Show new navigation
On
  • Log In
Columbia Basin Fish and Wildlife Program Columbia Basin Fish and Wildlife Program
  • Help
    • Help
    • Help Center
    • Data dictionary
    • EF&W Program documents
    • Request support
    • Send feedback
      • View all help topics
Columbia Basin Fish and Wildlife Program Columbia Basin Fish and Wildlife Program
  • Mitigation work
    Mitigation work View all mitigation work topics
  • Reporting
    Reporting View all reporting topics
  • Funding
    Funding View all funding topics
  • Search
RSS Feed for updates to Proposal RMECAT-1991-029-00 - Research, monitoring, and evaluation of emerging issues and measures to recover the Snake River fall Chinook salmon ESU Follow this via RSS feed. Help setting up RSS feeds?

Proposal Summary

Proposal RMECAT-1991-029-00 - Research, monitoring, and evaluation of emerging issues and measures to recover the Snake River fall Chinook salmon ESU

View the dynamic Proposal Summary

This Proposal Summary page updates dynamically to always display the latest data from the associated project and contracts. This means changes, like updating the Project Lead or other contacts, will be immediately reflected here.

Download a snapshot PDF

To view a point-in-time PDF snapshot of this page, select one of the Download links in the Proposal History section. These PDFs are created automatically by important events like submitting your proposal or responding to the ISRP. You can also create one at any time by using the PDF button, located next to the Expand All and Collapse All buttons.

Proposal History


Archive Date Time Type From To By
Download 7/29/2010 3:08 PM Status Draft ISRP - Pending First Review <System>
10/15/2010 5:55 PM Status ISRP - Pending First Review ISRP - Pending Final Review <System>
1/19/2011 2:43 PM Status ISRP - Pending Final Review Pending Council Recommendation <System>
7/8/2011 12:33 PM Status Pending Council Recommendation Pending BPA Response <System>

This online form is dynamically updated with the most recent information. To view the content as reviewed by the ISRP and Council for this review cycle, download an archived PDF version using the Download link(s) above.

Back To Top

Basics

Proposal Number:
   RMECAT-1991-029-00
Proposal Status:
 Pending BPA Response
Proposal Version:
 Proposal Version 1
Review:
 RME / AP Category Review
Portfolio:
 RM&E Cat. Review - RM&E
Type:
 Existing Project: 1991-029-00
Primary Contact:
 William Connor (Inactive)
Created:
 3/11/2010 by (Not yet saved)
Proponent Organizations:
 US Fish and Wildlife Service (USFWS)
US Geological Survey (USGS)
Project Title:
 Research, monitoring, and evaluation of emerging issues and measures to recover the Snake River fall Chinook salmon ESU
 
Proposal Short Description:
 Project 199102900 will collaboratively collect, disseminate, and analyze data to provide real-time information to update status and trend monitoring and assist in the development of data-supported models that inform adaptive management.
 
Proposal Executive Summary:
 Project 199102900 began in 1991 to provide some of the first biological data on the contemporary population of fall Chinook salmon Oncorhynchus tshawytscha in the Snake River basin that was eventually listed in 1992 under the Endangered Species Act (ESA; NMFS 1992) as the Snake River fall Chinook salmon evolutionary significant unit (ESU). As knowledge was obtained and more complicated issues emerged, the project was divided into three projects: (1) 199102900 focused on behavior, migration timing, and survival of natural-origin and hatchery-origin subyearlings and most of the fish studied were collected in riverine habitat, (2) 199801003 focused on spawning and adult behavior, and (3) 200203200 focused on behavior and survival of natural-origin and hatchery-origin juveniles collected in lower Snake River reservoirs that were destined to enter the ocean as yearlings. In agreement with BPA, we have reincorporated project 199801003 under project 199102900 as part of the present categorical review to streamline project administration and increase the efficiency of data processing. Adding the budgets of the two projects brings the annual budget of 199102900 to $534,112. As in past years, project 199102900 staffed by the U. S. Fish and Wildlife Service (USFWS) and U. S. Geological Survey (USGS) will complement and be coordinated with existing Snake River fall Chinook salmon ESU projects including staff of Idaho Power Company (IPC), the Nez Perce Tribe Department of Fisheries Resources Management (NPT) National Oceanographic and Atmospheric Administration (NOAA), Pacific Northwest Laboratory (PNNL), University of Idaho (UOI), and Washington Department of Fish and Wildlife (WDFW). We will summarize historical data and collect new data to make progress towards answering two questions posed in the draft MERR plan (i.e., Monitoring, Evaluation, Research and Reporting plan): (1) is the ESU abundant, diverse, productive, and spatially distributed; and (2) is the ESU responding to implemented actions as anticipated? We acknowledge that increasing the abundance of Snake River fall Chinook salmon ESU is well beyond the influence of scientists alone, however, accomplishing the data collection and analyses to produce the deliverables in this proposal will add to the history of modest contributions we have made to assist the natural resource management community in the Pacific Northwest as it strives to recover the Snake River fall Chinook salmon ESU. With this in mind, we recast the MERR plan questions as objectives: (1) increase the abundance, productivity, and spawning distribution of natural-origin adults, and (2) increase the abundance and diversity of natural-origin subyearlings during early freshwater rearing and migration.
Purpose:
 Programmatic
Emphasis:
 RM and E
Species Benefit:
 Anadromous: 100.0%   Resident: 0.0%   Wildlife: 0.0%
Supports 2009 NPCC Program:
 Yes
Subbasin Plan:
Fish Accords:
 None
Biological Opinions:

Back To Top

Contacts

Contacts:

Back To Top

Project Significance & Problem Statement

Describe how you think your work relates to or implements regional documents including: the current Council’s 2014 Columbia River Basin Fish and Wildlife Program including subbasin plans, Council's 2017 Research Plan,  NOAA’s Recovery Plans, or regional plans. In your summary, it will be helpful for you to include page numbers from those documents; optional citation format).
Project Significance to Regional Programs: View instructions
The 2008 Biological Opinion RPA 55.4 calls for the investigation, description, and quantification of key characteristics of the early life history of Snake River Fall Chinook Salmon in the mainstem Snake, Columbia, and Clearwater rivers. RPA 50.3 calls for testing different methods of estimating Snake River fall Chinook juvenile production and assessing the precision and accuracy of survival measurements. RPA 65.2 in the 2008 Biological Opinion calls for and evaluation of the fall Chinook hatchery program on the productivity of the fall Chinook salmon ESU. Alternative (RPA) 44 in the 2008 Biological Opinion calls for the development of strategies to reduce non-indigenous fish, recognizing that action to reduce predators may be warranted if they are found to negatively affect juvenile salmon. The Endangered Species Act Section 7(a)(2) Consultation Supplemental Biological Opinion Supplemental Consultation on Remand for Operation of the Federal Columbia River Power System,11 Bureau of Reclamation Projects in the Columbia Basin and ESA Section 10(a)(I)(A) Permit for Juvenile Fish Transportation Program called for information to address potential density-dependent impacts of FCRPS hatchery releases on listed species. The Snake Hells Canyon Subbasin Management Plan and the Supplement to this plan supported the continued development of stock-specific knowledge of interactions between hatchery and wild fish. The Draft Clearwater Subbasin Management Plan requested an increased understanding of the thermal impacts of Dworshak Dam operations on life history characteristics of fall Chinook salmon. The Draft Grande Ronde Subbasin Management Plan requested answers to questions relevant to six key variables, including abundance, survival/productivity, distribution, life history, and habitat. Two specific questions were: (1) how is freshwater productivity (e.g., smolt/female) and survival (e.g., SAR) of focal fish populations affected by hatchery practices and (2) how does habitat condition affect productivity of various life history stages of focal populations? The participants of the Anadromous Salmonid Monitoring Strategy Viable Salmonid Population Parameters and Subset of Tributary Habitat and Hatchery Effectiveness Columbia Basin Coordinated Anadromous Monitoring Workshop (Version 24052010) called for: (1) the estimation of Snake River fall Chinook salmon adults and juveniles for life cycle monitoring at the ESU scale and (2) the use of natural production, general hatchery production, and surrogate hatchery production to study efficacy of dam operation and passage strategies. In 2010, this group identified project 199102900 as a critical provider of Snake River fall Chinook salmon redd count and juvenile sampling data noting that the following were needed: (1) an estimate of annual juvenile production, (2) robust quantification of natural-origin juvenile survival and life history diversity, and (3) more information on the passage of passage of adults and juveniles relative to dam operations. The workgroup recommended: (1) testing of different methods to estimate Snake River fall Chinook juvenile production and more precise and accurate survival measurements, (2) increasing the number of natural-origin Chinook PIT tagged for estimating parr-to-smolt survival, and (3) additional monitoring and assessment on the effects of habitat and hatchery actions. Highest priority status was given to advancing the understanding of the role of juvenile life history diversity (prolonged emigration and ocean entry as sub-yearlings and yearlings) on abundance and productivity. Guidance for Monitoring Recovery of Pacific Northwest Salmon and Steelhead Recommendations for Data Collection, Evaluation, and Reporting suggested that Pacific Northwest agencies and tribes should obtain estimates of juvenile migrant abundance for at least one significant population within an ESU. The Adhoc Supplementation Work Group Final Report identified three critical research areas that if successfully addressed would greatly help the region in making both tactical and strategic decisions about how hatcheries are managed and how they might best be used in salmon recovery. These areas are: (1) determining the genetic, behavioral or physiological mechanisms which may cause low relative fitness in hatchery-origin fish, (2) determining the mechanisms by which supplementation reduces natural population productivity, and (3) the developing decision support tools to help managers make decisions about if and when to initiate and cease supplementation. Aspects of the proposed predation research are called for in the Independent Scientific Advisory Board’s recent report on non-native species impacts (ISAB 2008), and are related to recent publications on impacts of non-native species in the Columbia River Basin (e.g., Harvey and Kareiva 2005; Sanderson et al. 2009). We will summarize historical data and collect new data to make progress towards answering two questions posed in the draft MERR plan (i.e., Monitoring, Evaluation, Research and Reporting plan): (1) is the ESU abundant, diverse, productive, and spatially distributed; and (2) is the ESU responding to implemented actions as anticipated? The Northwest Power and Conservation Council’s 2009 Amendments to the Fish and Wildlife Program (NPCC 2009) list specific actions related to predation research. These include, “Evaluate and document the impact of predation in the mainstem in terms of ESA-listed fishes taken and the estimated impact on smolt-to-adult return ratios” (Page 41), and “The federal action agencies should work cooperatively with NOAA Fisheries, states, tribes, and the council to review, evaluate, develop, and implement strategies to reduce non-native piscivorous predation on salmon and steelhead, especially by smallmouth bass, channel catfish, and walleye” (Page 52). The Council’s Fish and Wildlife Program states, “The Council supports actions that suppress non-native populations that directly or indirectly adversely affect juvenile and adult salmonids”, (page 18). Results from the proposed predation work (if found to be negative for juvenile salmon) can be ameliorated, as the Council suggests, if managers take action to reduce predators in some areas. The 2008 Biological Opinion and RPA have received much attention from the resources management community in the Pacific Northwest. Most recently it was reviewed by the Obama Administration. This review led to an Adaptive Management Implementation Plan (AMIP). A full review of the AMIP is beyond the scope of this problem statement, but it builds on the 2008 Biological Opinion and parallels and supports the other regional actions outlined above. The AMIP advocates collecting more data and improving analytic tools to better inform future adaptive management decision making. It calls for enhanced research on salmon predators and invasive species including a determination of whether removals of smallmouth bass in areas of intense predation could reduce the mortality of juvenile salmonids. It supports enhanced RM&E actions to fill data gaps including: adult status and trend monitoring, juvenile status and trend monitoring, and the development expanded life-cycle and passage models. Hereafter, we develop the problem statement for project 199102900 and lay out how this project can support the AMIP actions and the corresponding regional programs. This problem statement places our proposed research for FY12–14 in the context of what work has been done, what is known, and what remains to be known.
In this section describe the specific problem or need your proposal addresses. Describe the background, history, and location of the problem. If this proposal is addressing new problems or needs, identify the work components addressing these and distinguish these from ongoing/past work. For projects conducting research or monitoring, identify the management questions the work intends to address and include a short scientific literature review covering the most significant previous work related to these questions. The purpose of the literature review is to place the proposed research or restoration activity in the larger context by describing work that has been done, what is known, and what remains to be known. Cite references here but fully describe them on the key project personnel page.
Problem Statement: View instructions

Adult Status and Trend Monitoring

 * = journal article published by past and present key personnel.

The literature suggests that the historical populations of Snake River basin fall Chinook salmon were abundant, diverse, productive, and spatially distributed (Fulton 1968).  These measures of status declined from the late 19th century to 1992.  The Interior Columbia Basin Technical Recovery Team (ICRT) reviewed available information on historical distributions and concluded that there were likely three relatively discrete populations of Snake River fall Chinook salmon.  These included one population each centered on the Swan Falls reach, the middle Snake River (a.k.a., the Marsing reach), and the lower Snake River and its major tributaries downstream of the middle Snake River (Figure 1; ICTRT 2003).

  

  

figure 1 

The construction of Swan Falls Dam eliminated production in the Swans Falls reach in 1910.  The abundance of adults that returned to the middle Snake River was first measured with some certainty by counting fish at Brownlee (1957) and Oxbow dams (1958–1964; Haas 1965; Craig 1965).  The adult counts declined from over 17,103 to 504.  Redd counts upstream of the dams declined from 3,794 to 222.  In 1961, an experimental incubation facility was constructed near the power house of Oxbow Dam and 30% of the adults trapped at the dam were retained for hatchery brood stock (Culpin 1963).  Spawning in the middle Snake River was eliminated in 1964 when all of the adults trapped at Oxbow Dam were retained for hatchery brood stock and all of the hatchery-reared juveniles were released downstream of the dam (Craig 1965).  The hatchery program was plagued with disease outbreaks and mortality.  It was disbanded by the early 1970s.  

