PROJECT OVERVIEW

The Pacific Northwest tags more fish and monitors fish movements more intensely than anywhere else in North America.  Tens of millions of dollars are spent on fish tagging and data retrieval each year.  However, there is no overriding analytical framework to the design and analyses of these studies to assure optimal performances or maximum benefits from the data.  The Columbia Basin Fish and Wildlife Program (CBFWP 1994-1995) recognized these needs in their call for a regional center for conducting analyses and the development of needed analytical tools and analyses (3.2F.1).  The plan also called for a coordinated information system on anadromous fish databases (3.3A.2) and the need to monitor populations, provide timely transfer of information, and develop needed monitoring technologies (4.3C.1).  Despite these overwhelming needs, given the high expenditures on tagging and data collection, no agreement on a coordinated information system for anadromous fish data, methods of their analyses, or timely dissemination of information to the public has been agreed upon.  This project exists to meet some of these pressing demands for sound statistical analysis of tagging data and the dissemination of data in a timely manner in order to evaluate and monitor mitigation activities in the Columbia Basin.  This program contributes to mitigation activities by providing sound information from historical or real-time tag detections in order to adapt management strategies to the most current information on salmonid migration and success.  This program also assists by resolving statistical and data analysis issues, so that managers can focus on biological or resource issues rather than on data analysis uncertainties.

Apart from its essential role in the Fish and Wildlife Program, Bonneville Power Administration (BPA) needs and uses the support provided by this project to accountably perform and preserve its ability to independently make decisions related to operations of the hydro system and commitment of fiscal and material federal resources for fish and wildlife mitigation programs.  This project also provides critical analysis for efficient use of limited mitigation funds on both a real-time and planning horizon basis.  This program also helps assist the BPA in the CBFWP (2000) requirement to produce an "annual report on flow augmentation" including "the benefits of flow augmentation for fish survival, and the precise attributes of flow they may make it beneficial."  To support real-time monitoring and information dissemination, the program provides real-time analyses of PIT-tag data and smolt passage indices to predict outmigration timing at eight Snake and Columbia River dam sites.  This information is coupled with travel time information and barging projections in the Snake River Basin.  Daily updates are provided for yearling and subyearling Chinook salmon, steelhead, and sockeye salmon from April through September of each year since 1994.  These predictions, along with supporting information, can be retrieved and independently analyzed using interactive software and graphs on the internet (http://www.cbr.washington.edu).

The second element this project provides is value-added analyses of historical tagging data by testing hypotheses, estimating parameters, and modeling interrelationships without the tremendous costs of additional field studies.  These analyses have provided information in the past to scientific groups like the Plan for Analyzing and Testing Hypotheses (PATH) forum.  Examples of analyses included examining the relationship between coastal coho salmon (Ryding and Skalski 1998) and Chinook salmon (Burgess and Skalski 2001) returns and oceanographic conditions.  Current efforts are using Program ROSTER to perform retrospective analyses of juvenile and adult PIT-tag data to estimate juvenile outmigration survival, transport effects, ocean survival, adult upriver survival, and smolt-to-adult ratios (SARs).  These life-cycle analyses are being used to characterize the status and trends of hatchery and wild steelhead and Chinook salmon in the Columbia River Basin and examine factors influencing return success.  Program ROSTER has also been used to examine post-bypass effects on return rates of adult salmonids.  Currently, efforts are underway to examine the factors that may be influencing the overshoot and fallback rates of adult steelhead through the hydrosystem.

As provisions for handling salmonid stocks have become more restricted, the value of retrospective analyses of existing data sets becomes increasingly important.  These investigations also provide needed information to perform sample size calculations and to design field investigations more precisely. The specific analyses performed each year changes as BPA information needs to shift to reflect the changing needs of the fisheries community.  A series of technical publications on tag analyses is published under the contract to disseminate information learned from these added-value analyses.  A report performed in 2013 examined the limitations of using general purpose historical data to identify mortality factors associated with SARs.

