The response was very thorough and well organized. Each issue raised in the previous ISRP review was explicitly addressed. The additional information on previous studies that have been conducted as part of the effort to restore the focal fish species in Lake Pend Oreille was especially helpful in clarifying the questions raised by the ISRP in the previous review.

The ISRP agrees that working in this large natural lake poses many difficult challenges, but the responses indicate that IDFG is making a good faith effort to incorporate the latest information into their studies and have enlisted the help of very qualified specialists. The ISRP appreciates that additional details about the results of previous investigations have been incorporated into the proposal. Links to annual reports and other reports summarizing data are useful, but they do add to the difficulty of assessing scientific merit when a link must be followed. Where possible, concise summaries of main findings, in addition to the links, are very much appreciated and make the review process more efficient. We also appreciate that the field methods pertaining to this study in Monitoringmethods.org have been reclassified so that details are now accessible.

Overall, the ISRP is satisfied that this project will continue to generate useful data on the management of Lake Pend Oreille and its fisheries, and are confident that the sponsors have thought carefully about addressing these issues in this complex lentic ecosystem.

ISRP Retrospective Evaluation of Results

The Lake Pend Oreille Kokanee Mitigation project is a good example of a study where project staff has done an excellent job of seeking outside assistance in tackling a very tough scientific problem. While the project title suggests that it focuses on kokanee, it is clear that the project's scope has broadened to other fishes as well as the limnological dynamics of the Pend Oreille ecosystem itself. This project is almost 20 years old, and a publication summarizing what has been learned over the last two decades would be a valuable contribution, as well as useful in informing fishery managers in other large lake systems.

The Lake Pend Oreille fishery has received a lot of attention because it focuses on the historically large non-native kokanee population, which is in decline although apparently recovering slowly, as well as a trophy rainbow and bull trout fishery, which is also depressed. Many restoration actions are occurring simultaneously, and it will be difficult to determine the efficacy of individual program elements on both the harvest and conservation objectives. Nevertheless, this project has contributed valuable information on the ecosystem processes supporting the lake's salmonid populations over the last decade, and it is likely to provide useful data in the future.

The ISRP requests clarification on several points before providing a final recommendation.

1. What is the likely role of lake whitefish in reducing abundance of Mysis?
2. Additional justification is requested for adding spawning gravel to select shorelines to increase kokanee spawning.
3. A summary of what has been learned over the past 15 years of management actions in the context of the overall objective of increasing harvest is needed.
4. What has been learned from Lake Pend Oreille research that has helped IDFG balance conservation and harvest objectives?
5. What are likely reasons why rainbow trout have increased in abundance by 50% from 2009 to 2010?
6. Other questions and concern are embedded in the comments provided below. The ISRP suggests the sponsors examine these items as a response is prepared.

Apart from specific questions, the ISRP feels the restoration of native resident bull trout and westslope cutthroat trout in Lake Pend Oreille deserves additional attention. This proposal devotes little attention to these species, even though other proposals in the region do. For example, there may be adfluvial populations of cutthroat trout that could or do provide important sport fisheries, and management could consider restoration actions in Lake Pend Oreille’s tributary habitats. Ongoing lake trout suppression would also benefit these other native species, but increased kokanee production would not likely benefit whitefish or most cutthroat trout

See the ISRP’s programmatic comments on fish stocking.

1. Purpose: Significance to Regional Programs, Technical Background, and Objectives

This project has been in place for a long time, and the plan of work was reviewed by the ISRP in 2006, when it was given a favorable assessment. It is important to note that Lake Pend Oreille represents a large natural lake with a highly altered fish community. Of the three primary focal species, two are not native (kokanee and Gerrard stock rainbow trout) and the third (bull trout) is primarily of interest from a conservation standpoint, not a harvest standpoint. Additionally, the food web in Lake Pend Oreille has been strongly affected by the invasion of a non-native zooplankton (Mysis diluviana), which has acted as a competitor with kokanee and also helped to fuel the expansion of the non-native lake trout population, a significant predator on mysids as well as kokanee and juveniles of other salmonid species. As with many large lakes with increasing human development in the watershed, management challenges in Lake Pend Oreille are complex.

The project sponsors have done a good job of describing the relationship of this project to other regional resident fish management efforts, and their description of the technical background was also well done.

The proposal makes clear that recovery of the Pend Oreille fishery is the project's primary goal. Conservation of the two native salmonid species, bull trout and westslope cutthroat trout, is acknowledged in the work, but the primary emphasis is either research that addresses factors limiting kokanee and trophy trout recovery or habitat improvements that benefit kokanee reproductive success, such as addition of spawning gravel. Reduction of the lake's population of lake trout, generally viewed as a negative influence in the Pend Oreille ecosystem, also figures prominently in the work.

As mentioned above, management challenges are complex and restoring a desired balance of species, that is a balance that favors angler harvest of kokanee and trophy trout, will require that a number of potential limiting factors be addressed simultaneously. This will essentially mean a trial and error approach, and that is what IDFW have been doing for the last 15 years. A strong monitoring program will be essential for detecting the signal of programs such as lake trout reduction, winter lake level manipulation, kokanee stocking adjustments, and possible nutrient additions.

The role of lake whitefish in reducing abundance of Mysis is mentioned once but is not addressed again. Could this be important?

