• Abstract and Figures
• Public Full-text

Project Title: Idaho Supplementation Studies (198909800)

A. Abstract

The Idaho Supplementation Studies (ISS) study design was intensively scrutinized and updated prior to the last funding cycle (programmatic Issue 10) and the ISRP agreed we have appropriate methodologies to make a meaningful contribution to the evaluation of supplementation. This proposal represents the ongoing efforts of the cooperating agencies in the ISS to take that study design to completion without change. The objectives of the program are to: evaluate the effects of supplementation on juvenile and adult Chinook abundance; evaluate changes in natural productivity after supplementation is stopped; evaluate various supplementation strategies; and develop supplementation recommendations. This work will help define the role of supplementation in Idaho, and will identify impacts of supplementation on natural populations. The ISS project addresses the objectives of the 2009 Fish and Wildlife Program to “restore healthy, naturally reproducing populations of salmon and steelhead” and “artificial production be implemented with an experimental design to evaluate risks, benefits, and scientific uncertainties”. It also addresses the critical uncertainty surrounding “the detrimental effects of supplementation on natural stocks” in the 2006 Columbia Basin Research Plan. The effects of supplementation will be evaluated by comparing juvenile production and survival (screw traps, PIT tagging), adult returns (multi-pass redd counts, weirs), DNA parentage, age structure, and variability between treatment and control streams. In addition to the evaluation of supplementation, ISS provides intensive and extensive VSP status and trend monitoring of Chinook populations throughout the Salmon and Clearwater sub-basins and support for steelhead status and trend monitoring called for in the Columbia Basin Regional RM&E Strategy. Under the current study design adult and juvenile evaluations will continue through 2012 and 2014, respectively, and the project will provide status and trend monitoring over that period. At the completion of the project, status and trend monitoring currently provided by ISS will need to be incorporated into new or ongoing programs.

B. Technical and/or scientific background

History of Hatcheries and Supplementation Hatcheries and supplementation activities have existed in the Columbia Basin for over 100 years. The first recorded supplementation of Chinook salmon Oncorhynchus tshawytscha in Idaho was in 1920 on the Lemhi River. The second record of out-planting was an attempt to reestablish Chinook salmon into the Clearwater River above Lewiston Dam. Some adults returned as a result, but the exact numbers and their spawning success are unknown. A second major attempt to reestablish Chinook salmon into the Clearwater River began in 1961 with the advent of the Columbia River Fisheries Development Program. Once again, adults returned as a result, but extent and spawning success were not evaluated.

Other federal actions attempted to use hatchery construction to mitigate for lost production stemming from hydropower development in the Columbia and Snake basins. The Mitchell Act, enacted in 1938, attempted to conserve fisheries resources in the Columbia River (NOAA Fisheries 2005). Later, in 1976, the Lower Snake River Compensation Plan was authorized to mitigate losses resulting from the construction of the four lower Snake River dams (Herrig 1990).

198909800 – Idaho Supplementation Studies 1 Role of Supplementation The utility of supplementation as a viable recovery tool continues to be the subject of much debate. Although sound evaluation has been lacking, there is little doubt that past supplementation efforts have rarely met with success (Smith et al. 1985; Miller et al. 1990; Steward and Bjornn 1990). The verdict on supplementation is still out because previous out- planting programs were typically directed by conventional hatchery guidelines and criteria, and not by current natural production and genetic conservation theory. The potential benefits as well as risks associated with supplementation warrant more thorough investigation prior to negating or embracing supplementation as a recovery tool. The following discussion provides a brief synopsis of current knowledge and theory on supplementation effects.

While there has been conflicting evidence, the majority of the research suggests that out-planting programs to boost natural production have generally not been successful (Reisenbichler and McIntyre 1986; Miller et al. 1990). Attempts to re-establish runs have shown some success. Miller et al. (1990) suggests that the introduction of "locally adapted" smolts will yield adults but smolt quality must be good (e.g., disease not a significant mortality factor). Also, fish from distant stocks do not survive as well as fish from the local stocks. Survival decreases as transfer distance increases (Kijima and Fujo 1984; Reisenbichler 1988).

Inter-basin stock transfers can result in “serious” risk to the fitness of native stocks. Several biologists have recommended that if a supplementation program is initiated, the hatchery brood stock should be taken from the stock to be supplemented. This will maintain genetic identity and avoid disrupting locally attuned co-adapted gene complexes (Bams 1976, Reisenbichler 1981, 1984; Chilcote et al. 1986; Currens et al. 1991; Kapuscinski et al. 1991).

With traditional hatchery practices, hatchery fish tend to become a different stock. They adapt to the hatchery and can become different genetically (altered heterozygosity, gene frequency shifts) from the natural/wild stocks from which they were derived (Reisenbichler and McIntyre 1977; Steward and Bjornn 1990). These changes can be observed in fitness, growth, survival, and disease resistance. Hatchery fish have shown increased straying rates compared to wild and natural fish (Steward and Bjornn 1990), which could pose a significant threat to non- target wild stocks.

It is generally felt that supplementation can increase natural production but not natural productivity (McClure et al. 2008; Berejikian and Ford 2004). Reductions in natural productivity can be minimized through proper supplementation strategies so that enhanced production more than compensates for reduced productivity (McClure et al. 2008). These same hatchery practices can minimize genetic drift of the hatchery stock away from the local stock from which it was derived by collecting eggs from throughout the run, using wild fish in the egg-take periodically and spawning males and females in a 1:1 ratio (Kapuscinski et al. 1991).

Offspring resulting from hatchery X wild/natural crosses can have lower fitness for the local habitats. Fitness was found to decrease as differences between hatchery and wild/natural fish increased (Bams 1976; Reisenbichler and McIntyre 1986; Chilcote et al. 1986). Quantification of the relationship between some measure of “distance” (e.g., geographic, genetic) between stocks and resulting fitness of crosses is lacking. Productivity of wild/natural stocks can also be reduced after introgression by hatchery fish (Snow 1974; Vincent 1987; Kennedy and Strange 1986; Petrosky and Bjornn 1988). Offspring of hatchery adults can have relatively low survival in natural habitats relative to wild/natural offspring (Chilcote et al. 1986; Nickelson et al. 1986). Genetic changes in hatchery fish even over a few generations can affect

198909800 – Idaho Supplementation Studies 2 survival negatively in the natural environment (Reisenbichler and McIntyre 1977; Steward and Bjornn 1990).

Description of Need The ISRP has stated (ISRP/ISAB 2005-15), “The consequences of not conducting these [supplementation evaluation] studies and continuing to assume no deleterious impacts from supplementation, and being wrong, are much greater than short-term changes in salmon abundance. The natural populations that may be lost if supplementation actually decreases their fitness are irreplaceable. On the other hand, if supplementation proves to be an aid to natural populations during distress, further application may be warranted. Both outcomes remain uncertain without adequate monitoring and evaluation, which will likewise guide best management practice and cost effectiveness”.

The following are also direct quotes from the ISRP (2005-14) “A good example of planning for large scale effectiveness monitoring in the Columbia River Basin with manipulative experiment was the original design of the Idaho Supplementation Study on Chinook salmon (Lutch et al. 2003).” Since implementation of treatments was a problem, the project has reverted to an observational quasi-experiment. “Inferences will be based on subjective judgment concerning the validity of assumptions, correlations, and models.” “If census or statistical monitoring is carried out in multiple similar observational or quasi-experimental studies over time and space, [then] corroborative results of the studies can provide compelling evidence for the actual effect of an action.” “The ISRP believes that this is the most useful type of study design for determining the effectiveness of management actions in large ecosystems.”

The ISS differs from general supplementation programs in that not only does the project supplement streams and monitor returns, but it uses supplementation as a research treatment and monitors production and productivity responses in treated populations to unsupplemented reference populations. Then as a final phase of evaluation, the program will continue to monitor production and productivity metrics in treatment and reference populations for a period after supplementation ceases to better understand the long term effects of supplementation. It is this aspect of the ISS study that makes it unique from other supplementation programs in the region. Supplementation treatments began in 1996 and continued through 2007. Post supplementation evaluation began in 2008 and will continue through 2014.

Literature Review Lutch et al. (2005) provides an updated study design for Phase III data collection and analysis of ISS program data. This document also provides detail on three analytical techniques (Mixed Model ANOVA, regression, and graphical) that will be used to evaluate the effects of supplementation. Revised protocols outline how additional effort will be put into additional carcass collections to better estimate the production by general production hatchery strays in ISS streams. Finally, the document provides a detailed response to ISRP recommendations to use DNA level parental analyses to assess the reproductive success and contribution of natural, ISS supplementation, and general production hatchery strays.

Goodman (2004) developed an evolutionary model of integrated hatchery and naturally spawning populations, which demonstrated the potential for decreased productivity in the integrated population. In this theoretical model productivity declined precipitously with increasing levels of natural spawning by hatchery fish. This model relies on six “straightforward” terms that are readily measurable and a seventh α (describing the negative correlation between natural and hatchery spawning replacement rates). The model is “strongly affected” by this term, but this value has never been measured in an integrated hatchery program. The ISS

198909800 – Idaho Supplementation Studies 3 program should contribute to addressing this critical uncertainty through its use of a defined protocol measuring the natural spawning replacement rate of naturally produced and hatchery supplementation fish at multiple locations for at least one or two generations.

McLean et al. (2004) used microsatellite parentage tests to determine if a newly established hatchery population of steelhead trout reproduced in the wild. They also compared the reproductive contribution of the two classes. While juveniles were successfully identified from both parental types, wild origin females produced approximately 19-25 smolts each, while hatchery females only produced between 1 and 1.3 smolts each. This study is important because it demonstrates the importance of the procedures used by the ISS to minimize differentiation of hatchery and wild populations. This study acts as a “worse case scenario” for a supplementation program – and should not be compared to conservation supplementation programs like ISS. The hatchery stock used here had intentionally altered spawn timing, was sourced from “a distant location”, and no control was employed on the proportion of hatchery fish allowed spawning access.

Leth (2005) used microsatellite DNA parentage tests on an ISS study stream to determine contribution, reproductive success, and random matings of ISS supplementation and natural origin Chinook salmon in the Pahsimeroi River. In this study he found vastly different results than those described above. The genetic contribution from adults was not significantly different regardless of origin or sex of the parents or life stage at which the juveniles were sampled. Juveniles were determined to have arisen from all four potential cross types at rates indicating random mating was occurring. Behavioral observations made during the spawning season supported the genetic analyses in that no differences in spawning behavior, timing, or distribution were observed between natural and ISS supplementation origin adults.

C. Rationale and significance to regional programs

2008 BIOP: RPA 50 – Fish Population Status Monitoring The ISS program works collaboratively with the ISEMP (200301700) project in the Lemhi and South Fork Salmon rivers through juvenile screw trap operations and multi-pass redd counts in these systems.

The ISS program contributes to productivity and status monitoring of numerous Snake River B run steelhead populations including S.F. Clearwater, Lochsa, Pahsimeroi, upper Salmon rivers, and Marsh Creek.

RPA 51 – Collaboration Regarding Fish Population Status Monitoring The ISS program provides PIT tag information on natural origin Chinook salmon steelhead of known stocks from 18 screw traps to PTAGIS, redd count data for Chinook salmon from 30 streams to Stream Net, and CWT returns to RMIS annually.

RPA 52 – Monitor and Evaluate Fish Performance within the FCRPS The ISS program tags natural origin juvenile Chinook salmon and steelhead of known stock annually that can be used for in-river and system survival estimates through the FCRPS.

Returning adults from ISS juvenile Chinook salmon and steelhead tagging efforts are used to monitor and evaluate adult Chinook and steelhead survival upstream through the FCRPS.

198909800 – Idaho Supplementation Studies 4 RPA 53 – Monitor and Evaluate Migration Characteristics and River Conditions ISS juvenile tagging activities contribute directly to aggregate and stock specific estimates of Chinook salmon and steelhead smolts passing index dams.

ISS juvenile tagging activities contribute directly to aggregate and stock specific estimates of Chinook salmon and steelhead smolt migration timing at index dams.

Returning adults from ISS juvenile tagging efforts can be used to monitor and enumerate adult Chinook and steelhead survival upstream through the FCRPS, identify potential problems and contribute to implemented solutions.

RPA 54 – Monitor and Evaluate Effects of Configuration and Operation Actions ISS juvenile tagging activities contribute directly to the first eight (8) Action Descriptions in this RPA for Chinook salmon and steelhead smolts.

Returning adults from ISS juvenile tagging efforts can be used to monitor and evaluate fish ladder configuration on adult Chinook and steelhead passage rates.

RPA 55 – Investigate Hydro Critical Uncertainties and Investigate New Technologies Juvenile Chinook salmon and steelhead PIT tagged by the ISS program can contribute to investigating and quantifying delayed differential effects (D-value) associated with transportation through the FCRPS.

Juvenile Chinook salmon and steelhead PIT tagged by the ISS program can contribute to investigating the post Bonneville mortality effect of fish arrival timing and transportation.

RPA 62 – Fund Selected Harvest Investigations The ISS program will provide CWT recoveries from spawning ground surveys to contribute to assessing survival and straying of hatchery fish to the spawning ground by stock, rearing facility, release treatment and location.

RPA 63 – Monitor Hatchery Effectiveness Through its evaluation of supplementation, the ISS program will directly contribute to determining the effect of safety net and conservation hatchery programs on the viability and recovery of targeted populations of Chinook salmon.

RPA 64 – Investigate Hatchery Critical Uncertainties By evaluating the effects of supplementation, the ISS program addresses the issue of determining if properly designed intervention programs can have a net positive effect on the recovery of listed Chinook salmon populations.

TRT’s Recovery Plan and VSP Criteria: The ISS program collects VSP criteria (abundance, productivity, spatial structure, and diversity) on a wide variety of Salmon and Clearwater sub-basin streams (Appendix A) following the guidelines in Crawford and Rumsey (2009). We conduct multiple pass redd counts and carcass surveys on 27 of 30 study streams (White Cap Creek and the upper Salmon and Lemhi river redd counts are done by air, but carcass collections are done near known spawning areas on the upper Salmon and Lemhi rivers). These surveys address both the abundance and spatial structure criteria. Abundance is estimated either from direct expansions from redd counts or through the use of mark/recapture estimates for streams with weirs on them. Spatial structure has been addressed by expanding the areas surveyed beyond traditional index areas to

198909800 – Idaho Supplementation Studies 5 encompass all probable spawning areas in these streams. Redd counts also provide an estimate of adult to adult productivity. Juvenile screw traps on 18 streams provide estimates of juvenile abundance and information on life history diversity present in these populations. Redd counts and juvenile abundance estimates are combined to provide adult to juvenile productivity estimates where applicable.

