Review of the Comparative Survival Study (CSS) Draft 2015 Annual Report

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The Northwest Power and Conservation Council’s 2009 amendments to the Columbia River Basin Fish and Wildlife Program called for a regular system of independent and timely science reviews of the Fish Passage Center’s (FPC) analytical products. The 2014 Program continues to call for these reviews, which include evaluations of the Comparative Survival Study’s draft annual reports. These ISAB reviews began five years ago with the evaluation of the CSS’s draft 2010 Annual Report (ISAB 2010-5), followed by a review of the draft 2011 Annual Report (ISAB 2011-5), the draft 2012 Annual Report (ISAB 2012-7), the draft 2013 Annual Report (ISAB 2013-4), and most recently the draft 2014 Annual Report (ISAB 2014-5). This ISAB review of the draft 2015 CSS Annual Report is the ISAB’s sixth review of CSS annual reports in response to the Council’s 2009 Program.

These reports are extremely valuable to many stakeholders in the Basin for many different purposes, and the data collection and reporting should be continued.


This ISAB review begins with an overview of the latest report (this section), then moves to suggesting topics for further CSS review (Section III), general comments on each chapter of the 2015 CSS Annual Report (Section IV), and ends with specific queries and suggestions (Section V).

The annual CSS report is a mature product, typically including only updates with the latest year of data and expansion of analyses as more data are acquired. Many of the methods have been reviewed in previous ISAB reports and so now receive only a cursory examination. As more data are acquired, new patterns and questions arise on the interpretation of the results – this is now the primary focus of the ISAB’s reviews. The ISAB appreciates the detailed response of the CSS to suggestions provided in previous reviews. The ISAB does not expect that the CSS would necessarily respond immediately to new requests for further analyses.

Chapter 1 is similar to previous years with the 2013 results added. The report now disaggregates results for Snake River wild steelhead and Chinook to the major population group (MPG) level. The results in Chapter 1 appear to show a natural experiment involving the effects of mainstem discharge on salmon survival with the proportion of downstream transportation of juveniles and proportion of spill being roughly constant since 2006, but total flow in the river differing among years. The ISAB suggests that focused analyses (graphs and formal analyses) be conducted on this natural experiment to test statistical relationships between flow and salmon population parameters such as survival, smolt-to-adult-return rate (SAR), and other response variables.

In Chapter 2, an updated Life Cycle Model (LCM) is presented that relates juvenile survival of transported and untransported cohorts of juvenile fish and a PIT-tag based indicator of powerhouse passage. This is useful refinement of the LCM, and the ISAB looks forward to additional refinements such as the inclusion of additional terminal areas and further partitioning of survival. The LCM was used to investigate the long-term impacts of increased salmon productivity and reduced dam effects on the long-term persistence of salmon populations. It would be helpful to reverse this analysis and evaluate what combinations of increased productivity and reduced dam contact might lead to sustainable populations.

Chapter 3 is mainly an update with the latest information on in-river effects on juvenile travel time, instantaneous mortality, and survival. A key finding is that there is large variation in the results among years and among cohorts. The variation among years is understandable; the variation within a year less so. Many figures (e.g., Figure 3.2) show a consistent pattern in fish travel time and survival over cohorts as the year progresses. The discussion lists potential explanations for the effect of “day.” Can planned or natural experiments be designed to distinguish among these hypotheses and is it worthwhile to do so? For example, do these relationships provide information on optimal timing of releases for hatchery fish? It is also not clear if these cohort effects continue to the final performance measures (e.g., SARs). Data are clearly too sparse to investigate this question for individual cohorts, but can a more gross separation be used (e.g., a simple split of cohorts into two parts – early vs. late)?

Chapter 4 described overall annual SARs and was updated with new data; details are presented in Appendices. Additionally, the authors investigate relationships between SARs and salmon population productivity (return per spawner) and inter-stock correlations among SARs. These chapters and appendices will continue to expand over time. Is there a better way to present the results than in an ever-expanding set of graphs and sets of tables? As indicated in the report, different SAR objectives will require different accounting locations (e.g., finer geographic locations) and methods (e.g., for persistence at local or basin levels). The current tables and plots are generally well done, but as can be imagined, this chapter could become overwhelming. The ISAB suggests that consideration be given to how to present these results in the future to best serve the various stakeholders. Perhaps an electronic report that can be customized for a particular interest group may be more useful than a static paper document? The CSS report could then focus on unexpected findings or relationships (such as that between SAR and productivity or inter-cohort relationships).

Chapter 5 is mostly an update on Snake River subyearling fall Chinook. As with Chapter 4, some consideration is needed on the best way to present an ever-increasing amount of data so that the results of the data analyses are useful for stakeholders. This chapter also includes a new power analysis indicating how much additional tagging is needed for fall Chinook above Lower Granite Dam (LGR). Is it feasible to tag the required number of fish? Also, these additional tagged-fish will provide added information on down-river detection rates – does this lead to improvements elsewhere in the CSS domain of study?