The objective to increase kokanee spawning success by adding spawning gravel to select shorelines needs additional scientific justification. When gravel is added in streams or lakes without addressing the hydrogeomorphic factors that create clean spawning gravel, for example upwelling and wave action, the usual result is that the gravel simply becomes unsuitable, requiring either more gravel or manual cleaning, all at great expense. Additionally, we wonder whether studies of kokanee egg survival in the laboratory and in boxes buried in lake substrate will answer the question of interest: what conditions are necessary for high survival, and how does survival vary with sediment deposition? It is clear that survival should be low when sediment is high, but at moderate levels of sediment, it is not clear whether human-placed egg boxes or eggs monitored in the laboratory will mimic those from egg pockets placed by female fish sufficiently to generate useful data. 

2. History: Accomplishments, Results, and Adaptive Management (ISRP Review of Results)

The proposal does a good job of summarizing the administrative accomplishments of the project. More details could have been given on results to date. A single graph was presented showing lake trout abundance from 1999 to 2008 but with only 5 years sampling data, while it would have been helpful to have seen similar summaries as graphs or tabular data for the other salmonid species. Over the last 15 years a variety of management actions have been implemented such as lake trout netting, experimental winter drawdowns, hatchery operations, and angler programs. A summary of what has been learned from these actions in the context of the overall objective of increasing harvest is needed. It does appear that predator control has had some success, but what about other efforts? Also, there was little mention of warm-water fishes. Have these introduced fishes had negligible impact on focal species in other areas of the lake?

More information is also needed on how the results of the Lake Pend Oreille research have been incorporated into management changes. In particular, the potential for conflict between conservation and harvest objectives needs additional clarification. What has been learned from the research that has helped IDFG balance these two important objectives?

Other questions on accomplishments include:

Why have rainbow trout increased in abundance by 50% from 2009 to 2010? Is this difference significant, or are the confidence intervals around these estimates wide? If the difference is real, and not owing to high variability, then what is the explanation – high recruitment rates of small fish?

Lake trout marking – lake trout are reported as being marked in 2011 to estimate abundance by mark-recapture, but in the rest of the proposal all the lake trout were removed. When and where were these lake trout marked, how many, and of what sizes?

Management changes have focused on better targeting lake trout removal efforts in response to new data, and thereby reducing bull trout bycatch. The project sponsors acknowledge pressure from kokanee and rainbow trout anglers to increase abundance of these fishes and expand the fisheries, but how has this pressure driven management decisions as opposed to a focus on conservation and restoration of resident native fishes?

ISRP Retrospective Evaluation of Results

It is clear that the food web dynamics in the lake are changing, but it also seems clear that the primary focal species have not returned to a level of abundance that support harvest objectives. There is no question that the studies proposed here will help address some of the most important problems; however, the proposal itself did not supply very many details about the results of previous management experiments, with the possible exception of the lake trout netting program. Sorting out the benefits of the various initiatives including predator control, habitat improvements, hatchery releases, and nutrient manipulations will be very difficult when they are all happening at the same time and will require very creative field experiments and analyses.

3. Project Relationships, Emerging Limiting Factors, and Tailored Questions for Type of Work (hatchery, RME, tagging)

Because this project has a long history and Lake Pend Oreille has been intensively studied, the suite of potentially limiting factors has been adequately characterized. The project also seems to be well integrated into other work taking place in the Pend Oreille watershed.

The questions being asked specific to kokanee restoration seem appropriate, for example, where do lake trout spawn and at what locations in their daily or seasonal movements will they be particularly vulnerable to capture? Additional work is needed on understanding the role of winter drawdown in regulating kokanee reproductive success, whether physical addition of gravel along shoreline spawning areas can be cost-effective, and whether deliberate nutrient supplementation can achieve desired food web benefits. Fortunately, the proposal contains elements that address these matters.

The proposal did not supply much detail regarding how salmonid releases from hatcheries would be carried out to maximize learning opportunities nor did it give many details about existing or planned monitoring efforts except for the acoustic tracking work on lake trout, which was adequately covered. It was also unclear how project staffs are exchanging information with other RME practitioners in the region, although the explicit call for an annual science review meeting to discuss results is an excellent idea.

4. Deliverables, Work Elements, Metrics, and Methods

The ISRP had several questions relative to project deliverables:

The proposal did not specify metrics and indicators in very much detail for some of the deliverables. Often the metrics were described in general terms, but not in a way that particular measurement protocols could be identified or assumed. Many of the protocols and methods in MonitoringMethods.org were in draft form and did not contain sufficient detail for scientific review.

The proposal also lacked information on what would be considered reference conditions for some of the deliverables. For example, if gravel is added to a kokanee spawning area, what would the reference condition be, pre-gravel enhancement egg survival or egg survival in an adjacent spawning area without gravel addition?

Can annual exploitation rates be accurately determined if only 30 lake trout are tagged with acoustic tags per year?

We were unsure why a gear efficiency study is necessary. Would it be more cost effective to buy a bigger boat and trawl and simply increase efficiency this way?

The ISRP provided a variety of comments on this proposal and we want to start by explaining our approach to responding.  Responses were specifically requested for five issues and we did this.  However, it also was requested that comments and questions embedded throughout the document be considered.  Thus, we responded to these to assure that ISRP had adequate information to evaluate the proposal.  There was a fair bit of repetitiveness in the ISRP comments and questions throughout the document.  We did our best to avoid repetition in our responses, but some may exist.  We included our responses directly below each series of ISRP comments so it was clear what questions we were addressing.  Also, hyperlinks for all citations provided in our responses can be found in the proposal.

