The sponsors have outlined their objectives more clearly in the response than in the proposal, especially those for assessing effects of Libby Dam. They have also demonstrated that they are conducting ongoing data analysis, and improving methods for analysis in many cases.

Additional suggestions that may assist in optimizing studies for the Libby Dam/Kootenai River include:

1. The revised objectives make the proposal much clearer. Setting up clear hypotheses and alternatives is an important step. However, is there no expectation about the direction of these? The statement of non-directional alternative hypotheses indicates that little is known about the consequences of actions proposed. However, with the benefit of past data and experience, it should be possible to formulate more specific hypotheses for more powerful tests.

In addition, the sponsors should become versed on the current thinking about the drawbacks of hypothesis testing vs. model selection, so they can couch their results in appropriate terms. A priori hypotheses are a good thing, but how they are tested and reported are important for acceptance by the scientific communities.

2. Will production of phytoplankton and zooplankton be estimated, or simply density or volume? 

3. It appears that the sponsors will fit models of Didymo thickness and other metrics as a function of various covariates such as phosphorus. It would be informative to compare these models and covariates using the methods developed for "model selection and multi-model inference" by Burnham and Anderson (2002). These methods are believed by many to be superior to strict hypothesis testing, and traditional methods of developing one reduced model from the global model by deleting variables that are not significant. We urge the sponsors to look into these newer methods.

4. Under Objective 11, it was unclear for what biological group the richness and evenness would be calculated.

5. The ISRP appreciates the details presented for the early attempts of analysis of survival for bull trout, sturgeon, and rainbow trout using MARK. Although past data often may be too sparse for robust estimates, this design and analysis method should prove useful for future work, and analysis of some past data. Again, we urge the sponsors to approach experts with MARK if questions arise. They are often glad to help.

6. As for depletion estimates of bull trout abundance, the sponsors argue that the software that Montana uses to analyze data for population estimates has only certain options available. Nevertheless, working with an expert like Dr. Paul Lukacs at the University of Montana would allow using even newer methods that can combine data across bull trout samples in various tributaries or regions of Montana to estimate more robust capture probabilities. Likewise, new estimators allow including length as a continuous covariate instead of forcing separate estimates by size classes. This would improve estimates and confidence intervals for this and other projects.

7. As to topography of stream mouths, the hypothesis presented seems rather uninformative, especially if the goal is to determine fish passage upstream or downstream. Would it be possible to determine a measure of minimum habitat needed for fish passage (thalweg depth?) and to compare this through time, in addition to overall topography?

8. It is not entirely clear why evaluations of condition, growth, CPUE, and contributions of hatchery and wild sturgeon for fish captured in Montana will be compared to fish collected in Idaho and British Columbia. How will this information be used to inform management decisions?

9. More details for the adaptive management plan should be provided for contracting and Council consideration. For example, what are the implications for decisions about dam operations resulting from various outcomes of the project? Who will be involved in making those decisions and who will have final authority? How will dam operation decisions influence habitat restoration and fisheries management planning? What are the consequences to other aspects of the project if Didymo control efforts fail?

10. The sponsors should provide evidence of a strong commitment to sharing successes and lessons learned with others in the region and beyond through workshops, meetings, agency reports, and peer reviewed scientific publications. The peer-reviewed publications provide the opportunity to learn from other scientists who review the work, as well as to create a permanent record of the research and management decisions that is easily accessible in other places and future times.

ISRP Retrospective Evaluation of Results

This project has been ongoing for six years, during which the flow regime has been changing in the Kootenai River but has been more stable in the Flathead River. Partly as a result of recent changes, project results are further advanced for the Flathead River system than the Kootenai. Key questions about effects of ramping rates and reservoir levels on bull trout habitat use and benthic invertebrates have been answered in the Flathead River, although further questions remain about potential effects on native mountain whitefish and an invasive diatom (Didymo). These are the subject of ongoing study. In contrast, data on the effects of the new regime in the Kootenai River have been collected for several years since the flow regime change in 2008, but it will take more years before sufficient data are available to compare to previous regimes. Five years of data after the regime change would be a minimum to allow useful analysis. Improved designs are being developed for analysis of these before-after comparisons to capitalize on the substantial data being collected in the Kootenai River.

 

The research in the Kootenai River needs more effective integration through time. The ISRP recommend that the project sponsors develop an integrated conceptual model of the system, which would facilitate identification of key hypotheses to be tested and the presenting and publishing of results when these questions are answered. The ISRP will be looking for this in the next project review.

Likewise, the ISRP will be looking for dissemination of new knowledge and insights in the form of presentations at scientific or regional management meetings; workshops held to present information on problems common to these and other similar regulated rivers; and especially in the form of peer-reviewed publications to make a permanent record of the findings.

This project will evaluate the changes in drawdown limits and ramping rates at Libby and Hungry Horse dams, the two dams in Montana where flows can be altered to potentially benefit resident native fishes including those with fluvial and adfluvial life histories. There is a long history of dam operation changes, with current changes at Libby Dam coming online in 2008.

The proposal makes clear that dam operations affect the entire river ecosystem, with effects cascading downstream and upstream, partly through the altered movements and migrations of fishes. For the Kootenai River, the proposal describes that large amount of data collected both before and after the 2008 operation changes on hydrology, geomorphology of tributary deltas, benthic algae, and fish populations. For the Flathead River, where flow regime changes and research of them have been ongoing longer, the proposal describes evaluation of regime effects on habitat for juvenile bull trout, PIT tagging of bull trout in North Fork tributaries, and recent work on movement of mountain whitefish.

Overall, there were several deficiencies with the proposal itself, and several objectives and deliverables that were not well justified. First, we list deficiencies with the proposal which should be corrected in further proposals, followed by identification of responses requested to address problems with objectives and deliverables.

A. Deficiencies with the proposal:

1. Objectives were not well organized into key components to be measured. For the Kootenai River, Objective 1 was too broad, and aimed at monitoring many physical and biotic components from river flows to fish survival, whereas 2 through 5 were much more specific. In the future, objectives could be divided into more logical key components, such as 1) physical changes to reservoirs and flow regimes, 2) changes in nutrients, periphyton, and invertebrates, 3) demographics and viability of listed fish species, 4) population analysis of other native and non-native species, and 5) potential for invasions by non-native fishes.

2. Within objectives, deliverables should focus on key questions phrased as hypotheses. Examples might include: 1) Is survival rate and population growth rate (lambda) of listed bull trout increasing, stable, or decreasing? And 2) are brook and brown trout invading above Kootenai Falls? Focused questions to be addressed were a key component missing in the proposal for the Kootenai River work.

3. Sections on accomplishments need much greater synthesis for the work on the Kootenai River. This section was long and lacked the critical analysis and synthesis needed. No questions were presented, and no statistical analysis was completed or presented. Although the ISRP understands that these data are recent, and often too few data have been collected since the flow regime change in 2008 to analyze appropriately, the work needs to provide useful summaries rather than so much relatively detailed data. Some parts, such as the figures of aggradation at delta mouths, were unreadable, and so unusable. Not all reviewers will be able to delve into the annual reports.

B. Deficiencies with objectives and deliverables that require response in this cycle:

1. Appropriate study designs were lacking for much of the work on the Kootenai River, although baseline data collected provide useful information to develop such designs. Given this background, future work needs to focus on specific questions, rather than attempting to address all aspects of the changes caused by the flow regimes. Specific points raised by the ISRP that need to be addressed in this cycle include:

a. Bull trout survival and population growth – in both river systems, much effort is being expended to capture and mark bull trout with PIT tags, but no information was given about how these data would be analyzed to yield robust estimates of survival or rates of population change (lambda). These are two key vital rates that must be evaluated to make management decisions. Program MARK (see website of Dr. Gary White at Colorado State University) provides a flexible method for analyzing these data to estimate these rates. It offers much better power at detecting differences between time periods or locations than, for example, the analysis described in the annual report for the Kootenai River (Sylvester and Stephens 2010, FY10 Annual Report). Examples of such integrated MARK analyses for mark-recapture data on fishes in major river systems are available in Bestgen et al. (2007) and Zelasko et al. (2010), both in Transactions of the American Fisheries Society. Expertise to conduct such analyses can be gained by consulting with experts such as Drs. Paul Lukacs (U of MT), Gary White or Kevin Bestgen (Colorado State U), and Paul Conn or Brett McClintock (NOAA Fisheries, Seattle), and/or attending one of the periodic workshops on MARK (after some self-study, the intermediate-level workshop might be best). Given the large effort and excellent datasets being collected, appropriate design and analysis are a key component missing from the proposed work. Without them, much effort and funding could be wasted. With them, the work could provide landmark information to help fuel sound management decisions.

Response requested: Provide information about how data will be analyzed to yield robust estimates of survival or rates of population change for bull trout.

b. Similar data will be collected for white sturgeon in the Kootenai River, and can profit from a similar design, although the ISRP recognizes that recaptures may be too few for robust analysis. Nevertheless, without a suitable design, it may be difficult to prove that survival is indeed low, or to place confidence intervals around this, or test the evidence for it.

Response requested: Provide information about how data will be analyzed to yield robust estimates of survival or rates of population change for white sturgeon.

c. Problems were reported about estimating survival of rainbow trout, based on concerns about inaccurate ageing using scales. The method proposed for estimating survival in the FY 2010 Annual Report is akin to using catch curves, which is based on many assumptions. It seems like it would be much more efficient to simply PIT tag rainbow trout, avoiding the ageing issues altogether, and estimate survival directly using MARK. This could be done within size classes of interest. Given this, some deliverables need to be modified or dropped.