The population centered downstream of the middle Snake River likely spawned in portions of the lower Snake River downstream of the Boise River mouth as well as lower portions of the Imnaha, Grande Ronde, Salmon, Selway, Clearwater, Palouse, and Tucannon rivers (e.g., Schoning 1947; Figure 1).  Abundance of the adults returning to these spawning areas was first measured by counting adults passing Ice Harbor Dam in 1964.  Adult counts at Ice Harbor Dam declined from a high in 1968 of 24,374 to a low of 1,475 in 1976 when management efforts refocused on establishing a hatchery stock of Snake River fall Chinook salmon.  Adults were trapped at dams such as Ice Harbor Dam, the offspring were reared at existing hatcheries, and the juveniles were largely released into the Snake River at various locations (Bugert et al. 1995).  Lyons Ferry Hatchery was completed and reared its first brood in 1984.  The Lyons Ferry program involved the release of subyearling and yearling smolts made on station and most of the returning adults that escaped to the Snake River returned to the hatchery where they were collected as broodstock.

Lower Granite Dam was completed in 1972.  The average number of adults counted at Lower Granite Dam during 1975–1992 was 1,489 (Figure 2).  Redd surveys made in the 1970s focused on the lower Snake River because few if any redds were counted in other areas when search effort was expended in these areas.  Mark data was first used in 1983 to reconstruct the adult run that arrived at Lower Granite Dam into natural-origin and hatchery-origin fish (Figure 2).  We define natural-origin fish as any fish that was produced by spawning in the wild regardless of parental origin.  For example, a hatchery-origin female that made a redd and spawned with a hatchery-origin male would produce natural offspring.  The hatchery-origin fish identified by run reconstruction were a combination of out-of-basin strays, Lyons Ferry Hatchery strays, and returns from hatchery releases made into the Snake River when developing Lyons Ferry Hatchery stock (Marshall et al. 2000*).  The contemporary major spawning areas upstream of Lower Granite Dam included lower Snake, Clearwater, and Grande Ronde rivers according to redd surveys made during 1986–1992.  However, the inter-annual average number of redds counted were low (Snake River = 50; Clearwater River = 13; Grande Ronde River = 1).

 

 

 

Figure 2

Our research group increased redd surveying effort after 1992 (Garcia and Groves 1998*; Groves and Chandler 1999; Table 1).  Counts upstream of Lower Granite Reservoir increased from 219 in 1993 to a high of 3,464 in 2009.  Inter-annual means of 60 ± 2, 28 ± 2, and 9 ± 2% of the basin-wide redds were counted in the lower Snake, Clearwater, and Grande Ronde rivers, respectively.  We fit a series of models and then estimated a redd capacity of 2,570 for the lower Snake River under a stable flow regime adopted for Hells Canyon Dam (Figure 1) during spawning to prevent redd dewatering (Connor et al. 2001a*).  We then worked with staff of the UOI and used field and laboratory methods to implicitly relate emergence success to substrate composition measured at fall Chinook salmon spawning sites in the Snake River.  Estimated that emergence success ranged from 29 to 48% (Bennett et al. 2003*).  Redd capacity estimates and spawning habitat quality analyses provided similar results for the Clearwater River (Arnsberg et al. 1992).  We concluded that spawning habitat availability and quality should not of itself limit recovery, but this conclusion needs to be tested given existing evidence for density dependent population regulation (Figure 3).

 

 

 

Table 1

  

 

 

Figure 3

The release of hatchery-origin fall Chinook salmon subyearlings and yearlings (of or derived from Lyons Ferry Hatchery stock) into the free-flowing lower Snake, Clearwater and tributaries, and Grande Ronde rivers to supplement production that began in 1996 had large potential to influence adult status and trends.  We refer to project 199801004 reports written by NPT for more details on supplementation (Table 2).  Notably, millions of hatchery-origin fish are released annually for supplementation and a large portion (e.g., 20% or more) have been and will continue to be unmarked.  This lead to enhanced efforts after 1998 to reconstruct the adult run at Lower Granite Dam that are presently led by NPT (Table 1).  Counts of both natural-origin and hatchery-origin adults increased after ESA listing (Figure 2).

This portion of the problem statement has briefly suggested adults from the historical populations of Snake River basin fall Chinook salmon were abundant, diverse, productive, and spatially distributed and that these measures of status declined from the late 19th century to 1992.  Adult abundance has increased since ESA listing in 1992 to the point where density dependent mechanisms appear to be in effect (Figure 3).  A stock-recruitment analysis that tests the influence of anthropogenic, biological, and environmental change on trends in adult counts (i.e., without use of run reconstruction) and the spatial distribution of redd counts observed since the middle of the 20th century has not been conducted.  We suggest that such an analysis would provide a useful historical perspective and propose it herein.

The ICRT (2003) recommended a minimum viability threshold of a geometric mean of 3,000 natural-origin adults over 10 years for the Snake River fall Chinook salmon ESU.  Run reconstruction indicates that 3,000 or more natural-origin adults have arrived at Lower Granite Dam during 5 of the last 10 years (Figure 2; geometric mean = 2,897).  A stock-recruitment analysis that tests the influence of anthropogenic, biological, and environmental change on the abundance of natural-origin adults observed after 1983 when reconstruction began would (1) help to understand why the abundance of natural-origin adults increased and (2) provide the ability to make predictions under “what if ?” scenarios for adaptive management.  We describe such an analysis in this proposal.

The ICRT (2003) also recommended explicit population level spatial structure criteria including the escapement of at least 2,500 natural-origin spawners to the lower Snake River.  Spawning by natural-origin adults in the Clearwater and Grande Ronde rivers is also important under these criteria.  Though run reconstruction provides an estimate of the abundance of natural-origin adults at Lower Granite Dam to assess status relative to the minimum viability threshold, it does not provide the information on spatial distribution of natural-origin spawners needed to assess status relative to the explicit population level spatial structure criteria.  A model with clearly stated assumptions that relates redd counts made since we intensified search effort and coverage in 1993 to the explicit population level spatial structure criteria would be useful.  This proposal describes one approach for developing such a model.

 

Juvenile Status and Trend Monitoring

 

Though research was not conducted to document the historical status of the juvenile populations, it is quite likely these populations reflected the abundance, diversity, productivity, and spatial distribution of the adults.  Spawning was spatially distributed across habitats with a wide range of temperatures and levels of growth opportunity that would have fostered variation in emergence timing, growth, and timing of seaward migration.  Moreover, the rivers leading to the sea were free-flowing with natural temperature regimes and the juveniles and predators had evolved sympatrically.   

Loss of the Swan Falls reach eliminated some of the most productive rearing habitat.  After the loss of the Swan Falls reach, Krcma and Raleigh (1970) used a “migrant dipper” trap to capture offspring of adult fall Chinook salmon that spawned along the middle Snake River prior to 1964.  Fry emergence was complete by the middle of April.  Approximately 98% of the juvenile population had grown to become subyearling parr and had started downstream dispersal from natal rearing areas by the end of May.  Graban (1964) and Haas (1965) described the historical attempts to pass juvenile migrants at Brownlee and Oxbow dams (Figure 1).  The juvenile fish bypass facility was considered a failure and the inability to successfully pass fish at these two dams was the primary reason attempts to maintain production in the middle Snake River were discontinued and the juvenile production in this reach of river was lost.  Mains and Smith (1964) collected subsamples of subyearlings in between the present locations of Lower Granite and Little Goose dams that likely included offspring of fall Chinook salmon that spawned throughout the Snake River basin.  Passage of subyearlings was complete by the end of June well before flow descended to base levels.  This stretch of river was completely impounded with the construction of Little Goose and Lower Granite dams in 1970 and 1972, respectively.

We began using beach seines to collect natural-origin subyearlings along in the lower Snake and Clearwater rivers in the early 1990s to study early life history timing and growth (Table 2).  Natural-origin subyearlings 60-mm and longer were implanted with passive integrated transponder (PIT) tags (Prentice et al. 1990a).  Connor et al. (2000*) and Burge and Connor (2003*) found that the fry emerged later and grew to become parr more slowly and later than observed by Krcma and Raleigh (1970) in the middle Snake River.  We also found that the subyearling migrants passed between Lower Granite and Little Goose dams a month or more later than reported by Mains and Smith (1964).  We concluded that dams in the Swan Falls reach and the middle Snake River had eliminated highly productive rearing habitat leaving juvenile production to habitat with relatively lower growth opportunity.  Further, dam construction in the lower Snake River had delayed seaward migration and young fall Chinook salmon were present in reservoirs during the warmest periods of the year when flows in the reservoir were at their lowest. 

 

 

Table 2

 

 

 

 

Summer flow augmentation is one action that has been implemented to mitigate delayed seaward migration and the associated reduction in survival of subyearling migrants.  Summer flow involves releasing relatively cool water from Dworshak Reservoir and relatively warm water in smaller volumes from reservoirs upstream of Hells Canyon Dam (Figure 1) and it decreases temperature and increases flow in Lower Granite Reservoir (Connor et al. 2003a*).  Through analyses of PIT tagging data (Table 2) and radio tag data we have concluded that summer flow augmentation has a slight affect on migration rate of subyearlings (Connor et al. 2003b*; Smith et al. 2003*; Tiffan et al. 2009a*) and has a large effect on survival and growth (Connor et al. 2003a*; Smith et al. 2003*; Tiffan et al. 2009b*).

The previously described release of millions of hatchery juveniles upstream of Lower Granite Dam is another implemented action we have helped to evaluate with PIT-tag data (Table 2).  The potential for interaction between natural-origin and hatchery-origin subyearlings likely decreases as the size of the hatchery-origin fish released increases (Connor et al. 2004*).  Hatchery-origin subyearlings released at sizes similar to natural-origin subyearlings (e.g, 70–75 mm fork length) disperse slowly downstream and they can interact while growing, feeding, and passing dams.  Hatchery-origin subyearlings released at average fork lengths of 90–95 mm actively migrate, spend little time feeding and growing, and pass dams earlier than natural-origin subyearlings.  Prior to release into riverine habitat, some hatchery-origin juveniles are acclimated for a period of three to six weeks at acclimation facilities (Figure 1) to allow the juveniles to recover from trucking and to increase homing.  Acclimated hatchery-origin subyearlings pass downstream faster and pass dams earlier than hatchery-origin subyearlings that were trucked and released directly to the river, thus acclimation reduces the potential for interaction with natural-origin subyearlings (Rosenberger et al. in preparation). 

In the last several years, we have observed an increase in densities of natural-origin subyearlings in the lower Snake River that might suggest a response to implemented actions such as summer flow augmentation and hatchery supplementation.  For example, in the Snake River during 1992–1999 the inter-annual mean CPUE was 3 ± 1 SE natural-origin juveniles per seine haul compared to an inter-annual mean of 29 ± 6 juveniles per seine haul for the years 2000–2008 (Connor, unpublished data).  In association with increases in rearing densities of natural–origin subyearlings and the number of hatchery-origin subyearlings released, we found that the amount of time the PIT-tagged natural-origin subyearlings spent in transit to Lower Granite Dam had decreased, passage timing of the PIT-tagged population at Lower Granite Dam had become earlier, the size of the fish at the time of dam passage had become smaller, and growth rates during downstream passage had decreased (Plumb et al. in preparation a,b).

This portion of the problem statement has briefly suggested juveniles from the historical populations of Snake River basin fall Chinook salmon were abundant, diverse, and spatially distributed and that these measures of status declined from the late 19th century to 1992.  It has also summarized how we have used PIT tags to understand the response of subyearlings to actions implemented including summer flow augmentation and hatchery supplementation.  Though the unique and individually based information collected with PIT tags has been and will be useful for research and management, PIT-tag data do not fully represent the natural population.  To compliment PIT-tag data and analyses and move the state of knowledge forward, estimates of passage abundance for the population of natural-origin subyearlings at Lower Granite Dam are needed.  This can be done by reconstructing the juvenile run.  Reconstructing the run of subyearlings would provide: (1) estimates of passage abundance of natural-origin subyearlings at Lower Granite Dam during the spring, summer, and fall, (2) the opportunity to increase understanding of the anthropogenic, biological, and environmental factors that influence trends in passage abundance, and (3) the opportunity to increase the understanding of how varying influential anthropogenic, biological, and environmental factors might increase passage abundance.  We describe the development and application of such an approach in this proposal.

The explanation for the apparent density-dependent population response shown in Figure 3 remains to be known.  We have not observed large-scale redd superimposition in the spawning areas and new spawning sites within an area are documented annually, thus it is not likely that the capacity of the spawning habitat is a large factor for the density dependent population response being observed (Groves et al. in preparation).  The Beverton Holt curve (Beverton and Holt 1957) in Figure 3 might suggest that competition for food and space during early freshwater rearing and seaward as an explanation of the decline in recruits as spawner abundance has increased.  This theory could be tested with the juvenile run reconstruction and modeling approach described above.  The Ricker curve (Ricker 1954) in Figure 3 might suggest overcompensation.  Predators in freshwater may have responded to increases in natural-origin and hatchery-origin subyearlings in riverine habitat by increasing in abundance or predatory effectiveness. 

 

Expanded Life Cycle and Passage Modeling

 

A number of life-cycle and passage models have been fitted to data collected on spring Chinook salmon and steelhead to help understand trends in abundance and productivity (e.g., Karieva et al. 2000; Zabel et al. 2006, 2008; Scheuerell et al. 2006; ICRT 2007; ICTRT & Zabel., 2007).  A major initiative under the AMIP will involve building on these models to develop improved tools for informing the evaluation of recovery efforts and the adaptive development of future actions.  Though some progress has been made in the past (e.g., Williams et al. 2008), a life-cycle and passage model has yet to be fully fitted from data collected on the Snake River fall Chinook salmon ESU.  Fitting such models is a high priority for NOAA as outlined in the AMIP.

 

 

 

 


Back To Top

Objectives

What are the ultimate ecological objectives of your project?