The ISAB understands that Chapter 6 in the 2014 report (PIT-tag versus CWT survival estimates) is currently in preparation for the next iteration of the CSS report. Rather than report on incomplete analyses, it was removed from this year’s report. The ISAB looks forward to its inclusion next year. Evaluating potential bias in survival rates of PIT-tagged fish is an important topic.

Suggested Topics for Further Review

In 2013, the ISAB recommended these topics (ISAB 2013-4, Page 1):

  1. Hypotheses on mechanisms regulating smolt-to-adult survival rates (SARs)
  2. Life-cycle modeling questions and Fish and Wildlife Program SAR objectives
  3. Data gaps
  4. Rationalization of CSS's Passive Integrated Transponder (PIT)-tagging, and
  5. Publication of a synthesis and critical review of CSS results

In 2014, the ISAB recommended these topics (ISAB 2014-5, pages 2-3):

  1. Hypotheses on mechanisms regulating smolt-to-adult return rates (SARs) [update from 2013 review]
  2. Life-cycle modeling questions and Fish and Wildlife Program SAR objectives [update from 2013 review]
  3. New PIT/CWT study to further investigate differential survival among these tag types

The CSS group has incorporated many of the ISAB’s suggestions into the current document. For example, the current report has a substantial discussion of correlations among SARs from different regions or effects of transport on SARs (#1 in 2013; #1 in 2014). The life cycle modeling now allows for variation in stream productivity and hydrosystem survival and simulates the correlative impacts of these changes on predicted future population abundances (#2 in 2013; #2 in 2014). Members of the CSS have now published many peer-reviewed articles synthesizing the results (#5 in 2013). The ISAB appreciates the CSS efforts to respond to the ISAB’s queries which in turn leads to further questions as noted below.

However, some of the recommendations from the ISAB appear to be beyond the scope of the CSS. For example, the ISAB identified several data gaps such as fish body mass metrics (#3 in 2013), but limited resources and questions about which agencies should collect this information have prevented acquisition of these data. The CSS expends considerable effort to coordinate PIT-tagging in the basin with other groups but does not feel that it is the appropriate body for a full rationalization of the PIT-tagging effort (#4 in 2013) along the lines recommended by the IEAB report (2013-1). Resolution of these issues may require higher-level policy discussions among the stakeholders in the Basin. The update of Chapter 6 from last year (#3 in 2014) has been deferred until the next report.

In 2015, the ISAB recommends the following four topics for future reports:

  1. Use SAR data to examine both intra- and interspecific density dependence during the smolt out migration and early marine periods.

ISAB (2015-1) found relatively little direct testing of density dependence during the smolt outmigration period when many natural and hatchery salmonids may co-mingle as they migrate toward the ocean. Would it be possible to use CSS SAR data to examine both intra- and interspecific density dependence during the smolt out migration and early marine periods? The potential for compensatory density dependence was suggested by bioenergetic estimates of numerous prey consumed by spring/summer Chinook as they migrate from Lower Granite Dam to Bonneville (ISAB 2011-1). Also, there was some evidence of depensatory mortality of smolts in the Snake River caused by foraging birds (see Fig. VII.1 of ISAB 2015-1).

  1. Propose actions to improve SARs to pre-1970s levels.

The Chapter 4 Discussion provides a good summary of key information, leading to the conclusion that pre-harvest SARs of ~4-7% are needed to improve productivity to pre-1970s levels. Given the range in observed survivals at sea (S.oa), to what extent might actions in the mainstem Columbia and Snake rivers allow this to occur? What are the key actions predicted to influence survival to reach SARs of 4-7%? For example, can the Life Cycle Model simulation study be run in “reverse” to help evaluate the relative benefit of alternative management actions? These evaluations might support an actual test (like a spill-experiment).

  1. Explore additional potential relations between SARs and climate and ocean conditions

The authors should consider further exploration of potential relationships between SARs and indices of climate and ocean conditions that have not been previously evaluated by CSS, e.g., the North Pacific Gyre Oscillation (NPGO; see Kilduff et al.2015; Miller et al. 2014), NOAA local biological indices (e.g., copepod biodiversity, northern copepod anomalies, biological spring transition, winter ichthyoplankton, juvenile catch-June), and Alaska Marine Ecosystem indicators. Similarly, can methods similar to Chapter 2 be used where years that are “similar” to those expected under future climate change scenarios are used to simulate the predictions for survival, SARS, and other population parameters under future climate scenarios.

  1. Consider ways to explore the variability of inter-cohort responses

Finally, the CSS report has studied effects on the "mean" response to various factors. For example, fish travel time reductions improve "mean" survival, but as noted, there is high inter-cohort variability. Perhaps a lower average survival with less inter-cohort variability would be more beneficial, i.e. a more robust response. Are there management actions that could reduce this intra-cohort variability? The current time series is now approaching a length where this could be investigated in the future. Some planning is required to ensure that data collected now are stored in a format that will be suitable for future investigations along these lines.

See the full ISAB report for detailed comments on each CSS report chapter.

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