By letter dated November 14, 1996 from Mark J. Schneider to Chip McConnaha, the National Marine Fisheries Service, Environmental & Technical Services Division (Portland, Oregon) requested that the Independent Scientific Review Board (ISAB) review its draft report to the Oregon Department of Environmental Quality. That report presents results of 1996 monitoring and evaluation related to the Department’s 1996 waiver of state water quality standards for total dissolved gas saturation in the Columbia and Snake rivers to facilitate salmonid outmigration with spill. This ISAB report is our response to that request.
Background
In April 1996, the Oregon Department of Environmental Quality (ODEQ) considered a request by the National Marine Fisheries Service (NMFS) for a waiver of water quality standards for dissolved gas saturation in the Columbia and Snake rivers. The waiver from the standard of 110% total dissolved gas saturation (TDGS) was requested for a period in spring when voluntary spill at eight dams might be used by fishery managers to assist migration of salmonid smolts to the ocean. Spill has been demonstrated to yield higher survival than turbine passage in studies of smolt survival at several species and several dams [Schoeneman et al. 1961 (chinook salmon at McNary Dam); Johnson and Dawley 1974 (chinook salmon at Bonneville Dam); Long et al. 1975 (steelhead at Lower Monumental Dam); Raymond and Sims 1980 (chinook salmon at John Day Dam); Weitkamp et al. 1980 (steelhead at Wells Dam); Heinle and Olson 1981 (coho salmon at Rocky Reach Dam); Ledgerwood et al. 1990 (chinook salmon at Bonneville Dam); Iwomoto et al. 1994 (chinook salmon at Little Goose Dam); Muir et al. 1995 (chinook salmon at Lower Monumental Dam). Spill also appears to pose less risk for fish at dams than some engineered fish bypasses (Ledgerwood et al. 1990).
However, spill contributes to an increase in TDGS in the river downstream of dams such that conditions well above the standard can be created, including levels that exceed those demonstrated to be lethal to juvenile salmonids in laboratory studies because of gas bubble disease (GBD) (Ebel 1969; Bouck 1980; Weitkamp and Katz 1980; USACE 1994). Despite these potential detrimental effects, the NMFS’ Endangered Species Act Section 7 Biological Opinion (NMFS 1995) includes as a “reasonable and prudent alternative” the spillage of water at dams during the migration season for the protection of juvenile spring/summer chinook salmon. Under the Biological Opinion, the NMFS directed the U.S. Army Corps of Engineers to achieve 80% fish passage efficiency (FPE) using spill. Because the prescribed spill program is likely to cause TDGS to exceed 110%, the NMFS seeks annual waivers from these standards in order to implement the spill program.
The spill program under the Biological Opinion operates in an environment in which spill may be necessary for other reasons. Spillage may be necessary because the volume of water flowing in the river exceeds the physical capacities of fully-operating turbines to pass it. Some turbines at a dam may not be operable (such as requiring maintenance), thus lessening the physical capability of the dam to pass water. Turbines may also not be used because there is no market for the electricity they would produce, thus the turbines are stilled and the water shunted over spillways. Spillage forced upon dam operators by the functional hydraulic capacity of their dams is generally called involuntary spill. Spillage under the Biological Opinion (or other requests by fishery managers) is generally termed voluntary spill. In high-water years such as 1996, spill is a mixture of voluntary and involuntary types.
Barging smolts is an alternative to assisting their natural in-river migration with spill. Fish that pass dams via spill are not available for collection in fish bypass systems for loading onto barges. An ongoing question is whether barge transportation or natural, in-river migration (with or without spill) is more effective for the survival of downstream migrating juvenile salmonids. Thus, the relative efficacies of barge transportation of fish and in-river migration enter into discussions of spill, as they did in the deliberations of the ODEQ.
The ODEQ granted NMFS the requested waiver, but with several stipulations. One stipulation was that the NMFS provide the ODEQ an annual report on several TDGS-related questions by January 15, 1997. The NMFS drafted the annual report and released it for peer and public review on December 1, 1996. The Independent Scientific Advisory Board (ISAB), established to assist the NMFS and the Northwest Power Planning Council in scientific review, was requested to provide peer review. This document is the ISAB review of the NMFS’ December 1, 1996 draft annual report. Seven topics were identified by the ODEQ for inclusion in the NMFS annual report. The NMFS organized the annual report in seven corresponding sections, each with an identified author or authors. The topics were (as given in the NMFS draft report):
- Statistical evaluation of the available PIT-tag data to determine week-by-week survival changes.