ISRP Comments:

The Lake Pend Oreille fishery has received a lot of attention because it focuses on the historically large non-native kokanee population, which is in decline although apparently recovering slowly, as well as a trophy rainbow and bull trout fishery, which is also depressed. Many restoration actions are occurring simultaneously, and it will be difficult to determine the efficacy of individual program elements on both the harvest and conservation objectives. Nevertheless, this project has contributed valuable information on the ecosystem processes supporting the lake's salmonid populations over the last decade, and it is likely to provide useful data in the future.

The ISRP requests clarification on several points before providing a final recommendation.

1. What is the likely role of lake whitefish in reducing abundance of Mysis?

RESPONSE: Lake whitefish biomass is higher than for any other species in Lake Pend Oreille, yet it does not appear that lake whitefish effectively regulate mysids in Lake Pend Oreille.  While lake whitefish do consume mysids (IDFG unpublished data), mysid densities are high relative to other lakes and have remained stable since reaching initial highs in the 1980’s following establishment (Wahl et al. 2011).  The lake whitefish population in Lake Pend Oreille (introduced in late-1800’s) is characterized by low natural mortality, slow growth, and late maturity (Hosack 2007).  Population parameters would likely be different (e.g., faster growth) if mysids represented a larger diet component.  ISRP commented that mysid reduction by lake whitefish was mentioned by us in the proposal; however, this was only a reference to an objective in the Pend Oreille Subbbasin Plan.  The lake whitefish portion of this subbasin plan objective has not been advanced for funding.  This has not been a priority given that the best available data show no indication that lake whitefish effectively regulate mysid abundance.

2. Additional justification is requested for adding spawning gravel to select shorelines to increase kokanee spawning.

RESPONSE: Winter lake level manipulations have been the management action chosen to address spawning habitat limitations for kokanee.  However, a raised winter lake level to benefit kokanee places demands on the hydrosystem.  Alternative approaches, such as gravel addition and cleaning sediments from gravels below the minimum winter elevation, have been suggested by Bonneville.  In the past, we have not evaluated these approaches because we believed the existing strategy had more potential to meet recovery goals.  We thought the scale at which gravel would need to be added to the lake would be prohibitive, and we questioned how long added gravels or cleaned gravels would remain usable to kokanee.  In recent years, demands on the hydrosystem have increased and providing a raised winter lake level has become increasingly costly and difficult.  Recognizing these constraints, we have given more thought to gravel additions.  It still may be unrealistic for gravel additions to completely replace the need for a raised winter lake level in years of high kokanee density, but we propose to evaluate whether it has potential to increase the threshold spawner density at which a higher winter elevation is needed.  In practice, this would allow a higher winter lake level to be requested less frequently.  In ordinary circumstances a habitat manipulation of this scale may be cost prohibitive, but Bonneville incurs considerable revenue losses by holding the lake higher.  This could make creation of spawning habitat a cost-effective action.  During the last year, we have had discussions with Bonneville about evaluating spawning gravel addition and inclusion of this work in our proposal was encouraged.

One of the justifications for initiating a recent kokanee spawning ecology graduate project was to learn more about substrate conditions that kokanee require for successful spawning and egg incubation.  In addition to evaluating egg incubation success in various habitats, we also are measuring physical characteristics at these sites (e.g., dissolved oxygen, intragravel flow, substrate size composition).  Results from this study are expected to aid in determining how to best create spawning habitat.  Further, we are currently conducting high-resolution bathymetric mapping and videography in portions of Lake Pend Oreille where gravel additions are likely to occur.  One of the justifications for this ongoing study was to identify candidate sites for gravel addition.  Specifically, we seek to identify areas where lake currents prohibit accumulation of sediments.  Adding gravels in these areas should minimize risks of sedimentation. 

3. A summary of what has been learned over the past 15 years of management actions in the context of the overall objective of increasing harvest is needed.

RESPONSE: This comment seems to be closely related to #4 below, so please also refer to that response.  Also, we are unclear as to what harvest objective this comment refers to, but assume that ISRP means kokanee harvest (Objective 1).  We also have an objective that relates to bull trout and rainbow trout harvest (Objective 3). 

Meeting our kokanee harvest objective depends on addressing limiting factors for the kokanee population so that abundance can increase.  We provided a detailed summary of the history of management actions designed to recovery kokanee in the Problem Statement section of the proposal.  Please refer to that for additional details to what we provide in this response.

When this project started in the mid-1990’s, the primary limiting factor identified for kokanee was spawning habitat.  A strategy for managing winter lake levels to provide more spawning habitat was developed and evaluated starting in 1996.  Unfortunately, a record flood event occurred in 1997 and caused major kokanee mortality (downstream entrainment).  Almost immediately afterwards, lake trout began a rapid population expansion and predation increased to the point that the kokanee harvest fishery was closed.  At this time, predation surpassed spawning habitat as the primary limiting factor for kokanee recovery.  The timing of these events severely limited our ability to reap the anticipated benefits from winter lake level manipulations.  Thus, this management action has not yet resulted in major gains towards our kokanee harvest objective. 

Instead, management actions were developed to address predation.  Predator removal began in 2006 and these actions have successfully reduced the lake trout population.  Current data indicate that lake trout are approaching their population size in 1999 (a population estimate in the spring of 2012 will better answer this).  As a result, predation has been lessened and appears to be near a point where it is no longer the primary limiting factor.  The kokanee population has responded positively with increasing abundance and survival since 2007.  Kokanee have recovered to near their abundance in 2000 when the fishery was closed.  Should this trend continue, we may be able to provide a limited harvest kokanee fishery again by 2013.  Given the success of predator removals, we are positioned to see continued improvements in the kokanee population and expect to see benefits from other management actions that have been overshadowed by predation for more than a decade.