Examples include:

Monitoring the status and trend of the spawner abundance of a salmonid population; Increasing harvest; Restoring or protecting a certain population; or Maintaining species diversity. A Project Objective should provide a biological and/or physical habitat benchmark by which results can be evaluated. Objectives should be stated in terms of desired outcomes, rather than as statements of methods and work elements (tasks). In addition, define the success criteria by which you will determine if you have met your objectives. Later, you will be asked to link these Objectives to Deliverables and Work Elements.
Objectives: View instructions
Increase the abundance, productivity, and spawning distribution of natural-origin adults (OBJ-1)
The success criteria for objective 1 will be: (1) an increased understanding of the anthropogenic, biological, and environmental factors that influenced historical and contemporary trends in adult abundance, (2) an increased understanding of how varying influential anthropogenic, biological, and environmental factors might facilitate meeting the minimum viability threshold, and (3) documentation of the status of escapement of natural-origin adults to the spawning areas relative to the explicit population level spatial structure criteria, and (4) support for expanded life cycle and passage modeling.
Increase the abundance and diversity of natural subyearlings during early freshwater rearing and migration (OBJ-2)
The success criteria for objective 2 will be: (1) estimates of passage abundance for natural-origin fall Chinook salmon subyearlings at Lower Granite Dam during the spring, summer, and fall, (2) an increased understanding of the anthropogenic, biological, and environmental factors that influence trends in passage abundance, (3) an increased understanding of how varying influential anthropogenic, biological, and environmental factors might increase passage abundance of natural-origin fall Chinook salmon subyearlings, (4) an increased understanding of the effect of predation in riverine habitat on passage abundance of natural-origin fall Chinook salmon subyearlings, and (5) support for expanded life cycle and passage models.

Back To Top

Project History

Financials

The table content is updated frequently and thus contains more recent information than what was in the original proposal reviewed by ISRP and Council.

Summary of Budgets

To view all expenditures for all fiscal years, click "Project Exp. by FY"

To see more detailed project budget information, please visit the "Project Budget" page

Expense SOY Budget Working Budget Expenditures *
FY2019 $1,366,605 $941,729
BiOp FCRPS 2008 (non-Accord) $1,359,994 $937,174
General - Within Year $6,611 $4,556
FY2020 $1,359,994 $1,359,994 $1,174,647
BiOp FCRPS 2008 (non-Accord) $1,359,994 $1,174,647
FY2021 $1,359,994 $1,630,207 $1,796,561
BiOp FCRPS 2008 (non-Accord) $1,630,207 $1,796,561
FY2022 $1,630,207 $1,630,207 $1,464,616
BiOp FCRPS 2008 (non-Accord) $1,630,207 $1,464,616
FY2023 $1,630,207 $1,630,207 $1,556,945
BiOp FCRPS 2008 (non-Accord) $1,630,207 $1,556,945
FY2024 $1,701,936 $1,701,936 $1,579,090
BiOp FCRPS 2008 (non-Accord) $1,701,936 $1,579,090
FY2025 $1,701,936 $1,701,936 $877,327
BiOp FCRPS 2008 (non-Accord) $1,701,936 $877,327

* Expenditures data includes accruals and are based on data through 31-Mar-2025

Actual Project Cost Share

The table content is updated frequently and thus contains more recent information than what was in the original proposal reviewed by ISRP and Council.

Current Fiscal Year — 2025   DRAFT
Cost Share Partner Total Proposed Contribution Total Confirmed Contribution
There are no project cost share contributions to show.
Previous Fiscal Years
Fiscal Year Total Contributions % of Budget
2024 $227,000 12%
2023 $227,000 12%
2022 $227,000 12%
2021 $217,000 12%
2020 $207,000 13%
2019 $167,000 11%
2018 $194,000 26%
2017 $194,000 25%
2016 $242,000 29%
2015 $396,250 40%
2014 $233,200 28%
2013 $288,000 35%
2012 $208,000 28%
2011 $1,200,000 69%
2010 $1,215,000 71%
2009 $1,215,000 73%
2008 $1,565,000 77%
2007 $45,000 9%

Discuss your project's recent Financial performance shown above. Please explain any significant differences between your Working Budget, Contracted Amount and Expenditures. If Confirmed Cost Share Contributions are significantly different than Proposed cost share contributions, please explain.
Explanation of Recent Financial Performance: View instructions
We have never overspent this projects budget. The FY2009 Expenditures were about $150,000 above the budget, but that was probably due to: (1) FY2008 budget expenditures hitting in FY2009, (2) we went through the BOG process to carry money over to complete work in FY2009. We can work with our administrative staff to any provide any additional information if needed.
Discuss your project's historical financial performance, going back to its inception. Include a brief recap of your project's expenditures by fiscal year. If appropriate discuss this in the context of your project's various phases.
Explanation of Financial History: View instructions
Years underway: 20 Past costs: FY90 = $300,000 Focused solely on natural production in Snake and Hanford Reach FY91 = $335,000 FY92 = $343,000 FY93 = $409,000 FY94 = $350,000 FY95 = $630,375 Increased natural and hatchery fish tagging (PIT and radio) and habitat work FY96 = $630,375 FY97 = $630,375 FY98 = $630,375 FY99 = $630,375 FY00 = $630,375 FY01 = $630,375 FY02 = $630,375 FY03 = $610,375 FY04 = $610,375 Discontinued hatchery fish PIT-tagging and radio tagging FY05 = $365,375 FY06 = $456,375 Began to work on diet, growth, and bioenergetics FY07 = $456,375 FY08 = $456,375 FY09 = $456,375 FY10 = $467,784 FY11 = $534,112 Merged projects 199102900 and 199801003

Back To Top

Reporting & Contracted Deliverables Performance

Annual Progress Reports
Expected (since FY2004):54
Completed:44
On time:34
Status Reports
Completed:168
On time:109
Avg Days Late:0

Historical from: 1998-010-03
                Count of Contract Deliverables
Earliest Contract Subsequent Contracts Title Contractor Earliest Start Latest End Latest Status Accepted Reports Complete Green Yellow Red Total % Green and Complete Canceled
4700 20366, 25263, 29840, 35778, 40522, 45097 199801003 EXP BIOP SPAWNING DISTRIBUTION OF SNAKE RIVER FALL CHIN US Fish and Wildlife Service (USFWS) 05/01/2001 11/30/2010 Closed 23 42 0 0 4 46 91.30% 1
Project Totals 183 433 41 0 42 516 91.86% 15

                Count of Contract Deliverables
Earliest Contract Subsequent Contracts Title Contractor Earliest Start Latest End Latest Status Accepted Reports Complete Green Yellow Red Total % Green and Complete Canceled
5362 18033, 22926, 27447, 33149, 37852, 42842, 47760, 53309, 56969, 61380, 65395, 69274, 72898, 75986, 79371, 81781, 84776, 87285, 90045, 92095, 94498, 96586 1991-029-00 EXP SNAKE R FALL CHINOOK RESEARCH & MONITORING US Geological Survey (USGS) 08/01/1996 03/31/2026 Pending 79 245 38 0 30 313 90.42% 10
5233 27429, 32819, 37853, 42841, 47759, 53310, 56968, 61379, 65396, 69273, 72899, 75987 1991-029-00 EXP USFWS EMERGING ISSUE/MEASURE S RIV FALL CHIN ESU US Fish and Wildlife Service (USFWS) 06/06/2001 05/31/2018 Closed 52 120 3 0 7 130 94.62% 2
26951 199102900 EXP EFFECTS OF SUMMER FLOW AUG ON JUV SNAKE R FALL CHIN Lotek Wireless, Inc. 04/15/2006 06/30/2006 Closed 0 0 0 0 0 0 0
32856 37899, 42600, 47127, 53169 1991-029-00 EXP BIOP UI EMERGING ISSUE/MEASURE SR FALL CHIN ESU University of Idaho 06/01/2007 08/31/2012 Closed 21 19 0 0 1 20 95.00% 1
BPA-9696 PIT Tags - Measure SR Fall Chinook ESU Bonneville Power Administration 10/01/2016 09/30/2017 Active 0 0 0 0 0 0 0
74314 REL 43 1991-029-00 EXP WDFW EMERGING ISSUE/MEASURE SNAKE R FALL CHIN ESU Washington Department of Fish and Wildlife (WDFW) 09/01/2018 08/31/2019 Closed 4 2 0 0 0 2 100.00% 0
BPA-10798 PIT Tag Readers - Measure SR Fall Chinook ESU Bonneville Power Administration 10/01/2018 09/30/2019 Active 0 0 0 0 0 0 0
81900 1991-029-00 EXP BIOMARK SNAKE R. FALL CHIN RESEARCH & MONITORING Biomark, LLC. 04/01/2019 03/31/2020 Closed 4 5 0 0 0 5 100.00% 1
BPA-12273 FY21 Pit Tags Bonneville Power Administration 10/01/2020 09/30/2021 Active 0 0 0 0 0 0 0
BPA-12909 FY22 PIT tags Bonneville Power Administration 10/01/2021 09/30/2022 Active 0 0 0 0 0 0 0
Project Totals 183 433 41 0 42 516 91.86% 15

Selected Contracted Deliverables in CBFish (2004 to present)

The contracted deliverables listed below have been selected by the proponent as demonstrative of this project's major accomplishments.

Projects that are the product of merges and/or splits from other projects may not have the complete list of historical deliverables included below. If you wish to highlight deliverables that are not listed, please refer to Pisces to determine the complete list and describe the missing deliverables in the Major Accomplishments section.

Contract WE Ref Contracted Deliverable Title Due Completed
27447 D: 162 Determine the migration history of two groups of tagged fish 12/1/2006 12/1/2006
27447 G: 157 John Day pool velocity measurements 4/6/2007 4/6/2007
27447 B: 158 Collect, Tag, and release fish 5/24/2007 5/24/2007
27429 C: 161 Management briefings 5/31/2007 5/31/2007
27429 F: 132 Annual report 5/31/2007 5/31/2007
27447 C: 157 Monitor movement of radio-tagged fish 6/30/2007 6/30/2007
33149 B: 157 Obtain morphological data 7/20/2007 7/20/2007
37852 G: 183 Published journal article 3/27/2009 3/27/2009
37899 D: 162 Analyses on factors affecting life stage progression 5/31/2009 5/31/2009
42842 C: 157 Collect growth data from fish 7/15/2009 7/15/2009
42841 E: 162 Analyses on factors affecting rearing survival 9/18/2009 9/18/2009
42841 F: 162 Analyses on acclimation effects 10/31/2009 10/31/2009
42841 G: 162 Analyses on surrogate performance 12/14/2009 12/14/2009
42842 F: 162 Estimate growth 5/24/2010 5/24/2010
42842 H: 162 Quantify habitat use 5/24/2010 5/24/2010
42841 B: 158 PIT tag wild fall Chinook salmon subyearlings 5/28/2010 5/28/2010
42841 C: 157 PIT-tag data uploaded to PITAGIS and summary of 2009 passage period. 5/28/2010 5/28/2010
42600 B: 161 Management briefings 5/31/2010 5/31/2010

View full Project Summary report (lists all Contracted Deliverables and Quantitative Metrics)

Discuss your project's contracted deliverable history (from Pisces). If it has a high number of Red deliverables, please explain. Most projects will not have 100% completion of deliverables since most have at least one active ("Issued") or Pending contract. Also discuss your project's history in terms of providing timely Annual Progress Reports (aka Scientific/Technical reports) and Pisces Status Reports. If you think your contracted deliverable performance has been stellar, you can say that too.
Explanation of Performance: View instructions
Our completion rate is not 100%, but it is relatively high (91%). In the past, it has not been uncommon for us to collect a set of data during one funding cycle as part of a given deliverable and then complete that deliverable in a subsequent funding cycle by publishing a journal article (e.g., Tiffan et al. 2009a,b). It is quite probable that the nine deliverables that have not been completed (9% rate of incompletion) will be completed in the near future.

Back To Top

Results: Reporting, Accomplishments, and Impact

  • Please do the following to help the ISRP and Council assess project performance:
  • List important activities and then report results.
  • List each objective and summarize accomplishments and results for each one, including the projects previous objectives. If the objectives were not met, were changed, or dropped, please explain why. For research projects, list hypotheses that have been and will be tested.
  • Whenever possible, describe results in terms of the quantifiable biological and physical habitat objectives of the Fish and Wildlife Program, i.e., benefit to fish and wildlife or to the ecosystems that sustain them. Include summary tables and graphs of key metrics showing trends. Summarize and cite (with links when available) your annual reports, peer reviewed papers, and other technical documents. If another project tracks physical habitat or biological information related to your project’s actions please summarize and expand on, as necessary, the results and evaluation conducted under that project that apply to your project, and cite that project briefly here and fully in the Relationships section below. Research or M&E projects that have existed for a significant period should, besides showing accumulated data, also present statistical analyses and conclusions based on those data. Also, summarize the project’s influence on resource management and other economic or social benefits. Expand as needed in the Adaptive Management section below. The ISRP will use this information in its Retrospective Review of prior year results. If your proposal is for continuation of work, your proposal should focus on updating this section. If yours is an umbrella project, click here for additional instructions. Clearly report the impacts of your project, what you have learned, not just what you did.
All Proposals: View instructions
  • For umbrella projects, the following information should also be included in this section:
  • a. Provide a list of project actions to date. Include background information on the recipients of funding, including organization name and mission, project cost, project title, location and short project summary, and implementation timeline.
  • b. Describe how the restoration actions were selected for implementation, the process and criteria used, and their relative rank. Were these the highest priority actions? If not, please explain why?
  • c. Describe the process to document progress toward meeting the program’s objectives in the implementation of the suite of projects to date. Describe this in terms of landscape-level improvements in limiting factors and response of the focal species.
  • d. Where are project results reported (e.g. Pisces, report repository, database)? Is progress toward program objectives tracked in a database, report, indicator, or other format? Can project data be incorporated into regional databases that may be of interest to other projects?
  • e. Who is responsible for the final reporting and data management?
  • f. Describe problems encountered, lessons learned, and any data collected, that will inform adaptive management or influence program priorities.
Umbrella Proposals: View instructions

This section includes work conducted under project 199801003, which has been merged with project 199102900.  We have completed all of our annual reports, but the dates in given later in this proposal might not match the dates given below because sometimes we worked on reports within a year but combined two years into one report.

Our staff has coauthored 32 peer-reviewed journal articles as part of project 199102900 and several more are in the hopper.

1991: Conducted aerial surveys of the Planned and implemented pilot beach seining and PIT tagging five days per week from May to July in the lower 50 kms of the Snake River from May to July.  Proofed and uploaded data to the PIT-tag Information System (PITAGIS) for public access.  Provided an in-season briefing to the FPAC to describe the first existing detection data at Lower Granite Dam.  Planned to build on existing redd survey efforts and techniques.  Administered project.