- Week-by-week estimates of the quantities of voluntary vs. involuntary spill. The factors causing the spill scenario shall be stated, i.e., hydraulic capacity, turbine outages, lack of power market, etc.
- Empirical estimate of survival associated with spill.
- Incidence of GBD signs in adult [salmonids] and estimates of upstream spawning delays of returning salmonids from increased spill.
- Survival estimates of transported vs. untransported fish at collector projects.
- Survival and incidence of GBD data from net pens below Bonneville Dam.
- Incidence of GBD signs in resident fish species collected from below Bonneville Dam.
Although the NMFS’ draft annual report attempts to address each topic, the agency found that responding to the exact wording of the stipulation was difficult due to the complexity of the issues. Thus, NMFS chose to respond in slightly different ways.
General Comments
The ISAB commends both the ODEQ and the NMFS for their agreement to identify topics of concern regarding modifications of the TDGS standard and to present the relevant information for the benefit of their agencies and others in the basin. Aided by peer review and revisions, this strategy should enhance mutual understanding of both what is known about TDGS effects and what still needs to be learned, with the ultimate benefit of reasonable and effective regulations.
Both the statement of topics and the provision of relevant information could be better refined to focus on the apparent items of concern. For example, the ODEQ did not specifically state that the survival data requested in topic 1 and the spill data requested in topic 2 should be from the same reaches of the river system, yet a comparison of survival with spill seems to be the obvious information need. However, the annual report provides survival data from the Snake River dams and spill data from the lower Columbia River dams, which cannot be compared. As a second example, topic 4 can be taken literally as questioning delays in actual spawning (deposition of eggs in redds) or as what seems to be the real concern, any delays in upstream spawning migrations caused by spill and high TDGS. The NMFS took a literal view and thus provided a somewhat unsatisfying response. Also, topic 6 requests information on GBD data from net pens below Bonneville Dam without specifying what species might be in those pens. The NMFS assumed that the ODEQ meant juvenile salmonids and noted that they did not do that type of study in 1996. Yet the information, including that for salmonids, is available in response to topic 7 on resident species.
We understand that at least one attempt was made to bring the respective staffs together for better mutual understanding of the topics and the information desired. If this annual report approach is taken in another year, the agencies could fruitfully spend additional time together to better understand what information is wanted and what kind of information can reasonably be provided.
The fact that 1996 was an especially high flow and spill year through the system should have provided an exceptionally good year for estimation of spill effects on fish survival. We were surprised that none of the responses referred to the monitoring data on gas bubble disease signs in fish collected by the Fish Passage Center. Although subject to some criticism in their own right, these data should have been germane to several of the topics discussed in the report. Clearly, more synthesis of 1996 data from all sources is needed. Timely interpretation is important before designing studies for 1997, which appears to be another opportunity to evaluate conditions under high involuntary spill.
Detailed Comments by Section
Introduction.
The firm statements in the second paragraph that migration routes over spillways or through bypass systems are the safest should be tempered by data that show some bypasses can be more damaging than some turbines. A review by Chapman et al. (1991) indicates delayed mortality due to effects of passage through the entire bypass system at Lower Granite Dam produced estimated losses of 7.6, 4.4, and 5.1% in 1984, 1985, and 1986, respectively. Ledgerwood et al. (1990) showed smolt survival through Bonneville Dam was less for fish using the bypass than for fish passing through the turbines. High mortality appears to be due to mechanical problems within the bypasses and placement of the bypass outfalls in zones of high predation. The first sentence needs reworking for tense correction.
The next to the last sentence in the final paragraph is unclear. This sentence is especially important as it is a concluding sentence for the report. Does it mean that both low percentages of fish with GBD signs and high observed survival rates occurred at times when TDGS levels were high and well above 110%?
Topic 1. Statistical evaluation of the available PIT-tag data to determine week-by-week survival changes.