4. What has been learned from Lake Pend Oreille research that has helped IDFG balance conservation and harvest objectives?

RESPONSE: Objectives for managing the Lake Pend Oreille fishery do target both conservation and harvest for multiple species.   There are major pressures from anglers to provide sport fishing and harvest opportunity in Lake Pend Oreille.  Fortunately, conservation of native species and providing anglers with recreational fishing opportunities are not mutually exclusive.  Historically, the Lake Pend Oreille fishery supported robust populations of native bull trout, nonnative kokanee, and nonnative Gerrard rainbow trout.  Native adfluvial cutthroat trout became much less abundant following alterations from human development (primarily blocked access to the Clark Fork river drainage and land use activities in smaller tributaries) and not because of their in-lake compatibility with nonnative species.  All of these species are desirable to anglers and kokanee are the primary prey source for bull trout, so by continuing to manage in favor of these species we can meet both conservation and sport fishing objectives.  Of note, in the early 2000’s we had emerging angler interest in lake trout fishing as their abundance increased.  In this situation, we proactively worked to educate the greater angling community that it was not in the best interest of the Lake Pend Oreille fishery to manage for lake trout.  The now overwhelming acceptance of the lake trout suppression program by anglers indicates the success of this effort to maintain balance between conservation and sport fishing objectives.

As previously mentioned, our objectives for conservation and harvest are not mutually exclusive.  However, our research has been instrumental in making management decisions relative to these objectives.  For example, our kokanee monitoring in the late-90’s indicated that survival and abundance were declining to levels that could not support harvest.  In response, we closed the kokanee fishery to harvest in 2000.  Subsequent predation research allowed us to determine that predation had become the primary limiting factor for kokanee, due to an exponentially increasing lake trout population (Hansen et al. 2008; Hansen et al. 2010).  In addition to posing a threat to our harvest-related objectives for the fishery, lake trout also were identified as a threat to conservation of native bull trout and cutthroat trout.  Thus, research in the early-2000’s focused on evaluating predator removal feasibility and developing techniques for removal and evaluation.  This led to the initiation of the predator removal program in 2006, which included a change in harvest regulations and institution of the Angler Incentive Program.  Our research then focused on identifying patterns in lake trout distribution via telemetry to most effectively target them for removal and simultaneously minimize bull trout bycatch.  We also explored new techniques, such as seismic air gun technology (Cox et al. In Press) and various net designs, to more effectively remove predators.  Bull trout bycatch analyses have allowed us to better understand the effects of incidental harvest on the population, which will be useful for determining how much recreational harvest this population can support while also meeting conservation objectives.  Rainbow trout population dynamics research has been useful for evaluating the success of the Angler Incentive Program.  This research effort will help determine when to end this program and return to managing for a trophy rainbow trout fishery.  Similarly, kokanee population monitoring indicates that abundance has increased to near pre-2000 levels when the fishery was closed.  If we continue to observe further increases, we will use these data to make an informed decision on when to re-open the kokanee harvest fishery.  These are some of the key examples of how our research results have been used to make management decisions that influence both conservation and harvest objectives.

5. What are likely reasons why rainbow trout have increased in abundance by 50% from 2009 to 2010?

RESPONSE: The population estimate for rainbow trout >406 mm was 10,251 (95% CI ± 35%) in 2009 and 14,779 (95% CI ± 30%) in 2010.  We may not have been clear enough in the proposal that this did not represent a statistically significant increase in the population.  Our interpretation of rainbow trout estimates that date back to 1999 is that abundance has remained stable despite the incentivized harvest that started in 2006.  Variation in abundance point estimates is likely attributed to sampling variability and natural population fluctuations.  Another population estimate will be conducted in 2012-13.  This information will be used to guide a management decision on whether to discontinue incentivized harvest for rainbow trout.

6. Other questions and concern are embedded in the comments provided below. The ISRP suggests the sponsors examine these items as a response is prepared.

RESPONSE: See below for our responses to all questions embedded ISRP comments.

ISRP: Apart from specific questions, the ISRP feels the restoration of native resident bull trout and westslope cutthroat trout in Lake Pend Oreille deserves additional attention. This proposal devotes little attention to these species, even though other proposals in the region do. For example, there may be adfluvial populations of cutthroat trout that could or do provide important sport fisheries, and management could consider restoration actions in Lake Pend Oreille’s tributary habitats. Ongoing lake trout suppression would also benefit these other native species, but increased kokanee production would not likely benefit whitefish or most cutthroat trout.

RESPONSE: In regard to ISRP concerns that this project is not focusing enough on native species in the lake, we respectfully disagree.  We have a specific objective (Objective 2) stated in the proposal to preserve native bull trout and westslope cutthroat trout.  A very large portion of the funds requested are to reduce lake trout abundance for the benefit of ESA listed, native bull trout.    Lake trout suppression is critical given that adfluvial bull trout populations cannot be sustained in the presence of introduced lake trout (Donald and Alger 1993; Fredenberg 2002).  Suppression of lake trout is also likely to benefit native cutthroat trout, which were eminently compatible with kokanee in other regional lakes (e.g., Priest Lake) prior to lake trout establishment.  Lake trout pose a major threat to cutthroat trout and others have initiated suppression programs (e.g., Yellowstone National Park) to reduce this threat (Martinez at al. 2009).  In addition to lake trout suppression, it should be noted that our efforts to increase kokanee abundance does more than provide angler opportunity.  Kokanee are the primary prey for bull trout and their recovery is essential for conservation of this native species in Lake Pend Oreille.  Additionally, numerous restoration actions for bull trout and cutthroat trout are ongoing in tributaries to Lake Pend Oreille.  The actions include, but are not limited to, funding watershed restoration projects at the third-order basin level, in-channel restoration, acquisition of fee title and conservation easements for lands on key spawning and rearing tributaries for bull trout and cutthroat trout, brook trout suppression, and restoring fish passage in both small tributaries and the mainstem Clark Fork River dams.  IDFG conducts this work using mitigation funding provided by Avista Utilities and in partnership with the state of Montana, federal agencies, Avista and others as part of the Clark Fork Settlement Agreement for the FERC relicensing of Avista’s Clark Fork River projects.  IDFG is charged with protecting, preserving, and perpetuating fish and wildlife in the state of Idaho.  We believe that our overall efforts in the Lake Pend Oreille Subbasin exemplify this charge, particularly with respect to native fish restoration. 