Columbia Basin Regional RM&E Strategy: Quantifying abundance, productivity, spatial scale, and diversity (VSP) of all populations is desired by fisheries managers, however it is not scientifically needed or financially possible to robustly quantify all VSP performance measures in all populations. Despite multiple recommendations for increased and improved monitoring (ISAB/ISRP 2009-1, ISRP 2008-4, ISRP/ISAB 2005-15, NPCC 2009, Botkin et al. 2000), a commonly accepted description of what type, location, and replication of RM&E that is needed in the Columbia River basin has been lacking until just recently. Columbia Basin natural resource managers, funding agencies, and regulatory entities worked together in 2009 to produce a coordinated anadromous monitoring strategy that establishes the scope, spatial coverage and desired precision for monitoring and evaluating population status and trends, hatchery, habitat, hydro, diversity, and data management and access of anadromous salmonids in the Columbia Basin (Coordinated Anadromous Workshop 2010 a-c1). The Snake River basin spring/summer Chinook salmon and steelhead strategies call for high precision estimates of adult abundance (coefficient of variation of 15% or less) in at least one population per life history type per Major Population Group (MPG). Several ISS streams have initially been recommended as having high precision monitoring populations. A strategy to implement high intensity hatchery effectiveness monitoring on select supplementation programs; LSRCP, Northeast Oregon Hatchery, Johnson Creek, and Idaho Salmon Supplementation and new/reformed supplementation programs with formal study designs was included.

The developing strategy for monitoring and evaluating the status of spring/summer Chinook salmon and steelhead in the Snake River basin is taking on a three tiered structure. Sampling at Lower Granite Dam will provide ESU, MPG, and possibly population level information. Individual populations within an MPG will also be monitored at one of two different levels. At least one population per MGP will be intensively monitored (fish in fish out) for high precision status and trend data. The remaining populations within the MPGs will also be monitored for status and trend information, but at a reduced level of intensity (extensive monitoring; Table 1). Both the RPA workgroup and a second group of State and Tribal managers recommended that the ISS program be funded for the next review cycle. The ISS program is currently doing intensive level monitoring for Chinook salmon at all locations where we operate screw traps (see Section F, Method 1) and provide support for steelhead intensive monitoring activities and hatchery effectiveness monitoring (Table 1) at these sites as well. Additionally, the ISS project is currently doing multi-pass redd counts and carcass surveys outlined for extensively monitored populations in all study streams (See Section F, Method 3), and an RRS study on the Pahsimeroi River summer Chinook salmon population. The ISS

1 These tables were compiled to provide the implementation strategies guiding the development of a regional Columbia Basin coordinated anadromous monitoring strategy for salmon and steelhead focused on Viable Salmonid Population parameters, tributary habitat effectiveness and hatchery effectiveness in the Columbia Basin. The November 2009 draft of the document describing this coordinated anadromous monitoring strategy is entitled "Columbia River Basin Monitoring Framework" and is available in the subfolder 'Anadromous Monitoring Strategy 2009/November 2009-Workshop' located at www.nwcouncil.org/dropbox.

198909800 – Idaho Supplementation Studies 6 program ends in 2014 and the strategy recommends the ISS infrastructure be consolidated into other new or ongoing programs to maintain prescribed status and trend monitoring. Additionally, after 2012, the ISS program will no longer need to do multi-pass redd counts or carcass surveys, and again the strategy recommends these aspect of the current program should be consolidated into other new or ongoing programs to maintain status and trend monitoring.

Two modifications for this project were identified in the RM&E strategy. The first was to operate a second screw trap on Marsh Creek, below Beaver Creek. This will provide intensive status and trend monitoring for the Marsh Creek Chinook salmon population, including Beaver, Cape Horn, Banner, Knapp, and Marsh creeks, and will improve our ability to monitor steelhead as well. The current ISS screw trap (which only covers Banner, Knapp, and Marsh creeks) will be operated at least through the end of the ISS program to maintain the integrity of the ISS study design and to calibrate production estimates from the two traps. The second modification identified was to test the predictive output of the AHA model and the HSRG standards using ISS data.

Table 1. Goals and strategies for monitoring and evaluation of the status of Snake River Chinook salmon and steelhead identified by the RM&E Collaborative Workshop.

Goal Strategy Obtain high precision status and trend data for at least one population per adult life history type per MPG (fish in, fish out monitoring). Estimate annually the number of adults and juveniles with a CV≤15%. Estimate SAR, smolts per spawner, and adult-adult productivity for life cycle monitoring. Select populations for high precision monitoring based on maximum synergy between BiOp RPA requirements, TRT recommendations, IMWs (habitat effectiveness monitoring), Fish Accord monitoring, hatchery effectiveness monitoring, representativeness of populations, and multiple species coverage. Obtain high precision estimates of fish reaching Lower Granite Dam. Estimate annually the number of adults and juveniles with a CV≤15%. Estimate SAR, smolts per spawner, and adult-adult productivity for life cycle monitoring. Establish annual run-reconstruction of natural and hatchery returns, harvest, and escapement to known and unknown population areas to provide abundance and age structure of escapement to Lower Granite Dam and including disposition of hatchery fish. Obtain status and trend data in every population per MPG (including populations with high precision monitoring). Lower precision will be acceptable for management in populations without intensive monitoring. Partition Lower Granite Dam escapement to MPGs (and populations as able) with CV estimates using genetic stock identification (GSI). Estimate age structure, smolts per adults, and adult to adult productivity by MPG and population. Validate GSI results with radio and/or PIT tag arrays in at least two MPGs. For Chinook, make low/moderate precision estimates of abundance and spatial structure on all populations via multi-pass extensive area redd counts and carcass surveys. Maintain existing index reach surveys. Estimate harvest and incidental mortality of natural origin adults in fisheries. Monitor genetic and life history diversity of all populations. Genotype wild populations on a rotating five year basis to maintain genetic

198909800 – Idaho Supplementation Studies 7 Goal Strategy baseline for GSI and to evaluate genetic population structure and diversity. Implement high intensity hatchery effectiveness monitoring on select supplementation programs including Idaho Supplementation Studies and Johnson Creek Artificial Production Evaluation Conduct RRS studies on at least six populations of Spring/Summer Chinook salmon throughout the Columbia River Basin

NPCC 2009 Fish and Wildlife Program (NPCC 2009): The Northwest Power and Conservation Council Fish and Wildlife Program (NPPC 2009) states that biological objectives have performance components which describe population responses in terms of capacity, abundance, productivity, and life history diversity. These biological objective components are intended to be empirically measurable based on explicit scientific rationale to meet Power Council objectives and vision of the Fish and Wildlife program. Strategies identified in the adult passage subsection (NPPC 2009) include evaluation of escapement numbers to spawning grounds. Under the Research, Monitoring and Evaluation subsection the primary RM&E strategies are identified as: 1) identify priority fish and wildlife and ecosystem elements of the Program that can be monitored in a cost-effective manner, evaluate the monitoring data and manage the Program based on results, 2) research and report on key uncertainties, 3) make information from this program accessible to the public, and 4) to the extent practicable ensure consistency with other processes. Monitoring and evaluation of tributary specific adult salmon abundance and productivity in ISS streams as a key biological performance measure is closely linked to biological objectives. Salmon abundance information from this project is quantified, has high accuracy and precision, is available to the public, is compared to supplementation program performance, and directly measures the effect of FCRPS (2008) conservation measures.

Listed below are specific strategies the ISS project implements:

“Significantly improve smolt-to-adult (SARs) return rates for Columbia River salmon and steelhead…” (Pg. 11) The ISS program PIT tags a large number of both Chinook salmon and steelhead that will be used to determine SARs and evaluate progress toward this objective.

“ Restore the widest possible set of healthy, naturally reproducing and sustaining populations of salmon and steelhead…” (Pg. 11). Completion of the ISS program will provide valuable insights into the potential usefulness of supplementation to rebuild self-sustaining Chinook salmon populations.

“ Artificial production must be implemented within an experimental, adaptive- management design that includes an aggressive program to evaluate the risks and benefits and addresses scientific uncertainties.” (Pg. 18). Determining the benefits and risk of supplementation is one of the primary objectives of the ISS program. Completion of the ISS program will provide better understanding of the potential benefits and risks.

Finally, the NPPC (2009) has adopted the subbasin plans. The Salmon and Clearwater Subbasin Management Plans’ biological objectives and strategies are discussed below, and contain direct linkages to the population level salmon adult abundance and productivity information that the ISS project collects.

Previous NPPC/NPCC Documents: The Northwest Power and Conservation Council (NPCC) – formerly the Northwest Power Planning Council (NPPC) - called “for immediate efforts to gather data on wild and

198909800 – Idaho Supplementation Studies 8 naturally spawning stocks, review impacts of the existing hatchery system and coordinate supplementation activities” to “develop a clear policy to guide the use of supplementation,” and to achieve its goal of doubling anadromous fish runs in the Columbia Basin (NPCC 1987, 1994). The ISS project is directly related to basin-wide needs and concerns addressed in the Columbia Basin Fish and Wildlife Program including sections 206(b)(1)(D) that mandated supplementation research to assess the potential of supplementation to increase natural production, 204(D) that stressed the importance of evaluating genetic and ecological effects from out-planting hatchery fish on natural populations, and 703(h)(1) the need to address supplementation questions for upriver stocks (NPPC 1987, 1994). The Council has also called for the implementation of high priority supplementation programs that included monitoring and evaluation, a recommendation that [supplementation] programs monitor and evaluate changes in natural productivity and genetic composition of target and adjacent populations following supplementation, programs document which methods are best for supplementing existing naturally reproducing populations and re-establishing naturally producing populations in stream where they have been extirpated, and that artificial production be implemented with an experimental design that includes an aggressive program to evaluate the risks and benefits (NPPC 1987, 1994, 2000). These priorities are directly addressed in the ISS study design (Bowls and Leitzingger 1991; Lutch et al. 2005).

The 2000 NPPC Fish and Wildlife Program (NPPC 2000) shifted from past programs that were a collection of measures that directed specific activities to a new program that established a basin-wide vision for fish and wildlife which included the outcome of the program, biological objectives, and action strategies all of which are consistent with the vision (NPPC 2000). NPCC 2000 called for the Fish and Wildlife Program to be implemented through adopted sub-basin management plans. The ISS program operates in both the Salmon and Clearwater river sub-basins and is directly linked to their respective management plans (Ecovista 2003, 2004).

Salmon Sub-basin Plan: The ISS program is intimately connected with the anadromous fisheries resources of the Salmon River sub-basin. Of the 22 identified spring/summer Chinook salmon populations in the sub-basin (ICTRT 2003), 12 are included in the ISS project including: South Fork Salmon River, Secesh River, East Fork South Fork Salmon River/Johnson Creek, Bear Valley Creek/Elk Creek, Marsh Creek, North Fork Salmon River, Lemhi River, Pahsimeroi River, East Fork Salmon River, Yankee Fork, Valley Creek, and the Salmon River above Redfish Lake.

The ISS program contributes directly to the following Aquatic Objectives identified in the Salmon River Sub-basin Management Plan (Ecovista 2004). Increase the number of naturally spawning adults to achieve recovery goals (Objective 1A). One strategy to achieve this is to determine population specific SAR’s. The ISS program PIT tags Chinook salmon for its own use and for Projects 199602000, 199005500, and 198712702, which contribute valuable “known source” individuals to these programs. The ISS also conducts “focused activities to understand small populations while preserving their genetic identity” (Objective 2A) through the application of identified strategies to 1) continue evaluation programs in areas where intervention has already occurred, 2) collecting steelhead abundance information via snorkel surveys, 3) evaluation of the effectiveness of a hatchery intervention program. The ISS program is also “addressing data gaps needed to measure freshwater productivity and survival” (Objective 3A). ISS is specifically named as an important contributor of this information. Data gaps have also been identified that limit our ability to monitor progress toward delisting (Objective 3C). ISS contributes data to the following data gaps 1) population specific adult and juvenile abundance information on index streams, 2) population specific SAR’s on index streams, 3) determine

198909800 – Idaho Supplementation Studies 9 population productivity on index streams, and 4) estimates of the reproductive success of hatchery Chinook salmon.

While the Technical Team stated that prioritization was not feasible (Ecovista 2004) their identification of research needs (see Ecovista 2004, Tables 12&13) and performance measures to evaluate success (see Ecovista 2004, Table 15) are actually de facto identification of high priority RM&E needs. The ISS program measures all the identified Performance Measures for Research Need 1 (life stage survival {egg:parr, egg:smolt, and parr:smolt} and population growth rate or lambda) and Research Need 3 (genetic diversity and spatial distribution of spawners). Additionally, of the eight measures identified in Research Needs 4 and 5 the ISS program measures all but one (juvenile rearing distribution). Thirty Objectives and their key performance measures are identified in Ecovista (2004, Table 15). The ISS program measures performance measures associated with 20 of these 30 Objectives (1A, 1B, 2A, 4C, 7A, 8A, 8B, 8D, 9A, 10A, 11A, 12A, 12B, 17C, 18A, 18B, 28A, 30A, 45A, and 46B).

Clearwater Sub-basin Plan: In Section 4.2.2 of the Clearwater Sub-basin Management Plan (CSMP; Ecovista 2003), Problem Statements, Objectives, and Strategies for the plan are outlined for the Biological Group – Anadromous Fish Species. The following discussion demonstrates how the Idaho Supplementation Studies (ISS) project is linked directly or indirectly to those problem statements, objectives, and strategies.

Problem 1 in the CSMP lists out of basin factors as the primary limiting factors in limiting adult recruitment in the Clearwater River sub-basin. Under this problem, the objective outlined is to increase the number of naturally spawning adults measured at Lower Granite Dam (LGD). One of the four strategies was to examine main stem and ocean mortality associated with differential migration timing and life histories of anadromous salmonids. The ISS program PIT tags thousands of juvenile Chinook salmon annually in the Clearwater River sub-basin to address this issue. A second strategy within the objective is “to define and establish anadromous index stocks within the Clearwater Sub-basin to evaluate Clearwater Sub-basin specific adult abundance, life history characteristics and spawner recruitment characteristics as a measure of productivity. Since 1991, this project has been evaluating these data in 11 treatment and 4 control streams within the Clearwater Sub-basin (Bowles and Leitzinger 1991, Lutch et al. 2003).

Problem 2 in the CSMP describes anadromous fish production as being limited by habitat quantity, quality, and connectivity in portions of the sub-basin. Under this problem, the Objective of the CSMP is to increase anadromous fish productivity and production, and life stage specific survival through habitat improvement. As stated in the CSMP “The most effective way to determine the degree to which the productivity of a certain life history stage of anadromous salmonid is being limited is to conduct spatially explicit examinations of respective populations, stratified by habitat types sharing common themes.” [The ISS program collects data that] “provides researchers with requisite life-stage specific survival information which will allow for focused and effective treatment of problems as well as baseline information against which restoration success can be assessed” (Ecovista 2003).

Problem 3 in the CSMP defines that management of hatchery and natural production are not adequately integrated to meet mitigation, restoration, harvest, and recovery goals. The two objectives listed in the CSMP for this problem are to 1) develop and integrated management plan to optimize the use of hatchery fish to meet recovery and harvest objectives; 2) use a mix of hatchery and natural production strategies for native, localized, and reintroduced populations

198909800 – Idaho Supplementation Studies 10 to meet sub-basin goals. Strategies to meet these objectives that the ISS program contribute to include 1) continue to develop stock specific knowledge of interactions between hatchery and wild fish and 2) maximize hatchery effectiveness, continue innovative hatchery production strategies to support fisheries, natural production augmentation and rebuilding, reintroduction, and research.