Our comments on this topic fall into two categories. One is related to the strictly statistical aspects. The other relates to the possible use of a more functional, alternative model for making evaluations of survival.
Statistical Aspects. We are unsatisfied with the statistical treatment as it is presented. We have several specific comments:
1. What exactly was the method used for estimating mortalities?
Initially the author calls the method Cormack-Jolly-Seber, and later just Jolly-Seber. What exactly is the formula used (for the estimate and for the standard error)? What is the reference? If packaged software was used, what package? If NMFS’ own software was used, where is it archived and where is documentation of its validation? What are the crucial assumptions in application of this method or where are they discussed (citation needed)? Were those assumptions verified to have been met, at least practically, in application to this particular study?
2. Where are the data?
The report does not display (by table or figure) or reference (by document number or Internet address) the actual data. The graphs provided are very remote from the actual data; they are smoothed graphs of a time series of estimates made from the data, and the smoothing procedure is essentially undefined (the S-plus package is notoriously bad about documentation of their methods). As a consequence the reader has no picture of what the original data looked like, and therefore no way to judge whether the analyses done were reasonable, whether the interpretations were reasonable, and whether alternative analyses might have lead to very different interpretations. If not actually presented in this report, a citation chain for the data and analysis methods would be helpful.
3. What are the conclusions?
With the material presented, the reader cannot draw any conclusion about the key question–a relationship between survival and the degree of gas supersaturation. The correlation analysis for daily data showed a very low correlation, but because of the way the results are reported we can't tell why the correlation is so low.
For example, we would like to know whether the low correlation is owing to the absence of a relationship, or to non-linearity in a relationship, or possibly to measurement noise superimposed on a relationship, or to a discernibly patterned perturbation superimposed on a relationship, or to random process variation superimposed on a relationship, etc. Exploration of these possibilities would indicate where we should look next: should we recommend a larger sample size (as is proposed in the Idaho PIT tag study); should we focus on a search for other factors which might modulate the influence of gas supersaturation on survival; should we go to a different kind of experimental design; or should we actually conclude that there is little or no relationship in practice? No one can even start to explore these questions without the data.
We note further that the pattern that does emerge from analysis of the "smoothed" time series of estimates is inconclusive, notwithstanding some reported p-values that superficially look "significant." The graphs of the smoothed time series showed that, grossly, there were three episodes during the period of observation: two of these (early season, late season) had high gas supersaturation, and one (mid-season) has less gas supersaturation. During one of the episodes with high supersaturation, survival was high; during the other, survival was low. During the one episode of lesser gas supersaturation, survival was high. What can we conclude from that?
It is not technically valid (and it is extremely misleading) to compute correlation coefficients for a smoothed time series of estimates of this sort. The p-values at face value are meaningless, and should not be reported. Even with disclaimers, such p-values should not be reported, for invariably they fall into the hands of those who would misrepresent them.
Alternative Model. The NMFS report provides important reach-specific survival data, assuming the statistical aspects are further explained, but conclusions are limited by a strictly statistical evaluation of the results. Although the statistical evaluations of survival and environmental variables are interesting and informative, this analysis could be improved by consideration of a dose-accumulation model for TDGS effects on migrating fish. In a dose-accumulation model, the time it takes for a toxicant to take effect is considered. Because of the time it takes juvenile salmonids to pass through Snake River reservoirs, the effects of upriver exposures may not be manifested until fish have reached the lower river reaches. Information on durations of exposure required for different levels of TDGS to cause biological effects is available in TDGS bioassay data in the literature (e.g., Blahm et al. 1975; Dawley and Ebel 1975; Fickeisen and Montgomery 1978; Bouck 1980; Colt et al. 1986; Jensen et al. 1986; Backman et al. 1991). Many of the relevant data are cited in recent reviews (e.g., Fidler and Miller 1993). The advantage of this approach will be evident as more detailed comments are made.
Even though much of the voluntary spill occurred downstream of McNary Dam, it apparently was not possible to develop PIT-tag-based survival estimates in that reach. A statement on page 4 about the distribution of PIT-tag data in relation to Biological Opinion spill seems needed (see topic 2). It would be useful to include a time schedule showing when it will be technically feasible to make survival estimates for reaches below McNary Dam.