Response requested: Provide an evaluation of using PIT tagged rainbow trout to estimate survival within size classes. How would using this approach affect currently proposed deliverables?                                                                       

d. Population estimation for salmonids can also be improved markedly with new methods in MARK (see Saunders et al. 2011 TAFS for an example), which can integrate analysis across all size classes and even among different locations or sites. This improves power greatly by estimating capture probabilities for a much larger sample of fishes, with a continuous covariate for fish length (Huggins model) and other covariates for sites or times. In contrast, the method proposed and commonly used of estimating abundance for several size classes of fish at each site separately produces estimates with wide confidence intervals because they are each based on small sample sizes.

Response requested: Provide an evaluation of using the new methods in MARK for population estimation.                                                                      

e. Questions about factors affecting Didymo invasions should be developed as alternative plausible models or hypotheses, which can be tested using model selection (see Burnham and Anderson 2002). This method allows evaluating the weight of evidence for alternative models, and estimating parameters using multi-model inference to more fully use the information gained. Expertise in these methods can also be gained from the people listed above. Moreover, there are several proposals from this region addressing the same topic, and all have substantial budgets, so the ISRP is interested for clarification on how the workload will be shared.

Response requested: Provide alternative models or hypotheses about factors affecting Didymo invasions and outline how current and future data could be used to evaluate the alternatives.                                                                      

f. The information on delta aggradation and potential blockage of bull trout migrations is very interesting and important, but no questions were developed, and no methods or statistical analyses discussed for evaluating these changes.

Response requested: Develop questions and identify methods of analysis to evaluate changes due to delta aggregation and potential blockage of bull trout migrations.                                                                      

g. Adaptive Management: Most material in the text is a small component of adaptive management. It is suggested that the sponsors develop an adaptive management process that is responsive to the resources as well as to the public and to management needs.

Response requested: Provide an Adaptive Management plan to describe a process that is responsive to the resource, public, and management needs.                                                                       

h. Emerging Limiting Factors: The sponsors seem to have a good understanding of most emerging factors. However, changes in winter icing conditions were not mentioned, and could become increasingly important with time.

Response requested: Identify how winter icing conditions would affect the proposed project objectives.

i. Data Management: What percentage of the total budget is dedicated to data management? How is data QA/QC addressed for specific projects activities? Please describe anticipated improvements in the data management system expected to occur over the next few years (e.g., cloud computing, new software, equipment upgrades).

Response requested: Provide a response addressing issues raised in item i.                                                                       

j. The sponsors need to improve their collective productivity by publishing peer-reviewed articles in professional journals.

Response requested: Describe plans to publish in peer-reviewed journals.                                                                       

2. On the Flathead River system, where work is apparently more advanced, several main points require response:

a. Analysis of bull trout survival and rates of population growth require a more robust approach using current capture-recapture analysis methods like those included in Program MARK. Please see point 1.A. above.

Response requested: Provide information about how data will be analyzed to yield robust estimates of survival or rates of population change for bull trout on the Flathead River system.

b. The accomplishments presented about whitefish tracking in the Flathead River were useful information, but no study plan of focused questions was presented for the future, and there was no indication about how these data will be analyzed to answer specific questions.

Response requested: Develop questions and identify methods of analysis to evaluate whitefish tracking data.                                                                      

c. Points 1.G., and 1.I. from above also need to be addressed for the Flathead River system.

Response requested: Provide an adaptive management plan to describe a process that is responsive to the resource, public, and management needs for the Flathead River system. Respond to the questions posed in item I above with respect to the Flathead River system.                                                                       

Retrospective Evaluation of Results: This project has been ongoing for six years, during which the flow regime has been changing in the Kootenai River, but has been more stable in the Flathead River. Partly as a result of recent changes, project results are farther advanced for the Flathead River system than the Kootenai. Key questions about effects of ramping rates and reservoir levels on bull trout habitat use and benthic invertebrates have been answered in the Flathead River, although further questions remain about potential effects on native mountain whitefish and an invasive diatom (Didymo). These are the subject of ongoing study. In contrast, data on the effects of the new regime in the Kootenai River have been collected for several years since the flow regime change in 2008, but it will take more years before sufficient data are available to compare to previous regimes. Five years of data after the regime change would be a minimum to allow useful analysis. Nevertheless, better designs are needed for analysis of these before-after comparisons to capitalize on the substantial data being collected in the Kootenai River.

Modified by Dal Marsters on 4/16/2012 10:54:15 PM.

Modified by Dal Marsters on 4/17/2012 12:41:03 PM.

200600800 - Mainstem Columbia Amendments Research at Libby Dam

Sponsor: Montana Fish, Wildlife and Parks (MFWP)

ISRP recommendation: Response requested

Comment: This project will evaluate the changes in drawdown limits and ramping rates at Libby and Hungry Horse dams, the two dams in Montana where flows can be altered to potentially benefit resident native fishes including those with fluvial and adfluvial life histories. There is a long history of dam operation changes, with current changes at Libby Dam coming online in 2008.

The proposal makes clear that dam operations affect the entire river ecosystem, with effects cascading downstream and upstream, partly through the altered movements and migrations of fishes. For the Kootenai River, the proposal describes that large amount of data collected both before and after the 2008 operation changes on hydrology, geomorphology of tributary deltas, benthic algae, and fish populations. For the Flathead River, where flow regime changes and research of them have been ongoing longer, the proposal describes evaluation of regime effects on habitat for juvenile bull trout, PIT tagging of bull trout in North Fork tributaries, and recent work on movement of mountain whitefish.

Overall, there were several deficiencies with the proposal itself, and several objectives and deliverables that were not well justified. First, we list deficiencies with the proposal which should be corrected in further proposals, followed by identification of responses requested to address problems with objectives and deliverables.

A. Deficiencies with the proposal:

ISRP Comment :1. Objectives were not well organized into key components to be measured. For the Kootenai River, Objective 1 was too broad, and aimed at monitoring many physical and biotic components from river flows to fish survival, whereas 2 through 5 were much more specific. In the future, objectives could be divided into more logical key components, such as 1) physical changes to reservoirs and flow regimes, 2) changes in nutrients, periphyton, and invertebrates, 3) demographics and viability of listed fish species, 4) population analysis of other native and non-native species, and 5) potential for invasions by non-native fishes.

MFWP Response: The following objectives were contained within the original proposal and have been updated as part of our response to ISRP comment #2. 

OBJ-1: Mainstem Amendment Modeling and Monitoring

Model and monitor the biological and physical effects of the Mainstem Amendment dam operations on the Kootenai and Flathead rivers and Libby and Hungry Horse reservoirs. Monitored metrics can include inflow, outflow, and surface elevations of Libby Reservoir, wetted perimeter, weighted usable area, fish growth and condition, population estimates, and annual survival estimates for various fish species. The baseline for comparison will be the same metrics during previous dam operating strategies and to pre-dam conditions if data are available. Results should provide information of how various dam operating strategies are affecting both the biological communities and physical habitat conditions upstream and downstream of Libby and Hungry Horse dams. Results may direct or possibly lead to modification of future water management and operational strategies at dams throughout the Columbia River basin.

OBJ-2: Didymosphenia geminata Monitoring

Continue to monitor D. geminata (didymo) mat production and relate biomass, thickness, and coverage information to dam operations and other metrics in the Kootenai and Flathead rivers as part of a coordinated effort to reduce or eliminate blooms altogether. Data collected during this monitoring combined with other research may lead to removal or large reductions of the species downstream of Libby and/or Hungry Horse dams with the goal of improving habitat conditions in those river systems. Reduction or elimination of D. geminata may improve the invertebrate community metrics and possibly growth and condition of fish downstream of Libby and Hungry Horse dams in Montana.

OBJ-3: Quartz Creek Monitoring

Continue to monitor the dynamics and status of the bull trout population, fish community, and thermal conditions in Quartz Creek, a tributary to the Kootenai River downstream of Libby Dam. Metrics monitored will include population estimates of juvenile bull trout, redd counts, juvenile and adult migration patterns, survival rates, growth, and water temperatures in an effort to identify limiting factors of the bull trout population. Bull trout population dynamics will be compared to other populations and juvenile to adult survival rates will be compared to those observed in an adfluvial population in Idaho and estimates being collected in the Flathead River drainage. If limiting factors of the population can be determined, mitigation or restoration efforts may be performed in order to reach recovery and delisting criteria for the species as specified by the United States Fish and Wildlife Service.

OBJ-4: White Sturgeon Monitoring

Increase the knowledge base of the population of white sturgeon in the Kootenai River, Montana and Idaho by continuing to assess the size and age structure, habitat use, effectiveness of hatchery stocking efforts, fish movement, document the presence of wild sturgeon, and other information related to spawning and reproduction in Montana. Almost no information has been collected for the species in Montana since the mid 1970's despite ongoing hatchery and recovery efforts in Idaho and British Columbia. Data and other information gathered will be used to evaluate the status of the species and ultimate goal of reaching recovery criteria and delisting of the species in the Kootenai River.