High priority RM&E needs are identified in the aquatics portion of the CSMP. Proposed research needed to answer critical uncertainties within the sub-basin is identified, and existing programs that are collecting data necessary to address the research needs are identified. The ISS project is named specifically as a potential data source to answer a number of these high priority research needs. The ISS is listed in the CSMP (2003) RM&E Plan for coordination potential as an ongoing population status monitoring program for the following proposed research questions in the aquatics section (4.3.1): I-1, I-2, I-3, II-1, II-2, II-3, III-1, III-2, IV-1, VIII- 1, VIII-2, VIII-3, and VIII-4. The ISS program also collects data directly related to the research proposed in Section V-1, and V-2. Also, due to the location of traps within the Clearwater Sub- basin, the ISS program is listed as a trapping source for Pacific lamprey (VI-3).

Idaho Department of Fish and Game “Fisheries Management Plan 2007-2012”: The Idaho Department of Fish and Game’s Fisheries Management Plan 2007-2012 (http://fishandgame.idaho.gov/fish/programs/fish_plan.pdf) identifies six management objectives to achieve management goals. The ISS program addresses three of these. The ISS program provides data to assess efforts to maintain genetic and life history diversity of natural salmonids by providing a large part of the state’s monitoring infrastructure. Juvenile trapping provides DNA necessary to establish and monitor the genetic health of populations and to identify the variety of life histories present within the state. A second goal is to rebuild natural populations for sport and tribal harvest by utilizing existing habitat to an optimal level. The ISS program will help us better understand if and how supplementation can be used to rebuild these populations. The third goal is to improve overall life cycle survival by addressing limiting factors identified in the all “H” model. The ISS program directly addresses potential hatchery effects and the potential benefits and risks of using artificial propagation to rebuild populations. The program also plays a large role in PIT tagging known origin, naturally produced Chinook salmon and steelhead to address hydro and associated survival issues. Finally, ISS works collaboratively with the ISEMP program (200301700) in the Lemhi River drainage to assess the effectiveness of habitat improvement projects.

WY-KAN-USH-MI WA-KISH-WIT Spirit of the Salmon (CRITFC 1996): This document lists a recommended action to develop experimental and monitoring programs in association with high priority supplementation projects to study relationships between natural and supplemented components of those populations. It further recommends establishing additional monitoring programs for each of the subbasin tributary systems to monitor adult escapement and resulting smolt production, and to evaluate (by measuring the number of adults returning) the ability of managers to meet goals set by the Columbia River Fish Management Plan (CRFMP). The results of this project will fill gaps in the knowledge about the impacts of using hatchery technology as a tool to increase natural salmon populations. For the supplementation approach of recovery, “there is a need to track the medium and long-term genetic and behavioral effects of hatchery technology on naturally spawning populations.” (CRITFC 1996).

D. Relationships to other projects Due to the large geographic scope of this study, study streams were partitioned among four resource management entities for implementation. These include Idaho Department of Fish

198909800 – Idaho Supplementation Studies 11 and Game, Nez Perce Tribe, Shoshone-Bannock Tribe, and the U.S. Fish and Wildlife Service. Allocations were based on interest, integration with ongoing programs, cost efficiency, logistics and, to a lesser extent, relative equity. Approximately one-half of the study will be implemented by Idaho Department of Fish and Game through the ISS contract with BPA. The Nez Perce Tribe and Shoshone-Bannock Tribe have similar commitments to ISS, each comprising approximately 20% of the study. Both of these components rely heavily on integration of existing or proposed tribal programs. The U.S. Fish and Wildlife Service-Idaho Fishery Resource Office implements about 10% of the project. The Idaho Department of Fish and Game is the lead agency regarding project development, coordination, and implementation.

In addition to the relationship with the cooperative studies mentioned above, ISS also coordinates field activities and data collection efforts within the Salmon River and Clearwater River sub-basins with projects including the Idaho Steelhead Monitoring and Evaluation Studies (199005500), Idaho Natural Production Monitoring (199107300), the Monitoring Smolt Migration of Wild Snake River Spring/Summer Chinook Salmon (199102800), Salmon River Habitat Enhancement (199405000), Captive Rearing Program for Salmon River Chinook Salmon (199700100), Salmon River Sockeye Salmon Captive Rearing Program (199107200), Integrated Systemwide Effectiveness Monitoring Program (200301700). All juvenile Chinook salmon PIT tagged in the ISS project are available for use in the Comparative Survival Studies (199602000) and other smolt monitoring programs utilizing PIT tag detections from known source naturally produced Chinook salmon and steelhead (e.g., 198712700). The Nez Perce Tribal Hatchery Monitoring and Evaluation project (198335003) collects the data associated with the ISS project in Lolo Creek, Eldorado Creek, and Newsome Creeks in the Clearwater River sub-basin. The monitoring and evaluation portion of the Johnson Creek Artificial Propagation Enhancement project (199604300) conducts the juvenile emigration and survival, adult escapement (weir and spawning ground surveys), and genetic monitoring associated with the ISS project in Johnson Creek. The Nez Perce Tribe Monitoring of Listed Stock Chinook Salmon Escapement project (BPA Number 199703000) operates a sonar weir to enumerate adult Chinook salmon entering the upper Secesh River. LSRCP hatchery personnel from Sawtooth, Pahsimeroi, McCall, and Clearwater hatcheries operate ISS weirs.

ISS cooperators collect a tremendous volume of data. These data are requested by other entities in the Salmon and Clearwater drainages including: Idaho Department of Fish and Game regions and headquarters, U.S. Forest Service, Bureau of Land Management, National Marine Fisheries Service, U.S. Fish and Wildlife Service, private landowners, hatchery managers, etc. Many entities rely on the information we collect in making management decisions.

The ISS program distributes data to appropriate regional databases and evaluation programs. ISS personnel upload PIT tag files daily to the PIT Tag Information System (PTAGIS; 199008000), and data from the ISS program are provided to STREAMNET (198810804) through our agency representative.

IDFG and NPT cooperators participated in the Ad Hoc Supplementation Workgroup (AHSWG), which designed an evaluation of supplementation for the entire Columbia River basin. The ISS project data are directly applicable to the design that was developed, and the workgroup strongly recommended the ISS project receive continued support based on the type, quality and applicability of the data produced by this project (Galbreath et al. 2008; pg 7, 23).

198909800 – Idaho Supplementation Studies 12 Personnel from the ISS program are also contributing to and collaborating in the Lemhi Habitat Conservation Plan (052 08 CW / NA06NMF4360290) funded by the Pacific Coast Salmon Recovery Fund.

Personnel from the IDFG and SBT have addressed concerns about potential conflicts between (200890400) and ISS (as well as the ISEMP project 200301700). The Salmon River Basin Nutrient Enhancement project identified several streams in their list of potential study streams that could have confounding effects on either or both the ISS and ISEMP programs. These included Smiley Creek (upper Salmon River), Elk Creek (tributary to Valley Creek; upper Salmon River), Hayden, and Big Timber creeks (Lemhi River). The potential confounding effect of nutrient enhancement on the ISS program would be potential (probable) changes in juvenile Chinook salmon productivity in treated streams above ISS or ISMEP screw traps. This is also a metric that ISS is investigating, and it would not be possible to differentiate the effect of nutrient enhancement from that of supplementation. The SBT demonstrated its commitment to the ISS project and agreed not to treat the identified streams, and, as now planned, the Salmon River Basin Nutrient Enhancement project should not affect the ISS study design.

E. Project history (for ongoing projects)

Project Numbers The Idaho Supplementation Studies (ISS) in Idaho Rivers started in 1989 as project 89098, (Idaho Department of Fish and Game, current project 198909800). In 1992, the U.S. Fish and Wildlife Service, Nez Perce Tribe, and Shoshone-Bannock Tribes were funded to assist in the ISS project as cooperative agencies with project numbers of 198909801, 198909802, and 198909803, respectively. In 2007 the four individual projects were combined into a single proposal to better reflect the cooperative nature of this program, and were funded under project number 198909800.

Funding:

The IDFG has been funded since 1989 under Project Number 198909800. During this time annual budgets have ranged from $850,000 to $1,400,000. The higher budgets were associated with the start-up of the project and included substantial capital acquisitions. Between 2003 and 2009 funding was $990,000. Funding in 2010 increased to $1,024,534.

The USFWS annual budget for Project Number 198909801 has ranged from $73,461 to $147,344. The higher budgets were associated with the start-up of the project and included substantial capital acquisitions. USFWS funding for ISS will be $90,241in 2010.

The NPT annual budget for Project Number 8909802 has ranged from $107,050 to $429,841. The higher budgets were associated with the start-up of the project and included substantial capital acquisitions after 1996. Funding for the NPT portion of the ISS program will be $544,032.

The SBT funding for Project Number 198909803 has averaged $173,256. In 2010, SBT funding for ISS will be 242,074.

Development of the Idaho Supplementation Studies The Idaho Department of Fish and Game (IDFG) spearheaded development of the Idaho Supplementation Studies (ISS) to address questions identified in the Supplementation Technical Work Group (STWG) Five Year Work-plan (STWG 1988), as well as help define the potential

198909800 – Idaho Supplementation Studies 13 role of supplementation in managing Idaho's anadromous fisheries and as a recovery tool for the basin. The development of the Experimental Design (Bowls and Leitzinger 1991) was a cooperative project involving all the members of the Idaho Supplementation Technical Advisory Committee (ISTAC). The committee was made up of representatives from the Forest Service (USFS) Intermountain and Northern regions, United States Fish and Wildlife Service (USFWS), Nez Perce Tribe (NPT), Shoshone-Bannock Tribes (SBT), Northwest Power Planning Council (NPPC), Bonneville Power Administration (BPA), Idaho Cooperative Fish and Wildlife Research Unit (ICFWRU), and Idaho Department of Fish and Game (IDFG). Their roles were to technically review and provide input on the research design and coordinate with their respective management, research, and user groups. This insured that the long- and short-term management plans of respective agencies and tribes would not be compromised by the supplementation research design and that management and research concerns of the respective agencies and tribes were represented in the supplementation research design.

The research goals of the Idaho Supplementation Studies are to: (1) assess the use of hatchery Chinook salmon to increase naturally reproducing populations of spring and summer Chinook in the Salmon and Clearwater River drainages; and, (2) evaluate the genetic and ecological impacts of hatchery Chinook salmon on naturally reproducing populations.

A thorough programmatic explanation of the experimental design and methods for analysis is provided in Bowles and Leitzinger (1991) and updated in Lutch et al. 2005. Sixteen treatment and fourteen control streams in both the Clearwater and Salmon basins have been divided among four resource management entities for implementation. Each cooperator is responsible for the activities on their respective streams. Individual ISS study streams (including ISS sampling infrastructure screw traps and weirs) and how they are spread across the Chinook salmon MPG designations are shown in Figure 1.

As the project transitioned from the treatment to the evaluation phase several challenges to the study design were identified. These issues were highlighted by the Independent Scientific Review Panel (ISRP) (ISRP 2001–12A) during the 2001 Provincial Review for the Mountain Snake Province as being problematic for the evaluation of ISS. The Northwest Power and Conservation Council, acting on technical review from ISRP, advised the ISS to complete a technical review of the study as part of the Fiscal Year 2002 Programmatic Issues document (Issue 10) to resolve the concerns stated above.

Jointly, the ISS cooperators submitted a response to the Council to address the ISRP concerns and recommendations. Through statistical consultation with the University of Idaho, a technical review of the ISS study was completed that included a preliminary statistical treatment of ISS data (Lutch et al. 2003). The ISRP completed their review of the ISS statistical review (ISRP 2003-8) and accepted the following responses: 1) the statistical prototype certified by Dr. Kirk Steinhorst, University of Idaho, satisfied the recommendation of a written protocol for statistical analysis using an independent statistical team, 2) ISRP agreed with ISS in the need to address general production hatchery and ISS hatchery production straying using carcass data to estimate the density of hatchery origin strays, and 3) the ISRP agreed that the timetable presented was an appropriate plan for implementation of Phase III of the ISS.

In response to ISRP (2003-8) the ISS cooperators prepared an updated study design and statistical treatment of Idaho Supplementation Studies (Lutch et al. 2005) to resolve the technical recommendations in ISRP (2003-8). We used the statistical review (Lutch et al. 2003) as a foundation to review other aspects of the ISS study, such as the status of other data types and the ability to use genetic analyses for project evaluation purposes. Independent statistical

198909800 – Idaho Supplementation Studies 14 consultation was provided through the University of Idaho. Due to the cost, complexity, and major change in program scope these analyses would represent the ISS response to this ISRP concern was addressed in a separate proposal in 2007 (Genetic Evaluation of Salmon Supplementation in Idaho Rivers 200725000). Although this proposal was not funded, the ISS program will continue to collect and archive DNA, and will continue RRS work on the Pahsimeroi River population.

The evaluation phase of the project commenced in 2008 with continued evaluation of natural production in all study streams to determine the production and productivity responses of the natural populations after supplementation ended. Adult evaluation will continue for one full Chinook salmon generation after the end of supplementation treatments (2012), and their resulting progeny will be evaluated through the smolt migration in 2014.

There are two categories of case histories for the project as a whole, supplementation of existing natural populations (Salmon River basin) and supplementation of extirpated populations (Clearwater River basin). Supplementation effects will be evaluated by comparing weir returns, redd counts, juvenile production, juvenile survival, fecundity, age structure, and genetic structure and variability in supplemented and un-supplemented streams of similar ecological parameters. An overview of these activities and the data collected are provided below. Treatment effects will be tested directly by hypothesis. The experimental units are the study streams themselves.

Adult Weirs. Escapement weirs to capture, enumerate, sample, and manage adult Chinook salmon are operated in the South Fork Salmon River, Pahsimeroi River, upper Salmon River, Crooked River, Red River, Crooked Fork Creek, Clear Creek, Lolo Creek, Newsome Creek, and Johnson Creek. Additionally, a sonar weir is operated on the Secesh River and video weir is maintained on Lake Creek. While adult sampling is not possible at the latter two sites, these weirs do provide annual estimates of Chinook salmon entering these streams. In treatment streams, adults of natural origin are passed above to spawn, while GP strays are excluded. In control streams with weirs, only Chinook salmon of natural origin are passed. Each fish passed over an ISS weir is fin clipped for a DNA sample and is given an opercle punch. The ratio of punched to un-punched carcasses collected is then used to estimate weir efficiency. In addition to adult enumeration, biological characteristics measurable with non-lethal methods are recorded for fish passed above weirs. Weirs were operated at all proposed locations during the previous funding cycle and will continue to be operated through 2012 (and beyond at hatchery locations).

Redd Count and Carcass Surveys. Each year, multiple redd counts and carcass surveys are conducted along designated reaches in all ISS treatment and control streams in the Clearwater and Salmon River sub-basins. Generally, ISS cooperators make at least three passes on each stream except three extremely remote streams that are surveyed once near the expected peak spawning period. Redds are flagged and GPS locations recorded. Carcasses are measured, scanned for tags, sex and percent spawned are verified, DNA collected, and dorsal fin rays are collected for age determination by Project Number 1991-073-00. Redd count and carcass surveys were completed in all proposed streams during the previous funding cycle. Fires prevented one or more passes on some streams (e.g., West Fork Yankee Fork and South Fork Salmon River, Crooked Fork Creek) in certain years, but this was not a common occurrence. Redd counts and carcass surveys will continue on all study stream during this cycle.