1992: Implemented weekly surveys for fall Chinook salmon redds from October to December over 173 km of the Snake River.  Tested SCUBA for counting redds that were too deep to observe from the air.  Proofed the survey data.  Collected habitat data at one spawning site.  Proofed the habitat data and provided it to IPC for use during re-licensing by the Federal Energy Regulatory Commission (FERC).  Presented and published the PIT-tag data at an American Fisheries Society (AFS) Symposium.  Expanded beach seining to 3-4 days a week covering 79 km of river from April to July.  Implanted PIT-tags into subyearling Chinook salmon and collected genetic samples (Table 3).  Proofed and uploaded data to the PITAGIS for public access.  Provided an in season briefing to the FPAC on passage timing at Lower Granite Dam to help implement summer flow augmentation.  Prepared the FY90 annual report to BPA. Administered project.

1993: Implemented weekly surveys for fall Chinook salmon redds from October to December over 173 km of the Snake River.  Used SCUBA and underwater video cameras for counting redds that were too deep to observe from the air throughout 142 km of the Snake River.  Proofed the survey data.  Collected habitat data at seven spawning sites.  Proofed the habitat data and provided it to IPC for use during FERC re-licensing.  Beach seined to 3-4 days a week covering 142 km of river from April to July, implanted PIT-tags into subyearling Chinook salmon, and took genetic samples (Table 3).  Proofed and uploaded data to the PITAGIS for public access.  Provided an in season briefing to the FPAC on passage timing at Lower Granite Dam to help implement summer flow augmentation.  Presented PIT-tag study results at an AFS meeting. Prepared the FY91 annual report to BPA.   Administered project. 

 

 

 

 

Table 3 

1994: Implemented weekly surveys for fall Chinook salmon redds from October to December over 173 km of the Snake River.  Used underwater video cameras for counting redds that were too deep to observe from the air throughout 142 km of the Snake River.  Proofed the survey data.  Collected habitat data at two spawning sites.  Proofed the habitat data and provided it to IPC for use during FERC re-licensing.  Beach seined to 3-4 days a week covering 142 km of river from April to July, implanted PIT-tags into subyearling Chinook salmon, and took genetic samples (Table 3).  Proofed and uploaded data to the PITAGIS for public access.  Provided an in season briefing to the FPAC on passage timing at Lower Granite Dam to help implement summer flow augmentation.  Contributed data and text to the proposed recovery plan for Snake River fall Chinook salmon.  Presented data on quantifying fall Chinook salmon habitat at an AFS meeting. Prepared the FY92 annual report to BPA.  Administered project.

1995: Implemented weekly surveys for fall Chinook salmon redds from October to December over 173 km of the Snake River.  Used underwater video cameras for counting redds that were too deep to observe from the air throughout 142 km of the Snake River from April to July.  Proofed the survey data.  Beach seined to 3-4 days a week covering 142 km of river from April to July, implanted PIT-tags into subyearling Chinook salmon, and took genetic samples (Table 3).  Proofed and uploaded data to the PITAGIS for public access.  Provided an in season briefing to the FPAC on passage timing at Lower Granite Dam to help implement summer flow augmentation.  Presented PIT-tag data and analyses at an AFS meeting. Prepared the FY93 annual report to BPA.  Administered project.

1996: Implemented weekly surveys for fall Chinook salmon redds from October to December over 173 km of the Snake River.  Used underwater video cameras for counting redds that were too deep to observe from the air throughout 142 km of the Snake River.  Proofed the survey data.  Prepared the FY94 annual report to BPA.  Beach seined to 3-4 days a week covering 142 km of river from April to July, implanted PIT-tags into subyearling Chinook salmon, and took genetic samples (Table 3).  Proofed and uploaded data to the PITAGIS for public access.  Provided an in season briefing to the FPAC on passage timing at Lower Granite Dam to help implement summer flow augmentation.  Presented PIT-tag data and analyses at a PSFMC workshop.  Prepared the FY94 annual report to BPA.  Administered project.

1997: Implemented weekly surveys for fall Chinook salmon redds from October to December over 173 km of the Snake River.  Used underwater video cameras for counting redds that were too deep to observe from the air throughout 142 km of the Snake River.  Proofed the survey data.    Beach seined to 3-4 days a week covering 142 km of river from April to July, implanted PIT-tags into subyearling Chinook salmon, and took genetic samples (Table 3).  Proofed and uploaded data to the PITAGIS for public access.  PIT-tagged and released 35,000 hatchery fall Chinook salmon to evaluate supplementation.  Proofed and uploaded data to the PITAGIS for public access.  Provided an in season briefing to the FPAC on passage timing at Lower Granite Dam to help implement summer flow augmentation.  Prepared the FY95 annual report to BPA. Administered project.

1998: Implemented weekly surveys for fall Chinook salmon redds from October to December over 173 km of the Snake River.  Used underwater video cameras for counting redds that were too deep to observe from the air throughout 142 km of the Snake River.  Proofed the survey data. Prepared the FY96 annual report to BPA.  Beach seined to 3-4 days a week covering 142 km of river from April to July, implanted PIT-tags into subyearling Chinook salmon, and took genetic samples (Table 3).  Proofed and uploaded data to the PITAGIS for public access.  PIT-tagged and released 35,000 hatchery fall Chinook salmon to evaluate supplementation.  Proofed and uploaded data to the PITAGIS for public access.  Provided an in season briefing to the FPAC on passage timing at Lower Granite Dam to help implement summer flow augmentation.  Presented the data collected on hatchery fish at a symposium on hatchery supplementation.  Prepared the FY96 annual report to BPA.  Published Connor et al. (1998) and Groves and Garcia (1998).  Administered project.

1999: Implemented weekly surveys for fall Chinook salmon redds from October to December over 173 km of the Snake River.  Used underwater video cameras for counting redds that were too deep to observe from the air throughout 142 km of the Snake River.   Beach seined to 3-4 days a week covering 142 km of river from April to July, implanted PIT-tags into subyearling Chinook salmon, and took genetic samples (Table 3).  Proofed and uploaded data to the PITAGIS for public access.  Provided the data collected on the 70,000 PIT-tagged hatchery fish to the PATH work group for analyses.  Provided an  in season briefing to the FPAC on passage timing at Lower Granite Dam to help implement summer flow augmentation.  Presented the data collected on hatchery fish at a symposium on hatchery supplementation.  Made two presentations on the PIT-tag data at AFS meetings.  Prepared the FY97 annual report to BPA.  Published Dauble et al. (1999).  Administered project.

2000: Implemented weekly surveys for fall Chinook salmon redds from October to December over 173 km of the Snake River.  Used underwater video cameras for counting redds that were too deep to observe from the air throughout 142 km of the Snake River.   Beach seined to 3-4 days a week covering 142 km of river from April to July, implanted PIT-tags into subyearling Chinook salmon, and took genetic samples (Table 3).  Provided an in season briefing to the FPAC on passage timing at Lower Granite Dam to help implement summer flow augmentation.  We also contributed data an analysis for the Snake River fall Chinook salmon component of the PATH process, and wrote the fall.  Chinook sections of Appendix M and Annex D of the Fish and Wildlife Coordination Act report.  Prepared the FY98 annual report to BPA Published Connor et al. (2000), Marshall et al. (2000), Tiffan et al (2000), and Venditti et al. (2000).   Administered project. 

2001: Implemented weekly surveys for fall Chinook salmon redds from October to December over 173 km of the Snake River.  Used underwater video cameras for counting redds that were too deep to observe from the air throughout 142 km of the Snake River.  Beach seined to 3-4 days a week covering 142 km of river from April to July, implanted PIT-tags into subyearling Chinook salmon, and took genetic samples (Table 3).  Proofed and uploaded data to the PITAGIS for public access.  Provided an in season briefing to the FPAC on passage timing at Lower Granite Dam to help implement summer flow augmentation.  Briefed the Independent Scientific Advisory Board (ISAB) to the NWPCC on summer flow augmentation.  Prepared the FY99 annual report to BPA.  Published, Connor et al.( 2001a,b,c) and Tiffan et al. (2001).   Administered project.

2002: Implemented weekly surveys for fall Chinook salmon redds from October to December over 173 km of the Snake River.  Used underwater video cameras for counting redds that were too deep to observe from the air throughout 142 km of the Snake River.  Beach seined to 3-4 days a week covering 142 km of river from April to July, implanted PIT-tags into subyearling Chinook salmon, and took genetic samples (Table 3). Proofed and uploaded data to the PITAGIS for public access.  Provided an in season briefing to the FPAC on passage timing at Lower Granite Dam to help implement summer flow augmentation.  Briefed the NWPCC on summer flow augmentation.  Prepared the FY00 annual report to BPA.   Published Connor et. al (2002), Garland et al. (2002), and Tiffan et al. (2002).  Administered project.

2003: Implemented weekly surveys for fall Chinook salmon redds from October to December over 173 km of the Snake River.  Used underwater video cameras for counting redds that were too deep to observe from the air throughout 142 km of the Snake River.    Beach seined to 3-4 days a week covering 142 km of river from April to July, implanted PIT-tags into subyearling Chinook salmon, and took genetic samples (Table 3).   Released 100 radio-tagged subyearlings in Hells Canyon to relate travel time to water velocity.  Proofed and uploaded data to the PITAGIS for public access.  Provided an in season briefing to the FPAC on passage timing at Lower Granite Dam to help implement summer flow augmentation.  Prepared the FY01 annual report to BPA.  Published Bennett et al. (2003), Connor et al. (2003a,b,c), Connor and Burge (2003), Smith et al. (2003), Rasmussen et al. (2003; co-published under project 200203200), and Tiffan et al. (2003).  Administered project.

2004: Implemented weekly surveys for fall Chinook salmon redds from October to December over 173 km of the Snake River.  Used underwater video cameras for counting redds that were too deep to observe from the air throughout 142 km of the Snake River.    Beach seined to 3-4 days a week covering 142 km of river from April to July, implanted PIT-tags into subyearling Chinook salmon, and took genetic samples (Table 3).  Proofed and uploaded data to the PITAGIS for public access.   Released 100 radio-tagged subyearlings in Hells Canyon to relate travel time to water velocity.  Provided an in season briefing to the FPAC on passage timing at Lower Granite Dam to help implement summer flow augmentation.  Presented two briefings to the NWPCC and the ISAB on fall Chinook salmon life history and survival.  Provided three briefings on life history and survival to the USACE and an interagency team developing a large scale study on transportation and spill.  Prepared the FY02 annual report to BPA.  Published Connor et al. (2004) and Garcia et al. (2004),   Administered project.

2005: Implemented weekly surveys for fall Chinook salmon redds from October to December over 173 km of the Snake River.  Used underwater video cameras for counting redds that were too deep to observe from the air throughout 142 km of the Snake River.  Beach seined to 3-4 days a week covering 142 km of river from April to July, implanted PIT-tags into subyearling Chinook salmon, and took genetic samples (Table 3).  Released 50 subyearlings tagged with temperature-sensing transmitters to determine temperature selection at the confluence of the Snake and Clearwater rivers during summer flow augmentation.  Uploaded the PIT-tag data to the central database for public access.  Participated on an interagency-tribal team to design a study to assess the effect of transportation and spill on smolt-to-adult return rates for fall Chinook salmon.  Provided an in season briefing to the FPAC on passage timing at Lower Granite Dam to help implement summer flow augmentation.  Presented a briefing to the NWPCC and the ISAB on fall Chinook salmon life history.  Prepared the FY03 annual report to BPA.  Published Connor et al. (2005; co-published under project 200203200).  Administered project.

2006: Implemented weekly surveys for fall Chinook salmon redds from October to December over 173 km of the Snake River.  Used underwater video cameras for counting redds that were too deep to observe from the air throughout 142 km of the Snake River.  Beach seined to 3-4 days a week covering 142 km of river from April to July, implanted PIT-tags into subyearling Chinook salmon, and took genetic samples (Table 3).  Uploaded the PIT-tag data to the central database for public access.  Participated on an interagency-tribal team to design a study to assess the effect of transportation and spill on smolt-to-adult return rates for fall Chinook salmon.  Presented a briefing to the NWPCC on fall Chinook salmon life history.  Participated and provided data to the TRT fall Chinook salmon life cycle model.  Prepared the FY04 annual report to BPA.  Published Connor and Garcia (2006), Haskell et al. (2006a,b), and Tiffan et al. (2006).  Administered project.

2007: Implemented weekly surveys for fall Chinook salmon redds from October to December over 173 km of the Snake River.  Used underwater video cameras for counting redds that were too deep to observe from the air throughout 142 km of the Snake River.  Beach seined to 3-4 days a week covering 142 km of river from April to July, implanted PIT-tags into subyearling Chinook salmon, and took genetic samples (Table 3).  Uploaded the PIT-tag data to the central database for public access.  Participated on an interagency-tribal team to design a study to assess the effect of transportation and spill on smolt-to-adult return rates for fall Chinook salmon.  Participated and provided data to the TRT fall Chinook salmon life cycle model.  Presented a briefing to the NWPCC on fall Chinook salmon life history.  Prepared the FY05 annual report to BPA.  Administered project.

2008: Implemented weekly surveys for fall Chinook salmon redds from October to December over 173 km of the Snake River.  Used underwater video cameras for counting redds that were too deep to observe from the air throughout 142 km of the Snake River.  Beach seined to 3-4 days a week covering 142 km of river from April to July, implanted PIT-tags into subyearling Chinook salmon, and took genetic samples (Table 3).  Uploaded the PIT-tag data to the central database for public access.  Participated on an interagency-tribal team to design a study to assess the effect of transportation and spill on smolt-to-adult return rates for fall Chinook salmon.  Presented a paper at an AFS meeting on hatchery supplementation and a briefing to the Lower Snake River Compensation plan on fall Chinook salmon life history.  Published Williams et al. (2008; co-published under project 200203200).  Prepared the FY06 annual report to BPA.  Administered project.

2009: Implemented weekly surveys for fall Chinook salmon redds from October to December over 173 km of the Snake River.  Used underwater video cameras for counting redds that were too deep to observe from the air throughout 142 km of the Snake River.  Beach seined to 3-4 days a week covering 142 km of river from April to July, implanted PIT-tags into subyearling Chinook salmon, and took genetic samples (Table 3).  Uploaded the PIT-tag data to the central database for public access.  Participated on an interagency-tribal team to design a study to assess the effect of transportation and spill on smolt-to-adult return rates for fall Chinook salmon.  Published Tiffan et al. (2009a,b).  Prepared the FY07 annual report to BPA.  Administered project.

