FY 2003 Mainstem/Systemwide proposal 200304100

Section 1. Administrative

Project location

Reasonable and Prudent Alternatives (RPAs)

Section 2. Past accomplishments

Section 3. Relationships to other projects

Section 4. Budget for Planning and Design phase

Task-based budget

Outyear objectives-based budget

Outyear budgets for Planning and Design phase

Section 5. Budget for Construction and Implementation phase

Task-based budget

Outyear objectives-based budget

Outyear budgets for Construction and Implementation phase

Section 6. Budget for Operations and Maintenance phase

Task-based budget

Outyear objectives-based budget

Outyear budgets for Operations and Maintenance phase

Section 7. Budget for Monitoring and Evaluation phase

Task-based budget

Outyear objectives-based budget

Outyear budgets for Monitoring and Evaluation phase

Section 8. Estimated budget summary

Itemized budget

Total estimated budget

Cost sharing

Reviews and recommendations

This information was not provided on the original proposals, but was generated during the review process.

Comment:

The objective is to use empirical experiments to quantify delayed effects associated with hydrosystem passage. There is a logical need to address the problem of assessing dam passage mortality and the team possesses the experience and background to address the problem.

The ISRP questions whether this experiment will settle the issue because concern was originally for extra mortality to Bonneville and it is not clear that results from this experiment will apply. In this proposal, although the objectives are clearly defined, the methods do not appear appropriate for determining a clear answer to the hypothesis being tested. Determination of significant differences in delayed mortality due to passage through 8 dams versus passage through 4 or fewer dams will not be possible with the current study. The proposal asserts that if the null hypothesis is rejected, it is highly likely that migration through Snake River dams does cause extra mortality in spring/summer chinook salmon smolts. An assumption (unstated) is that the effect due to transport is the same for fish experiencing dam passage plus transport stress as it is for fish experiencing only transport stress. Is this assumption justified? It is possible that some fish experiencing dam passage alone would survive but due to experiencing transportation stress prior to dam passage stress, they succumb. Therefore comparing extra mortality for transportation only with extra mortality for transportation plus dam passage may not provide an unbiased estimate of the dam passage effect.

Questions: Have the authors considered conducting a study on fall Chinook instead or in addition to spring/summer Chinook? Could something be done to estimate the effects of the different impacts of spill, turbines, and bypass system instead of merging everything in dam passage as one thing? Are there procedures in place to ensure that good estimates of expected mortality at the dams for fish migrating in-river are obtained so "extra mortality" is clearly defined?

An excellent effort was made to do a power analysis in order to determine adequate sample sizes. One correction necessary is to note that a one-tailed procedure is required so alpha should be used rather than alpha/2 in the sample size formula.

Action Agency/NMFS RME Group Comments:

HYDRO SUBGROUP -- The authors indicate the proposed research provides information useful in satisfying RPAs 188 and 195.

The objective of RPA 185 is to contrast productivity and hydrosystem effects (delayed) between wild stocks in upper Snake stocks and those in the Lower Columbia Basin. To accomplish this, the RPA calls for PIT-tagging both wild population complexes with PIT tags. This proposal relies heavily on hatchery stocks from the Snake drainage as the population monitored. Thus its ability to fully satisfy the intent of RPA 188 is not readily apparent. The primary objective of this research is to identify the existence and generally quantify the magnitude of extra mortality as associated with dam passage. The linkage to the RPA is not all that pronounced.

The objective of RPA 195 is to establish how much post-Bonneville mortality is attributable to natural causes or other processes, such as hydrosystem passage or general fish fitness. This proposal is relevant to the fundamental intent of this RPA, i.e., identify delayed effects associated with hydrosystem passage. The proposed research clearly addresses the hydrosystem contribution to any extra, unexplained mortality that may exist. The experimental approach appears sound. However, the sample sizes necessary to provide the precision targets are considerable (~ 236,000 PIT-tagged @ LGR) and may be a challenge to acquire in some brood years.

Ancillary Benefits. These tagged yearling chinook will also yield inriver survival estimates. The large sample sizes all but ensure improved precision over most extant smolt survival estimates. This could be advantageous to the extent these estimates can be incorporated into survival Performance Standards tests prescribed in the BO. The proposal does not discuss the suitability of these estimates for such evaluations. The RME Hydro Work Group encourages the authors to explore this application and incorporate it as a section in the proposal.

ISRP Remarks on RME Group Comments: The ISRP does not agree with the RME Workgroup comments that the experimental approach appears sound as noted above. Other RME Workgroup comments relate to RPA connections and ancillary benefits that are not noted in the ISRP review comments.