198909800 – Idaho Supplementation Studies 15 Emigrant Trap Operations. The ISS program operates emigrant screw-traps on a total of 18 different streams in the Clearwater and Salmon river drainages from March until freeze up in November or December. Juvenile Chinook salmon of various life stages (parr, pre-smolt, and smolt) have been PIT tagged at these traps since the beginning of the ISS program, although the number tagged each year varies based on brood year strength. Trap efficiency is then estimated from the recapture of tagged fish released above the trap, and life stage emigration estimates are computed using a Maximum Likelihood Estimator with Bailey’s modification (Steinhorst et al. 2004). Life stage survival is also estimated to Lower Granite Dam for each stream using the SURPH Model (Lady et al. 2001). Data from wild/natural Chinook salmon PIT tagged by this project have been used to help develop basin-wide SARs. During trapping operations, many other species of fish (anadromous and resident) are captured. Many of the steelhead Oncorhynchus mykiss and sockeye salmon Oncorhynchus nerka captured are tagged, measured, and enumerated to assist other ongoing BPA funded research activities. Resident species captured are enumerated, and if time permits, measured for length and weight. Screw traps were operated on all proposed streams during the previous funding cycle. High water, debris, or hatchery releases caused short-term interruption of trapping activities, but this cannot be avoided. Screw traps will be operated on all proposed streams during the upcoming funding cycle.

Snorkel Estimates. Due to a lack of available screw traps, access issues, and limited potential trap locations, we also use snorkelers to estimate the density of juvenile Chinook salmon in a number of ISS streams. Techniques and rationale for underwater observation to determine Chinook salmon parr abundance and density are described in Petrosky and Holubetz (1985), Hankin (1986), and Hankin and Reeves (1988). Counts are limited to periods when water temperature exceeds 10°C (Thurow 1994) unless the stream does not routinely reach this temperature (e.g., the American River). Prior to snorkeling, visibility is measured to determine the most efficient distance between snorkelers for viewing fish and enough personnel are then used to observe the entire stream width in one pass. All salmonids are identified, counted, and their total length estimated, and the length of each snorkel site is measured along with at least three wetted stream widths. Chinook salmon parr density (number per 100 m2) is calculated for each stream, and the presence or absence of non-salmonids is also recorded. Snorkeling was conducted throughout the previous cycle and will continue through the next cycle.

Database Development. Data management and dissemination of project results and data is just as important as collecting data itself, but often receives less attention. Protocols for this project ensure proper collection and validation of data, with redundant and secure storage. This project acknowledges the need to share updated information on adult natural origin salmon escapement, spawner abundance, and productivity as soon as it is available. The project in the past has used the annual report submissions to the BPA web site (http://www.efw.bpa.gov/searchpublications/) to make project information available. Annual reports are also available on the Nez Perce Tribe’s web site (Nez Perce Department of Fisheries Resources Management - Research) and IDFG’s website (https://research.idfg.idaho.gov/Fisheries%20Research%20Reports/Forms/Show%20All %20Reports.aspx). The project also maintains an annual distribution list of managers, researchers, ICTRT members, and other recovery planners who receive hard copies of annual reports and maintain electronic correspondence to share key data sets.

The ever-increasing volume of data collected by each of the cooperators on the ISS project has prompted the development of several new integrated database. During the last six years, IDFG has devoted considerable effort to the development of these databases that will centralize data collected by all cooperating agencies into common databases. This will allow

198909800 – Idaho Supplementation Studies 16 uniform and repeatable queries and analysis of the data set. All ISS cooperators are, or soon will be, sending data remotely into a central server at IDFG headquarters. Currently, the juvenile trapping data entry form and tables have been developed. A redd count and adult carcass information tables are being developed and will be useable for the 2010 spawning surveys. All project data on juvenile fish collected prior to 2001 is currently in an electronic format and uploaded into the new centralized database. When complete this will be one of the largest sets of life history and migration data for both anadromous and resident fish in the state of Idaho, and applicable data sets will be shared with STREAMNET, PSMFC, RMIS, etc. Redd count and carcass survey data collected prior to and including 2009 is in electronic format and is being uploaded to the database. Finally, IDFG and cooperators have designed and implemented a hatchery database that will be used at all IDFG hatcheries beginning in 2010. This database will directly benefit ISS by simplifying tracking of return and disposition data at several ISS locations. Database development will continue as needed throughout the next funding cycle.

Appropriate components of program data and results are currently provided to the following websites: Pacific States Marine Fisheries Commission (PSMFC), including: PIT Tag Information System (PTAGIS) and the Regional Mark Information System (RMIS); and StreamNet (StreamNet).

Parental Contribution. A small-scale study was conducted on the Pahsimeroi River to determine the spawn timing, distribution, and parental contribution of Chinook salmon of natural and ISS origin to juvenile production using microsatellite parental exclusion analysis (Leth 2005). We are continuing this sampling to determine the contribution of adults from the two origins to subsequent adult returns to the River. In addition, DNA samples have been collected from adult and juvenile Chinook salmon spawning in ISS study streams with adult weirs and screw-traps for similar analyses in response to concerns raised by the ISRP (ISRP 2003-8). Adult genotyping is complete through 2008 and the 2009 returns are currently being genotyped. Genotyping adults will continue through the upcoming funding cycle.

F. Proposal biological objectives, work elements, and methods:

To preserve the continuity of data collection, we propose to maintain all program objectives, work elements, and objectives from the previous funding cycle and add two new tasks. The proposed work is framed to be consistent with RPA needs and guidance from NOAA Fisheries (Crawford and Rumsey 2009). This work will provide an evaluation of a supplementation program as well as both intensive and extensive status and trend monitoring for Chinook salmon in the Salmon and Clearwater Sub-basins (Appendix A) and RRS information for a Salmon River population.

ISS field activities are scheduled to end during this funding cycle, and appropriate plans will need to be developed if ISS infrastructure is to be maintained for intensive and extensive VSP status and trend monitoring (Appendix A). After 2012, ISS cooperators will no longer be evaluating adult returns to study streams (i.e., redd counts and carcass surveys), and juvenile migration evaluation will be complete after smolt trapping in 2014 (brood year 2012). In order to maintain current levels of intensive and extensive status and trend monitoring, ISS infrastructure and sampling duties will need to be incorporated into new or existing programs. Additionally, select personnel from the ISS cooperating agencies will need to be funded for a period of time after 2014 to complete data analysis, a completion report, peer reviewed publications, and ensure ISS findings are communicated to and incorporated into other regional supplementation programs.

198909800 – Idaho Supplementation Studies 17 Overall Management Objective for Supplementation: The general expectation for supplementation among management entities and user groups in Idaho is to use artificial propagation to help build self-sustaining and harvestable populations of Chinook salmon in the Salmon and Clearwater River drainages without adversely impacting existing wild and natural populations.

The specific research goals of this project are: 1. Assess the use of hatchery Chinook salmon to increase natural populations of spring and summer Chinook in the Salmon and Clearwater River drainages. 2. Evaluate the genetic and ecological impacts of hatchery Chinook salmon on naturally reproducing Chinook populations.

The specific program research objectives and hypotheses are: Objective 1. Monitor and evaluate the effects of supplementation on parr, pre-smolt, and smolt production and spawning escapements of naturally produced salmon. H01a: Supplementation-augmentation of existing Chinook populations in Idaho does not affect natural production.

H01b: Supplementation-restoration utilizing existing hatchery stocks does not establish natural populations of Chinook salmon in Idaho.

Objective 2. Monitor and evaluate changes in natural productivity and genetic composition of target and adjacent populations following supplementation. H02a: Supplementation-augmentation of existing Chinook populations in Idaho does not reduce productivity of target or adjacent populations below acceptable levels (e.g. replacement).

H02b: Supplementation does not lead to self-sustaining populations at some enhanced level (e.g. 50% increase in abundance maintained over time.)

Objective 3. Determine which supplementation strategies (brood stock and release stage) provide the quickest and highest response in natural production without adverse effects on productivity. H03a: Utilization of existing hatchery brood stocks in Idaho is an effective strategy to supplement existing populations of Chinook salmon within local or adjacent sub-basins.

H03b: Development of new, local brood stocks with known natural component for supplementation does not provide an advantage over utilization of existing hatchery brood stocks for supplementation within the local or adjacent sub-basin.

H03c: The effects of supplementation on natural production and productivity do not differ among life stages (parr, pre-smolt, smolt) of hatchery fish released.

Objective 4. Develop supplementation recommendations.

Objective 5: Coordinate and transfer technology from supplementation research planning, field evaluation program activities and management recommendations between program cooperators, internal and regional databases.

198909800 – Idaho Supplementation Studies 18 The methods are not described by objective or work element here since all methodologies must be used in synchrony to test the research hypotheses, and each methodology tests more than one hypothesis. The methods are described relative to the overall experimental design, and all must be performed annually to successfully evaluate the production and productivity response variables and to meet the project objectives. The methods used and how they relate to specific Work Elements are described below.

Method 1. Operate screw traps during ice-free season, PIT tag and collect DNA from a predetermined proportion of parr, pre-smolts, and smolts.

Associated Work Element(s): 132 Produce joint annual reports 157 Operate juvenile screw traps 157 Collect juvenile DNA from ISS screw traps 158 Mark juvenile and adult Chinook salmon 159 Upload juvenile data to centralized databases 159 Manage PIT tag files 162 Estimate juvenile production in ISS streams 162 Estimate juvenile survival to Lower Granite Dam

Agency and streams where screw traps will be operated: IDFG Pahsimeroi River, Salmon River above Sawtooth Hatchery, American River, Lemhi River, Crooked River, Red River, South Fork Salmon River, Crooked Fork Creek, Marsh Creek, and Colt Killed Creek NPT Lake Creek and the Secesh River NPT Lolo Creek and Newsome Creek (by cooperative agreement with Project 198335003) NPT Johnson Creek (by cooperative agreement with Project 199604300) SBT West Fork Yankee Fork Salmon River and the East Fork Salmon River FWS Clear Creek

Completion of this task will provide the following objectives and metrics: 1) Life-stage population estimates to estimate production in treatment and control streams 2) Survival estimates to Lower Granite Dam and mainstem mortality 3) Productivity estimates for treatment and control streams (when combined with redd counts and/or adult escapement measures) 4) Reproductive contribution of natural, ISS, and/or GP hatchery stray origin adults (when combined with adult DNA samples) 5) Comparisons of genetic indices (e.g., allele frequency) over time for supplemented and unsupplemented populations 6) Spawner to recruit relationships when combined with weir or redd count data for treatment and control streams, which can further be used in population viability assessments 7) Estimates of smolt-to-adult return rates at the finest possible scale (when combined with other regional tagging programs e.g., 199602000) 8) Evaluation of these data will be necessary to develop informed recommendations on the future use of supplementation.

Method 2. Operate adult weirs to monitor adult escapement into study streams, and collect DNA and opercle punch all adults passed over the weirs.

Associated Work Element(s): 132 Produce joint annual reports 157 Monitor adult escapement into streams 157 Collect adult DNA from study weirs

198909800 – Idaho Supplementation Studies 19 157 Supplemental data collection 158 Mark juvenile and adult Chinook salmon 162 Estimate adult production in study streams 162 Perform parental exclusion tests

Agency and streams where adult weirs will be operated: IDFG Crooked Fork Creek, Crooked and Red River, and South Fork Salmon River IDFG East Fork Salmon River (by cooperative arrangement with Project Number 199700100) FWS Clear Creek NPT Lolo, Newsome, and Johnson creeks (by cooperative arrangement with Project Numbers 198335003, 199604300) NPT Secesh River and Lake Creek (sonar and/or video weirs; enumeration only)

Completion of this task will contribute to the following program needs: 1) Adult returns by natural, general hatchery production, and ISS origin 2) Production estimates for treatment and control streams 3) Productivity estimates for treatment and control streams (when combined with juvenile population estimates or previous adult escapement estimates). 4) Restrict GP hatchery strays from accessing spawning grounds 5) Weir efficiency estimates from the ratio of opercle punched to un-punched carcasses 6) Reproductive contribution of natural, ISS, and/or GP hatchery stray origin adults (when combined with juvenile DNA samples) 7) Comparisons of genetic indices (e.g., allele frequency) over time for supplemented and unsupplemented populations. 8) Evaluation of these data will be necessary to develop informed recommendations on the future use of supplementation. 9) Information from tags (e.g., CWT, PIT, jaw, radio, etc.) collected from these sites will be communicated with the appropriate agencies (e.g., PMFC, RMIS, U of I, WDFW).

Method 3. Conduct multiple pass carcass surveys on ISS study streams collecting the necessary biological samples to estimate sex ratio, pre-spawn mortality, parentage analyses, age structure, weir efficiency, and origin (natural, ISS, or GP hatchery).

Associated work element(s): 132 Produce joint annual report 157 Monitor adult escapement into study streams 157 Conduct redd count and carcass surveys 157 Conduct additional carcass surveys 157 Supplemental data collection 157 Provide snouts for CWT extraction and reading 162 Estimate adult production in study streams

Agency and streams where carcass surveys will be conducted: IDFG Multiple carcass surveys on Crooked Fork Creek, Marsh Creek, Brushy Fork Creek, North Fork Salmon River, South Fork Salmon River, American River, Red River Crooked River, Lemhi River, Pahsimeroi River, and Salmon River above Sawtooth Hatchery IDFG A single carcass survey on Big Flat Creek and Colt Killed Creek. FWS Multiple carcass surveys on Clear Creek and Pete King Creek. NPT Multiple pass carcass surveys on: Fishing Creek, Legendary Bear Creek, Lake Creek, Secesh River, and Slate Creek. NPT Multiple pass carcass surveys on: Lolo Creek, Newsome Creek, and Eldorado Creek (by

198909800 – Idaho Supplementation Studies 20 cooperative agreement with Project 198335003) NPT Multiple pass carcass surveys on: Johnson Creek (by cooperative agreement with Project 199604300) SBT Multiple pass carcass surveys on: West Fork Yankee Fork Salmon River, East Fork Salmon River, and Valley Creek. SBT Multiple pass carcass surveys on: Herd Creek and Bear Valley Creek (by cooperative agreement with Project 199405000)

Completion of this task will contribute to the following program needs: 1) Proportion of origin type of adults returning to treatment and control streams without weirs 2) Weir efficiency (based on the ratio of opercle punched:un-punched recoveries) 3) GP hatchery stray rates into treatment and control streams 4) Reproductive contribution of natural, ISS, and/or GP hatchery stray origin adults (when combined with juvenile DNA samples). 5) Comparisons of genetic indices (e.g., allele frequency) over time for supplemented and un- supplemented populations. 6) Evaluation of these data will be necessary to develop informed recommendations on the future use of supplementation. 7) Information from tags (e.g., CWT, PIT, jaw, radio, etc.) collected from these sites will be communicated with the appropriate agencies (e.g., PMFC, RMIS, U of I, WDFW).