2010: Implemented weekly surveys for fall Chinook salmon redds from October to December over 173 km of the Snake River.  Used underwater video cameras for counting redds that were too deep to observe from the air throughout 142 km of the Snake River.  Beach seined to 3-4 days a week covering 142 km of river from April to July, implanted PIT-tags into subyearling Chinook salmon, and took genetic samples (Table 3).  Uploaded the PIT-tag data to the central database for public access.  Participated on an interagency-tribal team to design a study to assess the effect of transportation and spill on smolt-to-adult return rates for fall Chinook salmon including two presentations at a work shop.  Wrote Connor et al. (in preparation), Groves et al. (in preparation), Plumb et al. (in preparation a,b), Rosenberger et al. (in preparation), Tiffan and Connor (in review), and Yanke et al.( in review). Prepared the FY08 annual report to BPA.  Administered project.


Back To Top

Past Council Recommendations and ISRP Reviews


The table content is updated frequently and thus contains more recent information than what was in the original proposal reviewed by ISRP and Council.

Review: 2019-2021 Mainstem/Program Support

Council Recommendation

Assessment Number: 1991-029-00-NPCC-20210312
Project: 1991-029-00 - Snake River Fall Chinook Research & Monitoring
Review: 2019-2021 Mainstem/Program Support
Proposal: NPCC19-1991-029-00
Proposal State: Pending Council Recommendation
Approved Date: 8/25/2019
Recommendation: Implement
Comments: Continue implementation through next review cycle, and address ISRP qualifications in next annual report. Given the relationship of this work project to the fall chinook production efforts in the Snake River, this project will be considered in context during the 2021 Habitat and Hatchery Review. See Programmatic issue for Hatchery-related work.

[Background: See https:/www.nwcouncil.org/fish-and-wildlife/fish-and-wildlife-program/project-reviews-and-recommendations/mainstem-review]

Independent Scientific Review Panel Assessment

Assessment Number: 1991-029-00-ISRP-20190404
Project: 1991-029-00 - Snake River Fall Chinook Research & Monitoring
Review: 2019-2021 Mainstem/Program Support
Proposal Number: NPCC19-1991-029-00
Completed Date: None
First Round ISRP Date: 4/4/2019
First Round ISRP Rating: Meets Scientific Review Criteria
First Round ISRP Comment:

Comment:

The ISRP was impressed by the proposal, results-to-date, and the project review presentation. There are, however, several items that the proponents should consider (these are detailed below). Most importantly, the ISRP would appreciate knowing the topics and timelines for completing the multi-part synthesis (i.e., peer-reviewed publications) over the next year or two.

1. Objectives, Significance to Regional Programs, and Technical Background

Project objectives are to (1) inform recovery actions taken to increase the abundance, productivity, and spawning distribution of natural-origin adults, and (2) inform recovery actions taken to increase the abundance and diversity of natural-origin subyearlings during early freshwater rearing and migration. The project objectives are well aligned with the Snake River fall Chinook salmon recovery plan, the current biological opinion, and the Council's 2014 Fish and Wildlife Program and 2017 Research Plan.

However, the proponents should establish quantitative objectives, specific timelines, and hypotheses to guide the research/monitoring. The stated objectives are actually work elements described in vague terms as to what is expected to be accomplished. Although the project objectives are not quantitative, the text associated with each objective identified criteria for success. That said, the ISRP would like to see a long-range vision articulated for the project, as well as criteria for success identified for that vision.

The proponents mention that several regional programs use the data that are generated by the project. However, it is not clear to the ISRP that these regional programs require those data. Please consider adding letters of support from those programs to future proposals.

2. Results and Adaptive Management

Status and trend monitoring of juvenile and adult fall Chinook are described and provide important information on the recovery of this ESU. The project's monitoring program revealed strong density dependence in fall Chinook salmon recruitment. The mechanism leading to this is unknown. The ISRP also notes that millions of hatchery fish are released with a large portion (20% or more) unmarked, leading to less certainty about the status of the natural population. The proponents and decision-makers associated with this project should carefully consider these issues in crafting future project actions.

 The proponents make a few statements that would benefit from further explanation:

·         Density dependence (p. 6): "Although it is not likely that the capacity of the spawning habitat is a large factor for the density dependent population response being observed (Groves et al. 2013*), we have observed large-scale redd superimposition at some spawning areas that could explain this." The ISRP is curious as to why other possible factors (e.g., juvenile growth) were not considered.

·         Is there a publication or document showing how the life-cycle and passage models are linked (see p. 16)? And how are the outputs from that linkage effective in improving population status and management?

·         The proponents state that they account for climate change, predation, and potential food web changes (p. 16) "by fitting stock-recruitment functions to predict changes in adult and juvenile abundance from covariates derived from empirical data collected on stream flow, temperature, and ocean conditions." This is confusing to the ISRP since the proponents do not collect data on these important factors. What is the origin of these data?

·         Budget (p. 22): It would be useful to know the amounts devoted to data synthesis and preparation of professional publications in each year, as well as for public outreach.

3. Methods: Project Relationships, Work Types, and Deliverables

Although specific methodology was not described in the proposal, annual reports provided more details. The reports noted that more accurate identification of redds is needed. Deliverables noted in the proposal included redd counts, spawner origin determination based on PBT (300 fish), stock-recruitment analysis, juvenile PIT tagging, juvenile run reconstruction, the life cycle model, and associated information. The project uses standard statistical methods.

Project relationships are described at several places in the proposal. However, the mechanisms underlying these relationships are not always clearly described. Are there any problems or issues associated with project relationships that ISRP could assist with in the near future?
Documentation Links:
Review: RME / AP Category Review

Council Recommendation

Assessment Number: 1991-029-00-NPCC-20100924
Project: 1991-029-00 - Snake River Fall Chinook Research & Monitoring
Review: RME / AP Category Review
Proposal: RMECAT-1991-029-00
Proposal State: Pending BPA Response
Approved Date: 6/10/2011
Recommendation: Fund (Qualified)
Comments: Implement with conditions through 2016: Implementation based on outcome of Lower Snake Comp Review process and relationship to and a regional hatchery effects.
Conditions:
Council Condition #1 Programmatic Issue: RMECAT #4 Hatchery Effectiveness—.

Independent Scientific Review Panel Assessment

Assessment Number: 1991-029-00-ISRP-20101015
Project: 1991-029-00 - Snake River Fall Chinook Research & Monitoring
Review: RME / AP Category Review
Proposal Number: RMECAT-1991-029-00
Completed Date: 12/17/2010
Final Round ISRP Date: 12/17/2010
Final Round ISRP Rating: Meets Scientific Review Criteria
Final Round ISRP Comment:
This ongoing project has collected field data on Snake River fall Chinook salmon spawning activity, juvenile recruitment, survival, and growth for almost two decades, and proposes to continue these studies. The project also manages a very ambitious PIT-tagging program, with almost 400,000 hatchery fall Chinook PIT tagged annually. This project has provided a large portion of the available data on the Snake River fall Chinook Salmon ESU. The data have been used for development of the recovery plan, for planning of the Lyons Ferry hatchery program, and for design of the summer flow augmentation program. The study documented overwintering of juvenile fall Chinook salmon in the hydropower system reservoirs, and contributed to the decision to extend the operation of the juvenile bypass system at Lower Granite Dam later into the fall. This project is a collaborative effort between the USFWS and the USGS, and will provide information essential to NOAA life-cycle modeling efforts. A number of additional Federal and State agencies are involved in data collecting and reporting. The activities funded by this proposal would not duplicate other efforts.

This project is well integrated with other regional RM&E efforts relating to Snake River fall Chinook, as would be expected of a project with a nearly 20-year history. The proposal addresses RPAs in the BiOp, the AMIP, and Council’s draft MERR plan. The 2008 BiOp calls for (continuing) investigations of the early life history of Snake River fall Chinook salmon and of the effects of the hatchery program on natural productivity. The NPCC’s Fish and Wildlife Program calls for research on the effects of predation in the mainstem on juvenile salmonids, as does the Adaptive Management Implementation Plan (AMIP). The AMIP also calls for the development of improved life-cycle and passage models for ESA-listed salmonid stocks. The proposal has easily identifiable objectives and tasks related to these needs.

This was a well-written proposal for a project with an excellent track record of success and accomplishment (e.g., 32 peer-reviewed journal articles) over its long history. Project proponents have made a number of presentations to the ISAB and ISRP over the years in which major findings have been analyzed and discussed. The project has clearly benefited Snake River fall Chinook salmon over the years and will likely continue to do so. In particular, this proposal seems to be especially good at describing how data collection and data analysis/modeling will work together. It is more than a monitoring project. It is truly a combination monitoring and research/modeling effort. Their proposal is thus a well-synthesized effort at data collection and high-level analyses with clear applicability to management. The itemized list of management changes that have resulted from the findings of this study constitutes strong evidence of adaptive management. Their general approach could (and should) be applied to other programs in the Basin.

Some limitations on the extent and reliability of data collected by this project have been resolved (differentiating between natural-origin Fall and Spring Chinook subyearlings and between natural-origin Fall Chinook and hatchery-origin subyearlings), while others have not (inability to tag subyearlings <49 mm, uncertainty about effects of flow on beach-seining efficiency, lack of data on passage of juveniles during winter months).

One of the highlights of the project’s discoveries has been the recognition of a reservoir overwintering life history attribute in some Snake River fall Chinook, and extension of operation of the juvenile bypass systems at the lower Snake dams reflects this new understanding of year-round movement patterns. The research questions have been refined and focused over the years, and are addressing some of the most critical data gaps concerning this ESU.

The technical background and objectives were clearly organized and explained. For each objective, detailed methods are provided. The project relies on standard field sampling methods. Deliverables, work elements, metrics and methods are well described in the proposal. The discussions of population modeling and the approaches to fitting stock-recruitment curves were especially thorough. Project proponents appear well equipped to carry out the work.

Of particular value in this proposed work are their analyses of abundance and growth data with stock recruitment relationships to address the idea of density dependence in supplementation programs. Post supplementation, there has been a significant decrease in smolt size. Hatchery supplementation has been associated with large increases in redd counts, followed by a leveling off/slight decline of natural fish. There are some indications that density dependent factors might be acting as stock size rebuilds. Whether or not density-dependence or other hatchery-wild interactions are occurring may be a contentious issue, but regardless of the outcome, addressing these questions with their long-term data sets is a highly important use of the data, and an appropriate approach for evaluating and shaping other supplementation projects in the basin as well. Results of the analysis should provide a biological basis for recovery goals. The proponents also have a riverine bass predation element to their project that will provide information related to survival. This project is exemplary in that it is making the attempt to truly assess a supplementation program not just through intermediate steps such as more smolts or more redds, but in terms of its ultimate impact on recovery, the wild stock, density effects, and other higher level population dynamics.
First Round ISRP Date: 10/18/2010
First Round ISRP Rating: Meets Scientific Review Criteria
First Round ISRP Comment:

This ongoing project has collected field data on Snake River fall Chinook salmon spawning activity, juvenile recruitment, survival, and growth for almost two decades, and proposes to continue these studies. The project also manages a very ambitious PIT-tagging program, with almost 400,000 hatchery fall Chinook PIT tagged annually. This project has provided a large portion of the available data on the Snake River fall Chinook Salmon ESU. The data have been used for development of the recovery plan, for planning of the Lyons Ferry hatchery program, and for design of the summer flow augmentation program. The study documented overwintering of juvenile fall Chinook salmon in the hydropower system reservoirs, and contributed to the decision to extend the operation of the juvenile bypass system at Lower Granite Dam later into the fall. This project is a collaborative effort between the USFWS and the USGS, and will provide information essential to NOAA life-cycle modeling efforts. A number of additional Federal and State agencies are involved in data collecting and reporting. The activities funded by this proposal would not duplicate other efforts. This project is well integrated with other regional RM&E efforts relating to Snake River fall Chinook, as would be expected of a project with a nearly 20-year history. The proposal addresses RPAs in the BiOp, the AMIP, and Council’s draft MERR plan. The 2008 BiOp calls for (continuing) investigations of the early life history of Snake River fall Chinook salmon and of the effects of the hatchery program on natural productivity. The NPCC’s Fish and Wildlife Program calls for research on the effects of predation in the mainstem on juvenile salmonids, as does the Adaptive Management Implementation Plan (AMIP). The AMIP also calls for the development of improved life-cycle and passage models for ESA-listed salmonid stocks. The proposal has easily identifiable objectives and tasks related to these needs. This was a well-written proposal for a project with an excellent track record of success and accomplishment (e.g., 32 peer-reviewed journal articles) over its long history. Project proponents have made a number of presentations to the ISAB and ISRP over the years in which major findings have been analyzed and discussed. The project has clearly benefited Snake River fall Chinook salmon over the years and will likely continue to do so. In particular, this proposal seems to be especially good at describing how data collection and data analysis/modeling will work together. It is more than a monitoring project. It is truly a combination monitoring and research/modeling effort. Their proposal is thus a well-synthesized effort at data collection and high-level analyses with clear applicability to management. The itemized list of management changes that have resulted from the findings of this study constitutes strong evidence of adaptive management. Their general approach could (and should) be applied to other programs in the Basin. Some limitations on the extent and reliability of data collected by this project have been resolved (differentiating between natural-origin Fall and Spring Chinook subyearlings and between natural-origin Fall Chinook and hatchery-origin subyearlings), while others have not (inability to tag subyearlings <49 mm, uncertainty about effects of flow on beach-seining efficiency, lack of data on passage of juveniles during winter months). One of the highlights of the project’s discoveries has been the recognition of a reservoir overwintering life history attribute in some Snake River fall Chinook, and extension of operation of the juvenile bypass systems at the lower Snake dams reflects this new understanding of year-round movement patterns. The research questions have been refined and focused over the years, and are addressing some of the most critical data gaps concerning this ESU. The technical background and objectives were clearly organized and explained. For each objective, detailed methods are provided. The project relies on standard field sampling methods. Deliverables, work elements, metrics and methods are well described in the proposal. The discussions of population modeling and the approaches to fitting stock-recruitment curves were especially thorough. Project proponents appear well equipped to carry out the work. Of particular value in this proposed work are their analyses of abundance and growth data with stock recruitment relationships to address the idea of density dependence in supplementation programs. Post supplementation, there has been a significant decrease in smolt size. Hatchery supplementation has been associated with large increases in redd counts, followed by a leveling off/slight decline of natural fish. There are some indications that density dependent factors might be acting as stock size rebuilds. Whether or not density-dependence or other hatchery-wild interactions are occurring may be a contentious issue, but regardless of the outcome, addressing these questions with their long-term data sets is a highly important use of the data, and an appropriate approach for evaluating and shaping other supplementation projects in the basin as well. Results of the analysis should provide a biological basis for recovery goals. The proponents also have a riverine bass predation element to their project that will provide information related to survival. This project is exemplary in that it is making the attempt to truly assess a supplementation program not just through intermediate steps such as more smolts or more redds, but in terms of its ultimate impact on recovery, the wild stock, density effects, and other higher level population dynamics.
Documentation Links:
Review: FY07-09 Solicitation Review

Council Recommendation

Assessment Number: 1991-029-00-NPCC-20090924
Project: 1991-029-00 - Snake River Fall Chinook Research & Monitoring
Review: FY07-09 Solicitation Review
Approved Date: 10/23/2006
Recommendation: Fund
Comments:
Assessment Number: 1998-010-03-NPCC-20090924
Project: 1998-010-03 - Spawning Distribution of Snake River Fall Chinook Salmon
Review: FY07-09 Solicitation Review
Approved Date: 10/23/2006
Recommendation: Fund
Comments:

Independent Scientific Review Panel Assessment

Assessment Number: 1991-029-00-ISRP-20060831
Project: 1991-029-00 - Snake River Fall Chinook Research & Monitoring
Review: FY07-09 Solicitation Review
Completed Date: 8/31/2006
Final Round ISRP Date: None
Final Round ISRP Rating: Meets Scientific Review Criteria
Final Round ISRP Comment:
This is a well-prepared proposal to continue a project that has been exceptionally productive and well organized. In many respects it is a model proposal. The project is devoted to Snake River fall Chinook and has a proven track record of providing important information necessary to this species' recovery and deserves to be continued.