OBJ-5: Delta aggradation

Periodic topographic assessments of deltas and comparison to previous surveys downstream of Libby Dam will allow calculation of aggradation rates and vertical changes at the confluences with the Kootenai River. Tributaries in need of restoration efforts to allow better fish passage into spawning tributaries may be identified. Formation of the deltas is suspected as a possible reason for declining redd counts of bull trout and may require mitigation actions to increase access to spawning tributaries and reach recovery criteria for the species.

OBJ-6: Mountain whitefish Monitoring

The native mountain whitefish have been detected in abundance throughout the Flathead River system (McMullin and Graham 1981), though little attention has been focused on the species until recently. Regionally reported declines based on minimal quantitative data along with its potential as a model species for evaluating dam impacts in a partially regulated system have directed attention towards this putatively abundant, sensitive, and long-lived species for which minute local data exists. Increasing local demographic and life history information, including movement, habitat use, distribution, age, growth, and abundances can lead to a better understanding of how this native may be impacted by dam operations, nonnative species interactions, or climate change.

ISRP Comment: 2. Within objectives, deliverables should focus on key questions phrased as hypotheses. Examples might include: 1) Is survival rate and population growth rate (lambda) of listed bull trout increasing, stable, or decreasing? And 2) are brook and brown trout invading above Kootenai Falls? Focused questions to be addressed were a key component missing in the proposal for the Kootenai River work.

MFWP Response: The primary purpose of this project is to identify the physical and biological impacts of the Mainstem Amendment dam operations upstream and downstream of Libby and Hungry Horse dams.  Six prior and current dam operating strategies were identified at Libby Dam based on changes to dam operations including elimination of power peaking and load following, elevated summer flo ws for anadromous salmon, experimental spring flows for white sturgeon, elimination of standard flood control operation, implementation of VARQ flood control operations, establishment of minimum flows for bull trout in the fall, implementation of more stringent ramping rates in the Kootenai River on seasonal and daily levels, and limiting the summer draft of Libby Reservoir.  The operational periods and seasons identified for data analysis include the following.

Period 1: Pre-dam (water years 1911-1971)

Characterized by unregulated discharges up to completion of Libby Dam.

 Period 2: Post-dam Pre-Biop (water years 1972-1994)

Characterized by regulated discharges, power peaking and load following, no limits to ramping rates of discharged water downstream of Libby Dam, with variable and occasionally deep drawdown of Libby Reservoir.

Period 3: Post-dam Biop (water years 1995-1999)

Characterized by more a normative shaped spring discharges and flow augmentation for anadromous salmon and Kootenai River white sturgeon with unnatural double summer peaks in the Kootenai River downstream of Libby Dam.

Period 4:  Post-dam Transition (water years 2000-2002)

Characterized by flow augmentation for Kootenai River white sturgeon after a recovery plan was established, water temperature management for the benefit of white sturgeon, reduced discharge variation, and establishment of base flows for bull trout.

 Period 5: Post-dam VARQ (water years 2003-2008)

Characterized by flow augmentation for white sturgeon, water temperature management, and seasonal bull trout minimum flows.  Switch from standard flood control operations to VARQ flood control operations. 

Period 6:  Post-dam Mainstem (water years 2009-present)

Characterized by flow augmentation for white sturgeon, reduced summer drawdown of Libby Reservoir (10 feet from full pool in upper 80% supply water years, 20 feet from full pool in lowest 20% water supply years),  stricter ramping rate limits to the discharge into the Kootenai River downstream of Libby Dam, water temperature management, and seasonal bull trout minimum flows.  

The following seasons were identified based on ambient air temperatures, changes to normative water temperatures, and typical hydrological years which begin October 1 and end September 30: fall = October-November, winter = December-March, spring = April- June, summer = July-September. 

Additional work is being performed to address impacts of dam operations on the diatom D. geminata which appeared in the Kootenai River in 2001, updating the status of the white sturgeon Acipenser transmontanus in Montana, assessing aggradation of deltas and potential impacts to migratory fish species downstream of Libby Dam, and assessing the benthic invertebrate community and fish diets along a gradient in the Kootenai River to compare to previously collected data during previous dam operating strategies. 

In order to more clearly focus the intent of Project 2006-008-00 based on comments #1 and #2 of the ISRP, we have revised the objectives included in the original proposal and included the key hypotheses being tested under each objective below.

Objective 1. Document changes to inflow and outflow patterns, surface elevation, refill frequency, draft and refill rates, and water residence time in Libby Reservoir resulting from changes of dam operating strategies.

H_o = annual and seasonal inflow to Libby Reservoir is equal among strategies

H_a = annual and seasonal inflow to Libby Reservoir is not equal among strategies

H_o = annual and seasonal outflow from Libby Dam is equal among strategies

H_a = annual and seasonal outflow from Libby Dam is not equal among strategies

H_o = annual and seasonal surface elevation of Libby Reservoir is equal among strategies

H_a = annual and seasonal surface elevation of Libby Reservoir is not equal among strategies

H_o = refill frequency (% of years) is equal among strategies

H_a = refill frequency (% of years) is not equal among strategies

H_o = annual and monthly water residence time of Libby Reservoir is equal among strategies

H_a = annual and monthly water residence time of Libby Reservoir is not equal among strategies

H_o = annual and seasonal draft rates of Libby Reservoir are equal among strategies

H_a = annual and seasonal draft rates of Libby Reservoir are not equal among strategies

H_o = annual and seasonal refill rates of Libby Reservoir are equal among strategies

H_a = annual and seasonal refill rates of Libby Reservoir are equal among strategies

Objective 2.  Document any changes to the modeled primary productivity, primary productivity washout, and zooplankton in Libby and Hungry Horse reservoirs resulting of changes to dam operating strategies.

H_o = annual and seasonal primary productivity is equal among strategies

H_a =  annual and seasonal primary productivity is not equal among strategies

H_o = annual and seasonal primary production washout is equal among strategies

H_a = annual and seasonal primary production washout is not equal among strategies

H_o = annual and seasonal zooplankton production is equal among strategies

H_a = annual and seasonal zooplankton production is not equal among strategies

Objective 3.  Assess changes in the species composition of fish captured in Libby Reservoir  between dam operating strategies and evaluate any changes in fish condition.

            H_o = bull trout condition in the spring is equal among operating strategies

            H_a = bull trout condition in the spring is not equal among operating strategies

            H_o = spring species composition is equal among operating strategies

            H_a = spring species composition is not equal among operating strategies

            H_o = fall species composition is equal among operating strategies

            H_a = fall species composition is not equal among operating strategies

            H_o = kokanee condition in the fall is equal among operating strategies

            H_a = kokanee condition in the fall is not equal among operating strategies

Objective 4.  Assess the status of white sturgeon Acipenser transmontanus in Montana including evaluations of abundance, growth, catch per unit effort, condition, contributions from hatchery vs. wild fish, assessing movement using recaptured fish, and effectiveness of stocking efforts in Montana and Idaho.

H_o = condition of white sturgeon captured in Montana and Idaho are equal

H_a = condition of white sturgeon captured in Montana and Idaho are not equal

H_o = the number of wild and hatchery white sturgeon in Montana are equal

H_a = the number of wild and hatchery white sturgeon in Montana are not equal

H_o = growth of white sturgeon captured in Montana and Idaho are equal

H_a = growth of white sturgeon captured in Montana and Idaho are not equal

H_o = catch per unit effort in Montana and Idaho are equal

H_a = catch per unit effort in Montana and Idaho are not equal

Objective 5.  Assess changes in physical habitat conditions and productivity of the Kootenai River using RIVBIO & IFIM models and water temperatures to evaluate physical conditions occurring in the Kootenai River under various dam operating strategies.

H_o = annual and seasonal wetted perimeter is equal among strategies

H_a = annual and seasonal wetted perimeter is not equal among strategies

H_o = annual and seasonal weighted usable area (WUA) for juvenile rainbow trout is equal among strategies

H_a = annual and seasonal weighted usable area (WUA) for juvenile rainbow trout is not equal among strategies

H_o = annual and seasonal weighted usable area (WUA) for adult rainbow trout is equal among strategies

H_a = annual and seasonal weighted usable area (WUA) for adult rainbow trout is not equal among strategies

H_o = annual and seasonal nighttime weighted usable area (WUA) for juvenile bull trout is equal among strategies

H_a = annual and seasonal nighttime weighted usable area (WUA) for juvenile bull trout is not equal among strategies

H_o = annual and seasonal daytime weighted usable area (WUA) for juvenile bull trout is equal among strategies

H_a = annual and seasonal daytime weighted usable area (WUA) for juvenile bull trout is not equal among strategies

H_o = annual and seasonal weighted usable area (WUA) for adult bull trout is equal among strategies

H_a = annual and seasonal weighted usable area (WUA) for adult bull trout is not equal among strategies

H_o = annual and seasonal modeled benthic biomass is equal among strategies

H_a = annual and seasonal modeled benthic biomass is not equal among strategies

H_o = annual and monthly water temperatures are equal among strategies

H_a = annual and monthly water temperatures are not equal among strategies

H_o = annual and monthly degree days are equal among strategies

H_a = annual and monthly degree days are not equal among strategies

Objective 6.  Assess fish condition and survival of rainbow and bull trout in the Kootenai River and investigate if changes to dam operations can explain any observed changes.