Method 4. Conduct redd counts on index and expanded reaches of ISS study streams

Associated work element(s): 132 Produce joint annual report 157 Monitor adult escapement into study streams 157 Conduct redd counts and carcass surveys 162 Estimate adult production in study streams

Agency and streams where redd counts will be conducted: IDFG Multiple pass redd counts on Crooked Fork Creek, Marsh Creek, Brushy Fork Creek, North Fork Salmon River, South Fork Salmon River, American River, Red River Crooked River, Lemhi River, and Pahsimeroi River. IDFG A single pass redd count on Big Flat Creek and Colt Killed Creek. IDFG A single aerial redd count will be done on the Salmon River above Sawtooth Hatchery, the Lemhi River, Alturas Lake Creek, and White Cap Creek FWS Multiple pass redd counts on Clear Creek and Pete King Creek. NPT Multiple pass redd counts on: Fishing Creek, Legendary Bear Creek, Lake Creek, Secesh River, and Slate Creek. NPT Multiple pass redd counts on: Lolo Creek, Newsome Creek, and Eldorado Creek (by cooperative agreement with Project 198335003) NPT Multiple pass redd counts on: Johnson Creek (by cooperative agreement with Project 199604300) SBT Multiple pass redd counts on: West Fork Yankee Fork Salmon River, East Fork Salmon River, and Valley Creek.

SBT Multiple pass redd counts on: Herd Creek and Bear Valley Creek (by cooperative agreement with Project 199405000)

Completion of this task will contribute to the following program needs: 1) A standardized index of adult escapement comparable across treatment and control streams with and without weirs.

198909800 – Idaho Supplementation Studies 21 2) A standardized index of natural production comparable across treatment and control streams with and without weirs. 3) Productivity estimates for treatment and control streams where juvenile abundance is estimated. 4) Spawner to recruitment relationships when combined with juvenile production estimates for treatment and control streams, which can further be used in population viability assessments. 5) Evaluation of these data will be necessary to develop informed recommendations on the future use of supplementation. 6) Data from ISS redd counts will be made available to STREAMNET

Method 5. Perform snorkel surveys along index and probabilistically determined sites on select ISS study streams to estimate Chinook salmon parr and other salmonid density

Associated work element(s): 132 Produce joint annual report 162 Estimate juvenile production in study streams

Agency and streams where snorkel surveys will be conducted: NPT Fishing Creek, Legendary Bear Creek FWS Pete King Creek SBT Valley Creek, Bear Valley Creek, Herd Creek

Completion of this task will contribute to the following program needs: 1) Natural production estimates comparable across streams sampled by snorkeling (IDFG regional activities, Projects 199005500, and 199107300) following the procedures of (Stevens and Olsen 2004). 2) Productivity estimates when combined with redd count data 3) Production trend data for additional ISS streams without screw traps 4) Additional snorkel transects will be conducted in ISS study streams based on probabilistic sampling through the INPMEP project (199107300) 5) Evaluation of these data will be necessary to develop informed recommendations on the future use of supplementation.

Method 6. Maintain, update, upload data to, and improve project databases, servers, and websites.

Associated work element(s): 132 Produce joint annual reports 159 Upload juvenile data to centralized database 159 Manage PIT tag files 160 Maintain project servers and databases

Agency and associated database responsibility: IDFG Provide personnel and expertise for ISS database and web site construction and maintenance IDFG Perform regularly scheduled maintenance to ISS web servers and web based databases to maintain functionality, security, and accessibility every two months IDFG Replace or repair hardware as needed to ensure functionality, security, and accessibility IDFG Upload data from cooperators to the centralized database IDFG Provide cooperators with field versions of databases for field data collection NPT Provide IDFG with an electronic copy of ISS data annually for uploading to centralized database

198909800 – Idaho Supplementation Studies 22 SBT Provide IDFG with an electronic copy of ISS data annually for uploading to centralized database FWS Provide IDFG with an electronic copy of ISS data annually for uploading to centralized database

Method 7. Coordinate between project cooperators to ensure that the necessary joint statements of work and reports are completed.

Associated work element(s): 119 Produce SOW, budget, and inventory 191 Inter- and intra-agency coordination

Agency and reporting responsibility: IDFG Prepare annual draft ISS statement of work for review by cooperators IDFG Submit joint ISS statement of work after review and approval by cooperators SBT Review draft ISS statement of work and provide IDFG with corrections and changes NPT Review draft ISS statement of work and provide IDFG with corrections and changes FWS Review draft ISS statement of work and provide IDFG with corrections and changes ALL Information contained in ISS centralized databases will be made available as appropriate to other regional databases (e.g., STEAMNET, PSMFC, PNAMP, and RMIS)

Method 8 (NEW). Develop a new location and install a second screw trap on Marsh Creek to provide intensive VSP status and trend monitoring to include Beaver, Cape Horn, Knapp, and upper Marsh creeks.

Associated Work Element(s): 157 Operate juvenile screw traps 157 Collect juvenile DNA from screw traps 158 Mark juvenile and adult Chinook salmon 159 Upload juvenile data to centralized databases 159 Manage PIT tag files 162 Estimate juvenile production in ISS streams 162 Estimate juvenile survival to Lower Granite Dam

Agency and reporting responsibility IDFG Data from this location will be reported as an appendix to ISS annual reports.

Completion of this task will contribute to the following program needs: 1) Fish in, fish out intensive VSP status and trend monitoring data for this population when combined with ongoing multi-pass redd counts and carcass surveys . 2) Calibration of past production and productivity estimates with the new screw trap on Marsh Creek. 3) Survival estimates to Lower Granite Dam and mainstem mortality

Method 9 (NEW). Verify AHA and AHSWG model assumptions and predictions using ISS data. To this point, these models are somewhat theoretical. We propose to use historic ISS juvenile release, survival, and adult return data in these models and compare actual adult returns to those predicted. The need for this type of model scoping has been identified by the ISRP/ISAB (ISRP/ISAB 2005-5).

Agency and reporting responsibility IDFG Data from this activity will be reported as an appendix to an ISS report

198909800 – Idaho Supplementation Studies 23 Completion of this task will contribute to the following program needs: Validation of the predictive capacity of the models Model usefulness for future supplementation implementation Assessment of some of the “boiler plate” values used in the model (e.g., baseline productivity, capacity) Will identify areas of future investigation to assess the sensitivity of AHA to assumptions made in choosing values of its numerous input variables

Methods for Data Analysis: We propose using two approaches for the statistical analysis of the ISS: 1) the experimental evaluation of treatment and control streams to determine cause and effect relationships, and 2) a modeling approach to estimate treatment effects (Table 2). The ISRP has reviewed our proposed analyses and determined it was an appropriate approach (ISRP 2005-18) The first approach maintains the original experimental analysis prescribed in Bowles and Leitzinger (1991). The second approach considers the ISS as an observational study per recommendation by ISRP and places more emphasis on modeling and estimating effects from supplementation treatments (see Lutch et al. 2005).

We also include a third evaluation approach for the ISS using a much finer scale that will focus on individual study streams. This includes the ongoing reproductive contribution study in the Pahsimeroi River (and similar data being collected in the upper Salmon River) that is examining the parental genetic contribution of ISS supplementation and natural origin Chinook salmon to F1 generation offspring and their survival to adulthood (as measured by smolt-to- adult and adult-to-adult return rates).

Expected Results – We expect this research will broaden our understanding of how supplementation affects target populations of Chinook salmon both in the short- and long-term, as well as the potential for using the technique to rebuild naturally spawning populations. It will also document the potential benefits and risks to these populations. This research will also explore the applicability of supplementation to re-establish naturally producing populations in streams where Chinook salmon have become extirpated. Because study streams have different ecological characteristics, supplementation effects and recommendations will likely be different for different streams.

Potential Risks – The risks associated with ISS were evaluated under the 1991 draft RASP criteria. ISS treatment streams already have on-going hatchery programs. Consequently, ISS protocols should pose minimal ecological risk to Chinook salmon populations in these streams. Risks are primarily associated with not conducting ISS and failing to identify and implement the best recovery measures. This could result in the continued decline or extinction of these populations or other adverse impacts to wild\natural populations through the use of inappropriate supplementation due to lack of information. Outmigrant traps and weirs impose a limited risk to individual animals in terms of direct mortality and migration alteration.

198909800 – Idaho Supplementation Studies 24 Table 2. Proposed ISS evaluation, data set, and statistical method for meeting objectives one and two.

Evaluation Evaluation Study Statistical Objective Measure Approach Phase Analysis Supplementation effects on Natural Mixed Model Production Redd Counts Global I, II, III Regression Regression Mixed Model Juvenile Migration Global I, II, III Graphical ISS Parental Exclusion Small Scale II, III Parental Exclusion Supplementation Regression effects on Productivity Juvenile Survival Global I, II, III Graphical Regression Smolt to adult Global I, II, III Graphical Recruits per Regression spawner Global I, II, III Graphical ISS Parental Exclusion Small Scale II, III Parental Exclusion

G. Facilities and equipment

IDFG personnel participating in this project are stationed at the IDFG Nampa Research Office and at IDFG Regional Offices in Lewiston, McCall, and Salmon, Idaho. The project utilizes existing hatchery facilities in the state. All major equipment needed has been purchased through previous contracts for the project. Equipment on hand includes, but is not limited to juvenile screw traps, PIT-tag stations, field computers for PIT-tag stations, office computers, printers, photocopiers, other field equipment including nets, seines, wet suits, trailers for field lodging, and camping gear for remote field work.

The USFWS-IFRO operates out of the Dworshak Fisheries Complex in Ahsahka, Idaho. This portion of the ISS program relies on existing hatchery personnel and facilities at both Kooskia and Dworshak National Fish Hatcheries for handling fish at the Clear Creek weir. Juvenile trapping is accomplished with the use of one rotary screw trap. The USFWS-IFRO also has a PIT-tag station that is shared by the Dworshak Fisheries Complex, and uses standardized PIT-tag protocols. The program also has the necessary desktop and laptop computers.

The Nez Perce Tribe’s portion of the ISS project is primarily conducted out of the field office in McCall, Idaho. This office houses NPT Fisheries and support personnel from three other BPA funded projects. At this time, the office facilities are adequate for all administrative and personnel needs. The ISS project has adequate computer power for office and field operations.

Field operations located in the Secesh River drainage consist of juvenile rotary screw traps, travel trailer, and other support equipment and vehicles. The Nez Perce Tribe currently uses six rotary screw traps to collect data for the ISS project. Two of these traps have been purchased with ISS funding, the other four traps are coordinated with associated BPA projects. One spare trap is available for emergency use when primary traps are damaged.

198909800 – Idaho Supplementation Studies 25 Personnel from the SBT participating in this project are stationed at the Fort Hall Fisheries Department in Fort Hall, Idaho. All major equipment needed has been purchased through previous contracts for the project. Equipment on hand includes, but is not limited to, vehicles, juvenile screw traps, PIT-tag stations, field computers, office computers, printers, photocopiers, other field equipment including wet suits, a trailer for field lodging, and camping gear for remote field work.

198909800 – Idaho Supplementation Studies 26 Figure 1. Location of ISS study streams in the Salmon River and Clearwater River sub-basins relative to spring/summer Chinook salmon MPG spawning habitat. Streams are identified by color as to whether they are treatment (supplemented) or control (un-supplemented), and icon shape indicates what type of ISS sampling infrastructure, if any, is present.

198909800 – Idaho Supplementation Studies 27 H. References Reference (include web address if available online) Bams, R.A. 1976. Results of a pink salmon transplant suing males native to the recipient stream. Fisheries and Marine Service Technical Report No. 642. Berejikian, B.A., and M.J. Ford. 2004. Review of relative fitness of hatchery and natural salmon. US Department of Commerce, NOAA Tech. Memo. NMFS-NWFSC-61, 28 pp. Botkin, D. B., D. L. Peterson, and J. M. Calhoun (technical editors). 2000. The scientific basis for validation monitoring of salmon for conservation and restoration plans. Olympic Natural Resources Technical Report. University of Washington, Olympic Natural Resources Center, Forks, Washington, USA. Bowles, E. and E. Leitzinger, 1991. Salmon Supplementation Studies in Idaho Rivers. Experimental Design to the U.S. Department of Energy, Bonneville Power Administration. Project No. 89-098. Contract No. DE-B179-89BP01466. Chilcote, M.W., S.A. Leider, and J.J. Loch. 1986. Differential reproductive success of hatchery and wild summer-run steelhead under natural conditions. Transactions of the American Fisheries Society. 115:726-735. CBFWA (Columbia Basin Fish and Wildlife Authority). 1990. Integrated system plan for salmon and steehead production in the Columbia Ricer Basin Public Review Draft. Prepared for the Northwest Power Planning Council, Portland, Oregon. Coordinated Anadromous Workshop (Columbia Basin Coordinated Anadromous M&E Workshop). 2010a. Table 1 Critical Steelhead Contracts and Identified Gaps Combined Edits - as revised 8 January 2010. Columbia Basin Fish and Wildlife Authority, Portland, Oregon. Available: http://www.cbfwa.org/ams/FinalDocs.cfm. Accessed January 8, 2010. Coordinated Anadromous Workshop (Columbia Basin Coordinated Anadromous M&E Workshop). 2010b. Table 2 Critical spring chinook contracts and gaps COMBINED edits - as revised 8 January 2010. Columbia Basin Fish and Wildlife Authority, Portland, Oregon. Available: http://www.cbfwa.org/ams/FinalDocs.cfm. Accessed January 8, 2010. Coordinated Anadromous Workshop (Columbia Basin Coordinated Anadromous M&E Workshop). 2010c. Basin Funding Prioritization Tables as revised 15 December 2009. Columbia Basin Fish and Wildlife Authority, Portland, Oregon. Available: http://www.cbfwa.org/ams/FinalDocs.cfm. Accessed January 8, 2010. Crawford, B.A., and S. Rumsey. 2009. DRAFT Guidance for monitoring recovery of salmon and steelhead. NOAA Fisheries Service – Northwest Region. http://www.cbfwa.org/ams/files %5CNOAA_M&E_Guidance_External_DraftVersion_4-27-09.pdf. Accessed January 14, 2010. Currens, K.P., C.A. Busack, G.K. Meffe, D.P. Phillip, E.P. Pister, F.M. Utter, and S.P. Yount. 1991 (MS). A hierarchical approach to conservation genetics and production of anadromous salmonids in the Columbia River Basin. Product of the 1990 Sustainability Workshop, Northwest Power Planning Council, Portland, Oregon. Ecovista. 2003. Draft clearwater subbasin management plan. Prepared for the Northwest Power and Conservation Council, Portland, Oregon.

Ecovista. 2004. Draft salmon subbasin management plan. Prepared for the Northwest Power and Conservation Council, Portland, Oregon. Franklin, I.R. 1980. Evolutionary change in small populations. Pages 135-149 in M.E. Soule’ and B.A. Wilcox (eds.). Conservation Biology: an evolutionary – ecological perspective. Sinauer Associates, Sunderland, Massachusetts. Galbreath, P.F., C.A. Beasley, B.A. Berejikian, R.W. Carmichael, D.E. Fast, M.J. Ford, J.A. Hesse, L.L. McDonald, A.R. Murdoch, C.M. Pevin, D.A. Venditti. 2008. Recommendations for Broad Scale Monitoring to Evaluate the Effects of Hatchery Supplementation on the Fitness of Natural Salmon and Steelhead Populations; Final Draft Report of the Ad Hoc Supplementation Monitoring and Evaluation Workgroup. http://www.nwcouncil.org/fw/program/2008amend/uploadedfiles/95/Final%20Draft%20AHSWG %20report.pdf. Accessed January 12, 2010.