The technical and scientific background is very well written with a clear explanation of the project's history and a persuasive rationale for the work. A point the sponsors may wish to consider is that the use of F1 and F2 generations for supplementation seem ambiguous, and probably inappropriately used here. Is the F1 generation those individuals that are of hatchery-origin, and the F2 those individual born in the wild from the F1 (hatchery-origin) parents? In at least some circles, the hatchery-origin adults spawning in the wild would be the P1 generation; the progeny of these hatchery fish spawning naturally the F1 generation, and their progeny the F2 generation.

The proposal does a very good job of relating the work to the FCRPS BiOps, the Council's Fish and Wildlife Program, and the various COE programs. Subbasin plans aren't mentioned although Snake River fall Chinook do enter the lower reaches of several subbasins. There is a good description of the relationship of this project to other work.

The proposal sets a standard for a concise year-by-year summary of the project's history, along with the reports and peer-reviewed publications. The proposal sets an example for others by identifying the adaptive management implications of their investigations.

Objectives, hypotheses, and methods are clearly described, along with the timelines for completion. The proposal was very explicit, right down to the sample size and statistical tests in many instances. The methods have a proven track record. One statement that may be in error is that "growth of parr and smolts will be directly proportional to temperature." Actually, this statement will only be true over the cooler range and if food availability increases in direct proportion to temperature and provides enough to compensate for the increased basal metabolic requirements of the fish that accompany higher temperatures. At higher temperatures, generally above about 18°C for Chinook salmon, growth rate normally declines because of over-riding metabolic demands. In other words, there may be some scenarios in which growth of parr and smolts is inversely proportional to temperature if temperatures are high and food resources are inadequate. An accurate estimation of food availability is needed, especially when making inferences about the potential for reduced growth of wild fish in the face of large numbers of supplemented fish (these comments apply to Objective 2).

The project will be thoroughly monitored and evaluated. The statistical analyses have been peer-reviewed (in prior publications) and are suitable. The proposal gives a good description of how the results can feed back into hydrosystem operations decisions, e.g., summer spill.

An excellent feature of the proposal is clear identification of how they are going to use their primary data to test prevailing assumptions about the state of nature, and then the implications of the inference for the next steps in developing management options. Most proposals fail to make a clear connection between the studies they are proposing and deciding among (or designing new) management schemes.

The results will be made available in reports, peer-reviewed publications, internet postings, and presentations. Plans for long-term storage of data and meta-data are not completely described, but they are assumed to be adequate. The project staff are some of the best publishers among all BPA projects.

In summary, this is a fine example of an effective proposal.
Documentation Links:
Assessment Number: 1998-010-03-ISRP-20060831
Project: 1998-010-03 - Spawning Distribution of Snake River Fall Chinook Salmon
Review: FY07-09 Solicitation Review
Completed Date: 8/31/2006
Final Round ISRP Date: None
Final Round ISRP Rating: Meets Scientific Review Criteria (Qualified)
Final Round ISRP Comment:
The ISRP is not requesting a response, but qualifies this fundable recommendation because this is such a small activity or component of the Fish and Wildlife Program. It would be better if it was more clearly integrated into a larger project. Furthermore, sponsors do not justify sufficiently why this project is critical and how it fits into and relates to other projects. At a regional scale, it is not clear why this project should continue. How is this used and related to other projects? Does this project have application beyond this site? Can this approach be applied some other places at low cost?

Besides the usefulness of the method in this particular case, the method may have potential application elsewhere. A key factor would be to develop the ability to see redds in places not easily accessible. The project should not only emphasize current usage of the method but look for ways to improve the method so that the application could be more widespread. The project history was brief, with little development of past findings. The budget seems reasonable given the scope and potential value of the work.
Documentation Links:
Explain how your project has responded to the above ISRP and Council qualifications, conditions, or recommendations. This is especially important if your project received a "Qualified" rating from the ISRP in your most recent assessment. Even if your project received favorable ratings from both the ISRP and Council, please respond to any issues they may have raised.
Response to past ISRP and Council comments and recommendations: View instructions
Our project did not have any qualifications or conditions.

Back To Top

Adaptive Management


Project Level: Please discuss how you’ve changed your project (objectives, actions, etc) based on biological responses or information gained from project actions; because of management decisions at the subbasin state, regional, or agency level; or by external or larger environment factors. Specifically, regarding project modifications summarize how previous hypotheses and methods are changed or improved in this updated proposal. This would include project modifications based on information from recent research and literature. How is your new work different than previous work, and why?
Management Level: Please describe any management changes planned or made because of biological responses or information gained from project actions. This would include management decisions at the subbasin, state, or regional level influenced by project results.
Management Changes: View instructions
1) Contributions were made to the proposed recovery plan relative to critical habitat and hydrosystem operation. 2) Lyons Ferry Hatchery fall Chinook salmon were incorporated into the Snake River fall Chinook salmon ESU in part because of the genetic analyses we published with WDFW. 3) Summer flow augmentation was timed annually according to the project's PIT-tag data and eventual changes in the timing of summer flow augmentation were based in part on the project's publications. 4) The project validated the IPC interim recovery measure of stabilizing flows during spawning. 5) The project provided instream flow data to support the Snake River Basin Water Adjudication process and FERC re-licensing of the Hells Canyon Complex. 6) We worked with WDFW and validated the size at release criteria for Lyons Ferry Hatchery fall Chinook salmon released for supplementation. 7) The project confirmed that acclimating hatchery-origin juveniles resulted in the return of adults to the locations desired by managers. Moreover, the project has shown that acclimation increases smolt survival. In the future, we will compare SARs of direct and acclimated releases with our NPT and WDFW colleagues as data become available. For the present; the time, effort, and money spent developing the acclimation program appears to have been well spent. 8) First peer-reviewed documentation of reservoir-overwintering which partly contributed to extended operation of the juvenile fish bypass system at Lower Granite Dam. 9)The project has provided key personnel and data to help design and conduct the consensus transportation/spill study: Evaluating the Responses of Snake and Columbia River Basin fall Chinook Salmon to Dam Passage Strategies and Experiences (www.fpc.org/documents/ fallchinook_planningteam_documents.html). 10) The project has provided managers and researchers with the best scientific information available including in season statistical support. Staff has given face-to-face briefings to all the major forums in the regions including the NPCC, TMT, Columbia River Basin Fish and Wildlife Authority (CBFWA), FPAC, ISAB, Independent Scientific Review Group (ISRG), Technical Recovery Team (TRT), and the AFS.

Back To Top

Project Documents & Reports

The table content is updated frequently and thus contains more recent information than what was in the original proposal reviewed by ISRP and Council.

Public Attachments in CBFish

ID Title Type Period Contract Uploaded
21708-1 Identification of the Spawning, Rearing and Migratory Requirements of Fall Chinook Salmon in the Col Progress (Annual) Report 08/1991 - 07/1992 8/1/1993 12:00:00 AM
21708-3 Identification of the Spawning, Rearing, and Migratory Requirements of Fall Chinook Salmon in the Co Progress (Annual) Report 10/1992 - 09/1993 1/1/1994 12:00:00 AM
21708-4 Identification of the Spawning, Rearing, and Migratory Requirements of Fall Chinook Salmon in the Co Progress (Annual) Report 10/1993 - 09/1994 8/1/1996 12:00:00 AM
21708-5 Identification of the Spawning, Rearing and Migratory Requirements of Fall Chinook Salmon in the Col Progress (Annual) Report 10/1994 - 09/1995 7/1/1997 12:00:00 AM
21708-6 Identification of the Spawning, Rearing and Migratory Requirements of Fall Chinook Salmon in the Col Progress (Annual) Report 10/1995 - 09/1997 2/1/1999 12:00:00 AM
21708-7 Post-Release Attributes and Survival of Hatchery and Natural Fall Chinook Salmon in the Snake River Progress (Annual) Report 10/1997 - 09/1998 12/1/1999 12:00:00 AM
00000161-1 Post-Release Attributes and Survival of Hatchery and Natural Fall Chinook Salmon in the Snake River Progress (Annual) Report 10/1998 - 09/1999 1/1/2001 12:00:00 AM
00005362-1 Post-Release Attributes and Survival of Hatchery and Natural Fall Chinook Salmon in the Snake River Progress (Annual) Report 10/1999 - 09/2001 5362 2/1/2003 12:00:00 AM
00005362-2 Effects of Summer Flow Augmentation on the Migratory Behavior and Survival of Juvenile Snake River F Progress (Annual) Report 10/2001 - 09/2003 5362 10/1/2003 12:00:00 AM
00005362-3 Effects of Summer Flow Augmentation on the Migratory Behavior and Survival of Juvenile Snake River F Progress (Annual) Report 10/2002 - 09/2004 5362 2/1/2005 12:00:00 AM
00005362-4 Effects of Summer Flow Augmentation on the Migratory Behavior and Survival of Juvenile Snake River F Progress (Annual) Report 10/2003 - 05/2004 22926 3/1/2006 12:00:00 AM
P102644 Effects of summer flow augmentation Progress (Annual) Report 06/2005 - 05/2006 27447 6/26/2007 9:14:12 AM
P107567 EFFECTS OF SUMMER FLOW AUGMENATION ON THE MIGRATORY BEHAVIOR AND SURVIVAL OF JUVENILE SNAKE RIVER FALL CHINOOK SALMON Progress (Annual) Report 06/2006 - 05/2007 37852 8/1/2008 3:27:54 PM
P112356 Water velocity, turbulence, and migration rate of subyearling fall Chinook salmon in the free-flowing and impounded Snake River Other - 37852 7/6/2009 10:02:34 AM
P113539 RESEARCH, MONITORING, AND EVALUATION OF EMERGING ISSUES AND MEASURES TO RECOVER THE SNAKE RIVER FALL CHINOOK SALMON ESU Progress (Annual) Report 06/2007 - 05/2008 42842 9/30/2009 1:14:02 PM
P115643 Chart showing redd counts of Fall Chinook from 1993-2003 Other - 3/18/2010 6:38:11 PM
P115644 Map of the Snake River basin including the historical core area of production Other - 3/18/2010 6:39:10 PM
P118208 Research, monitoring, and evaluation of emerging issues and meausers to recover the Snake River fall Chinook salmon ESU Progress (Annual) Report 06/2008 - 05/2009 47760 9/30/2010 3:15:16 PM
P122690 RESEARCH, MONITORING, AND EVALUATION OF EMERGING ISSUES AND MEASURES TO RECOVER THE SNAKE RIVER FALL CHINOOK SALMON ESU Progress (Annual) Report 06/2009 - 05/2010 53309 8/25/2011 1:54:21 PM
P127078 RESEARCH, MONITORING, AND EVALUATION OF EMERGING ISSUES AND MEASURES TO RECOVER THE SNAKE RIVER FALL CHINOOK SALMON ESU Progress (Annual) Report 06/2010 - 05/2011 53309 6/22/2012 3:09:00 PM
P132109 Research, Monitoring, and Evaluation of Emerging Issues and Measures to Recover the Snake River Fall Chinook Salmon ESU Progress (Annual) Report 06/2011 - 05/2012 56969 5/22/2013 2:07:22 PM
P132140 Research, Monitoring, and Evaluation of Emerging Issues and Measures to Recover the Snake River Fall Chinook Salmon ESU; 1/11 - 12/11 Progress (Annual) Report 01/2011 - 12/2011 56968 5/29/2013 11:08:45 AM
P137822 RM&E of Emerging Issues and Measures to Recover the Snake River fall Chinook Salmon ESU Progress (Annual) Report 01/2012 - 12/2013 61379 7/25/2014 10:58:28 AM
P139646 Research, Monitoring, and Evaluation of the Snake River Basin fall Chinook Salmon Population/ESU Progress (Annual) Report 01/2013 - 12/2013 65396 11/24/2014 8:43:10 AM
P139946 Research, monitoring, and evaluation of emerging issues and measures to recover the Snake river fall Chinook salmon ESU Progress (Annual) Report 01/2013 - 12/2013 65395 11/24/2014 10:49:13 AM
P143326 Research, Monitoring, and Evaluation of Emerging Issues and Measures to Recover the Snake River Fall Chinook Salmon ESU Progress (Annual) Report 01/2014 - 12/2014 65395 4/15/2015 3:32:22 PM
P143033 Research, Monitoring, and Evaluation of Emerging Issues and Measures to Recover the Snake River Fall Chinook Salmon ESU; 1/14 - 12/14 Progress (Annual) Report 01/2014 - 12/2014 65396 4/15/2015 3:38:05 PM
P148972 Research, Monitoring, and Evaluation of Emerging Issues and Measures to Recover the Snake River Fall Chinook Salmon ESU; 1/15 - 12/15 Progress (Annual) Report 01/2015 - 12/2015 69274 6/2/2016 1:58:00 PM
P154616 Research, Monitoring, and Evaluation of Emerging Issues and Measures to Recover the Snake River Fall Chinook Salmon ESU; 1/16 - 12/16 Progress (Annual) Report 01/2016 - 12/2016 72899 6/5/2017 11:07:01 AM
P155752 Research, Monitoring, and Evaluation of Emerging Issues and Measures to Recover the Snake River Fall Chinook Salmon ESU; 1/16 - 12/16 Progress (Annual) Report 01/2016 - 12/2016 72898 9/6/2017 10:22:50 AM
P160478 Research, Monitoring, and Evaluation of Emerging Issues and Measures to Recover the Snake River Fall Chinook Salmon ESU; 1/17 - 12/17 Progress (Annual) Report 01/2017 - 12/2017 75986 5/14/2018 8:05:12 AM
P163118 Bibliography of Published Journal Articles Other - 81781 12/18/2018 2:33:33 PM
P166057 Research, Monitoring, and Evaluation of Emerging Issues and Measures to Recover the Snake River Fall Chinook Salmon ESU; 1/18 - 12/18 Progress (Annual) Report 01/2018 - 12/2018 79371 7/10/2019 8:41:53 AM
P168765 Snake River brood years 2009-2018 outmigrant Chinook salmon run ID Other - 74314 REL 43 11/7/2019 9:06:06 AM
P175195 Research, Monitoring, and Evaluation of Emerging Issues and Measures to Recover the Snake River Fall Chinook Salmon ESU Photo - 5/7/2020 5:44:05 PM
P175196 Research, Monitoring, and Evaluation of Emerging Issues and Measures to Recover the Snake River Fall Chinook Salmon ESU Photo - 5/7/2020 5:44:05 PM
P176701 Research, monitoring, and evaluation of emerging issues and measures to recover the Snake River fall Chinook salmon ESU 1/19-12/19 Progress (Annual) Report 01/2019 - 12/2019 84776 6/17/2020 11:15:16 AM
P186658 Monitoring Native, Resident Nonsalmonids for the Incidence of Gas Bubble Trauma Downstream of Snake and Columbia River Dams, 1/21-12/21 Progress (Annual) Report 01/2021 - 12/2021 87285 8/31/2021 9:35:49 AM
P186757 Research, Monitoring, and Evaluation of Emerging Issues and Measures to Recover the Snake River Fall Chinook Salmon ESU 1/20-12/20 Progress (Annual) Report 01/2020 - 12/2020 87285 9/2/2021 1:53:10 PM
P196313 Snake River Fall Chinook Salmon Research and Monitoring Progress (Annual) Report 01/2021 - 12/2021 90045 12/19/2022 11:10:58 AM
P197308 Monitoring Native Nonsalmonids for the Incidence of Gas Bubble Trauma Downstream of Snake and Columbia River Dams During the Spring Spill Season, 2022 Progress (Annual) Report 01/2022 - 12/2022 90045 2/6/2023 12:40:48 PM
P206973 Nonsalmonid Gas Bubble Trauma Investigations Progress (Annual) Report 04/2023 - 03/2024 92095 2/5/2024 11:02:05 AM
P210114 Snake River Fall Chinook Salmon Research and Monitoring Progress (Annual) Report 01/2022 - 12/2022 92095 7/1/2024 9:52:03 AM