H_o =  condition of bull trout is equal among strategies

H_a = condition of bull trout is not equal among strategies

H_o = condition of rainbow trout is equal among strategies

H_a = condition of rainbow trout is not equal among strategies

H_o = condition of mountain whitefish is equal among strategies

H_a = condition of mountain whitefish is not equal among strategies

H_o = annual and cohort survival rates of rainbow trout are equal among strategies

H_a = annual and cohort survival rates of rainbow trout are not equal among strategies

Objective 7.  Assess juvenile to adult bull trout survival in Quartz Creek and compare survival estimates and population dynamics (emigration and immigration patterns, size and age structure, return rates, influence of biological and physical conditions) and to compare to data collected in the Flathead River drainage in an effort to identify limiting factors of bull trout and any influence of dam operations (e.g., spill).

H_o = return rates of age-1, 2, 3, and 4 emigrants are equal

H_a =  return rates of age-1, 2, 3, and 4 emigrants are not equal

H_o = emigration is equally distributed temporally throughout the year

H_a =  emigration is not equally distributed temporally throughout the year

Objective 8.  Monitor water temperatures in the primary spawning tributary (i.e., West Fisher River, Bear Creek, Pipe Creek, Quartz Creek, Keeler Creek, O’Brien Creek, and Callahan Creek)  and migratory corridors downstream of Libby Dam (i.e., Fisher River, Libby Creek, and Lake Creek) to assess if water temperatures may be limiting bull trout populations within the Kootenai River drainage.

H_o = maximum daily temperature is less than 15^oC  or 60^oF

H_a =  maximum daily temperature is greater than 15^oC  or 60^oF

H_o = average monthly temperatures in each tributary are equal

H_a =  average monthly water temperatures in each tributary are not equal

H_o = water supply forecast does impact average monthly and maximum daily water temperatures

H_a =  water supply forecast does not impact average monthly and maximum daily water temperatures

Objective 9.  Monitor the seasonal growth patterns of Didymosphenia geminata and assess potential impacts of dam operations (i.e., discharge variation /volume / fluctuation) on reducing or eliminating nuisance blooms of mat materials.

H_o = the monthly average percent coverage and thickness of D. geminata mats is equal

H_a = the monthly average percent coverage and thickness of D. geminata mats is not equal

H_o = discharge (peak and volume) affects D. geminata coverage and thickness 

H_a = discharge (peak and volume) does not affect D. geminata coverage and thickness 

H_o = water quality parameters and habitat conditions at sites with and without D. geminata are equal

H_a = water quality parameters and habitat conditions at sites with and without D. geminata are equal

Objective 10.  Assess aggradation and degradation of tributary deltas to assess if build up of materials may be resulting in or causing reductions in bull trout redd counts downstream of Libby Dam.

H_o = the topography (i.e., elevation) of each delta is the same as previous survey(s)

H_a = the topography (i.e., elevation) of the delta is not the same as previous survey(s)

Objective 11.  Assess the benthic invertebrate community, fish diets, fish condition, and water temperatures to identify potential limiting factors of trout in three sections of the Kootenai River including Libby Dam to the Fisher River, Flower Creek to Pipe Creek, and Troy.

H_o = species composition of benthic invertebrates is equal among sections of the Kootenai River

H_a = species composition of benthic invertebrates is not equal among sections of the Kootenai River

H_o = biomass of aquatic invertebrates is equal among sections of the Kootenai River

H_a = biomass of aquatic invertebrates is not equal among sections of the Kootenai River

H_o = length frequency distribution and size structure of rainbow trout is equal among sections of the Kootenai River

H_a = length frequency distribution and size structure of rainbow trout is not equal among sections of the Kootenai River

H_o = richness / evenness are equal among sections of the Kootenai River

H_a = richness / evenness are not equal among sections of the Kootenai River

H_o = the numbers of individuals in each fish stomach is equal among sections of the Kootenai River

H_a = the numbers of individuals in each fish stomach is not equal among sections of the Kootenai River

H_o = the volume of stomach contents in each fish is equal among sections of the Kootenai River

H_a = the volume of stomach contents in each fish is not equal among sections of the Kootenai River

H_o = monthly water temperatures are equal among sections of the Kootenai River

H_a = monthly water temperatures are not equal among sections of the Kootenai River

H_o = density of aquatic invertebrates is equal among sections

H_a = density of aquatic invertebrates is not equal among sections

H_o = the species composition of diets in each section  is equal to the benthic composition

H_a = the species composition of diets in each section is not equal to the benthic  composition

Objective 12.  To assess impacts of dam influenced sections of the Flathead River drainage on growth, condition, and habitat use of mountain whitefish.

H_o = mountain whitefish detected in dam-influenced portions of the Flathead River spend > 50% of their adult lives in those areas.
H_a = mountain whitefish detected in dam-influenced portions of the Flathead River spend ≤ 50% of their adult lives in those areas.

H_o = mountain whitefish detected in dam-influenced portions of the Flathead River use pool, riffle, and run habitat equally, regardless of discharge and water temperature.
H_a = mountain whitefish detected in dam-influenced portions of the Flathead River do not use pool, riffle, and run habitat equally, regardless of discharge and water temperature.

H_o = the relative weights (Wr) of mountain whitefish detected in dam-influenced portions of the Flathead River are equal to those found in Hungry Horse Reservoir.
H_a = the relative weights (Wr) of mountain whitefish detected in dam-influenced portions of the Flathead River are not equal to those found in Hungry Horse Reservoir.

H_o = age and growth distributions of mountain whitefish detected in dam-influenced portions of the Flathead River are equal to those found in Hungry Horse Reservoir.
H_a = age and growth distributions of mountain whitefish detected in dam-influenced portions of the Flathead River are not equal to those found in Hungry Horse Reservoir.

ISRP Comment:

3. Sections on accomplishments need much greater synthesis for the work on the Kootenai River. This section was long and lacked the critical analysis and synthesis needed. No questions were presented, and no statistical analysis was completed or presented. Although the ISRP understands that these data are recent, and often too few data have been collected since the flow regime change in 2008 to analyze appropriately, the work needs to provide useful summaries rather than so much relatively detailed data. Some parts, such as the figures of aggradation at delta mouths, were unreadable, and so unusable. Not all reviewers will be able to delve into the annual reports.

MFWP Response: 

At this time the original proposal was being written, the Mainstem Amendment operations had only been implemented for 2 complete years, which both had below average snowpack (i.e., approximately 80%) and the third year of implementation was about 90% complete, and included well above average snowpack (i.e., approximately 130%).  We were not comfortable making statements about the impacts of the Mainstem Amendment operations on physical conditions and biological communities with limited data and we feel at least 2 to 3 more years of implementation are needed so that at least one or two cohorts of fish have only been exposed to the Mainstem operations.  Model simulations and statistical analysis regarding the impacts of the Mainstem Amendment operations are not completed until the water year was complete and we are in the process of performing this analysis based on the first 3 years of implementation.  Once the Mainstem Amendments have been implemented for approximately 5-7 years, we will be able to summarize impacts of dam operations more thoroughly including statistical comparisons and provide a more thorough summary of impacts.  At that time, we will also provide recommendations about continued implementation of the Mainstem operations or propose modifications to dam operations.

B. Deficiencies with objectives and deliverables that require response in this cycle:

ISRP Comment:

1. Appropriate study designs were lacking for much of the work on the Kootenai River, although baseline data collected provide useful information to develop such designs. Given this background, future work needs to focus on specific questions, rather than attempting to address all aspects of the changes caused by the flow regimes. Specific points raised by the ISRP that need to be addressed in this cycle include:

a. Bull trout survival and population growth – in both river systems, much effort is being expended to capture and mark bull trout with PIT tags, but no information was given about how these data would be analyzed to yield robust estimates of survival or rates of population change (lambda). These are two key vital rates that must be evaluated to make management decisions. Program MARK (see website of Dr. Gary White at Colorado State University) provides a flexible method for analyzing these data to estimate these rates. It offers much better power at detecting differences between time periods or locations than, for example, the analysis described in the annual report for the Kootenai River (Sylvester and Stephens 2010, FY10 Annual Report). Examples of such integrated MARK analyses for mark-recapture data on fishes in major river systems are available in Bestgen et al. (2007) and Zelasko et al. (2010), both in Transactions of the American Fisheries Society. Expertise to conduct such analyses can be gained by consulting with experts such as Drs. Paul Lukacs (U of MT), Gary White or Kevin Bestgen (Colorado State U), and Paul Conn or Brett McClintock (NOAA Fisheries, Seattle), and/or attending one of the periodic workshops on MARK (after some self-study, the intermediate-level workshop might be best). Given the large effort and excellent datasets being collected, appropriate design and analysis are a key component missing from the proposed work. Without them, much effort and funding could be wasted. With them, the work could provide landmark information to help fuel sound management decisions.

Response requested: Provide information about how data will be analyzed to yield robust estimates of survival or rates of population change for bull trout.

MFWP Response:

The original proposal for this project proposed to assess the impacts of dam operations (i.e., both past and present) on both physical and biological components of the Kootenai River upstream and downstream of Libby Dam.  One of the metrics proposed to evaluate the effects of modifications to dam operations was estimating survival rates (i.e., cohort and annual survival estimates) of fish species (i.e., primarily rainbow trout and possibly bull trout) in the Kootenai River downstream of Libby Dam.  At that time, authors proposed to use catch curves using historical length and age data collected during the past 3 decades to estimate annual and cohort survival estimates and compare those vital rates to the rates experienced under the Mainstem Amendment operating strategy. 