Gebhards, S.V. 1959. The effects of irrigation on the natural production of Chinook salmon

198909800 – Idaho Supplementation Studies 28 (Oncorhynchus tshawtscha) in the Lemhi River, Idaho. Master’s thesis, Utah State University, Logan, Utah. Hankin, D. G. 1986. Sampling designs for estimating the total number of fish in small streams. USDA Pacific Northwest Research Station, Research Paper PNW-360. 33 p. Hankin, D. G., and G. H. Reeves. 1988. Estimating total fish abundance and total habitat area in small streams based on visual estimation methods. Canadian Journal of Fisheries and Aquatic Sciences 45:834-844. Hesse, J. A., and J. R. Harbeck. 2004. Northeast Oregon hatchery spring/summer Chinook salmon conceptual monitoring and evaluation plan. Report prepared for the Bonneville Power Administration, Portland, Oregon, DOE/BP-3267. Herrig, D.M. 1990. A review of the Lower Snake River Compensation Plan hatchery program. U.S. Fish and Wildlife Service, Lower Snake River Compensation Plan Office, Boise, Idaho. HSRG (Hatchery Scientific Review Group. 2005. Hatchery reform in Washington state: Principles and emerging issues. Fisheries 30:11-23. Idaho Department of Fish and Game. 1985. Anadromous fisheries management plan, 1986-1990. Boise, Idaho. Idaho Department of Fish and Game. 1991. Anadromous fisheries management plan, 1991-1995. Boise, Idaho. Idaho Department of Fish and Game, Nez Perce Tribe of Idaho, and Shoshone-Bannock Tribes of Fort Hall. 1990. Salmon River sub-basin salmon and steelhead production plan. Northwest Power Planning Council, Portland, Oregon. ISAB (Independent Scientific Advisory Board). 2003-3. Review of salmon and steelhead supplementation. Northwest Power and Conservation Council, Portland, Oregon ISRP. 2001-12A. Final review of fiscal year 2002 project proposals for the Mountain Snake and Blue Mountain Provinces. Independent Scientific Review Panel review presented to the Northwest Power and Conservation Council. ISRP. 2003-8. Review of Idaho supplementation studies. Independent Scientific Review Panel programmatic review provided to the Northwest Power Planning Council. ISRP. 2005-14. Independent scientific review panel retrospective report 1997 – 2005. Presented to the Northwest Power and Conservation Council. ISRP. 2005-18. Review of the updated study design and statistical analysis of Idaho supplementation studies (IDFG Report Number 05-35). Memorandum to the Northwest Power and Conservation Council ISRP/ISAB. 2005 - 5. Review of the All-H Analyzer. http://www.nwcouncil.org/library/isrp/isrp2005- 5.htm. Accessed January 15, 2010. ISRP/ISAB. 2005 - 15. Monitoring ands evaluation of supplementation projects. Joint Independent Scientific Review Panel and Independent Scientific Advisory Board report to the Northwest Power and Conservation Council, 11 pages. Kapucinski, A.R., C.R. Steward, M.L. Goodman, C.C. Krueger, J.H. Williamson, E.C. Bowes, and R. Carmichael. 1991 (MS). Genetic conservation guidelines for salmon and steelhead supplementation. Product of the 1990 Sustainability Workshop, Northwest Power Planning Council, Portland, Oregon. Kennedy, G.J.A., and C.D. Strange. 1986. The effects of intra- and interspecific competition on the survival and growth of stocked juvenile Atlantic salmon Salmo salar L., and resident trout Salmo trutta L., in an upland stream. Journal of Fish biology 28:479-490 Kijima, A., and Y. Fujio. 1984. Relationship between average heterozygosity and river population size in chum salmon. Bull. Jpn. Soc. Sci. Fish. 50:603-608. Kim, J.E., W.E. Withler, C. Ritland, and K.M. Cheng. 2004. Genetic variation within and between domesticated chinook salmon, Oncorhynchus tshawytscha, strains and their progenitor porulations. Environmental Biology of Fishes 69:371-378. Lady, J.M., P. Westhagen, and J.R. Skalski. 2001. Survival under proportional hazards (SURPH 2.1). Prepared for the U.S. Department of Energy, Bonneville Power Administration, Project Number 8910700, Portland, Oregon.

Leth, B. 2005. Reproductive success of hatchery and natural origin Chinook salmon (Oncorhynchus

198909800 – Idaho Supplementation Studies 29 tshawytscha) in a stream with a history of supplementation management. Master’s thesis. University of Idaho, Moscow, Idaho. Lutch, J., C. Beasley, and K. Steinhorst. 2003. Evaluation and statistical review of Idaho supplementation studies. Scientific Findings Report to the Bonneville Power Administration, Project Number 198909800, Portland, Oregon. Lutch, J., J. Lockhart, C. Beasley, K. Steinhorst, and D.A. Venditti. 2005. An updated study design and statistical analysis of Idaho supplementation studies. Technical Report, Project Number 199809800, to the Bonneville Power Administration, Portland, Oregon. McClure, M.M., and nine coauthors. 2008. Evolutionary effects of artificial propagation programs: implications for viability of endangered anadromous salmonids. Evolutionary Applications 1:356-375/ McLean, J.E., P. Bentzen, and T.P. Quinn. 2004. Differential reproductive success of sympatric, naturally spawning hatchery and wild steelhead, Oncorhynchus mykiss. Environmental Biology of Fishes 69:359-369. Miller, W.H., T.C. Coley, H.L. Burge, and T.T. Kisanuki. 1990. Analysis of salmon and steelhead supplementation: emphasis on unpublished reports and present programs. Part 1 in W.H. Miller (ed.). Analysis of salmon and steelhead supplementation, Parts 1-3. Technical Report 88-100, Bonneville Power Administration, U.S. Department of Energy, Portland, Oregon. Nez Perce Tribe of Idaho and Idaho Department of Fish and Game. 1990. Clearwater River sub- basin salmon and steelhead production plan. Prepared for Northwest Power Planning Council, Portland, Oregon. Nickelson, T.E., M.F. Solazzi, and S.L. Johnson. 1986. Use of hatchery coho salmon (oncorhynchus kisutch) presmolts to rebuild wild populations in Oregon coastal streams. Canadian Journal of Fisheries and Aquatic Sciences 43(12):2443-2449. NPPC (Northwest Power Planning Council). 1987. Columbia River Basin Fish and Wildlife Program. Portland, Oregon. NPPC (Northwest Power Planning Council). 1994. Columbia River Basin Fish and Wildlife Program. Portland, Oregon.

Northwest Power Planning Council (NPPC). 2000. Columbia River Basin Fish and Wildlife Program. Portland, Oregon. NOAA Fisheries. 2005. Data obtained from NOAA Northwest Regional Office’s website. http://www.nwr.noaa.gov/Salmon-Harvest-Hatcheries/Hatcheries/Mitchell-Act-Programs.cfm NPCC (Northwest Power and Conservation Council). 2009. Columbia River Basin Fish and Wildlife Program 2009 Amendments. Portland, Oregon. www.nwcouncil.org NRC (National Research Council). 2004. Adaptive Management for Water Resources Project Planning Panel on Adaptive Management for Resource Stewardship, Committee to Assess the U.S. Army Corps of Engineers Methods of Analysis and Peer Review for Water Resources Project Planning, National Research Council. ISBN: 0-309-09191-8, 138 pages, 6 Petrosky, C.E., and T.C. Bjornn. 1988. Response of wild rainbows (Salmo gairdineri) and cutthroat trout (S. Clarki) to stocked rainbow trout in fertile and infertile streams. Canadian Journal of Fisheries and Aquatic Sciences 45(12):2087-2105. Petrosky, C. E., and T. B. Holubetz. 1985. Idaho habitat evaluation for off-site mitigation record. Idaho Department of Fish and Game, Annual Report for FY 1984 to U.S. Department of Energy, Bonneville Power Administration, Division of Fish and Wildlife, Portland, Oregon. Contract DE-A179-84BP 13381, Project 83-7. 207 p. Reisenbichler, R.R. 1981. Columbia River salmonid broodstock management – annual progress report (unpublished). National Fishery Research Center, U.S. Fish and Wildlife Service, Seattle, Washington. Reisenbichler, R.R. 1984. Outplanting: potential for harmful genetic change in naturally spawning salmonids. Pages 33-39 in J.M. Walton, and D.B. Houston (eds.). Proceedings of the Soviet- American symposium on aquaculture. National Fisheries Research Center, U.S. Fish and Wildlife Service, Seattle, Washington.

Reisenbichler, R.R. 1988. Relation between distance transferred from natal stream and recovery

198909800 – Idaho Supplementation Studies 30 rate for hatchery coho salmon. North American Journal of Fisheries Management 8:172-174. Reisenbichler, R.R., and J.D. McIntyre. 1986. Requirements for integrating natural and artificial production of anadromous salmonids in the Pacific Northwest. Pages 365-374 in R.H. Stroud (ed.). Fish Culture in Fisheries Management. American Fisheries Society, Bethesda, Maryland. Reisenbichler, R.R., and J.D. McIntyre. 1977. Genetic differences in growth and survival of juvenile hatchery and wild steelhead trout, Salmo gairdneri. Journal of the Fisheries Research Board of Canada 34:123-128. Smith, E.M., B.A. Miller, J.D. Rodgers, and M.A. Buckman. 1985. Outplanting anadromous salmonids – a literature survey. Bonneville Power Administration, U.S. Department of Energy, Project 85-68, Portland, Oregon. Snow, H.E. 1974. Effects of stocking northern pike in Murphy’s Flowage. Wisconsin Department of Natural Resources Technical Bulletin 79, Madison. Steinhorst, K., Y. Wu, B. Dennis, and P. Kline. 2004. Confidence intervals for fish out-migration estimates using stratified trap efficiency methods. Journal of Agricultural, Biological, and Environmental Statistics 9:284-299. Steward, C.R., and T.C. Bjornn. 1990 Supplementation of salmon and steelhead stocks with hatchery fish: a synthesis of published literature. Part 2 in W.H. Miller (ed.). Analysis of salmon and steelhead supplementation, parts 1-3. Project 88-100, Bonneville Power Administration, U.S. Department of Energy, Portland, Oregon.

STWG (Supplementation Technical Work Group). 1988 Supplementation research-proposed five year work plan. Northwest Power Planning Council, Portland, Oregon. Thurow, R. F. 1994. Underwater methods for study of salmonids in the Intermountain West. USDA Forest Service, Intermountain Research Station, Ogden, Utah. General Technical Report INT- GTR-307. 28 p. Verspoor, E. 1988. Reduced genetic variability in first-generation hatchery populations of Atlantic salmon (Salmo salar). Canadian Journal of Fisheries and Aquatic Sciences 45:1686-1690. Vincent, E.R. 1987. Effects of stocking catchable-sized hatchery rainbow trout on two wild trout species in the Madison River and Odell Creek, Montana. North American Journal of Fisheries Management 7:91-105.

198909800 – Idaho Supplementation Studies 31 Appendix A. Specific Snake River Spring/Summer Chinook salmon VSP information collected in by the ISS project 2007-2009 that will continue into this funding cycle.

Viable salmonid population criterion Major population Population Abundance Productivity Spatial structure Diversity group South Fork Salmon South Fork Salmon Multi-pass redd Adult ages Redd distribution Adult ages River counts Juveniles per redd Adult spawn timing Adult escapement (weir Adult to adult Juvenile migration mark/recapture) returns timing

Juvenile migrants Hatchery fraction (trap mark/recapture)

Secesh River/Lake Adult escapement Adult ages Redd distribution Adult ages Creek (video/DIDSON weirs) Juveniles per redd Adult spawn timing

Multi-pass redd Adult to adult Juvenile migration counts returns timing

Juvenile migrant Hatchery fraction estimates

Middle Fork Marsh Creek Multi-pass redd Adult ages Redd distribution Adult ages Salmon River counts Juveniles per redd Adult spawn timing Juvenile migrant estimates Adult to adult Juvenile migration returns timing

Hatchery fraction

Bear Valley/Elk Multi-pass redd Adult ages Redd distribution Adult ages Creek counts Hatchery fraction Parr occurrence Adult spawn timing Parr density

Upper Salmon North Fork Salmon Multi-pass redd Adult ages Redd distribution Adult ages River counts Adult to adult Adult spawn timing returns

Hatchery fraction

Lemhi River Multi-pass redd Adult ages Redd distribution Adult ages counts Juveniles per redd Adult spawn timing Juvenile migrant estimates Adult to adult Juvenile migration returns timing

Hatchery fraction

Pahsimeroi River Multi-pass redd Adult ages Redd distribution Adult ages counts Juveniles per redd Adult spawn timing Adult escapement (weir Adult to adult Juvenile migration mark/recapture) returns timing

Juvenile migrants Hatchery fraction (trap mark/recapture) RRS

198909800 – Idaho Supplementation Studies 32 Viable salmonid population criterion Major population Population Abundance Productivity Spatial structure Diversity group East Fork Salmon Multi-pass redd Adult ages Redd distribution Adult ages counts Juveniles per redd Adult spawn timing Adult escapement (weir Adult to adult Juvenile migration mark/recapture) returns timing

Juvenile migrants Hatchery fraction (trap mark/recapture)

Herd Creek Multi-pass redd Adult ages Redd distribution Adult ages counts Adult to adult Adult spawn timing returns

W. Fork Yankee Multi-pass redd Adult ages Redd distribution Adult ages Fork counts Juveniles per redd Adult spawn timing Juvenile migrants (trap Adult to adult Juvenile migration mark/recapture) returns timing

Hatchery fraction

Valley Creek Multi-pass redd Adult ages Redd distribution Adult ages counts Adult to adult Parr occurrence Adult spawn timing Parr density returns

hatchery fraction

Upper Main Multi-pass redd Adult ages Redd distribution Adult ages Salmon/Alturas counts Lake Creek Juveniles per redd Adult spawn timing Adult escapement (weir Adult to adult mark/recapture) returns

Juvenile migrants Hatchery fraction (trap mark/recapture) RRS

Main stem Salmon Slate Creek Multi-pass redd Adult ages Redd distribution Adult ages River counts Adult to adult Parr occurrence Adult spawn timing Parr density returns

Dry Clearwater Crooked River Multi-pass redd Adult ages Redd distribution Adult ages counts Juveniles per redd Adult spawn timing Adult escapement (Weir Adult to adult mark/recapture) returns

Juvenile migrants Hatchery fraction (trap mark/recapture)

Red River Multi-pass redd Adult ages Redd distribution Adult ages counts Juveniles per redd Adult spawn timing Adult escapement (weir Adult to adult mark/recapture) returns

198909800 – Idaho Supplementation Studies 33 Viable salmonid population criterion Major population Population Abundance Productivity Spatial structure Diversity group Juvenile migrants Hatchery fraction (trap mark/recapture)

American River Multi-pass redd Adult ages Redd distribution Adult ages counts Juveniles per redd Adult spawn timing Juvenile migrants (trap Adult to adult mark/recapture) returns

Hatchery fraction

Wet Clearwater Crooked Fork Multi-pass redd Adult ages Redd distribution Adult ages Creek counts Juveniles per redd Adult spawn timing Adult escapement (weir Adult to adult mark/recapture) returns

Juvenile migrants Hatchery fraction (trap mark/recapture)

Colt Killed Creek Single pass redd Adult ages Redd distribution Adult ages counts Juveniles per redd Juvenile migrants (trap Adult to adult mark/recapture) returns

Hatchery fraction

Clear Creek Multi-pass redd Adult ages Redd distribution Adult ages counts Juveniles per redd Adult spawn timing Adult escapement (weir Adult to adult mark/recapture) returns

Juvenile migrant estimates

Pete King Creek Multi-pass redd Adult ages Redd distribution Adult ages counts Adult to adult Adult spawn timing returns

Squaw Creek Multi-pass redd Adult ages Redd distribution Adult ages counts Adult to adult Adult spawn timing returns

Papoose Creek Multi-pass redd Adult ages Redd distribution Adult ages counts Adult to adult Adult spawn timing returns

198909800 – Idaho Supplementation Studies 34 I. Key personnel by Cooperating Agency

Bill Schrader FTE = 0.33

Bill Schrader is the principal fishery research biologist who supervises the IDFG anadromous natural production research group in Nampa. He has 22 years of experience as a professional fisheries biologist, most of which has been conducting trout population assessments and research for management purposes in Eastern Idaho. He has seven years experience in the Columbia River anadromous arena where he has worked on predator-prey research, upper Salmon River management, and wild steelhead and Chinook salmon research and monitoring. Beyond the publications listed below, he has written over 30 technical fisheries reports.