ISRP: See the ISRP’s programmatic comments on fish stocking.

RESPONSE: We have read the above mentioned comments regarding stocking.  There are both positives and negatives associated with hatchery stocking programs.  We believe the ongoing hatchery program on Lake Pend Oreille is well-designed and compatible with restoration of naturally reproducing kokanee.  Without our hatchery program, there is a high probability that the lakewide population would have completely collapsed during the past decade of intense predation.  Moving forward, we have proposed work that will allow us to refine our stocking practices to maximize the benefit that stocking has for meeting kokanee recovery objectives.

ISRP: 1. Purpose: Significance to Regional Programs, Technical Background, and Objectives

This project has been in place for a long time, and the plan of work was reviewed by the ISRP in 2006, when it was given a favorable assessment. It is important to note that Lake Pend Oreille represents a large natural lake with a highly altered fish community. Of the three primary focal species, two are not native (kokanee and Gerrard stock rainbow trout) and the third (bull trout) is primarily of interest from a conservation standpoint, not a harvest standpoint. Additionally, the food web in Lake Pend Oreille has been strongly affected by the invasion of a non-native zooplankton (Mysis diluviana), which has acted as a competitor with kokanee and also helped to fuel the expansion of the non-native lake trout population, a significant predator on mysids as well as kokanee and juveniles of other salmonid species. As with many large lakes with increasing human development in the watershed, management challenges in Lake Pend Oreille are complex.

The project sponsors have done a good job of describing the relationship of this project to other regional resident fish management efforts, and their description of the technical background was also well done.

The proposal makes clear that recovery of the Pend Oreille fishery is the project's primary goal. Conservation of the two native salmonid species, bull trout and westslope cutthroat trout, is acknowledged in the work, but the primary emphasis is either research that addresses factors limiting kokanee and trophy trout recovery or habitat improvements that benefit kokanee reproductive success, such as addition of spawning gravel. Reduction of the lake's population of lake trout, generally viewed as a negative influence in the Pend Oreille ecosystem, also figures prominently in the work.

As mentioned above, management challenges are complex and restoring a desired balance of species, that is a balance that favors angler harvest of kokanee and trophy trout, will require that a number of potential limiting factors be addressed simultaneously. This will essentially mean a trial and error approach, and that is what IDFW have been doing for the last 15 years. A strong monitoring program will be essential for detecting the signal of programs such as lake trout reduction, winter lake level manipulation, kokanee stocking adjustments, and possible nutrient additions.

RESPONSE: ISRP notes above that our approach has been based on trial and error.  While we have attempted a variety of management strategies and evaluated their success, we have learned from each of these actions and used that information to modify our strategies.  This adaptive management approach has been valuable for working towards our project objectives in such a large and complex lake system and has produced successful results for both desirable nonnative species and native bull trout and westslope cutthroat trout.

ISRP: The role of lake whitefish in reducing abundance of Mysis is mentioned once but is not addressed again. Could this be important?

RESPONSE: This comment is directly addressed in our response to Issue #1 above.

ISRP: The objective to increase kokanee spawning success by adding spawning gravel to select shorelines needs additional scientific justification. When gravel is added in streams or lakes without addressing the hydrogeomorphic factors that create clean spawning gravel, for example upwelling and wave action, the usual result is that the gravel simply becomes unsuitable, requiring either more gravel or manual cleaning, all at great expense. Additionally, we wonder whether studies of kokanee egg survival in the laboratory and in boxes buried in lake substrate will answer the question of interest: what conditions are necessary for high survival, and how does survival vary with sediment deposition? It is clear that survival should be low when sediment is high, but at moderate levels of sediment, it is not clear whether human-placed egg boxes or eggs monitored in the laboratory will mimic those from egg pockets placed by female fish sufficiently to generate useful data. 

RESPONSE: Our response to Issue #2 above addresses the portion of this comment related to spawning gravel addition. 

We understand ISRP’s concerns about the kokanee egg survival studies.  This study has been challenging to design given the inherent difficulty associated with conducting early-life history research.  However, we think this approach can help us better understand kokanee spawning requirements.  We rely on annual estimates of egg-to-fry survival as a key metric to evaluate success of the lake level management strategy.  This metric is designed to assess the recruitment response on a lakewide basis, but does not allow direct evaluation of egg incubation success in various habitat types.  Better understanding the habitat conditions that lead to improved egg incubation success is important, both for evaluating existing lake level manipulations and for investigating whether new ideas, like spawning gravel addition, can be effective.  For instance, results from this study will allow us to better identify sites for adding spawning gravel, the size of substrate to add, and provide methods for evaluating egg incubation success in the added spawning gravels.  Burying eggs in substrate and conducting laboratory trials are commonly used approaches for answering egg incubation questions (Reiser and White 1988; Fincel et al. 2009).  Further, we are focused on determining relative differences in survival among habitat types, rather than absolute survival rates.  In addition to egg incubation, physical habitat measurements (e.g., dissolved oxygen, substrate composition, upwelling currents) will be taken.  Relative survival in different physical habitat conditions will help us determine what conditions are needed for kokanee spawning.  We can then try to provide these habitat conditions by managing lake levels, adding spawning substrate, or some combination of the two.  ISRP should note that a graduate project is underway to address these questions and funds requested in this proposal will be for the final year of the current graduate project.  Continued work beyond 2013 will be determined based on success of the first phase of the project.        