A third element of this project is to develop the statistical tools and analyses to monitor and evaluate the status and trends of salmonid stocks and the hydro system.  Numerous performance measures and recovery goals have been established (e.g., BiOp. RM&E Hydro Working Group, Remand) to monitor the recovery of the Columbia Basin system.  Despite all the discussions of recovery and performance measures, no public source of readily available information exists.  In preparation for the recovery status "check ins," this project is compiling and summarizing the myriad of endpoints identified in recovery documents.  Performance measures compiled include adult return counts, harvest numbers, SARs, smolt outmigration and travel times, stream escapement, transport–inriver ratios, ocean survival (i.e., Bonneville to Bonneville Dam), upriver adult survival, and compliance with flow, temperature, and dissolved gas targets.  This project is reporting the information and developing analysis tools to assist the public and agencies in independently assessing the status of recovery in the Basin.  Currently, we are comparing estimates of overshoot and fallback rates generated by state agencies using simple PIT-tag tally methods versus multistate mark-recapture models.  The information and statistical tools to examine the status and trends of performance measures are placed in the DART database managed by the University of Washington for public dissemination (http://www.cbr.washington.edu/dart/dart.html).  Collaborating with the National Marine Fisheries Service (NMFS) and the action agencies will continue to refine and expand the capabilities to interpret recovery data.

PROJECT GOAL

The project goal is to provide state-of-the-art analysis and interpretation of life-cycle information for monitoring and evaluation of salmonid stocks.

PROJECT OBJECTIVES

1. Provide real-time predictions of smolt runtime through the hydro system to better manage water resource in the Columbia Basin.

2. Provide integrated analysis of historical tagging  data to improve the understanding of salmonid life history information and the effects of hydro system operations on salmon recovery.

3. Develop state-of-the-art statistical methods for monitoring and evaluating the status and trends of the Columbia Basin hydro system and associated salmonid stocks.

4. Provide the BPA with technical assistance on topics, proposals, technical reports, and data analyses of interest to them on an "as needed" basis, and to extend this statistical service to other agencies.

5. Provide ready public access to information on the status and trends of performance measures related to salmonid recovery in the Columbia Basin on the internet.

6. Provide technical guidance to the fisheries community on the design and performance of monitoring studies and provide recommendations on the most cost-efficient and effective approaches.

PROJECT ACCOMPLISHMENTS

Integration, Coordination, and Information Transfer

This program, in addition to fulfilling BPA-mandated responsibilities, addresses essential issues in the Columbia Basin Fish and Wildlife Program (CBFWP 2000).  This program--through data compilation, analysis, and dissemination--is consistent with the Council's scientific principles of ecological management (i.e., Principle 7).  This program strives to understand the dynamics of the aquatic systems and anthropogenic effects by analyzing historical tagging data and providing real-time access to the monitoring data to the public, fisheries managers, and the Technical Management Team (TMT).  Under the Hydro system Passage and Operations section of the CBFWP, this program has made the following contributions:  (a) developed, measured, and monitored juvenile fish passage; (b) monitored and evaluated adult passage, and provided technical support to the installing adult PIT-tag counters; (c) evaluated the effects of flow and spill strategies on outmigration success; (d) assist the BPA in preparing an annual report on flow augmentation; (e) provided mitigation information and specialized data summaries to the TMT; (f) investigated biological measures of mainstem operations; and (g) investigated key uncertainties associated with mainstem migration and transportation.  Under the Council's Ocean Condition section, this program has made the following coordinated contributions:  (a) helped better understand conditions salmon face in the ocean, (b) identify factors critical to ocean survival, (c) help distinguish ocean effects from other effects on adult returns, (d) separate the effects of ocean-related mortality from that caused in the freshwater part of the life cycle, (e) characterize smolt transport effects on adult returns, (f) compare performance measures of hatchery and wild stocks of steelhead and Chinook salmon, g) helped refine estimates of straying, overshoot, and fallback rates of adult steelhead.

Equally important, this program has contributed to the Council's call for "Research, monitoring and evaluation" in all three critical areas they have identified:  (a) identify and resolve key uncertainties, (b) monitor and evaluate, (c) make information readily available.  This program provides statistical support, software development, and publicly accessible interfaces for data interpretation as part of the internet data capabilities of the Columbia River Data Access in Real Time (DART).