Education: M.S. Fish and Wildlife Management. Montana State University, 1989. B.S. Biological Sciences (Fish and Wildlife Management Option). Montana State University, 1984.

Employment: 2007-Present. Principal Fishery Research Biologist, IDFG, Nampa, ID. 1993-2007. Senior Fisheries Research Biologist, IDFG, Idaho Falls, ID. 1992-1993. Senior Fisheries Research Biologist, IDFG, Eagle, ID. 1991-1992. Senior Fisheries Research Biologist IDFG, Idaho Falls, ID. 1990-1991. Regional Fisheries Biologist, IDFG, Salmon, ID. 1988-1990. Fishery Biologist, United States Fish and Wildlife Service, Cook, WA.

Selected Publications: Van Kirk, R.W., L. Battle, and W.C. Schrader. 2010. Modeling competition and hybridization between native cutthroat trout and nonnative rainbow and hybrid trout. Journal of Biological Dynamics 4:158-175. Meyer, K.A., D.J. Schill, F.S. Elle, and W.C. Schrader. 2003. A long-term comparison of Yellowstone cutthroat trout abundance and size structure in their historical range in Idaho. North American Journal of Fisheries Management 23:149-162 Schrader, W.C., and M.D. Jones. 2000. Use of radio telemetry to describe movement patterns of adult trout in the Teton River, Idaho. Pages 59-67 in J.H. Eiler, D.J. Alcorn, and M.R. Neuman, editors. Biotelemetry 15: Proceedings of the 15th International Symposium on Biotelemetry. International Society on Biotelemetry, Wageningen, The Netherlands. Schrader, W.C., and C.E. Petrosky. 1994. Idaho habitat/natural production monitoring: Part III. Annual Report 1992 (Project 91-73), Bonneville Power Administration, Portland. Rich, B.A., W.C. Schrader, and C.E. Petrosky. 1993. Idaho habitat and natural production monitoring: Part I. Annual Report 1991 (Project 91-73), Bonneville Power Administration, Portland. Schrader, W.C. 1991. Assessment of potential interactions between catchable rainbow trout and sockeye salmon relative to the federal Endangered Species Act. Position paper submitted to National Marine Fisheries Service. Idaho Department of Fish and Game, Boise. Petersen, J.H., M.G. Mesa, J. Hall-Griswold, W.C. Schrader, G.W. Short, and T.P. Poe. 1990. Magnitude and dynamics of predation on juvenile salmonids in Columbia and Snake River reservoirs. Annual Report 1989 (Project 82-003), Bonneville Power Administration, Portland.

198909800 – Idaho Supplementation Studies 35 David A. Venditti FTE = 1 [email protected]

Montana Sate University. M.S. 1994. Fish and Wildlife Management. South Dakota State University. B.S. 1989. Wildlife and Fisheries Science. Northland College. Biology. August 1985 – April 1987.

Idaho Department of Fish and Game, Senior Fishery Research Biologist, September 2004 - present. I am responsible for coordinating the research activities of the four agencies participating in the Idaho Salmon Supplementation Studies. I am responsible for project long- term planning and integration with other research and management programs in the state. I supervise one permanent and five temporary technicians and oversee project field activities. Idaho Department of Fish and Game, Fishery Research Biologist, August 2000 – August 2002; Senior Fisheries Research Biologist, August 2002 – September 2004. I planned and conducted research to develop and evaluate culture methods to rear Chinook salmon to maturity and evaluate their spawning performance in natal streams. U.S. Geological Survey, Research Fishery Biologist, March 1999 – August 2000. I was responsible for the design and implementation of field and laboratory research to determine the prevalence and severity of gas bubble disease in fishes below Grand Coulee Dam. U.S. Geological Survey, Fishery Biologist, March 1994 – March 1999. Duties involved designing and implementing field research into various aspects of fall Chinook salmon emigration and early life history.

Expertise: Planning, implementing, logistics, and coordination of landscape scale research programs Conducting research on hatchery effectiveness and the behavior, ecology, and reproductive performance of fishes

Major Publications: Copeland, T., and D.A. Venditti. 2009. Contribution of three life history types to smolt production in a Chinook salmon (Oncorhynchus tshawytscha) population. Canadian Journal of Fisheries and Aquatic Sciences 66:1658-1665. Gadomski, D., D.A. Venditti, C. Robinson, J. Beeman, and A.G. Maule. 2004. Distribution and relative abundance of fishes in littoral areas of Chief Joseph Reservoir, Columbia River. Northwest Science 78:48-58. Venditti, D.A., J.M. Kraut, and D.W. Rondorf. 2000. Thermal exposure of wild juvenile fall chinook salmon in Little Goose Reservoir, Snake River . Pages 313-321in J.H. Eiler, D.J Alcorn, and M.R. Neuman (editors). Biotelemetry 15: Proceedings of the 15th International Symposium on Biotelemetry. Juneau, Alaska. International Society on Biotelemetry. Wageningen, The Netherlands. Venditti, D.A., D.W. Rondorf, and J.M. Kraut. 2000. Migratory behavior and forebay delay of radio-tagged juvenile fall chinook salmon in a lower Snake River impoundment. North American Journal of Fisheries Management 20:41-52. Beeman, J.W., D.W. Rondorf, M.E. Tilson, and D.A. Venditti. 1995. A non-lethal measure of smolt satus of juvenile steelhead based on body morphology. Transactions of the American Fisheries Society, 124:764-769.

Professional Development: American Fisheries Society “Certified Fisheries Professional”. April 16, 2002, August 15, 2007. Life Member of the American Fisheries Society. November 2001.

198909800 – Idaho Supplementation Studies 36 Bruce Barnett FTE = 1 Idaho Department of Fish and Game 1414 E. Locust Lane Nampa, ID 83686 208-465-8404 e-mail: [email protected]

EXPERIENCE June 2000 - Current Employer: The Idaho Department of Fish and Game, Nampa Research Center Title: Senior Fisheries Technician

June 1999 - August 1999 Employer: USDA Forest Service, Boise National Forest, Cascade Ranger District Title: Fisheries Technician

May 1998 – August 1998 Employer: Boise State University, Boise, Idaho Title: Research Assistant

May 1996 – August 1997, seasonal Title: Research Assistant Employer: Boise State University

EDUCATION Boise State University, Boise, ID Bachelor’s of Science in Biology, May 2000, Emphasis in Zoology

HONORS AND ACTIVITIES Member of Sigma Xi, The Scientific Research Society, and the American Fisheries Society. I served a term as president of Societas biophilia in 1997. Distinguished academic graduate and squad leadership award, Primary Leadership Development Course, US Army. Four Army Achievement Medals, One Good Conduct Medal.

198909800 – Idaho Supplementation Studies 37 Kimberly A. Apperson FTE = 0.5

Kim Apperson is a Regional Anadromous Fisheries Biologist with Idaho Department of Fish and Game, stationed in McCall. Kim has 22 years experience as a professional fisheries biologist, working in both research and management realms. For the past 17 years she has participated as a cooperator on several anadromous research projects, including Idaho Supplementation Studies, Idaho Natural Production Monitoring and Evaluation Program, and Idaho Steelhead Monitoring and Evaluation Studies. She is also responsible for the monitoring program on the annual sport Chinook salmon fishery on the South Fork Salmon River. Kim was a primary contributor to the development of the Draft Salmon Subbasin Summary (2001) prepared for the Northwest Power Planning Council.

Education: M.S. Zoology, University of Idaho, Moscow, 1987. B.A. Biology, minor in Geology, California State University, Fresno, 1980.

Employment: 1993-present: Regional Anadromous Fisheries Biologist, Idaho Department of Fish and Game, McCall. 1987-1993: Senior Fisheries Research Biologist, Idaho Department of Fish and Game, Coeur d’Alene. 1987-1987: Senior Fisheries Technician, Idaho Department of Fish and Game, Salmon. 1984-1987: Instructional Assistant, University of Idaho, Moscow. 1983-1984: Fishery Biologist, private consultant.

Selected Publications: Venditti, D.A., A. Kohler, K.A. Apperson, A. Brimmer, B. Bowersox, C. Bretz, and J. Lockhart. 2008. Idaho supplementation studies brood year 2005 cooperative report. Annual progress report to Bonneville Power Administration. Project numbers 1989-098-00, 1989-098-01, 1989-098-02, and 1989-098-03. Portland Oregon. (co-author on all previous annual progress reports for the above project)

Copeland, T., J. Johnson, K. Apperson, J. Flinders, and R. Hand. 2009. Idaho natural production monitoring and evaluation, 2008 annual report. Idaho Department of Fish and Game Report 09-06. Prepared for U.S. Department of Energy, Bonneville Power Administration, Division of Fish and Wildlife. Project 1991-073-00. Portland, Oregon.

Apperson, K.A. Summer Chinook salmon sport fisheries on the South Fork Salmon River, Idaho, 2000, 2001, and 2002. Idaho Department of Fish and Game. Report Number 03- 25. (author or co-author on all other reports on this annual activity)

Rieman, B.E., and K. A. Apperson. 1989. Westslope cutthroat trout synopsis and analysis of fishery information. Project F-73-R-11, Subproject II, Study I, Job I. Idaho Department of Fish and Game, Boise.

Apperson, K.A. M. Mahan, and W.D. Horton. 1988. North Idaho streams fishery research. Study completion report, Project F-73-R-10, Subproject IV, Study IV, Jobs 1-3. Idaho Department of Fish and Game, Boise.

198909800 – Idaho Supplementation Studies 38 Brett Bowersox (208)553-8297 FTE = 0.5 3316 16th St, Lewiston, ID 83501 [email protected]

Professional Experience

Idaho Department of Fish and Game, Lewiston, ID October 2006 - Present

Regional Fishery Biologist Responsibilities:  Oversee regional ISS responsibilities on the South Fork Clearwater River  Oversee Potlatch River Steelhead Monitoring and Evaluation Project

Oregon Department of Fish and Wildlife, Lakeview, OR January 2005 – October 2006

Assistant District Fish Biologist Responsibilities:  Coordinated multi-million dollar fish passage project on Chewaucan River, OR  Conducted and assisted on a variety of endemic fish species monitoring and research  Monitored, set regulations and stocking rates for regional fisheries  Worked cooperatively with local landowners and other agency personnel on fish habitat, fish passage and fish screening projects

Idaho Department of Fish and Game, Lewiston, ID March 2004 – January 2005

Senior Fisheries Technician Responsibilities:  Provided field support and logistical planning for regional ISS and NPM projects  Conducted population monitoring on Potlatch River, ID  Wrote final report for Potlatch River steelhead assessment

Education

University of Idaho, Moscow, ID M.S. Fishery Resources May 2004

Calvin College, Grand Rapids, MI B.S. Biology May 2000

198909800 – Idaho Supplementation Studies 39 Jon Flinders FTE = 0.5

Jon Flinders is regional fishery biologist who oversees the Idaho Steelhead Monitoring and Evaluation and Idaho Supplementation (ISS) studies in the Salmon region. He has been a biologist with IDFG for approximately a year. Prior to working for IDFG he was pursuing a Ph.D. in fisheries at the University of Arkansas (UA). His research at the UA was examining the effectiveness of trout catch-and-release regulations in tailwaters using a bioenergetics modeling and stable isotope analysis approach. He also has experience as a regional fishery biologist with Arizona Game and Fish Department where he worked on the Colorado River system on native (e.g. razorback sucker, bonytail chub) and sportfish (e.g. flathead catfish, largemouth bass) species.

Education: Ph.D. Biological Sciences. University of Arkansas, expected completion 2010. M.S. Wildlife and Fisheries Science. University of Arizona, 2003. B.S. Fisheries and Wildlife Biology. Utah State University, 2000.

Employment: 2009-Present. Regional Fishery Biologist, Idaho Department of Fish and Game, Salmon, ID. 2004-2008. Graduate Research Assistant, University of Arkansas, Fayetteville, AR. 2003-2004. Regional Fisheries Biologist, Arizona Game and Fish Department, Yuma, AZ. 2001-2002. Graduate Research Assistant, University of Arizona, Tucson, AZ.

Selected Publications: Flinders, J.M. and S.A. Bonar. 2008. Growth, condition, diet, and consumption rates of northern pike in three Arizona reservoirs. Lakes and Reservoir Management 24:99-111.

Flinders, J.M. 2004. Alamo Lake, Status of the Largemouth Bass Fishery 1998-2004. Fisheries Technical Report 03-02. Statewide Fisheries Investigations, Federal Aid Project F-7-M-45. Arizona Game and Fish Department, Phoenix, Arizona.

Flinders, J.M. 2004. Colorado River Imperial Division Fish Management Report 2000-2004. Fisheries Technical Report 03-03. Statewide Fisheries Investigations, Federal Aid Project F-7-M-45. Arizona Game and Fish Department, Phoenix, Arizona.

Flinders, J.M. 2003. Lake Havasu fish management report 2000-2002. Fisheries Technical Report 02-01. Statewide Fisheries Investigations, Federal Aid Project F-7-M-45. Arizona Game and Fish Department, Phoenix, Arizona.

Flinders, J.M. 2003. Palo Verde Division fish management report 1997-2002. Fisheries Technical Report 02-02. Statewide Fisheries Investigations, Federal Aid Project F-7-M- 45. Arizona Game and Fish Department, Phoenix, Arizona.

Flinders, J.M. 2003. Cibola Division fish management report 1997-2002. Fisheries Technical Report 02-03. Statewide Fisheries Investigations, Federal Aid Project F-7-M-45. Arizona Game and Fish Department, Phoenix, Arizona.

Bonar, S.A., J.M. Flinders, W.J. Matter, and E.G. Maughan. 2002. Factors associated with razorback sucker recruitment in a small Arizona pond. Arizona Cooperative Fish and Wildlife Research Unit, Fisheries Research Report 01-02.

198909800 – Idaho Supplementation Studies 40 Shoshone-Bannock Tribes:

Project Leader: Doug Taki FTE = 0.5

Education: Bachelor of Science: Idaho State University Major in Biology- Fish Ecology focus.