Kootenai River Bull Trout Survival

A skewed size structure, low sample size, and entrainment of bull trout (DeHaan and Adams 2011) in all sections of the Kootenai River makes survival rates impossible to calculate based on catch curves in the Kootenai River.  We now have MARK and have begun using it to estimate vital statistics using PIT tagging information for bull trout in the Kootenai River. 

Preliminary analyses using MARK indicated that small sample sizes of bull trout (fish handled and later recaptures) limited model selection and only annual estimates of survival were calculated from 2004-2010.  Annual estimates of survival ranged from 32.5% to 63.2%, with capture probabilities ranging from 0.08 to 0.19.  Confidence intervals of the estimates were large (i.e., approximately 10-90% for each year and goodness-of-fit tests were not able to be performed due to small sample sizes of tagged fish and later recaptures.   A pooled recapture probability was estimated which affected annual estimates of survival (range 40.8% to 64.8% and confidence interval were slightly better, ranging from approximately 25 to 75% and again the goodness-of-fit test could not be run.  The average number of bull trout handled in the mainstem Kootenai River is about 50-75 per year, with the exception of 2004, when about 300 fish were handled.  Because no model fit could be evaluated, covariates could not be added to the model as this would only decrease the number of recaptures and further limit analysis.

ISRP Comment:

b. Similar data will be collected for white sturgeon in the Kootenai River, and can profit from a similar design, although the ISRP recognizes that recaptures may be too few for robust analysis. Nevertheless, without a suitable design, it may be difficult to prove that survival is indeed low, or to place confidence intervals around this, or test the evidence for it.

Response requested: Provide information about how data will be analyzed to yield robust estimates of survival or rates of population change for white sturgeon.

MFWP Response:

Kootenai River white sturgeon survival and monitoring

At this time we are not proposing to estimate survival or rates or population change of white sturgeon in the Montana portion of the Kootenai River as sample sizes are too small (N = 2 to 7 per year from 2009-2011, 13 total captures and no recaptures of fish previously captured in Montana).  This portion of our project was designed to update the status of the species in Montana as almost no data had been collected for white sturgeon since harvest was closed in 1979.  Several of the fish captured in Montana were previously included in survival estimates in Justice et al. (2009) and KTOI (2008) which included covariates such as mean length at stocking and number of fish stocked.   Minimum survival estimates for release or tagged brood year cohorts for sturgeon captured in Montana could be made based on number of fish stocked and the numbers captured in Montana by brood year using information from the Kootenai Tribe of Idaho and Idaho Department of Fish and Game.  Much larger sample sizes of white sturgeon would be necessary to estimate vital rates for white sturgeon captured in Montana.  Data collection in Montana is being used to supplement ongoing data collected in Idaho to evaluate effectiveness of hatchery stocking, growth, condition, and to update the status of the species in 20% of the lotic habitat and if survival estimates are updated in the future, capture information from white sturgeon in Montana will be included in that analysis.  Evaluations of condition, growth, CPUE, and contributions of hatchery and wild sturgeon will be made for fish captured in Montana and compared to data collected in Idaho and British Columbia.

ISRP Comment:

c. Problems were reported about estimating survival of rainbow trout, based on concerns about inaccurate ageing using scales. The method proposed for estimating survival in the FY 2010 Annual Report is akin to using catch curves, which is based on many assumptions. It seems like it would be much more efficient to simply PIT tag rainbow trout, avoiding the ageing issues altogether, and estimate survival directly using MARK. This could be done within size classes of interest. Given this, some deliverables need to be modified or dropped.

Response requested: Provide an evaluation of using PIT tagged rainbow trout to estimate survival within size classes. How would using this approach affect currently proposed deliverables?        

MFWP Response:

Kootenai River Rainbow Trout Survival

The original proposal for this project proposed to assess the impacts of dam operations on both physical and biological components of the Kootenai River upstream and downstream of Libby Dam.  One of the metrics proposed to evaluate the effects of dam operations was estimating survival (i.e., cohort and annual survival estimates) of fish species in the Kootenai River downstream of Libby Dam under different strategies.  Oncorhynchus spp. (rainbow and cutthroat trout) population estimates and representative scales samples have been collected since the 1970’s in the Flower-Pipe section of the Kootenai River and provides the best long term data set to evaluate the impacts of modified dam operations on survival, growth, and condition of fish in relation to dam operations but other limited data sets are available covering the past 10-15 years.

At the time of the original proposal, we proposed to use catch curves of historical length and age data collected during the Pre-Biop, Biop, Transition, and Transition operating strategies (i.e., WY 1972-2008) and compare those vital rates to the rates experienced under the Mainstem Amendment operations which were fully implemented in October 2009.  Survival of rainbow trout using catch curve analysis can provide estimates of annual and cohort survival assuming accurate estimates of age can be made. However, based on limited information collected to date,  fish >300 mm collected near Libby Dam cannot be accurately aged.  Therefore, the utility of using catch curves to estimate fish survival throughout the Montana portion of the Kootenai River requires additional work to evaluate the feasibility by validating age estimates for all sizes of rainbow and cutthroat trout, including fish of all sizes.  This work will include collection of adequate samples of fish across a variety of length sizes from several sections of the Kootenai River over the next few years in cooperation with the Libby Mitigation Project (199500400).   

A large PIT tagging effort was initiated in four sections of the Montana portion of the Kootenai River in 2011 during annual population estimates to estimate survival, validate age estimates, and assess growth in the Kootenai River.  Survival estimates will be calculated using MARK and covariates such as section and length may be added depending on the number of recaptures.  Typical capture efficiencies between the mark and recapture run typically range from 10-15% but survival of fish from one year to the next is unknown.  MFWP used approximate numbers fish handled in each of the four sections of the Kootenai River and made some assumptions about annual survival rates to assess potential numbers of recaptures in future sampling efforts.  We expect annual marking (PIT tagging) sample sizes of fish of  to be: Dam-Fisher 300-500, Rereg 300-500 per year, Flower-Pipe 1300-1500 per year, and Troy 500 fish per year.  Sample sizes differ between sections due to differences in abundance between sections.  The numbers of PIT tags deployed over 3-5 years during this effort are much higher than those used for bull trout from 2004-2010 in the Kootenai River and should provide more robust estimates of survival and allow inclusion of covariates such as length and river section if sufficient numbers of recaptures are encountered.  The duration of this study is expected to be 3-5 years and it is a cooperative effort between the Libby Mitigation Project 199500400, the Mainstem Amendment Project 200600800, and the MFWP fisheries management program.       

Recaptured fish during future estimates will allow validation of age estimates as each fish has scales collected when originally marked and again on each recapture event.  Validation of age estimates will allow us to determine if proceeding with catch curve analysis will continue.  However, if age estimates are not accurate, estimates of survival using catch curves will not be pursued further to assess the impacts of past and present dam operations and only survival estimates using PIT tags beginning in 2012 will be used for comparisons to future estimates of survival under future operating strategies. 

ISRP Comment:                                                     

d. Population estimation for salmonids can also be improved markedly with new methods in MARK (see Saunders et al. 2011 NAJFM for an example), which can integrate analysis across all size classes and even among different locations or sites. This improves power greatly by estimating capture probabilities for a much larger sample of fishes, with a continuous covariate for fish length (Huggins model) and other covariates for sites or times. In contrast, the method proposed and commonly used of estimating abundance for several size classes of fish at each site separately produces estimates with wide confidence intervals because they are each based on small sample sizes.

Response requested: Provide an evaluation of using the new methods in MARK for population estimation.            

MFWP Response:

We are qualifying this response: we assume it was meant for juvenile bull trout abundances in Quartz Creek based on Saunders et al. (NAJFM 2011).

See 1C above. 

MFWP has a current state standard program for data analysis of population estimate data including mark-recapture and depletion techniques.  MFWP is currently in the process of upgrading the program and software our agency utilizes to analyze population estimates obtained using mark recapture and depletion methodologies.  The new software within our  Fisheries Information System includes the options listed below:  

            Depletion Methods

Depletion methods include: the Leslie Method - Step-by-Step Regression, Leslie Depletion, DeLury - Step-by-Step Regression, DeLury – Depletion, K-Pass Removal - Step-by-Step MLE, and Zippin's K-Pass Removal techniques.

            MRCap Closed Population

            Closed population estimators can be run for single or combined species, with or without replacement, by user specified length groups, and calculation methods include those using a single census such as Petersen, Chapman,  Ricker, and Bailey.  Multiple census techniques are also available and include: Schnabel and Schumacher Eschmeyer.  All estimates can be performed with inclusion of user specified confidence intervals.

            MRCap Open Population

Open populations can be estimated using Jolly-Seber Estimate of Abundance and can utilize covariates. Models included are: CJS open population and Huggin’s closed population. Link functions include: logit, sine, and hazard. Model selection, model averaging routines, and plots are also available. CJS methods produce estimates of population size using the Horvitz-Thompson estimator.

Thank you for providing us the valuable references regarding potentially better analysis methodologies in MARK.  We will explore the capabilities of Program MARK and our new data analysis package which includes many of the same options and capabilities as MARK.  