Biological/Ecological Results to Date

Since 1991, this project has evaluated historical tagging studies to help design future research and determine the reliability of existing information.  This project has explored possible relationships between juvenile survival and adult returns with river flows, abundance of hatchery stocks, pulsing, ocean conditions, and ambient river conditions.  This project has also developed new approaches and statistical tools which generate online, internet-based information including real-time in-season predictions of migration status.  This information, along with flow predictions and transportation levels, provides fish managers with the opportunity to integrate the status of the smolt migration with river management options.  Run-timing predictions are available for the Snake, Mid-Columbia, and Lower Columbia hydro projects for NMFS ESUs as well as river runs as a whole for spring and fall Chinook salmon, steelhead, and sockeye salmon.

Specific biological results of the project to date include the following:

1. Evaluation of travel time information contained in freeze-brand data.
2. Evaluation of the annual pattern of adult salmon returns to the upper Snake River from PIT-tag data.
3. Recommendations for complete life-cycle survival studies using combined PIT/CWT releases.
4. Evaluation of the relationship between Priest Rapids hatchery fall Chinook adult returns and river conditions.
5. Evaluation of effects of river pulsing on smolt travel times.
6. Evaluation of the benefits of smolt transportation at Priest Rapids and McNary dams.
7. Evaluation of coho salmon--ocean survival relationships.
8. Evaluation of Chinook salmon--ocean survival relationships.
9. Evaluation of the internal consistency of hydroacoustic, PIT-tag, and balloon-tag studies in explaining project survival at Lower Granite Dam.
10. Evaluation of the relationship between turbine passage survival and turbine operating efficiency, and the efficiency of the "1% turbine efficiency rule."
11. Examined flow and spill--survival relationships during smolt outmigration.
12. Using joint juvenile and adult PIT-tag data, estimated juvenile inriver survival, ocean survival, adult upriver survival, smolt-to-adult ratios (SARs), transport–inriver ratios, and examined the effects of transportation on adult upriver migratory success of hatchery and wild salmonid stocks.
13. Compared inriver, ocean, and transport performance of hatchery and wild salmonid stocks.
14. Estimated unaccountable loses among adult migrants and the effects of fallbacks at dams on migration success.
15. Examined post-bypass effects on adult salmonid returns.  
16. Examined the limitations of assessing delayed hydrosystem effects using historical data.  
17. Conferred with agency biologists on the best approaches to summarize adult steelhead overshoot, fallback, and migratory success rates.
18. Effects of ladder passage at Lower Granite Dam on subsequent adult salmonid migration success.  

Together, these biological results are helping to evaluate past management decisions and improve future efforts to enhance wild salmonid stocks.

Nonbiological Results to Date

The most visible product of this project is the annual forecasts of smolt outmigration timing each spring and summer.  As many as 66 salmonid stocks, ESUs, and composite groups are monitored each year to produce the "percentage of passage by date" and the "date to specific passage percentiles" at hydro projects throughout the Columbia Basin.  Each year, these run-timing predictions are evaluated post-season to report on predictive accuracy and precision.

This project has also focused on the added value analyses of historical tagging data.  Using information collected over time and enumerable investigations, this project has sought to understand salmonid life history and hydro project effects at scales larger than the extent of individual investigations.  Such investigations have examined the effects of ocean conditions on early ocean survival of fall Chinook and coho salmon.  Other investigations have been used to provide information to better design future tagging studies such as the proposed summer spill study in 2004, the subyearling transport effects studies in the Snake and Columbia rivers, and turbine efficiency trials at McNary Dam.

More recent results have focused on compiling and summarizing performance measures as stated in the BiOp and Remand as the fisheries community approaches the recovery "check-ins."  These efforts have included evaluating statistical methods to assess status and trend data, and to summarize recovery status.

Specific accomplishments by year include:

1991:  Report on historical brand release data for the Snake River.  Report identified serious bias in travel time estimation using freeze-brand data and the difficulties establishing travel time relationship with existing data.

1992:  Report on a "strawman" smolt monitoring design for Snake/Columbia River systems.  This strawman became the conceptual design for the existing PIT-tag detection system for the Snake River.

1993:  Report on adult PIT-tag returns.  Results showed annual patterns of adult returns differed across years even for closely related river systems.

1994:  Developed and implemented statistical software called Program RealTime PIT Forecaster using pattern recognition to predict the outmigration timing of spring runs of wild Snake River spring/summer Chinook at Lower Granite Dam in real time.