Other Project Documents on the Web


Back To Top

Back To Top

Project Relationships

The Project Relationships tracked automatically in CBFish provide a history of how work and budgets move between projects. The terms "Merged" and "Split" describe the transfer of some or all of the Work and budgets from one or more source projects to one or more target projects. For example, some of one project's budget may be split from it and merged into a different project. Project relationships change for a variety of reasons including the creation of efficiency gains.
Project Relationships: This project Merged From 1998-010-03 effective on 12/1/2010
Relationship Description: Effective 12/1/10, work from 1998-010-03 is moved to 1991-029-00. Since contract ends 11/30/10, 6-months of work will be added to contract 47759. The 2 projects will start a new contract 6/1/11 with a combined FY11 budget under project 1991-029-00.


Additional Relationships Explanation:

All of the work proposed herein depends on coordinated, collaborative, complimentary efforts that are not duplicative.

Adult Status and Trend Monitoring FY12–14

See Table 1.

USACE counts adults at Ice Harbor, Lower Monumental, Little Goose, and Lower Granite dams.  NPT leads run reconstruction at Lower Granite Dam.  NPT counts redds in the Clearwater, Salmon, and Grande Ronde rivers.  We count redds in the lower Snake River and Imnaha River upstream of Lower Granite Reservoir with cost sharing from IPC and the BLM.  Redds are counted downstream of Lower Granite Dam by WDFW and PNNL.  A large group of biologists monitors harvest (Table 1).  Common methods are used and the data are shared and co-analyzed.  Staff of IPC, NPT, NOAA, PNNL, USFWS, USGS, and WDFW has agreed to conduct joint analyses to accomplish objective 1 in this proposal.  

Juvenile Status and Trend Monitoring FY12–14

See Table 2.

The Pacific States Marine Fisheries Commission operates oversees the collection and dissemination of PIT-tag tagging and detection data.  NPT beach seines and PIT tags natural-origin subyearlings in the Clearwater River.  We beach seine and PIT tags natural-origin subyearlings in the lower Snake River upstream of Lower Granite Reservoir.  USGS beach seines and PIT tags natural-origin subyearlings in Lower Granite and Little Goose reservoirs to study habitat use.  NPT PIT tags subsamples of the hatchery-origin subyearlings released at the Nez Perce Tribal Hatchery and the acclimation facilities upstream of Lower Granite Reservoir.  IPC PIT tags subsamples of the hatchery-origin subyearlings reared at Oxbow Hatchery and released at Hells Canyon Dam.  FPC oversees the smolt monitoring program that subsamples the subyearling outmigration and reports daily passage indices at collector dams.  The USGS studies factors affecting the behavior and survival in the upper end of Lower Granite Reservoir of subyearlings destined to become yearling migrants.  A large group of biologists is involved with the consensus study: Evaluating the Responses of Snake and Columbia River Basin fall Chinook Salmon to Dam Passage Strategies and Experiences (www.fpc.org/documents/
fallchinook_planningteam_documents.html) funded by USACE.  The corps pays for nearly all of the PIT-tagging of natural-origin and hatchery-origin subyearlings described above and cost shares the analyses of data with BPA.  FPC collects subsamples of subyearlings from the run-at-large at Lower Granite, Little Goose, Lower Monumental, McNary, John Day, and Bonneville dams and calculates smolt passage indices.  Recently, FPC staff began reporting a population passage index for subyearling Chinook salmon at Lower Granite Dam.  This index is described in more detail later in this proposal under deliverable 2A.  Staff of NPT, NOAA, USFWS, and USGS has agreed to conduct joint analyses to accomplish objective 1 in this proposal.

Expanded Life Cycle and Passage Modeling

Fitting such a model is presently a high priority for NOAA as outlined in the AMIP.  Our staff has collaborated with NOAA in the past (e.g., Williams et al. 2008), was recently asked to participate on the modeling group steering committee, and will readily provide experience, data, and analyses compiled over last 20 years to NOAA as modeling efforts proceed.  The stock-recruitment based models we propose herein differ from expanded life cycle and passage models because the stock recruitment models do not fully link life stages or include fine scale predictors (e.g., pre-spawning mortality, fecundity, passage survival at a given dam), but comparing the final output of both modeling processes will help to inform adaptive management.  Moreover, our proposed work will produce models to predict abundance of natural-origin adults (deliverable 1B described later) and the abundance of natural-origin juveniles (deliverable 2A described later).  Though abundance of natural-origin adults and juveniles are inexorably linked, our models will be separate.  Expanded life cycle and passage models will link these life stages and they will be modified according to results produced by projects such as 199102900.


Back To Top

Focal Species

Primary Focal Species
Chinook (O. tshawytscha) - Snake River Fall ESU (Threatened)

Secondary Focal Species
None

Describe how you are taking into account potential biological and physical effects of factors such as non-native species, predation increases, climate change and toxics that may impact the project’s focal species and their habitat, potentially reducing the success of the project. For example: Does modeling exist that predicts regional climate change impacts to your particular geographic area? If so, please summarize the results of any predictive modeling for your area and describe how you take that into consideration.
Threats to program investments and project success: View instructions
Climate change will likely result in: (1) early peak flows, (2) a decrease in peak flows, and (3) an increase in water temperature (ISAB 2007).  The ISAB proposed that climate change will have the most significant impacts on the early life stages of fall Chinook salmon, which rear in mainstem habitats.  In summary, the ISAB hypothesized that climate change will lead to: (1) earlier fry emergence, (2) a smaller size at emergence, (3) earlier departure from protective rearing habitat, (4) reduced survival due to changes in rearing behavior due to predation, (5) increased metabolism and decreased growth if food resources are limited in less optimal habitat in down-river reaches, (6) forebay delay, (7) decreased smolt survival, and (8) a reduction in life history diversity if late summer temperatures become lethal and kill that later summer migrants and those fish destined to become fall migrants or to overwinter in reservoirs.  This proposal takes climate change and predation into account by fitting stock recruitment functions to predict changes in adult and juvenile abundance from covariates derived from empirical data collected on stream flow, temperature, and ocean conditions.

Back To Top

Types of Work

Work Classes

Tagging

Please explain why the tagging technology used in this project was selected. Include a discussion of how the cost and applicability of the selected tagging technology influenced your selection. Enter "NA" if not applicable to your project.
We use PIT tags to tag natural-origin subyearlings because: (1) subyearlings as small as 60-mm (1992 to 2007) and 50-mm (2008 to present) fork length can be tagged to insure a large portion of the juvenile population can be represented in the study, (2) each tag has a unique code that allows data to be collected at the level of the individual fish, (3) the effect of the tags on survival, growth, and behavior have been well studied and the limitations of the method are largely known, and (4) tagging and detection data are uploaded in a regional database and are readily available to the public, and (5) BPA purchases millions of tags annual at a reduced price.
Describe any of the innovative approaches that your projects proposes that are in direct support of the ISAB/ISRP's recommendations to improve techniques for surgical insertion of internal tags, or external attachment of acoustic, radio, or data storage tags that reduce handling time, fish injury and stress. Enter "NA" if not applicable to your project.
NA
For specific tagging technologies, please address the tagging report's recommendations for genetic markers, otolith thermal marking, PIT tags, acoustic tags and radio tags for improving technologies in any way applicable. Enter "NA" if not applicable to your project.
All PIT-tagging of the natural and hatchery juveniles that make up the Snake River fall Chinook salmon ESU have been coordinated under study Consensus Research Proposal: Evaluating the Responses of Snake and Columbia River Basin fall Chinook Salmon to Dam Passage Strategies and Experiences (www.fpc.org/documents/fallchinook_planningteam_documents.html).
If your project involves ocean port sampling and lower river sampling for coded wire tag (CWT) recovery, address the tagging and tag recovery issues (statistical validity of tagging rates, tag recovery rates, and fishery sampling rates) presented in the Pacific Salmon Commission's Action Plan to Address the CWT Expert Panel (PSC Tech. Rep. No. 25, March 2008).
NA
Explain how your tagging and tag recovery rates ensure a statistically valid result for your project. Enter "NA" if not applicable to your project.

We have always balanced our large river sampling effort with an understanding safety, logistical restraints and cost effectiveness.  The strength and statistical validity of tagging data collected can be assessed based on the productivity of the project.  In the past, when the abundance of natural subyearlings was relatively low (described earlier in the Problem Statement), the sample size of natural subyearlings we PIT tagged consistently produced statistically valid results reported in peer reviewed articles on genetic lineage (Marshall et al. 2000*; Rasmussen et al. 2003*), pre-spawning movement of natural adults we had PIT tagged as juveniles (Connor and Garcia 2006*), early life history of natural subyearlings (Connor et al. 2001b,c*; Connor et al. 2002*), growth and body morphology (Tiffan et al. 2000; Connor and Burge 2003*), forecasts of juvenile survival and passage timing (Connor et al. 2000*), and the effects of summer flow augmentation on survival and migration rate (Connor et al. 1998*, 2003a,b*).  The data used in these articles have also made modest contributions to biological opinions and inseason mangement.  Presently, our sample sizes of tagged fish are larger than in the past (Table 3 in major accomplishments) and should continue to produce valid statistical results.  These new results and the data from which they are based will be published and shared with others to continue the modestly productive history of this project.  Hereafter, we high light the limitations of our tagging design and rates and how the project has evolved to address the limitations when possible.

 

Though we collect biological data on every natural-origin subyearling captured, we cannot PIT tag natural-origin subyearlings that disperse from riverine habitat into Lower Granite Reservoir before growing to the minimum size for tagging.  We began using the new 8.5-mm PIT tags in 2008 to increase the size range of fish we could represent in the natural-origin population.  In 2010, we also increased the proportion of the population represented with PIT tags by beach seining and PIT tagging natural-origin subyearlings in Lower Granite and Little Goose reservoirs as part of a study funded by the U. S. Army Corps of Engineers (Table 2 in problem statement).  We will continue to follow advancements in technology in search of a tag for 36–49 mm fish.

 

A second limitation is the inability to separate the effects of capture efficiency during beach seining and emigration when examining spatial and temporal trends in PIT tagging.  For example, increases in flow are sometimes followed by decreases in the number of fish seined and tagged.  However, it is not technologically or logistically possible to determine if the decrease in catch was the result of a reduction in beach seining efficiency due to high flow or a reduction in the fish population due to flow induced emigration. 