ISRP: 2. History: Accomplishments, Results, and Adaptive Management (ISRP Review of Results)

The proposal does a good job of summarizing the administrative accomplishments of the project. More details could have been given on results to date. A single graph was presented showing lake trout abundance from 1999 to 2008 but with only 5 years sampling data, while it would have been helpful to have seen similar summaries as graphs or tabular data for the other salmonid species. Over the last 15 years a variety of management actions have been implemented such as lake trout netting, experimental winter drawdowns, hatchery operations, and angler programs. A summary of what has been learned from these actions in the context of the overall objective of increasing harvest is needed. It does appear that predator control has had some success, but what about other efforts? Also, there was little mention of warm-water fishes. Have these introduced fishes had negligible impact on focal species in other areas of the lake?

A summary of results to date were provided in both the Problem Statement and Major Accomplishments sections.  These results were supported with citations for our annual reports and publications.  Because hyperlinks to most documents were provided, we anticipated that they would be easily accessible by ISRP if more in-depth results and discussion were desired.  However, in an attempt to provide the ISRP with more details, we added additional results to the proposal (see Problem Statement for additional figures).  As noted, the graph showing lake trout abundance from 1999-2008 does only have five data points; however, we would like ISRP to consider 1) the massive undertaking of estimating total abundance of lake trout in a large lake, and 2) that it is not practical (bull trout bycatch concerns) or necessary to estimate lake trout abundance annually to monitor trend.  Also note that we are currently in the final stages of completing a new population estimate that will add to this data set.  Other metrics are examined annually, such as trap net catch rates and exploitation rates, and are now reported in the proposal to further illustrate the rapid decline of the lake trout population.  We have added figures that show trends for kokanee, rainbow trout, and bull trout populations.  A summary of management actions over the past 15 years was requested.  Refer to our responses for Issues #3 and #4, which directly address this request.

RESPONSE: We did not feel it was necessary to discuss warmwater species in the proposal, with the exception of describing walleye in the Emerging Limiting Factors section.  Lake Pend Oreille supports a variety of nonnative warmwater and coolwater species, including walleye, smallmouth bass, largemouth bass, and northern pike.  Only smallmouth bass are widespread and abundant, but they are found in shoreline habitats and have limited habitat overlap with the focal species we seek to benefit.  Walleye exist in low abundance and primarily are located in the Pend Oreille River; however, this population could expand and result in predation on focal species.  Using Avista mitigation funding, IDFG initiated a fall walleye index netting protocol in 2011.  This sampling will be repeated in future years to monitor the walleye population.  We would like to know more about warmwater and coolwater species in the lake, but this has not been a research priority given that they currently appear to pose a minimal risk to meeting project objectives.  If this changes in the future, we will adjust accordingly.

ISRP: More information is also needed on how the results of the Lake Pend Oreille research have been incorporated into management changes. In particular, the potential for conflict between conservation and harvest objectives needs additional clarification. What has been learned from the research that has helped IDFG balance these two important objectives?

RESPONSE: This comment is directly addressed in our response to Issues #3 and #4 above.

ISRP: Other questions on accomplishments include:

Why have rainbow trout increased in abundance by 50% from 2009 to 2010? Is this difference significant, or are the confidence intervals around these estimates wide? If the difference is real, and not owing to high variability, then what is the explanation – high recruitment rates of small fish?

RESPONSE: This comment is directly addressed in our response to Issue #5 above.

ISRP: Lake trout marking – lake trout are reported as being marked in 2011 to estimate abundance by mark-recapture, but in the rest of the proposal all the lake trout were removed. When and where were these lake trout marked, how many, and of what sizes?

RESPONSE: All lake trout captured during netting operations are removed, except those fish that are used for periodic mark-recapture population estimates and telemetry research.  Lake trout captured in trap nets during September through November of 2011 were marked and released.  A total of 239 lake trout (>450 mm) were marked with spaghetti tags behind the dorsal fin and with individually-numbered coded wire tags in the snout.  Coded wire tags allowed all tagged fish harvested by anglers to be recovered because lake trout heads must be turned in for anglers to receive their reward payment.  A random gill netting design is being used for the recapture event.  A total of 100 random netting locations have been selected throughout the lake and will be sampled during February and March of 2012.  Additionally, angler recaptures will be used to generate a separate population estimate that will be compared to the netting estimate.  We plan to evaluate whether anglers can effectively be used as the recapture method in future years.  Random locations will be re-sampled an additional time if recaptures are not sufficient to generate an estimate with a coefficient of variation that is less than 25%.  Population estimate methods were developed by Dr. Mike Hansen of University of Wisconsin – Steven’s Point (Hansen et al. 2008).

ISRP: Management changes have focused on better targeting lake trout removal efforts in response to new data, and thereby reducing bull trout bycatch. The project sponsors acknowledge pressure from kokanee and rainbow trout anglers to increase abundance of these fishes and expand the fisheries, but how has this pressure driven management decisions as opposed to a focus on conservation and restoration of resident native fishes?