1995:  Refinement of Program RealTime PIT Forecaster statistical software and initial testing of RealTime Passage Index Forecaster to predict outmigration timing of summer/fall runs of juvenile subyearling Chinook salmon at Lower Granite Dam based on Fish Passage Center (FPC) passage indices.  Report on transportation benefit analysis methods showed estimation differences among investigators may be related to analysis methods they selected.  Recommendations on proper statistical models provided.

1996:  RealTime prediction algorithm of this project linked with CRiSP model of Project 89-108 to extend predictions of migration timing to include Lower Snake River hydro projects and McNary Dam.  Investigated extending real-time outmigration prediction to Mid-Columbia hydro projects. Expansion of Internet access to cover historical run timing and flow data at all major hydro projects.  Expansion of online interactive information to include in-season time series of PIT detections for National Marine Fisheries Service (NMFS) Snake River Basin ESUs (i.e., ESA-listed juvenile spring/summer Chinook, fall Chinook and sockeye salmon) as they pass through the Federal Columbia River Power System (FCRPS).  Report on Priest Rapids hatchery returns of fall Chinook salmon versus river conditions found upstream-downstream study designs to be of limited quantitative reliability.

1997:  Program RealTime projections continued, along with the addition of Redfish Lake sockeye salmon and steelhead.  Investigations included the study of the effects of river pulsing on smolt travel times, the estimation of fish guidance efficiency (FGE) and spill effectiveness (SE) from PIT-tag data, and the estimation of season-wide survival rates and smolt growth rates.

1998:  Completed study of the relationships between coho age-at-return CWT data and early ocean survival as a function of ocean conditions.  Assessed internal consistency of hydroacoustics, PIT-tag, and balloon-tag studies in explaining Lower Granite Dam project survival of outmigrating smolts.

1999:  Assessed the validity of using Rice Island PIT-tag recoveries in estimating smolt survival through the Bonneville project.   Assessed the feasibility of using hatchery rearing information to assess smolt quality and subsequent downriver migration performance in cooperation with the US Geological Survey.

2000:  Completed study of relationships between fall Chinook salmon age-at-return CWT data and early ocean survival as a function of ocean conditions.  Developed optimal weighting schemes to improve the predictive performance of smolt outmigration timing for Program RealTime.  Completed synthesis and comparison of smolt survival estimates as generated with different technologies and experimental protocols.  Assessed the effects of the detection efficiency of adult PIT-tag detection facilities at Bonneville Dam on the performance of transportation evaluation studies and estimation of ocean survival.

2001:  Evaluated the statistical behavior of proposed statistical tests for recovery in the NMFS BiOp based on annual estimates of smolt survival.  Proposed methods were found to have low-to-moderate chance of identifying the correct status of recovery.  Alternative statistical methods were developed to assess recovery that had much higher probabilities of correctly identifying the true status of recovery.  Examined the statistical bias of treatment/control returns for assessing transportation benefits under the conditions of low adult return numbers and developed bias-corrected estimators.

2002:  Compiled estimates and associated standard errors on smolt-to-adult ratios (SARs) using CWT recoveries for 90 Columbia Basin hatcheries from the 1970s to the present.  Currently compiling inriver survival and travel time information using PIT-tag detections for approximately 20 Columbia Basin hatcheries and screw traps from the 1990s to the present.  Results of the CWT and PIT-tag analyses are available in DART for examination and analysis with ambient river data, power operations, and ocean conditions.  Assisted NMFS in developing multidimensional decision rules for 2005 and 2008 progress "check-ins," and 2010 compliance with BiOp smolt survival performance measures.

2003:  Completed compilation of smolt travel time and survival estimates from PIT-tag releases, mid-1990s to 2002 (http://www.cbr.washington.edu/pitSurv/).  Also updated PIT-tag survival and travel times for the spring outmigration in 2003, and awaiting completion of the summer outmigration to complete the 2003 summaries.  Provided assistance to NOAA Fisheries on better statistical decision rules for recovery.  Compiled adult escapement data and associated NOAA interim recovery goals for 24 stocks and tributaries in the Columbia Basin.  A new website with adult escapement trends and goals will be established in January 2004.