Employment Background: Shoshone-Bannock Tribes July 1993 - present Mr. Taki is responsible for every aspect of the Shoshone-Bannock Tribes (SBT) Snake River sockeye research project and for ensuring that all contractual obligations are met. He is the direct liaison between Tribal government and the IDFG, NMFS, BPA, IDEQ, and the USFS for all sockeye related management or research related issues. He represents the SBT on the Stanley Basin Technical Oversight Committee and Anadromous Fish Managers forum and shares responsibility on the Fish Passage Advisory Committee.

Mr. Taki supervises one biologist, four full-time and one temporary technician, oversees several sub-contractors, and coordinates field work with the IDFG whenever there is a need for help by either agency.

StreamNet Steering Committee Shoshone-Bannock Tribes October 1996 - 1999 Mr. Taki’s duties included evaluating proposed changes to our website, coordination of data transfers, integration of genetic data between researchers and StreamNet, and assisting others when needed.

Resident Fisheries Manager Shoshone-Bannock Tribes November 1991 - July 1993 Mr. Taki was responsible for managing the fisheries resources on the 544,000 acre Fort Hall Indian Reservation.

Expertise: 1) Techniques and methodologies for evaluating stream and riparian habitats, 2) Techniques and methodologies for evaluating lentic habitats, 3) experience with equipment necessary to sample fish (e.g. screw traps, weir operations, gill nets, electrofishers, etc.) and subsequent evaluations, 4) All phases of using PIT tags for evaluating migration of anadromous fish, 5) All phases of conducting and analyzing hydroacoustic surveys, 6) SCUBA certified

Publications: Flagg, T.A., C.W. McAuley, P.K. Kline, M.S. Powell, D. Taki, J.C. Gislason. 2004. Application of captive broodstocks to preservation of ESA-listed stocks of Pacific Salmon: Redfish Lake sockeye salmon case example. Pages 387-400 in Nickum, M., P. Mazik, J. Nickum, and D. MacKinlay, editors. Propagated fish in resource management. American Fisheries Society Symposium 44, American Fisheries Society, Bethesda, Maryland. Griswold, R.G., D. Taki, and J. G. Stockner. 2003. Redfish Lake sockeye salmon: nutrient supplementation as a means of restoration in J. G. Stockner, editor. Nutrients in Salmonid Ecosystems: sustaining production and biodiversity. American Fisheries Society, Symposium 34, Bethesda, Maryland. Hebdon, J.L., P. Kline, D.Taki, and T.A. Flagg. 2004. Evaluating reintroduction strategies for Redfish Lake sockeye salmon captive broodstock progeny. Pages 401-413 400 in Nickum, M., P. Mazik, J. Nickum, and D. MacKinlay, editors. Propagated fish in resource management. American Fisheries Society Symposium 44, American Fisheries Society, Bethesda, Maryland.

198909800 – Idaho Supplementation Studies 41 Project Biologist: Andy Kohler FTE = 1

EDUCATION: Masters of Science: Washington State University Bachelors of Science: Lewis and Clark College, Portland, OR 97219-7899, November 93 Major in Biology- Ecology focus.

Employment Background: Research Biologist April 2001 - present SHOSHONE-BANNOCK TRIBES FORT HALL, ID 83203 Duties: Collect, compile, and analyze data for all aspects of the sockeye and ISS projects. Includes report writing, dissemination of data, and field supervision of co-workers.

Regional Habitat Biologist, Salmon and Steelhead Habitat Inventory and Assessment Program- Northwest Indian Fisheries Commission, Jan. 2000 – April 2001. Duties: Collect, analyze, and compile aquatic resource data regarding fish distribution and utilization, stream habitat type, fish passage barriers, water quality, hydromodifications, and riparian corridor assessments for the Salmon and Steelhead Habitat Inventory and Assessment Program (SSHIAP). These data are then integrated into an Access database and linked to an ArcView GIS platform for spatial analysis at the watershed scale. Additional duties include consultation with tribal and federal resource managers to provide SSHIAP data for limiting factors analysis and fish productivity modeling efforts being undertaken by the Washington Conservation Commission and the National Marine Fisheries Service. Other duties include developing analysis tools and analyzing data using GIS and remote sensing techniques, developing and employing SSHIAP methodologies, and coordinating activities with co- managers and other resource management entities.

Biologist III- Johnson Controls World Services, Inc. January 1999 – April 2000. Duties: Conducted ecological research and monitoring in the Klamath River Basin for the USGS Biological Resources Division, Klamath Falls Duty Station. Working as a contract biologist for the USGS Biological Resources Division in Klamath Falls, OR, I was involved in planning, designing, and implementing aquatic surveys and research examining the effects of long-term operation of the Klamath Project on the endangered Lost River and shortnose sucker. In cooperation with the Bureau of Reclamation, I helped conduct water quality, fish habitat, and fish population investigations in Upper Klamath Lake and the Lost River sub-basin. Specific duties included Lost River sub-basin water quality assessments, Lost River sub-basin fish community investigations, investigation of Juvenile sucker/micro habitat associations, Lost River sub-basin macroinvertebrate biomonitoring, Lost River and shortnose sucker spawning surveys, and sucker spawning habitat assessments. At the duty station I was a field supervisor for a crew of 6 biologists and was in charge of scheduling and field operations. When not in the field, my time was spent analyzing data and preparing reports for the Klamath Falls USGS BRD duty station.

198909800 – Idaho Supplementation Studies 42 Nez Perce Tribe:

Jay Hesse

Education  Master of Science degree in Fisheries. Michigan State University, 1994.  Bachelor of Science degree in Fisheries and Wildlife. Michigan State University, 1992.

Current Employment Director of Biological Services (Research Division). Nez Perce Tribe, Department of Fisheries Resources Management. June 2004 – present.  Research Division management: technical and procedure supervision/support of project leaders associated with 15 research projects with focus on population status assessment, hatchery effectiveness evaluations, and conservation throughout the Snake River basin.  Department management: participation in fisheries management team activity coordination across all five divisions of the Department of Fisheries Resources Management; development and implementation of long-term Strategic Management Plan; and incorporation of technical data into management decisions and policy recommendations.  Regional management: technical and management representation of Nez Perce Tribe in multiple Columbia River basin fisheries co-management forums including the Northwest Power and Conservation Council Fish and Wildlife Program project reviews, Recovery Implementation Science Team, U.S. vs Oregon, Columbia Basin Fish and Wildlife Authority, Snake River fall Chinook coordination meetings, Ad Hoc Supplementation Work Group; routine coordination and collaboration with state, tribal, and federal co-managers.

Past Employment  Fisheries Research Coordinator. Nez Perce Tribe, Department of Fisheries Resources Management. October 1997 – June 2004.  Fisheries Research Biologist - Project Leader. Nez Perce Tribe, Department of Fisheries Resources Management. July 1994 - October 1997.

Expertise Expertise in anadromous fish population dynamics, hatchery effectiveness research, strategic planning, effective communications and multi-entity collaboration.

Relevant Recent Reports Beasley C.A, B.A. Berejikian, R.W. Carmichael, D.E. Fast, M.J. Ford, P.F. Galbreath, J.A. Hesse, L.L. McDonald, A.R. Murdoch, C.M. Peven, and D.A. Venditti). 2008. Recommendations for Broad Scale Monitoring to Evaluate the Effects of Hatchery Supplementation on the Fitness of Natural Salmon and Steelhead Populations. Final Report of the Ad Hoc Supplementation Monitoring and Evaluation Workgroup (AHSWG). 82 pgs.

RIST (Recovery Implementation Science Team; G. M. Brown, Jr, C. Busack, R. Carmichael, T. Cooney, K. Currens, M. Ford, G. Helfman, University of Georgia, J. Hesse, P. Lawson, M. McClure, P. McElhany, G. Reeves, B. Rieman, M. Ruckelshaus, B. Thompson). 2009. Hatchery Reform Science; A review of some applications of science to hatchery reform issues. 93 pgs.

198909800 – Idaho Supplementation Studies 43 Scott Everett FTE = 1

Education  Master of Science degree in Fisheries Resources. University of Idaho, 1995.  Bachelor of Science degree in Fisheries Management. University of Idaho, 1999.

Current Employment Project Leader (Research Division). Nez Perce Tribe, Department of Fisheries Resources Management. January 2010 – present.

Project implementation, management and coordination, budget preparation and management, contract and subcontract preparation and management, report writing, personnel supervision, technical representative in meetings with regional co-managers, research agencies and private consultants, data analysis, computer modeling, public speaking and presentations, and proposal development.

Past Employment  Fisheries Production Biologist – Hatchery Supervisor. Nez Perce Tribe, Department of Fisheries Resources Management. January 2007 – January 2010.  Fisheries Research and Production Biologist – Project Leader. Nez Perce Tribe, Department of Fisheries Resources Management. October 2000 – January 2007.  Fisheries Research Biologist – Assistant Project Leader. Nez Perce Tribe, Department of Fisheries Resources Management. May 1997 – October 2000.

Expertise Anadromous fish population dynamics, hatchery management and effectiveness research, strategic plan development and multi-agency collaboration.

Reports Beasley, C.A., S.R. Everett, C. Davenport, and R.L. Johnson. 2004. Coho Salmon Master Plan, Clearwater River Basin. Report submitted to the Bonneville Power Administration. P.O. Box 365, Lapwai, ID 83540.

Everett, S.R. and J.A. Hesse. 2005. Nez Perce Tribe White Sturgeon Management Plan in the Snake River Between Lower Granite and Hells Canyon Dams. Report submitted to the Bonneville Power Administration. P.O. Box 365, Lapwai, ID 83540.

198909800 – Idaho Supplementation Studies 44 Wesley Keller FTE = 1 Nez Perce Tribe, Department of Fisheries Resources Management P. O. Box 1942, 125 South Mission McCall, Idaho 83638 Telephone: 208-634-5290 FAX: 208-634-4097 email: [email protected]

EDUCATION: University of West Florida, Pensacola, FL. Major: MS in Biology 2004

Bermuda Biological Station for Research, Bermuda. Summer Semester on Tropical Marine Invertebrates 2003

Hanover College, Hanover, IN. Major: BS in Biology May 1995

PROFESSIONAL EXPERIENCE: 2005-Present: Nez Perce Tribe, Biologist II in conjunction with the Idaho Supplementation Studies

2002-2005: Department of Environmental Protection: Pensacola, Fl. Water quality data collection. Aquatic insect taxonomy.

2000-2002: University of West Florida. Destin, FL. Beach erosion study, environmental impact of porous groynes on benthic macroinvertebrates and fish populations

1999: Army Corps of Engineers. McNary Dam. Umatilla, OR Fishery Technician.

1998: Army Corps of Engineers. Lower Granite Dam. Pomeroy, WA. Fishery Technician.

1996: SaltWater Inc., Anchorage, AK. Biological Observer on Alaskan fishing vessels collecting fishery data for National Marine Fisheries.

PUBLICATIONS: Keller, W.J. 2004. Local effect of porous groynes on marine macroinvertebrates. Masters Thesis, 2004. University of West Florida. Keller, W., and C.Pomory. 2008. Effects of Porous Mesh Groynes on Macroinvertebrates of a Sandy Beach, Santa Rosa Island, Florida, U.S.A. Gulf of Mexico Science (1) pp.36-45.

198909800 – Idaho Supplementation Studies 45 Ryan Kinzer FTE = 1

Nez Perce Tribe, Department of Fisheries Resources Management P. O. Box 1942, 125 South Mission McCall, Idaho 83638 Telephone: 208-634-5290 FAX: 208-634-4097 email: [email protected]

Education: University of Idaho, Moscow, ID. Major: BS in Wildlife Resources, 2001

Professional Experience: 2003-Present: Nez Perce Tribe, Biologist with Idaho Supplementation Studies 2001-2003: Nez Perce Tribe, Fisheries Technician with Idaho Supplementation Studies 1998-2000: Idaho Fish and Game, Bio-aid with the McCall Fish Hatchery

198909800 – Idaho Supplementation Studies 46 U.S. Fish and Wildlife Service:

Carrie B. Bretz FTE = 0.5 U.S. Fish and Wildlife Service PO Box 18 Ahsahka, ID 83520 (208) 476.7242 FAX (208) 476.7228

EDUCATION Master of Science: Appalachian State University 2002 Major: Biology

Bachelor of Science: Kennesaw State University 1997 Major: Biology Minor: Anthropology

EXPERIENCE Fishery Biologist 2003-Present U.S. Fish and Wildlife Service Ahsahka, ID Principle investigator for the Tucannon River Antenna Project. Duties include: (1) leading field crews and coordinating field activities related to PIT tagging juvenile and sub adult bull trout in the Tucannon River basin, (2) downloading, analyzing and reporting data collected from streamwidth passive integrated transponder tag antennas. Field biologist for the Tucannon River Radio Telemetry Project. Duties include: (1) leading field crews in hook and line sampling for bull trout, (2) performing radio tag insertion surgery on adult and sub adult bull trout, (3) tracking bull trout using radio telemetry equipment.

Interim project leader for the Idaho Supplementation Studies. Lead field crews in redd surveys, carcass recovery, juvenile collection using screwtraps and hook and line sampling. Analyze data using PTAGIS and SURPH software and summarize results in annual reports.

PIT tag coordinator for the Idaho Fishery Resource Office (IFRO). Coordinate the tagging of summer steelhead and spring Chinook smolts for research projects originating from the IFRO.

I have extensive knowledge of PIT tagging techniques, equipment and the PTAGIS database. Provide a cumulative report of PIT tagging activities and smolt survival to Snake and Columbia river hydropower facilities for inclusion into annual reports.

Biological Science Technician 2002 U.S. Forest Service Nebo, NC Conducted surveys of resident and migratory birds populations in Linville Gorge Wilderness Area using visual and auditory identification. Designed sampling protocol to investigate the effects of wildfire on vegetation. Completed statistical analysis of habitat usage by resident and migratory birds.

198909800 – Idaho Supplementation Studies 47 J. Environmental Compliance & Permitting

All program cooperators work closely with BPA COTRs and Environmental Compliance personnel and other State and Federal agencies to assure timely completion of these tasks. IDFG permitting and reporting of take of juvenile and adult Chinook salmon and steelhead are coordinated through the NOAA Fisheries 4(d) online system and include: IDFG – Permit 14706 (pending for 2010) SBT – Permit USFWS – Permit

Nez Perce Tribe take of Chinook salmon and steelhead is covered under NOAA Fisheries Section 10 Permit 1134

IDFG trapping of sockeye salmon in the upper Salmon River are covered under NOAA Fisheries Section 10 Permit 1454.

Permitting and reporting of IDFG take of listed resident species is coordinated with the U.S. Fish and Wildlife Service through an existing ESA Section 6 permit.

Permitting and reporting of NPT take of listed resident species is coordinated with the U.S. Fish and Wildlife Service through permit TE001598-3.

As necessary, Special Use Permits from the U.S. Forest Service have been acquired to operate juvenile screw traps and temporary adult fish weirs on Forest Service land. These permits are identified below: IDFG Crooked Fork Creek screw trap and weir and Colt Killed Creek screw trap authorization ID POW82. This permit expires in 2017. IDFG Marsh Creek Authorization ID YFK36. This permit expires 2023. IDFG South Fork Salmon River at Knox Bridge Holder No. 1001-18. This permit is currently being renewed. IDFG Red, Crooked, and American rivers Authorization No. ELK3. This permit expires in 2016.

198909800 – Idaho Supplementation Studies 48

Load more

  48

Copy Link