Juvenile estimate data in Quartz Creek is analyzed using depletion techniques with a lumped capture probability for all fish >75mm but estimates can be split into user defined length group(s).  Juvenile bull trout densities are reported as the number of fish >75 mm per 100m². Output from analysis includes capture probabilities for the  length group(s) specified by the user and includes 95% confidence interval(s) for the estimate and capture probabilities.

Many of the streams containing bull trout are only sampled once per year by performing depletion estimates (i.e., 2-3 pass depending on capture probability performed by 5-6 people) of juvenile bull trout >75mm in one 150 meter reach near bridge crossings, including Quartz Creek.  Sampling during these estimates involves using 2-3 backpack electrofishing units and block nets.  While some of the data collected during these efforts is being used by this project (i.e., we PIT tag fish during these estimates and report some of the data in our reports), most of our work in Quartz Creek uses different sampling techniques due to staff size limitations and field logistics.  We are evaluating emigration patterns and returns rates of emigrating juvenile bull trout in Quartz Creek.  Ten to fifteen reaches (100-200m long) are sampled annually throughout the drainage using single pass electrofishing without the use of block nets.  Usually, only 2 staff members are available during electrofishing which makes depletion techniques difficult to perform in remote locations due to stream size, increased gear demands, stream access, floating debris, and MFWP electrofishing safety protocols. 

Approximately 40-50% of the bull trout PIT tagged annually emigrate from Quartz Creek into the Kootenai River and the number of recaptured bull trout in Quartz Creek annually is low (i.e., <20 per year) despite tagging hundreds of fish.  We generally do not see many juvenile or adult bull trout in the sections of the Kootenai River adjacent to the confluence of Quartz Creek.  We will look into more detailed analysis methods including mark-recapture data for open populations in MARK and our new system using the PIT tag information and recaptures in Quartz Creek. 

ISRP Comment:

e. Questions about factors affecting Didymo invasions should be developed as alternative plausible models or hypotheses, which can be tested using model selection (see Burnham and Anderson 2002). This method allows evaluating the weight of evidence for alternative models, and estimating parameters using multi-model inference to more fully use the information gained. Expertise in these methods can also be gained from the people listed above. Moreover, there are several proposals from this region addressing the same topic, and all have substantial budgets, so the ISRP is interested for clarification on how the workload will be shared.

Response requested: Provide alternative models or hypotheses about factors affecting Didymo invasions and outline how current and future data could be used to evaluate the alternatives.    

MFWP Response:

Prior to 2009, there was almost no temporal and spatial data collected on the seasonal growth patterns, biomass, and coverage of D. geminata despite being present for almost a decade in the Kootenai River downstream of Libby Dam.   We now have 2-3 years of data showing the seasonal growth cycle of D. geminata in the Kootenai River.  Blooms of mat material typically occur during the winter months (January-May) but can persist throughout much of the year depending on discharge from Libby Dam.  Biomass and coverage are highest directly downstream of Libby Dam and generally decrease as distance from the dam increases.  D. geminata has been observed as far as 35 miles downstream of Libby Dam. These finding are being used to direct more focused research hypotheses and research proposed by the Libby Mitigation Project (199500400).  Recent research indicates that the concentration of SRP / DRP (soluble reactive phosphorus / dissolved reactive phosphorus) may be the major factor affecting presence of blooms of D. geminata.  Under potentially limited conditions of SRP, blooms of D. geminata occur and result in increased stalk length (Kilroy and Bothwell 2011 and 2012, Bothwell and Kilroy 2010).  Alternative mechanisms for D. geminata blooms have been proposed including biochemical pathways including utilization of iron and phosphorus (Sundareshwar, 2011-2012, personal communication).  Both of these hypotheses (i.e., SRP and iron/phosphorus) are scheduled to be tested in the Kootenai River in the next few years under the Libby Mitigation Project in hopes of identifying mitigation or control actions to greatly reduce or eliminate blooms in the Kootenai River.  This scope of monitoring under this project is being reduced.  We will continue monthly monitoring in the Kootenai River to provide more baseline data on the biomass, coverage, and thickness to assess the effectiveness of any treatments or changes to dam operations resulting from research hypotheses under the Libby Mitigation Project beginning in 2012.  Analysis of the 2009-2011 Kootenai River data are currently being conducted using correlation and regression techniques to investigate the relationship between several abiotic factors and the biomass, coverage and thickness of D. geminata in the system and impacts of dam operations and influences of water quality parameters.

Didymo has been observed in the past several years within the Flathead River system; however, only recently has attention been directed toward documenting its distribution, growth, seasonal abundance, and other variables potentially associated with its presence. Monitoring was initiated in July 2011 to quantify growth, biomass, coverage, and possible associated water quality variables, including nutrient chemistry (e.g., SRP, total P, iron, etc.), pH, ultraviolet light, dissolved oxygen, conductivity, flow, and temperature. Results will be compared to conditions in the Kootenai system and will render a better understanding of seasonal variation in didymo presence as well as factors associated with blooms. Hypotheses to be tested are shown below (also listed earlier), and may be refined as more information is gathered:

H_o = The monthly average percent coverage and thickness of D. geminata mats is equal

H_a = The monthly average percent coverage and thickness of D. geminata mats is not equal

H_o = The monthly ash free dry mass of D. geminata mats is equal

H_a = The monthly ash free dry mass of D. geminata mats is not equal

H_o = The annual ash free dry mass of D. geminata mats is equal

H_a = The annual ash free dry mass of D. geminata mats is not equal

H_o = Discharge (peak and volume) does not affect D. geminata coverage and thickness 

H_a = Discharge (peak and volume) does not affect D. geminata coverage and thickness 

H_o = Water quality parameters at sites with and without D. geminata are equal

H_a = Water quality parameters at sites with and without D. geminata are equal

The USACE and KTOI are currently collecting monthly water samples for analysis of TP and SRP in the Kootenai River throughout the year to assess if seasonal differences exist.  All data are frequently discussed and updated and collaborative efforts require communication and coordination of efforts and information between the numerous agencies and staff involved in both Montana and Idaho.

Kilroy, C. and M. L. Bothwell.  2011. Environmental control of stalk length in the bloom-forming, freshwater benthic diatom Didymosphenia geminata (Bacillariophyta).  J. Phycology. In Press.

Kilroy, C. and M. L. Bothwell.  2012. Didymosphenia geminata growth rates and bloom formation in relation to ambient dissolved phosphorus concentration.  Freshwater Biology, pages 1-13.

Bothwell, M. L. and C. Kilroy.  2010. Phosphorus limitation of the freshwater benthic diatom Didymosphenia geminata determined by the frequency of dividing cells. Freshwater Biology 56: 565–578.

 P. V. Sundareshwar, South Dakota School of Mines and Technology, Rapid City, South Dakota, USA, personal communication.

ISRP Comment:                                                     

f. The information on delta aggradation and potential blockage of bull trout migrations is very interesting and important, but no questions were developed, and no methods or statistical analyses discussed for evaluating these changes.

Response requested: Develop questions and identify methods of analysis to evaluate changes due to delta aggregation and potential blockage of bull trout migrations.     

MFWP Response:

Point location data including X, Y, and Z coordinates at each delta will be imported into Microsoft Excel from the survey equipment and then into ArcMap 9.3 (ESRI 2009).  Point data are used to create 3D surfaces of the topography at each delta.  Contours and surfaces will be interpolated by converting point locations coordinates (X, Y, and Z) collected in the field to a raster dataset using the Natural Neighbor technique and a raster cell size of 1.  Comparisons of changes to the topography between historical survey(s) and recent survey(s) at Quartz Creek, Pipe Creek, O’Brien Creek, and Libby Creek will be / were performed using Spatial Analyst extension in ArcMap.  We will use the initial survey shapefile at each delta as the base or zero layer to calculate the elevation difference between surveys using the MINUS and NEGATE function in the Spatial Analyst extension.  This will calculate the elevation change (i.e., + or -) between surveys over common survey areas of the delta for spatial analysis.  Pictures will be taken of each delta periodically to document any significant changes in elevations that occur.  Conversion of location and elevation data from local coordinates to UTM’s and actual elevations may be necessary at Libby Creek and Quartz Creek deltas to allow longer term comparisons to data presented and collected by Zelch (2003) at Libby (1995 and 2002) and Quartz Creek (1987 and 2002).   

Zelch, Karen. 2003.  Aggradation of alluvial fans in tributaries to the Kootenai River, Idaho and Montana.  Master’s Thesis. University of Idaho, Moscow.  2003.

H_o = The topography (i.e., elevation) of each delta is the same as previous survey(s)

            H_a = The topography (i.e., elevation ) of each delta is not the same as previous survey(s)

Monitoring of stream channel and delta elevations combined with assessments of a time series of data will be performed to assess aggradation at six deltas in the Montana portion of the Kootenai River.  Recent changes to dam operations including establishment of bull trout minimum flows and average or below average water supply forecasts compared to the pre-Biop period (WY1972-1994) may be leading to behavioral and physical barriers for migratory fish species.  This may be one potential cause for declines in bull trout redd counts in some tributaries downstream of Libby Dam.  Measurements of stream channel slope, water depths, and water velocities should be recorded periodically during the spawning season(s) at tributaries with more vertically developed deltas. 

ISRP Comment:                                              

g. Adaptive Management: Most material in the text is a small component of adaptive management. It is suggested that the sponsors develop an adaptive management process that is responsive to the resources as well as to the public and to management needs.