RESPONSE: This comment is directly addressed in our responses to Issues #3 and #4 above. 

ISRP Retrospective Evaluation of Results

It is clear that the food web dynamics in the lake are changing, but it also seems clear that the primary focal species have not returned to a level of abundance that support harvest objectives. There is no question that the studies proposed here will help address some of the most important problems; however, the proposal itself did not supply very many details about the results of previous management experiments, with the possible exception of the lake trout netting program. Sorting out the benefits of the various initiatives including predator control, habitat improvements, hatchery releases, and nutrient manipulations will be very difficult when they are all happening at the same time and will require very creative field experiments and analyses.

RESPONSE: In an effort to keep the proposal as concise as possible, we tried to describe key results in a broad context and cite annual reports and publications to support these results.  Because mostl documents were hyperlinked in the proposal, we thought ISRP would be able to easily refer to these documents if more detailed information was desired.  Given the above comment by ISRP, we have modified our proposal to provide additional details (see Problem Statement in particular).  The ISRP accurately notes that we are addressing multiple limiting factors simultaneously and will need appropriate monitoring to gauge success of these actions.  This project includes extensive monitoring intended to allow the various management actions to be assessed.  We have developed an effective monitoring program to evaluate predator removal.  We retained existing monitoring methods that have proven to be effective for evaluating kokanee spawning habitat limitations and hatchery contributions.  But, we also have included new approaches that we believe will improve our monitoring efforts.  Nutrient manipulation was mentioned in the ISRP comment above, but please note that we are not proposing to add nutrients to the lake.  Work is included to assess whether this strategy has merit, but actual additions are not planned.

ISRP: 3. Project Relationships, Emerging Limiting Factors, and Tailored Questions for Type of Work (hatchery, RME, tagging)

Because this project has a long history and Lake Pend Oreille has been intensively studied, the suite of potentially limiting factors has been adequately characterized. The project also seems to be well integrated into other work taking place in the Pend Oreille watershed.

The questions being asked specific to kokanee restoration seem appropriate, for example, where do lake trout spawn and at what locations in their daily or seasonal movements will they be particularly vulnerable to capture? Additional work is needed on understanding the role of winter drawdown in regulating kokanee reproductive success, whether physical addition of gravel along shoreline spawning areas can be cost-effective, and whether deliberate nutrient supplementation can achieve desired food web benefits. Fortunately, the proposal contains elements that address these matters.

The proposal did not supply much detail regarding how salmonid releases from hatcheries would be carried out to maximize learning opportunities nor did it give many details about existing or planned monitoring efforts except for the acoustic tracking work on lake trout, which was adequately covered. It was also unclear how project staffs are exchanging information with other RME practitioners in the region, although the explicit call for an annual science review meeting to discuss results is an excellent idea.

RESPONSE: Kokanee are the only species stocked in Lake Pend Oreille.  IDFG operates the Cabinet Gorge fish hatchery using internal agency funds, and the purpose of this facility is to raise kokanee for release into Lake Pend Oreille.  Two water sources are present at the hatchery and are used to thermally mark the otoliths of all kokanee stocked into the lake.  This allows us to distinguish hatchery and wild kokanee during our annual monitoring.  The contribution to the lakewide kokanee population by both hatchery and wild fish will be estimated annually.  To date, the hatchery program has been critical for sustaining the kokanee population, especially over the past decade of intense predation when the wild population reached record low abundance.  However, hatchery stocking alone has not been sufficient to meet kokanee recovery objectives.  We seek to better understand factors influencing survival of hatchery kokanee, especially fry, and use this information to refine stocking practices if opportunities to improve survival exist.  Deliverable-11 is aimed specifically at answering questions about fry survival.  Similar questions existed in previous years, but we were unable to adequately address them because of the low kokanee density in the lake.  With a rebuilding kokanee population, this should be feasible in the proposal period.  The hatchery program will also play a role in evaluating spawning gravel additions.  We plan to use eggs from the hatchery facility to conduct egg survival studies at these study sites. 

The ISRP indicated that details were lacking for monitoring activities, with the exception of lake trout telemetry work (DELV-3).  However, we proposed deliverables describing population monitoring for lake trout (DELV-2),  rainbow trout (DELV-5), and kokanee (DELV-8).  Additonally, we plan to assess bull trout bycatch effects (DELV-4) and other IDFG work (outside this project) using Avista funding will be used to monitor bull trout and cutthroat trout in tributaries, including redd counts.  While the deliverable descriptions themselves do not provide detailed methods for this work, the Protocols and Methods developed in MonitoringMethods.org do provide details.  It was brought to our attention that ISRP may not have been able to view our Methods on the website because they were in “draft” state (as instructed).  We have since advanced all of our Methods to “proposed” state in MonitoringMethods.org so that they are available for review.  In summary, this project contains a substantial amount of monitoring work, but we believe this work is critical for evaluating the multiple management actions that are being implemented.