Comment:

Comment:

Comment:

It has been argued by process of elimination that "extra mortality" is attributable to conditions experienced by smolts of Snake River stocks of chinook in their outmigrations through the hydrosystem. Arguments purporting to demonstrate the existence of "extra mortality" are primarily based on unconvincing comparisons with SARs of Lower Columbia River Basin stocks that are outside the Snake River. Since the differences observed favor the lower river stocks to a larger degree than expected based upon the "measured" in-river losses of upriver stocks, it was postulated that there might be an element of "delayed or extra mortality" that occurred in the ocean after the fish passed Bonneville Dam, the point of the last "measurement". In fact, the "measurements" consist of projections of average losses measured in the Snake River that are assumed to apply from McNary Dam to below Bonneville Dam. In our view, the assumptions and the methods used to develop the projections are of highly questionable validity.

The present proposal is adopting a definition of "extra mortality" as a component of mortality in a MCN-BON SAR attributed to conditions experienced previously in the in-river smolt passage LGR-MCN. This has a narrower focus than the PATH definitions, since it does not include the MCN-BON reach for smolt passage.

This is a design with two treatments and no control. The design measures MCN-to-BON SAR for two treatment groups: fish that were truck-transported as smolts LGR-ICE, and fish that spent equivalent truck transportation time going nowhere followed by in-river passage LGR-ICE. The truck-only treatment group is subject to "delayed mortality," and the truck-followed-by-in-river treatment group is subject to "delayed mortality" plus "extra mortality." This experiment provides information about delayed effects of transport plus passage through a differing number of dams for the two groups. It does not provide information about the effect of differing number of dam passages alone. There is an implicit assumption of additivity for these effects. With the additivity assumption, and the assumption that "delayed mortality" does not begin to be expressed until the fish are below MCN, one could calculate "extra mortality" as the difference between the mortality rates measured in the MCN-BON SAR for the two treatment groups. Regardless of the assumptions, there would be no opportunity just with this design to estimate "delayed mortality." Delayed mortality and extra mortality might be isolated by providing an additional experimental group not transported, as recommended in item 2 below.

A power to detect a 20% difference, with 95% confidence, 80% of the time, for the data from one year may be inadequate. This scenario is probably a best-case calculation, since variation between the within-year replicates may turn out to be large. If possible, the sample size should be increased.

The ISRP strongly recommends:

1. reaching an agreement so that the PIT tagged fish from the truck-followed-by-in-river treatment group from this project will always be returned to migrate in-river, rather than taken into transport, whenever they hit a bypass detector. This can be done automatically with the "sort by code" hardware at the collector dams (LGO and LMO). This will preserve sample size for this treatment group, and it will also present opportunities for stratifying on the number of bypass detections between LGR and MCN.
2. developing a method to estimate "delayed mortality" by using PIT tagged fish from outside this study but with coordinated release dates from the hatcheries to match batches of treatment groups from this study. An alternative would be to include an additional real control group of PIT tagged fish that are allowed to migrate in river from LGR to MCN, without the truck detour. This would permit estimation of "delayed mortality," which is not possible with the present design.
3. creating a CD of the "consensus interpreted data" as part of its annual reporting process. This would allow statistical researchers to try various statistical methods for analyzing these data, without the confounding issue of how the different researchers made their decisions about which data to cull.

1. increasing the budget to create another treatment group that is collected at LGR and barged to the tail race of ICE. This would allow investigation of the question concerning whether the "delayed mortality" from truck transportation is the same as from barges.
2. estimating mortality from recoveries of fish released below Lower Granite Dam and recovered downstream. Similarly, estimating mortality for fish released below Ice Harbor Dam and detected at McNary Dam. This would allow directly estimating the mortality in transportation itself rather than assuming the usual 5% mortality rate used in modeling transportation.

Finally, it should be noted that the ISRP recommends that NMFS, CBFWA, and the Corps of Engineers concentrate on development of better estimates of SARs that will directly answer critical questions for recovery of endangered stocks in the Columbia Basin. For example, direct answers are needed to questions concerning return rates of transported versus in-river migrating fish, adequacy of return rates needed to recover stocks, indirect mortality, extra mortality, "D", etc. The ISRP has recommended elsewhere in this report, and again emphasizes the importance of installation of a PIT tag reader in the corner collector at Bonneville 2 (project 199302900). Data collected there will provide information that would more directly estimate SARs for groups of in-river migrants than the efforts in this project.

If funded, this project should be coordinated with other monitoring projects to ensure compatibility of objectives, common methods and protocols. This coordination could be accomplished under the favorably reviewed CBFWA proposal #35033.

Comment:

Comments
NMFS proposal. Comment is inappropriate

Already ESA Required?
No

Biop?
Yes

Comment:

Comments:
Correct budgets are needed.

Comment:

Sponsor comments: See comment at Council's website