The stated “small number of detections below McNary Dam” (lst paragraph on p. 4) could be interpreted as being caused by mortalities in the lower reach of river that resulted from accumulated exposures to high TDGS in upper reaches rather than a problem of lack of detectors at downriver sites. Presentation of both possibilities would be informative and set the stage for further investigation. Beyond the question of simple “toxicity” of TDGS, the interactive effects of predation, food web capacity, and high temperature would influence the survivorship of fish stressed earlier in their migration.
The presentation on environmental variables at the top of page 7 seems to suggest that fish receive their exposures at the dams. In fact, the exposure is in the reservoirs between dams and dosage is likely related to travel time and travel depth between dams. Thus, the statistical model leaves out an important feature of the TDGS exposure–its duration. Again, small number of detections at John Day and Bonneville dams may be due to mortalities below McNary due to accumulated doses from upstream. Thus, the urgency for adequate detectors at lower-river dams.
Constant high survival between Lower Granite Dam and Lower Monumental Dam noted in the middle of page 7 may not indicate good conditions there. Effects of TDGS may be accumulating but not yet having an effect on survival. Table 1 indicates that the poorest survival occurs at the lower reaches from Lower Monumental Dam (LMO) to McNary Dam (MCN). There are two main interpretations of this information. One interpretation is that TDGS conditions in the lower Snake are worse than upstream (and the effects are shown there). Another interpretation is that doses of high gas accumulate in the fish as they migrate downstream and reduction in survival is exhibited primarily when fish have reached the lower river reach. The lower survival probabilities on the last set of dates may indicate that the accumulation of damaging doses occurs more rapidly at warmer temperatures (as has been demonstrated in previous studies such as Nebeker et al. 1979) and is manifested sooner (i.e., farther upstream) than at cooler temperatures. Alternatively, the especially high TDGS levels noted for Ice Harbor Dam tailrace may have been occurring upstream as well (no data are given). Such a dose-accumulation model does not seem to have been explored by the authors as an explanation for observed effects. We believe it should be.
Lack of statistical significance in survival between Lower Granite Dam and McNary Dam noted at the bottom of page 7 is likely a matter of data dilution. That is, as data from the upstream reaches showing high survival are combined with the data showing mortalities in the lower reaches, the statistical ability to detect lowered survival through the whole reach is decreased. This is another very good reason for considering a dose accumulation model rather than a statistical one for establishing causes.
In Figure 2, it is unclear what the purpose would be for drawing a line at 130% TDGS at Ice Harbor Dam. The line unrealistically gives an impression that values above it may be bad while those below it are good. Without this line, it is clear that fish survival declines markedly after a general rise in TDGS from near 120%. Again, it is the integrated dose between Lower Granite Dam and McNary Dam that is pertinent, not necessarily the TDGS value at Ice Harbor Dam. Moreover, the figure is unclear about the dates. Fish dated on the figure according to when they left Lower Granite Dam would experience TDGS at a time different from the Ice Harbor TDGS data by some unstated number of days (their migration time).
In the discussion, the overall conclusion that there is a demonstrated effect of high TDGS is justified by the data and statistical correlations, especially for steelhead. But, the analysis would have been improved by consideration of duration of exposure of fish to high TDGS (integrated doses during migration downriver), which might explain many details of the observed effects, such as seeming anomalies between dates. The general concept of accumulation of doses (similar to temperature degree-days) during outmigration would explain a general trend toward high survival between upper river dams and lower survival downriver (where the accumulated doses would show their effects). The notion of steelhead becoming residualized that is introduced in the discussion would be better received if supported by some data or citations.
As a direct response to the ODEQ topic, we would recommend that data on fish survival be obtained from the lower Columbia River, where voluntary spill is implemented This is especially important at The Dalles Dam, because the reach below John Day Dam is of special concern for high TDGS levels.
Topic 2. Week-by-week estimates of the quantities of voluntary vs. involuntary spill.