The ISRP requested information about our communication with other RME practitioners.  We believe that communication is a strength of this project and its staff.  During the past proposal period, we routinely attended and presented project results at professional conferences.  These included meetings of the ldaho Chapter and Parent Society AFS, North American Lake Management Society, and International Kokanee workshops.  These meetings allowed us to interact with RME practitioners in the region and interact with others outside the region.  Additionally, we formally participated in two science reviews for lake trout suppression on Yellowstone Lake.  In addition to meetings, we routinely have informal communication with other RME practitioners about various topics related to our projects.  Beyond interactions with RME practitioners, we have put a great deal of effort into involving outside experts in our project.  Dr. Mike Hansen of University of Wisconsin-Steven’s Point, a noted lake trout population dynamics expert, has played a major role in our predator removal efforts and meets with us annually to review our results.  Dr. Mike Quist of the University of Idaho is now actively involved in our kokanee research and is assisting with evaluation of our kokanee monitoring methods.  Dr. Frank Wilhelm of the University of Idaho is assisting us to investigate the role of mysids, zooplankton, and nutrient dynamics in kokanee recovery.  Darren Brandt of Advanced Eco-Solutions is helping us understand productivity changes that have occurred in Lake Pend Oreille.  These are just some of the primary individuals who we have engaged to assist with our efforts, but others are also involved.  Recently, we have placed more emphasis on publishing our research to get valuable peer review of our results.  Since 2008, five peer reviewed manuscripts have been published in fisheries journals and another is currently in review.  We plan to continue publishing more than historically occurred on this project.

ISRP: 4. Deliverables, Work Elements, Metrics, and Methods

The ISRP had several questions relative to project deliverables:

The proposal did not specify metrics and indicators in very much detail for some of the deliverables. Often the metrics were described in general terms, but not in a way that particular measurement protocols could be identified or assumed. Many of the protocols and methods in MonitoringMethods.org were in draft form and did not contain sufficient detail for scientific review.

RESPONSE: We have attempted to provide some more detail in the proposal; however, this comment is not clear as to what specific deliverables were lacking information.  If more direction is provided, we can give more detail.  As instructed, all Protocols on the MonitoringMethods.org website were advanced to “proposed” state.  All of the Methods in MonitoringMethods.org were in “draft” state, but the instructions indicated that this was satisfactory.  It was recently brought to our attention that ISRP may not have been able to view our Methods on the website because they were in “draft” state and not viewable.  We have since advanced all of our Methods to “proposed” state in MonitoringMethods.org so that they are now available for review.  We hope this will address ISRP concerns mentioned above and will be happy to provide more detail upon request.

ISRP: The proposal also lacked information on what would be considered reference conditions for some of the deliverables. For example, if gravel is added to a kokanee spawning area, what would the reference condition be, pre-gravel enhancement egg survival or egg survival in an adjacent spawning area without gravel addition?

RESPONSE: As with the last comment, it is difficult for us to know what deliverables are in question.  However, we can address reference conditions for the spawning gravel addition deliverable.  Methods are currently being developed for studying egg survival as part of a recently initiated graduate project that will be completed in 2013.  We plan to use these methods for burying eggs in the substrate to evaluate egg survival in added spawning gravels.  Egg survival will be examined concurrently in adjacent habitats.  Further, the graduate project will yield egg survival data in various habitat conditions around the lake, including actively used spawning areas.  We plan to compare relative survival rates in added gravels to those documented in other habitats, with the goal of having survival rates in added substrates that meet or exceed those present in existing spawning areas.

ISRP: Can annual exploitation rates be accurately determined if only 30 lake trout are tagged with acoustic tags per year?

RESPONSE: A larger sample size would be ideal; however, release of additional acoustic-tagged fish is costly (about $600/transmitter).  Different tag types (e.g., spaghetti tags) could be used to increase the number of marked fish, but we have been reluctant to release any more lake trout than is absolutely necessary.  Because of the suppression program, annual exploitation is high and we typically recapture 20-60% of tags that are deployed.  If exploitation was lower we would have more concern about sample size leading to biased conclusions from a small number of recaptured tags.  If annual exploitation was the only metric being used to evaluate lake trout suppression success we might be more concerned.  However, we also conduct periodic population estimates, monitor standardized trap net catch rates, and examine gill net catch rates.  Examining combined metrics allows us to effectively monitor changes in the lake trout population.  Comparing multiple years of exploitation data to trends observed in trap net catch rates and population estimates indicates similar trends across metrics.  This increases confidence that exploitation data are meaningful. 

ISRP: We were unsure why a gear efficiency study is necessary. Would it be more cost effective to buy a bigger boat and trawl and simply increase efficiency this way?

RESPONSE: We operate a 29’ trawl boat and a fixed frame midwater trawl.  This is about the largest boat we can reasonably operate ourselves.  Standardized sampling methods for kokanee have been developed using this gear and we do not want to disrupt long-standing trend data sets that have been collected with this gear.  Instead, we would like to conduct a gear efficiency study and develop a model that allows for catches in our existing trawls to be corrected based on capture efficiencies at varying kokanee densities.  To do this, we plan to conduct a paired study using our standard trawl equipment and a larger, commercial-grade trawl net (towed behind a bigger boat).  Kokanee exhibit density-dependent growth and at low densities we have reduced capture efficiencies because larger fish are more capable of avoiding our existing trawl net.  The commercial net we plan to use in this study is sufficiently large to safely make the assumption that all fish are equally vulnerable to capture at all densities.  It is more practical to conduct a gear efficiency study than to operate a bigger boat and trawl net.  While there is a higher cost associated during the study period, it will be cheaper over the long-term if we can continue using our existing trawl equipment and not have to subcontract commercial fishermen to operate a larger boat and trawl net.  Additionally, kokanee do not survive after being sampled in trawl gear and a larger net would result in higher kokanee mortality.  This sampling limitation is not unique to Lake Pend Oreille.  All midwater trawling for kokanee is vulnerable to reduced capture efficiencies when larger kokanee are present.  Thus, this study will have application beyond Lake Pend Oreille.