Response requested: Provide an Adaptive Management plan to describe a process that is responsive to the resource, public, and management needs.

MFWP Response: 

Impacts of the Mainstem Amendment operations were supposed to be monitored throughout the Columbia River basin but entities in the lower portions of the basin have not monitored the impacts to date.  Changes to discharges in the lower Columbia River system resulting from changes at Libby and Hungry Horse dams were very small and nearly undetectable.  Consequently, lower basin entities  indicated that observed impacts could not be related to the Mainstem operations.  Potential impacts at higher trophic levels are being quantified in Montana while addressing impacts to other variables physical variables such as water temperatures, discharge patterns, draft and refill rates, discharge variation, water residence times, and physical habitat.

All work plans developed for the Mainstem Amendment monitoring project are reviewed by the Regional Fisheries Manager and any concerns are discussed between the Fisheries Manager and the Mitigation Coordinator.  Additional staff meetings may also be held to discuss issues regarding proposed work.  The mitigation and research efforts in this project are intended to inform fisheries management staff about the life history, trends and status of fish populations, and provide information regarding impact of dam operations on the fisheries of the Kootenai and Flathead rivers with assistance and cooperation of the Libby (199500400) and Hungry Horse Mitigation (199101903) projects.  This project is also designed to inform action agencies, system operators, and policy makers about the impacts of recent modifications to dam operations on the physical and biological communities upstream and downstream of Libby and Hungry Horse dams.

Development and establishment of goals and quantifiable objectives for the fisheries in the Kootenai and Flathead River drainages will allow better decisions to be made and allow more adaptive and focused management, mitigation, research, and monitoring efforts.  A statewide MFWP Fisheries Management Plan is presently in development and will guide the synthesis and implementation of goals and objectives that blend conservation of shared aquatic resources, public needs and desires, and management priorities.

If the Mainstem Amendment or other recent dam operations result in significant positive impacts on the biological and physical aspects of the Kootenai and Flathead rivers or at Hungry Horse or Libby reservoirs, continuation or reimplementation of those operations may be proposed while considering the new constraints of the system, political and public interests, documents such as biological opinions, seasonal discharge and flood control requirements, life histories and requirements of various listed fish species, and critical habitat designations.  However, if negative impacts are documented, modifications to dam operations or other mitigation efforts may be proposed.  Mechanisms for the negative impacts must be explained and documented and any modifications will involve a large numbers of agencies, staff, and publics throughout the Columbia River Basin in the United States and British Columbia.

If significant aggradation is occurring at deltas downstream of Libby Dam, stream restoration or mitigation efforts including modifying discharges of the Kootenai River, physical removal of materials at each delta, and restoration of the stream channels to increase mobilization of materials may be proposed to eliminate or reduce any physical or behavioral barriers.

Fish growth and diet information combined with the benthic invertebrate and fish survival information may be used to direct fisheries management activities including modifications to regulations, size limits, and seasons in the Kootenai River.  Additionally, if physical aspects of the Kootenai River are shown to impact growth of fishes (e.g., water temperature), modifications to dam operations may be proposed including changes to the thermal targets and possible addition of nutrients to reduce the severity of D. geminata blooms.  Other mitigation efforts including addition of large woody debris and detritus are being considered because inputs of these materials to the Kootenai River downstream of Libby Dam over the past 40 year have been greatly reduced.  Inputs of woody debris, sediments, and detritus downstream of the Fisher River are more normative and restoration of the 3.5 miles between Libby Dam and the Fisher River.  Diversification of habitat conditions by placing or creating larger substrates, scour pools, and woody debris between Libby Dam and the Fisher River are also being considered.       

White sturgeon monitoring from 2009 to 2011 in Montana resulted in new information on the status of the species in the Kootenai River.  If the white sturgeon captured between 2009 and 2011 remain in Montana until they are sexually mature (i.e., another 5-10 years), monitoring efforts to document spawning may be warranted.  Habitat conditions for spawning in Montana are better than current white sturgeon spawning locations in Idaho because of increased substrate sizes.  Much of the Montana portion of the Kootenai River contains gravel and cobble substrates which are preferred over the sand and clay substrates currently being used in Idaho.  Spawning of white sturgeon has not been previously documented in Montana but few monitoring efforts have been performed over the past 30 years.  Movement of fish into Montana combined with potential spawning may lead to increased natural recruitment of the species in the Kootenai River which would be a step towards recovery and delisting of the species.

ISRP Comment:                           

h. Emerging Limiting Factors: The sponsors seem to have a good understanding of most emerging factors. However, changes in winter icing conditions were not mentioned, and could become increasingly important with time.

Response requested: Identify how winter icing conditions would affect the proposed project objectives.

MFWP Response:

Winter icing is not a concern in the Kootenai River downstream of Libby Dam in Montana unless severe drought occurs resulting in complete evacuation of the Libby and Hungry Horse Reservoir pools and extended periods of cold weather which could result in winter icing similar to pre-dam conditions.  Winter outflow water temperatures from Libby Dam averaged 36.8^oF from 1977-2010 during January and February, which is the period on record with selective withdrawal.  The minimum water temperature recorded downstream of Libby Dam was 34^oF during periods of deep drawdown in 1986 but more recent operations typically result in minimum temperatures of 37-40^oF during shallower drafts of Libby Reservoir. 

Winter icing in tributaries may be an issue in some streams based on observed anchor ice formation in downstream reaches and water temperature information collected over the past few years.  Anchor ice formation occurs in some streams if air temperatures near or below -5 to -10^oC or 15-20^oF for a period of about a week.  It will be difficult to quantify these any impacts as many higher elevation locations are nearly inaccessible during the winter months due to snow depth and could result in hazardous sampling conditions.  We are assessing juvenile density estimates by cohort in Quartz Creek and attempting to quantify potential impacts of rain on snow events, large spring outflows, or other anomalous weather conditions observed.  Several missing or greatly reduced cohorts have been observed since 1997.

ISRP Comment:

i. Data Management: What percentage of the total budget is dedicated to data management? How is data QA/QC addressed for specific projects activities? Please describe anticipated improvements in the data management system expected to occur over the next few years (e.g., cloud computing, new software, equipment upgrades).

Response requested: Provide a response addressing issues raised in item i. 

MFWP Response:

We estimate that data management (entry / uploading, QA / QC, data management / organization) is approximately 5-10% of our personnel budget. 

The data this project utilizes comes from many sources including those collected in the field or uploaded or obtained from external sources (e.g., United States Army Corps of Engineers, Idaho Department of Fish and Game, Kootenai Tribe of Idaho) on an annual basis.  This project currently uses Microsoft Excel to manage the majority of the data as state policy does not allow use of ACCESS to create databases without permission.  All data is currently managed locally on personal computers and is backed up on servers daily.  No new data management systems are anticipated in the next few years although MFWP is finalizing a new statewide data repository and analysis system including fish population estimates, fish tagging, gill netting, water quality, fish condition, and other information. This system is near completion and some of these data will be stored and managed as part of this system. 

QA/QC is addressed in all activities involving collection or acquisition of data.  All data collected during fish handling activities (including species, length, weight, injuries, PIT tag codes, injuries, other marks, etc.) are recorded on datasheets in the field.  All PIT tag codes are read in various PIT tag readers and downloaded and saved (error rates roughly 1 per 1 million scans).   Length and weight data are plotted and any outliers are removed or checked on the original datasheets.  After checking original data, relative weights are checked and any high ((>150) or low (<50) relative weights are removed.  Downloaded data from the USGS or USACE including discharge and temperature are also checked for inaccurate data or missing data.  Population modeling and statistical analyses in the new information system came from R and includes linear and nonlinear modeling, classical statistical tests, time-series analysis, classification, clustering, and graphing.  Other spatial and statistical analysis and modeling is performed using SAS, SPSS, ArcMap, AutoCAD, MARK, and other programs. 

ISRP Comment:

j. The sponsors need to improve their collective productivity by publishing peer-reviewed articles in professional journals.

Response requested: Describe plans to publish in peer-reviewed journals.          

MFWP Response:

Although the impacts of the Mainstem Amendment operations are not far enough along to make definitive conclusions about the impacts on either the physical or biological components of the Kootenai and Flathead River systems, the Instream Flow Incremental Methodology (IFIM) research conducted in both systems has been published (Muhlfeld et al. 2010) or is near completion.  While this project has received funding for 6 years, it was not fully staffed until 2008 and the MA operations were not in effect until October 2008.  At least 2-3 more years of continued implementation and monitoring of the Mainstem Amendment operations may be necessary before meaningful analysis and interpretation of impacts will be possible.  However, at that time, we anticipate publishing results in peer-reviewed journals.

ISRP Comment:  

2. On the Flathead River system, where work is apparently more advanced, several main points require response:

a. Analysis of bull trout survival and rates of population growth require a more robust approach using current capture-recapture analysis methods like those included in Program MARK. Please see point 1.A. above.

Response requested: Provide information about how data will be analyzed to yield robust estimates of survival or rates of population change for bull trout on the Flathead River system.

