (i.e., five years). Determining population response after supplementation ceases will provide valuable insight into the long-term effects of supplementation.  Currently, the project is in transition between Phase II and III.

In response to ISRP recommendations, the program’s data sets were assessed, and the original ISS study design was updated in 2005.  The data set review indicated the data will be sufficient to address the program’s two main goals (defined above) and that the ANOVA technique proposed in the original study design would be appropriate for much of the analysis.  Alternatively, regression and graphical techniques were also developed for some data sets as recommended by the ISRP.  The effect of general production hatchery strays into ISS study streams was also addressed in the updated study design.  Additional carcass collections were initiated to better quantify the magnitude of this unintended supplementation and will be continued throughout the remainder of the program.  We also developed a supplemental proposal to use microsatellite DNA parentage analyses to address the relative reproductive success of natural, supplementation, and general production fish in a subset of study streams.  However, this would represent a large and costly commitment by the region, and would require additional funding to undertake.

Of the 30 streams involved in the ISS program, the NPT portion of the project encompasses nine (9) streams; 5 in the Clearwater River sub-basin (Lolo Creek, Eldorado Creek, Newsome Creek, Fishing Creek, and Legendary Bear Creek) and 4 in the Salmon River sub-basin (Slate Creek, Secesh River, Lake Creek, and Johnson Creek).  Treatment streams include Lolo Creek, Newsome Creek, Fishing Creek, Legendary Bear Creek, and Johnson Creek.  The remainder are control streams (Eldorado Creek, Slate Creek, Secesh River, and Lake Creek).  The Nez Perce Tribal Hatchery program (NPTH) (BPA Project No. 1983-350-03) collects all data required by the ISS program in Eldorado Creek and operates adult weirs on Lolo Creek and Newsome Creek as well as juvenile traps on Lolo Creek and Newsome Creek.  All data that is collected is provided to the cooperative ISS project as needed.  The Johnson Creek Artificial Propagation Enhancement program (JCAPE) (BPA Project No. 1996-043-00) collects all data required by the ISS program and operates an adult weir on Johnson Creek as well as a juvenile trap on Johnson Creek.  All data that is collected is provided to the cooperative ISS project as needed.  The Chinook Salmon Adult Abundance Monitoring in Secesh River, Idaho program (BPA Contract No. 1997-030-00) operates a DIDSON weir in Secesh River for adult abundance estimates.  All data that is collected is provided to the cooperative ISS project as needed.  The NPT ISS project (BPA Project No. 1989-098-02) collects all ISS data in Fishing Creek, Legendary Bear Creek, Slate Creek, Lake Creek, and Secesh River and operates juvenile traps in Lake Creek and Secesh River.  In 2007 and beyond, if funding is available and the activity is approved, the NPT ISS project wishes to operate the video weir on Lake Cr..  All data that is collected is provided to the cooperative ISS project as needed.  Coordination between all projects is required to maintain standardization of all data collected by all factions involved within ISS.  When personnel or equipment shortages might occur within cooperating agencies, NPT ISS personnel and equipment are available for temporary use to install or operate equipment or to collect other data as needed to maintain consistent operations and data for the entire cooperative ISS program.  

Since the streams involved in the ISS program are encompassed within numerous National Forests, National Forest Ranger Districts, State, and private lands, coordination amongst numerous Federal, State, Local, and private organizations is required.  Additionally, whether taken directly or indirectly, listed species are taken and coordination with the Federal agencies that are responsible for recovery is necessary (NMFS, USFWS, and State).  A core group of project leaders from each cooperative agency collects and assembles all the data for evaluation and report writing.  Annual reports (based on brood year) are assembled by cooperators, routed to cooperator agencies for approval, and sent to BPA for posting on their website.  As with all cooperators, NPT ISS is available to assist temporarily any cooperator install or maintain equipment, collect data, or coordinate activities as needed.