This section of the NMFS report gives valuable information, but not for the appropriate reaches. The ISAB believes that it is implicit in the sequence of topics 1 & 2 that the nature of spill was being requested in the reaches for which survival data were available. As it stands, survival data are provided from Lower Granite Dam on the Snake River to McNary Dam on the Columbia River, yet the spill characterization is given from McNary Dam to Bonneville Dam. These are completely non-overlapping reaches. Although the ODEQ perhaps should have made the topics more explicit, the NMFS response could have foreseen the importance of using data from the same reaches.
Moreover, the points in the discussion of this section generally are not well supported by the data in Table 7. For example, whereas the text notes that “most of the spill above 120% TDGS occurred due to the lack of turbine capacity,” the table has only 6 of 36 entries where lack of turbine capacity was the highest category, and this occurred in only 3 of 9 weeks. All the rest of the entries attributed the highest spill to Biological Opinion voluntary spills. Thirteen of 36 entries (36%) were only Biological Opinion voluntary spills. Thus, the Biological Opinion spills appear to be the dominant spill type in this accounting.
It is not clear why the accounting in Table 7 began with May 15 and ended with July 10. Was there no spill before and after these dates? The responses to topic 1 indicate much upriver spill before May 15. It would be helpful if the selection of these dates for data presentation were justified.
The “NMFS Note” needs further explanation with specific reference to quantities in Table 7. If the spills would have occurred anyway because of lack of turbine capacity in the face of high flows in a wet year, why are the spills not tallied as “lack of turbine” spills instead of Biological Opinion spills? Why were spills at The Dalles Dam never attributed to reasons other than Biological Opinion voluntary spills? Surely there must have been times when there was no market for power from that dam or turbine capacity was exceeded.
In general, this section gives little confidence that the accounting for spills is undertaken in a consistent and logical manner that gives a true picture of involuntary and voluntary spills. Moreover, the lack of geographic overlap of spill data with fish survival data makes conclusions about relationships impossible.
Topic 3. An empirical estimate of survival associated with spill.
The restriction of the response to voluntary spill seems unreasonable, based on the general nature of the stated topic. The statement that very little spill occurring in 1996 was voluntary spill is not consistent with the data given in Table 7.
The discussion of limitations in experimental procedures for responding to the topic seem inconsistent with the presentation for Topic 1, in which correlations were calculated for the various factors that may have contributed to survival estimates. Clearly, spill was one of the significant correlates. If the spill data from Topic 2 and the survival data from Topic 1 had been on the same reaches, a better estimate of effects of spill type might have been drawn. The monitoring data from the Fish Passage Center, which included the reaches reported in Topic 2, might have been referenced. The fact that 1996 was an especially high spill year (for whatever reason) through the system should have provided an exceptionally good year for estimation of spill effects on fish survival.
Although estimation of survival associated with spill is a complex subject, this response does not appear to be adequate for communication with the ODEQ, given the information presented elsewhere in this annual report.
Topic 4. Incidence of GBD signs in adult [salmonids] and estimates of upstream spawning delays of returning salmonids from increased spill.
This response would be better if it were directed in a more straightforward manner to the clear the intent of the topic. As noted in the general comments, it appears that concern for delays in upstream migration is the second part of the topic, not actual spawning. A consistent use of GBD throughout the report would be better than using gas bubble trauma (GBT) here.
The text is somewhat inconsistent with Table 8, which is not called out in the text, in its description of the incidence of signs. At Lower Granite Dam, four salmon were found with signs of GBT, not three as the text states. In addition, the table lists headburns, which some people consider to be a biological sign of high TDGS, in 128 fish (about 5%) distributed throughout the sampling period when adults were fairly abundant. No data on run timing were presented in response to the second part of the topic.
The discussion point that few adult salmon showed GBD signs despite high flows (and high TDGS) is a fair summary of the signs data. However, the discussion of delays seems to avoid the clear intent of this issue. Data should have been available from dam counts to determine whether adult migration rates were any slower (or faster) in this year of high flows and high spills compared to years with little spill. If the reports cited already do an adequate job of making this comparison, then their results could have been given, as was done for the Bjornn and Peery (1992) study.
We take exception to the “bottom line” given in the last sentence of the section. The purpose of the report to ODEQ, as we understand it, is to obtain the data needed to establish the risk to adult salmon from increased spill. It is not to obtain a restatement that someone has already accepted the (unquantified) risk as a matter of policy. With the requested data, spill can more validly be included in an overall management strategy.