MFWP Response:

Flathead River bull trout survival

A multi-year study was initiated in 2005 to estimate survival of juvenile bull trout to adulthood in Trail Creek, a tributary to the North Fork Flathead River containing an adfluvial population of the species. An additional, parallel study was initiated in another North Fork Flathead tributary, Big Creek, in 2009. These studies used passive integrated transponder (PIT) technology to determine both instream survival and survival from emigration to adult return. Quantification of survival to emigration was performed by enumerating PIT-tagged juveniles as they departed their stream of origin (using fixed monitoring antennas), accounting for an estimated conservative tag loss rate of 3% (Prentice 1990; Ombredane et al. 1998; Zydlewski et al. 2001; Bateman and Gresswell 2006) and antenna efficiency (95% confidence intervals = 95.21% ± 0.02% for Trail Creek post-2009 antenna replacement, 99.50% ± 0.01% for Big Creek). Similarly, survival from emigration to adulthood was to be quantified as the proportion of emigrated fish returning to spawn, accounting for detection efficiency and tag loss. About 30% of juveniles survived to emigration in Trail Creek, with 28% successfully emigrating from Big Creek. To date, one putative pre-spawning adult has returned to Trail Creek out of 1,289 fish tagged. However, variables including antenna malfunctions prior to system replacement and upgrade in 2009 (Trail Creek), the limited number of bull trout tagged annually, and the subsequent cessation of tagging efforts in both drainages has restricted the capacity of data analyses. These issues, in addition to concerns associated with handling weak stocks of ESA-listed fish, have limited the project to continuous operation, periodic maintenance, and efficiency evaluation of antenna arrays at minimal cost to optimize the likelihood of detecting a tagged fish returning to spawn.

ISRP Comment:

b. The accomplishments presented about whitefish tracking in the Flathead River were useful information, but no study plan of focused questions was presented for the future, and there was no indication about how these data will be analyzed to answer specific questions.

Response requested: Develop questions and identify methods of analysis to evaluate whitefish tracking data.              

MFWP Response:

Questions addressed through the tracking of radio telemetry-tagged mountain whitefish in the Flathead River system included:

What proportion of tagged fish remained in dam-influenced areas of the system for the duration they were tracked?

How far from the original tagging location were fish tracked? What time of year did this occur?

What habitat types (e.g., pool, run, riffle) were used during different flow and temperature regimes?

What proportion of fish putatively spawned?

What are the relative weights (Wr) of tagged fish?

How old are tagged fish?

Acknowledging that data collection is ongoing and analyses thus far are based on one tagging season’s worth of data, the following describes the results of analyses conducted (which will continue with additional data input from 2011 efforts).

 What proportion of tagged fish remained in dam-influenced areas of the system for the duration they were tracked?

 The proportion of tagged mountain whitefish that resided within dam-influenced areas for the duration of their tag lives (20 of 29, or 69%) was the result of a simple analysis of tracking data collected during April-December 2010. Specifically, fish tracked outside dam-influenced portions of the Flathead system (i.e., upstream of the South Fork Flathead confluence or downstream of the Stillwater River confluence) were recorded as having spent a portion of their radio tag lives outside dam-influenced areas. Most fish (7 of 9) spent more of their tag battery lives within dam-influenced portions of the river than outside (i.e., below Hungry Horse ground station) (Table 1). Median number of days spent above dam-influenced areas was 51 (range = 2-140) where as the median number of days spent within dam-influenced areas was 95 (range = 67-245). The median proportion of tag battery lives spent outside of dam-influenced areas was 32% (range = 1-67%).

Table 1. Movements of mountain whitefish implanted with radio telemetry tags in the Flathead River during 2010. Only fish that moved upstream of dam-influenced portions of the Flathead are described. DIA = dam influenced area.

Fish tag ID	Days above DIA	Days within DIA	Proportion of tag life above DIA
45	12	95	11%
47	51	245	17%
50	135	67	67%
54	22	82	21%
55	107	138	44%
57	140	85	62%
58	44	93	32%
64	2	243	1%
66	121	124	49%

 How far from the original tagging location were fish tracked? What time of year did this occur?

The average distance moved by these nine fish from the furthest downstream to the most upstream location (home range) was 54.8 km (range 27.9-100.0 km). All nine fish moved upstream of the South Fork Flathead confluence. Four of the nine fish entered the Middle Fork of the Flathead River, four entered the North Fork Flathead River, and one moved upriver (above the confluence of the South Fork Flathead River) into Hungry Horse Canyon. No fish were documented entering tributaries to spawn. The average date of movement upstream of the South Fork confluence was July 25 (range 6/28-10/8), returning an average of 3 months later (October 26; range 9/10-11/28).

What habitat types (e.g., pool, run, riffle) were used during different flow and temperature regimes?

More detailed habitat use information was collected beginning in 2011 and will be analyzed once tags expire (mid-late June 2012). However, analyses will include comparisons of habitat use (characterized as riffle, pool, or run) with ambient discharge and temperature. Location of fish laterally along the river corridor will also be compared to physical parameters.

What proportion of fish putatively spawned?

Spawning was determined to have taken place if a fish moved up or downstream of its “home range” (i.e., the portion of river inhabited outside of spawning season) and into a habitat unit characteristic of spawning (i.e., pool tail-out or riffle). Kick-netting for egg collection was performed in areas of putative spawning to corroborate this assumption. Although spawning can occur without pronounced up or downstream movements, we could not confirm this empirically and therefore categorized fish that did not act as indicated above as “non-spawners” (Northcote and Ennis 1994). The nine fish that were tracked upstream of dam-influenced portions of the Flathead were assumed to have spawned based on movement and by the production of eggs through kick-netting in the immediate vicinity of tagged fish.

What are the relative weights (Wr) of tagged fish?

Relative weight (Wr) was calculated to determine the condition of each fish at tagging. A standard weight equation for mountain whitefish was used to compute these indices (Rogers et al. 1996). Relative weights (Wr) of fish collected in 2010 ranged from 74-97 (median = 90).

How old are tagged fish?

 

Scales were collected from radio-tagged fish for age and growth calculations. Blind age calculations were independently performed on samples from 28 fish by three individuals to quantify variability in age assignments using the coefficient of variation (CV). Only 25 of the 28 samples were readable by all three reviewers, however. Growth analyses will be combined with additional samples collected in 2011, paired with otolith analyses, further quantifying the validity of scale-based aging in this long-lived species.

Age determination and analyses of CV indicated disparities among reviewer age assignments. Identical ages were determined by all three reviewers for only two fish, with the greatest difference in assigned age for any given fish being 4 years (age 7 versus age 11). The median CV for age assignments was 15.7 from a range of 0-28.9. These results support the future pairing of otoliths with scales in addition to the employment of multiple blind reviewers to most accurately and precisely estimate age (and in the near future, growth) of mountain whitefish.

Although we have gained pertinent information regarding basic mountain whitefish movement and life history information, concern for the species’ sensitivity to radio telemetry tagging and electrofishing has directed our near-future efforts toward investigating micro-elemental and isotopic ratios throughout the lower Flathead system as partial surrogates for active tracking. Analyses of temporal and spatial microchemical differentiation in Ba:Ca, Sr:Ca, and Sr isotope ratios will be tested in 2013 (Muhlfeld et al. 2005). If significant differences are detected, otolith and scale samples will be collected from mountain whitefish in 2014 to determine residence time within and outside of dam-influenced portions of the river.

ISRP Comment:                      

c. Points 1.G., and 1.I. from above also need to be addressed for the Flathead River system.

Response requested: Provide an adaptive management plan to describe a process that is responsive to the resource, public, and management needs for the Flathead River system. Respond to the questions posed in item i above with respect to the Flathead River system.

MFWP Response:

The Adaptive Management Plan described in response to the ISRP’s request for the Kootenai system applies to the Flathead as well because both drainages are managed by the same regional and state-level entities.

In response to item 1.I, we estimate (as in the Kootenai system) an approximate allocation of 5-10% of our personnel budget and less than 1% of our operations budget are dedicated to data management, QA/QC, and system improvements.

Data management begins at the study design level, organizing databases, data sheets, and personnel to gather and store data efficiently and accurately to address the intended purpose of its collection.  Field data is entered into Microsoft Access and subsequently organized, queried, and exported to various programs as needed (e.g., Microsoft Excel).  Data are checked for errors as it is entered, and checked again once it is exported for analyses.  Data are shared with the MFWP statewide Fisheries Information System, MFISH, and distributed in annual report form. External data acquired from sources such as the USGS, NPS, USFS, and others are examined for errors prior to use.  Software used for analyses can include but are not limited to R, ArcMap, ArcGIS, SigmaPlot, FSTAT, Genepop, and STRUCTURE.  MFWP upgrades employee operating systems every five years, and as a result we will be replacing one machine within the next two years.

Retrospective Evaluation of Results: This project has been ongoing for six years, during which the flow regime has been changing in the Kootenai River, but has been more stable in the Flathead River. Partly as a result of recent changes, project results are farther advanced for the Flathead River system than the Kootenai. Key questions about effects of ramping rates and reservoir levels on bull trout habitat use and benthic invertebrates have been answered in the Flathead River, although further questions remain about potential effects on native mountain whitefish and an invasive diatom (Didymo). These are the subject of ongoing study. In contrast, data on the effects of the new regime in the Kootenai River have been collected for several years since the flow regime change in 2008, but it will take more years before sufficient data are available to compare to previous regimes. Five years of data after the regime change would be a minimum to allow useful analysis. Nevertheless, better designs are needed for analysis of these before-after comparisons to capitalize on the substantial data being collected in the Kootenai River.