2004:  Developed an interactive status-and-trends database on DART to permit cross-examination of a variety of performance measures.   Users can sort and cross-tabulate information based on stock, location, years, and performance measures.  Summaries of user-specified searches are tabulated for ease of interpretation and examination.  Compiled smolt survivals and travel times through the hydro system based on 21 wild and hatchery PIT-tagged stocks in 2003.  Updated historical data on survival and travel times of summer 2004 migrants.  Developed new web page on adult fallback rates of salmonids at Bonneville Dam using PIT-tag information.  Compiled historical information on annual flows (since 1950s) and dissolved gas levels (since mid-1980s) and performance compliance at 10 Columbia Basin dams.  

2005:  Expanded interactive Status and Trends website to include "report card" summaries of progress toward recovery goals.  Reports cards indicate progress toward recovery on a performance-by-performance-measure basis as well as across performance measures.  Prototype database developed for monitoring and retrieving information on habitat mitigation activities in the tributary and estuary environments.  Updated CWT estimates of SARs for 90 Columbia Basin hatcheries, and smolt survivals and travel times for 20 hatchery stocks.  

2006:  Historical information on inriver and ocean salmonid harvest added as performance measures to Status and Trends website (http://www.cbr.washington.edu/trends/index.php).  New NMFS recovery goals associated with monitoring data added for stream escapement.  Status and trends data can be searched by province, subbasin, and hydrological unit code using either tabular or geographic interfaces.   Joint juvenile and adult PIT-tag data analyzed using Program ROSTER to estimate juvenile inriver survival, SARs, transportation effects on Chinook salmon (1996-2002) and steelhead (1996-2002) and posted results on DART.

2007:  A 1996-2003 retrospective report on hatchery steelhead and Chinook salmon juvenile and adult PIT-tag performance measures completed.  The report includes juvenile inriver, ocean, and adult upriver survival estimates  as well as estimates of dam and systemwide transport/inriver ratios and D.  Web page with 11 oceanographic indices added to DART under Status and Trends.

2008:  A 1996-2004 retrospective report on wild steelhead and Chinook salmon juvenile and adult PIT-tag performance measures completed. The report includes juvenile inriver, ocean, and adult upriver survival estimates as well as estimates of dam and systemwide transport/inriver ratios and D.  Comparison of hatchery and wild performance measures performed.  Development of an interactive, geographic-based website for simultaneously displaying and analyzing multiple performance measures as a prototype for technology transfer.

2009:  Compared migration performance of hatchery and wild yearling Chinook salmon.  Found hatchery summer Chinook salmon and wild yearling Chinook salmon had similar downriver survivals, ocean survival (i.e., BON-to-BON), upriver adult survival, SARs, and T/I ratios.

2010:  Published papers on the surrogacy of summer hatchery yearling Chinook salmon for wild Chinook salmon migration performance and a statistical review of adult escapement/spawner abundance estimation techniques.

2011:  Life-cycle analyses of the joint juvenile-adult PIT-tag data using Program ROSTER found ocean survival (i.e., BON-to-BON) to vary tenfold between the years 1999 and 2006 (range of 0.002-0.024) and constituted an average of 86.2% of the total mortality during LGR-to-LGR migration for yearling Chinook salmon.  Inriver mortality of juveniles constituted, on average, only 9.4% of the total mortality pressure on yearling Chinook salmon. Project ROSTER was used to compare adult PIT-tag returns across different bypass histories.  Strong evidence was found between the number of times a juvenile salmonid was bypassed and lower adult return rates.  The magnitude of the bypass effect on a smolt was also dependent on which dams it bypassed.  

2012:  Extended status and trends reporting to include results of HCP and BiOp compliance testing of smolt survival through hydroprojects or dams and corresponding 2009 Fish Accord performance measures.

2013:  An evaluation of the limitations of correlative analyses to identify inriver and oceanographic factors affecting the survival of salmon smolts and adult returns was performed.  The review recommended much stronger use of the hypo-deductive method and advanced regression analyses such as generalized additive models (GAMs).

2014:  The interface for the presentation of monitoring and trends data received a major facelift.  The hatchery PIT-tag releases have become more distributed in recent years requiring analysis and reporting, not only by hatchery, but also by release location.  The PIT-tag survival results are now presented using a graphical interface.

2015:  Evaluated the effects of different operational and structural configurations at Bonneville Dam on PIT-tag detection efficiencies at that site, along with the consequence to precision of system-wide (i.e., LGR-to-BON)  juvenile survival estimates.  Additional work has investigated how PIT-tag detectors at the sluiceways and weirs in the FCRPS would improve the precision of system-wide estimates of juvenile passage survival.  