Topic 5. Survival estimates of transported vs. untransported fish at collector projects.
Although the answer is technically correct with respect to the 1996 outmigration, it does not seem responsive to the ODEQ. There is an opportunity here to summarize the existing data on transported and in-river fish from previous years that differed in amounts of spill. The high-spill year of 1996 will certainly add to the existing data in important ways, but it does not represent much of what we know about the subject (Williams et al. in press). The taggings in 1996 could have been put into perspective with reports of previous taggings (cited), and the importance of the high-flow 1996 for recoveries made in subsequent years emphasized.
Topic 6. Survival and incidence of GBD data from net pens below Bonneville Dam.
The note seems unduly unresponsive, if only in tone. The topic listed by the ODEQ was not restricted to salmonids, as implied by the note. As described in Section 7, there actually were net pen studies below Bonneville Dam. A more positive statement seems warranted that the responses to topics 6 and 7 have been combined because they result from a combined study of resident fish and salmonids that were collected from the river and subsequently held in pens.
Topic 7. Incidence of GBD signs in resident fish species collected from below Bonneville Dam.
This appears to be a well planned and conducted study that has yielded important results. Our comments are mainly editorial. In background, it is mentioned that spill has diurnal fluctuations. This point seems not to have been addressed in any of the other topic responses, and perhaps should be. Under Findings, the first heading might better say Prevalence of GBD Signs in Non-Captive Fish. The same addition might be useful in the legend for Table 10 (to avoid confusion with the subsequent net-pen-held fish). The legend for Table 11 might note that it is for all species combined, and by weeks at three depths. Figure 6 could use some explanation and description of the results in the text rather than the simple callout on page 38.
Summary
The ISAB commends the ODEQ and the NMFS for identification of topics of concern for modifications of the TDGS standard and for presentation of relevant information for the benefit of their agencies and others in the basin. We have reviewed NMFS’ draft report to ODEQ from the scientific perspectives of factual accuracy, openness of discussion, and alternative interpretations that may yield further gains in understanding and ability to manage the hydropower system and its living resources.
Both the statement of topics and the provision of relevant information could be better refined to focus on the apparent items of concern. If this annual report approach is taken in another year, we strongly urge that the agencies spend more time together to better understand what information is wanted and what kind of information can reasonably be provided. Some responses show very literal interpretations of the topic, which restricted the usefulness of the data presented and the discussion. Some discussions did not match the data. Injection of a policy conclusion as a response to a request for factual information was inappropriate.
The analysis suffered from the seven sections essentially being done independently. Although the geographic mismatch of survival and spill data is the most obvious example, other sections could have benefited from a more synthetic approach. As it stands, some sections border on publishable research reports whereas others suggest that the request was not taken seriously and there was an effort to minimize the time and effort required to respond. We suggest that topics needing additional discussion in the report be bolstered by citation of existing analyses (e.g., the transportation issue) and indication that more extensive discussion can follow the January 15 deadline, perhaps in an annual report for 1997.
A better categorization of types of spill appears essential for meaningful progress toward managing the resource. This report highlighted an accounting system for spill that is confusing, at best, and misleading, at worst.
Finally, for meaningful evaluation of salmonid survival in different spill regimes it is essential that survival and spill data be collected from the same reaches of river and that survival be considered a cumulative response to sequential exposures over time of migration. We have suggested an alternative analytical tool, the cumulative dose-response model, as appropriate for understanding the distribution of mortalities in relation to TDGS values throughout the migration route and season. There is a fundamental disjunction in this report between spill, TDGS exposure, and survival that undermines confidence that there is an integrated plan for study and evaluation of spill, TDGS, and their biological effects.
References
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Colt, J. E., G. Bouck, and L. E. Fidler 1986. review of current literature and research on gas supersaturation and gas bubble trauma. Special Publication No. 1, Division of Fish and wildlife, Bonneville Power Administration, Portland, Oregon.
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Drafted 12/13/96, reviewed by subcommittee and then whole ISAB, revised 1/6/97. C. C. Coutant for the ISAB.