2016:  Evaluated changes in juvenile outmigration timing at Bonneville and Lower Granite dams.  Made recommendations on how to improve the timing of spill programs.  Examined patterns in adult steelhead overshoot and fallback rates for 19 hatchery and wild stocks in the Columbia Basin.

2017:  Evaluated how adult route of passage through the adult ladder at Lower Granite Dam affects subsequent migration success.  Developed new website for real-time adult fallback rates.  

Project Accomplishments:  1 January 2017 - 31 December 2017

Major milestones accomplished this last year include the following:

1. Program RealTime monitored the timing of smolt outmigrations of 66 stocks, ESUs, and composite groups through 6 different hydro projects in 2017.

2. Updated CWT SARs for over 400 hatchery x  stock combinations currently monitored on DART.  

3. Updated smolt inriver survival estimates and travel times for 25 hatchery and wild salmonid stocks monitored on DART.

4. Developed and implemented new page on DART to monitor adult salmonid fallback rates at major Columbia River Basin dams.  

5. One peer-reviewed paper was published in a peer-reviewed journal in 2017.

     a. Deng, Z. D., J. J. Martinez, H. Li, R. A. Harnish, C. M. Woodley, J. A. Hughes, X. Li, T. Fu, J. Lu, G. A. McMichael, M. A. Weiland, M. B. Eppard, J. R. Skalski, and R. L. Townsend.  2017.  Comparing the survival rate of juvenile Chinook salmon migrating through hydropower systems using injectable and surgical acoustic transmitters.  Scientific Reports 7, 42999; DOI: 10.1038/srep42999.
  
6. Three other papers were submitted for publication in 2017:

     a. Deng, Z. D., X. Li, T. Fu, R. Brown, J. Martinez, G. McMichael, B. Trumbo, M. Ahmann, J. Reynolds, J. Skalski, and R. Townsend.  2017.  Three-dimensional migration behavior of juvenile salmonids at a mid-reach location and dam forebay locations on the snake river, Washington.  Fisheries Research (submitted).
     b. Richins, S. M., and J. R. Skalski.  2017.  Influence of the reservoir environment on steelhead overshoot and fallback rates in the Columbia/Snake River Basin.  North American Journal of Fisheries Management (submitted).
     c. Richins, S. M., and J. R. Skalski.  2017.  Steelhead overshoot and fallback rates in the Columbia/Snake River Basin and the influence of rearing, barging, and age at return.  North American Journal of Fisheries Management (submitted).

7. One M.S. thesis was completed in 2017.

     a. Richins, S. M.  2017.  Influence of juvenile and adult experiences on tributary overshoot and fallback by steelhead in the Columbia River basin.  M.S. thesis.  School of Aquatic and Fishery Sciences, University of Washington, Seattle, Washington, USA.

8.The following presentations were provided in the November 2016 AFEP review:

     a. Appy, E., J. Reams, T. Williamson, D. Swope, G. McMichael, J. Purlsey, M. Demarchi, N. Hentze, J. Skalski, and B. Hazell.  2016.  2016 Lower Columbia River estuary double crested cormorant nesting status evaluation.  U.S. Army Corps of Engineers, 2016 Anadromous Fish Evaluation Program (AFEP) Annual Review, November 29–30, 2016, Portland, OR.
     b. Johnson, P., P. Mugunthan, J. Miller, S. Haffey, M. Weiland, J. Murauskas, J. Skalski, R. Townsend, D. Passero, and J. DiGiulio.  2016.  Post-construction evaluation of adult fishway temperature differential reduction at Lower Granite Dam in 2016.  U.S. Army Corps of Engineers, 2016 Anadromous Fish Evaluation Program (AFEP) Annual Review, November 29–30, 2016, Portland, OR.
     c. McMichael, G., M. Weiland, T. Carlson, D. Deng, J. Miller, S. Haffey, J. Martinez, J. Murauskas, K. W. Jung, K. Carter, J. Lu, D. Hance, M. Gray, S. Titzler, and J. Skalski.  2016.  Lower Granite Dam construction sound and vibration monitoring.  U.S. Army Corps of Engineers, 2016 Anadromous Fish Evaluation Program (AFEP) Annual Review, November 29–30, 2016, Portland, OR.