 

The third limitation is that every natural-origin subyearling we PIT tag is not a fall Chinook salmon.  Some natural-origin spring Chinook salmon disperse from natal tributaries into the Snake River where they are captured during our beach seining (Table 3 in major accomplishments).  We published three additional journal articles that addressed this limitation.  Connor et al. (2001b,c) showed that natural-origin subyearling spring Chinook salmon that dispersed into the lower Snake River and shared the rearing environment of natural-origin subyearling fall Chinook salmon essentially exhibited the early life history characteristics of natural-origin subyearling fall Chinook salmon, but the spring-run fish were slightly larger and migrated slightly earlier.  Connor et al. (2001b) fitted a discriminant function that distinguished between natural-origin subyearling spring and fall Chinook salmon with 75% accuracy and recommended using such a function when estimating natural-origin subyearling fall Chinook salmon abundance at Lower Granite Dam.  When describing the early life history timing of natural-origin subyearlings in the lower Snake River, however, Connor et al. (2002) simplified the run terminology by referring to the fish in the lower Snake River solely as fall Chinook salmon at the request of a reviewer who did not believe the differences in life history timing documented by (Connor et al. 2001b) were large enough to justify confusing the reader with the spring-run vs. fall-run terminology.  We have continued to collect data on the genetic lineage of the natural-origin juveniles during beach seining and the percentage of our catch made up of natural-origin spring Chinook salmon has generally declined over years as fall Chinook salmon adult abundance and redd counts have increased (Table 3 in major accomplishments).

 

The fourth limitation is the potential to misidentify unmarked hatchery-origin fall Chinook salmon as natural-origin subyearling fall Chinook salmon.  We overcame this limitation as follows.  We used body morphology to distinguish between natural-origin and hatchery-origin subyearling fall Chinook salmon Oncorhynchus tshawytscha in rearing areas of the Snake River and at a downstream dam during seaward migration (Tiffan and Connor in review).  Field personnel, using subjective eye and body shape characteristics, correctly classified 89.9-100% of natural-origin subyearlings (N = 626) and 90.0–100% of hatchery-origin subyearlings (N = 867) in rearing areas from 2001 to 2008.  The morphological characteristics used by field personnel proved to have a quantitative basis as shown by digital photography and principal-components analysis.  Natural-origin subyearlings had smaller eyes and pupils, smaller heads, deeper bodies, and shorter peduncles than their hatchery counterparts during rearing and at the dam.  A discriminant function fitted from this set of morphological characteristics classified origin of fish during rearing and at the dam with over 97% accuracy.

 

A fifth limitation of our project design is the seasonal schedule for passing water into the juvenile fish bypass and PIT-tag detection systems at collector dams.  These systems are dewatered from late fall of year t through early spring each year t + 1, thus PIT-tagged fish that pass at these times are not detected.  This is why objective 2 of the present proposal focuses on the portions of the natural population that migrates during spring, summer, and fall of year t.

 

Data Management

Please explain how you manage the data and corresponding metadata you collect.
<No answer provided>
Describe how you distribute your project's data to data users and what requirements or restrictions there may be for data access.
<No answer provided>

RM&E

What type(s) of RM&E will you be doing?
Status and Trend Monitoring
Uncertainties Research (Validation Monitoring and Innovation Research)
Where will you post or publish the data your project generates?

Back To Top

Location

Loading ...
Layers
Legend
Name (Identifier) Area Type Source for Limiting Factor Information
Type of Location Count
The Dalles Dam to John Day Dam Mainstem None
John Day Dam Mainstem None
The Dalles Dam Mainstem None
Confluence of Snake and Columbia River to Priest Rapids Dam Mainstem None
Ice Harbor Dam to Lower Monumental Dam Mainstem None
Confluence of Snake and Columbia River to Ice Harbor Dam Mainstem None
McNary Dam to Confluence of Snake and Columbia River Mainstem None
John Day Dam to McNary Dam Mainstem None
Priest Rapids Dam to Wanapum Dam Mainstem None
McNary Dam Mainstem None
Ice Harbor Dam Mainstem None
Priest Rapids Dam Mainstem None
Lower Monumental Dam Mainstem None
Little Goose Dam Mainstem None
Little Goose Dam to Lower Granite Dam Mainstem None
Lower Monumental Dam to Little Goose Dam Mainstem None
Lower Granite Dam Mainstem None
Lower Granite Dam to Hells Canyon Dam Mainstem None
Wanapum Dam Mainstem None
Dworshak Dam Mainstem None
Chief Joseph Dam to Grand Coulee Dam Mainstem None
Wells Dam to Chief Joseph Dam Mainstem None
Chief Joseph Dam Mainstem None
Grand Coulee Dam to Keenleyside Dam Mainstem None
Wells Dam Mainstem None
Rocky Reach Dam to Wells Dam Mainstem None
Rocky Reach Dam Mainstem None
Rock Island Dam to Rocky Reach Dam Mainstem None
Wanapum Dam to Rock Island Dam Mainstem None
Rock Island Dam Mainstem None
Grand Coulee Dam Mainstem None
Bonneville Dam to The Dalles Dam Mainstem None
Bonneville Dam - Powerhouse 1 Mainstem None
Bonneville Dam - Spillway Mainstem None
Bonneville Dam - Powerhouse 2 Mainstem None
Dworshak Reservoir Mainstem None
Hells Canyon Dam Mainstem None
Hungry Horse Dam beginning of Hungry Horse Reservoir Mainstem None
Kerr Dam Mainstem None
Kerr Dam to Hungry Horse Dam Mainstem None
Hungry Horse Dam Mainstem None
Libby Dam to end of Mainstem Kootenay River Mainstem None
Corra Linn Dam to Libby Dam Mainstem None
Libby Dam Mainstem None
Albeni Falls Dam into Lake Pend Oreille Mainstem None
Box Canyon Dam to Albeni Falls Dam Mainstem None
Albeni Falls Dam Mainstem None
Confluence of Snake and Clearwater River to Dworshak Dam Mainstem None
Confluence of MF and CF Willamette River to Confluence of MF Willamette River and Fall Creek Mainstem None
Detroit Reservoir Mainstem None
Detroit Dam Mainstem None
Big Cliff Dam to Detroit Dam Mainstem None
Green Peter Reservoir Mainstem None
Foster Dam to Green Peter Dam Mainstem None
Confluence of North and South Santiam River to Foster Dam Mainstem None
Confluence of North and South Santiam River to Big Cliff Dam Mainstem None
Confluence of Willamette and Santiam River to Confluence of North and South Santiam River Mainstem None
Big Cliff Dam Mainstem None
Foster Dam Mainstem None
Green Peter Dam Mainstem None
Fern Ridge Reservoir Mainstem None
Confluence of Willamette and Long Tom River to Fern Ridge Dam Mainstem None
Fern Ridge Dam Mainstem None
Dexter Dam to Lookout Point Dam Mainstem None
Lookout Point Dam to Hills Creek Dam Mainstem None
Fall Creek Reservoir Mainstem None
Blue River Lake Mainstem None
Cougar Reservoir Mainstem None
Leaburg Dam to Confluence of McKenzie and Blue River Mainstem None
Confluence of Willamette and McKenzie River to Leaburg Dam Mainstem None
Leaburg Dam Mainstem None
Confluence of McKenzie and Blue River to Blue River Dam Mainstem None
Blue River Dam Mainstem None
Confluence of McKenzie and South Fork McKenzie River to Cougar Dam Mainstem None
Cougar Dam Mainstem None
Confluence of McKenzie and Blue River to Confluence of McKenzie and South Fork McKenzie River Mainstem None
Confluence of Willamette and Columbia River to Confluence of MF Willamette and CF Willamette River Mainstem None
Confluence of MF Willamette River and Fall Creek to Fall Creek Dam Mainstem None
Confluence of MF Willamette River and Fall Creek to Dexter Dam Mainstem None
Fall Creek Dam Mainstem None
Lookout Point Dam Mainstem None
Dexter Dam Mainstem None
Hills Creek Reservoir Mainstem None
Hills Creek Dam Mainstem None
Cottage Grove Lake Mainstem None
Dorena Lake Mainstem None
Confluence of MF and CF Willamette River to Confluence of CF Willamette and Row River Mainstem None
Dorena Dam Mainstem None
Confluence of CF Willamette River and Row River to Cottage Grove Dam Mainstem None
Cottage Grove Dam Mainstem None
Confluence of CF Willamette River and Row River to Dorena Dam Mainstem None

Back To Top

Project Deliverables

Project Deliverable definition: A significant output of a project that often spans multiple years and therefore may be accomplished by multiple contracts and multiple work elements. Contract Deliverables on the other hand are smaller in scope and correspond with an individual work element. Title and describe each Project Deliverable including an estimated budget, start year and end year. Title: A synopsis of the deliverable. For example: Crooked River Barrier and Channel Modification. Deliverable Description: Describe the work required to produce this deliverable in 5000 characters or less. A habitat restoration deliverable will contain a suite of actions to address particular Limiting Factors over time for a specified Geographic area typically not to exceed a species population’s range. Briefly include the methods for implementation, in particular any novel methods you propose to use, including an assessment of factors that may limit success. Do not go into great detail on RM&E Metrics, Indicators, and Methods if you are collecting or analyzing data – later in this proposal you’ll be asked for these details.
Project Deliverables: View instructions
Models that explain and predict historical and contemporary variations in adult abundance (DELV-1)
The first set of models (hereafter, deliverable 1A) will provide a historical retrospective across eras that will rely on adult counts made without distinction of adult origin, but with redd counts made throughout the Snake River basin from 1947 to 2012. We will fit a stock-recruitment model with covariates separate for four eras distinguished based on temporal and spatial changes in adult counts and management effort. The four eras will be: the middle Snake River (1947–1972), the Clearwater River (1952–1972), and the lower Snake River and tributaries (1958–1974), and the lower Snake River and tributaries (after 1974). These models will accomplish the following scientific objectives: (1) describe the numerical trends in the adult counts within each era, (2) describe the numerical and spatial trends in redd counts within each era; (3) evaluate changes in the ability to use redd counts as accurate and precise predictors of adult within each era, and (4) increase the understanding of how the numerical trends in the adult counts during each era were influenced by anthropogenic, biological, and environmental change. Our project does not operate on a standard fiscal year schedule as its fiscal year begins on June 1 of yeat t +1 instead of October first of year t. The FY12–FY14 activities begin on June 1, 2012 and end on May 31, 2015. We will continue to develop the models annually, add new data as it becomes available including the redd count data we collect in the Snake River and the basinwide redd data collected by our research group (Table 1), and strive to complete a journal manuscript describing the results by the end of June 2013. The models and the manuscript will confirm completion of the objective 1 success criterion 1.

The second set of models will focus on estimated counts of natural-origin adults at Lower Granite Dam from run construction and on redd counts made upstream of Lower Granite Reservoir after 1982 (hereafter, deliverable 1B). It will accomplish the following scientific objectives: (1) increase the understanding of how the numerical trends in the estimated counts of natural-origin adults during 1983–2013 were influenced by anthropogenic, biological, and environmental change, (2) predict how varying influential anthropogenic, biological, and environmental factors might affect the status of natural-origin adults relative to the minimum viability threshold, and (3) predict the status of escapement of natural-origin adults to the spawning areas relative to the explicit population level spatial structure criteria. We will continue to develop the model annually, add new data as it becomes available including the redd count data we collect in the Snake River and the basinwide redd data collected by our research group (Table 1), and strive to complete a journal manuscript describing the results by the end of June 2014. The model and the manuscript will confirm completion of objective 1 success criteria 2 and 3.
Types of Work:
Models that explain and predict variation in passage abundance of natural-origin subyearlings (DELV-2)
The first set of models will focus on natural-origin subyearlings at Lower Granite dam during 1992–2014 (hereafter, deliverable 2A). The scientific objectives will be to: (1) describe numerical trends in passage abundance of natural-origin fall Chinook salmon subyearlings estimated by reconstructing the run; (2) compare annual passage timing distributions calculated using different methods, (3) increase the understanding of how the numerical trends in passage abundance were associated with anthropogenic, biological, and environmental change, (4) use the results from scientific objectives 1 and 2 to predict how varying influential anthropogenic, biological, and environmental factors might increase abundance of natural-origin fall Chinook salmon subyearlings. We will continue to develop the models annually, add new data as it becomes available, and strive to complete a journal manuscript describing the results by the end of June 2015. The models and the manuscript will confirm completion of objective 2 success criteria 1, 2, and 3.

The second set of models effort will focus on predation by smallmouth bass in riverine rearing habitat along the lower Snake River during 1997–2014 (hereafter, deliverable 2B). The scientific objectives will be to: (1) estimate the abundance of smallmouth bass, (2) describe the diet of smallmouth bass, and (3) estimate subyearling loss to predation by smallmouth bass. We strive to complete a journal manuscript describing the results by the end of June 2015. The models and the manuscript will confirm completion of objective 2 success criterion 4.
Types of Work:

Back To Top

Objectives & Project Deliverables

Objective: Increase the abundance, productivity, and spawning distribution of natural-origin adults (OBJ-1)
Project Deliverables How the project deliverables help meet this objective*
Models that explain and predict historical and contemporary variations in adult abundance (DELV-1)
Objective: Increase the abundance and diversity of natural subyearlings during early freshwater rearing and migration (OBJ-2)
Project Deliverables How the project deliverables help meet this objective*
Models that explain and predict variation in passage abundance of natural-origin subyearlings (DELV-2)
*This section was not available on proposals submitted prior to 9/1/2011

Back To Top

RM&E Protocols and Methods

RM&E Protocol Deliverable Method Name and Citation
Historical variation in Snake River basin fall Chinook salmon adult abundance and distribution v1.0
Understanding the status of Snake River basin fall Chinook salmon relative to recovery criteria v1.0
Variation in passage abundance of natural Snake River basin fall Chinook salmon juveniles v1.0
Smallmouth bass predation of juvenile fall Chinook salmon in Hells Canyon (1991-029-00) v1.0

Back To Top

Project Deliverables & Budget

Project Deliverable Start End Budget
Models that explain and predict historical and contemporary variations in adult abundance (DELV-1) 2012 2015 $686,283
Models that explain and predict variation in passage abundance of natural-origin subyearlings (DELV-2) 2012 2015 $1,289,931
Total $1,976,214
Requested Budget by Fiscal Year

Fiscal Year Proposal Budget Limit Actual Request Explanation of amount above FY2010
2012 $500,000 $534,112 Constant cost at full level
2013 $500,000 $534,112 Constant cost at full level
2014 $500,000 $534,112 Constant cost at full level
2015 $500,000 $373,878 Expectation of continued monitoring of recovery
Total $2,000,000 $1,976,214
Item Notes FY 2012 FY 2013 FY 2014 FY 2015
Personnel $386,830 $386,830 $386,830 $270,780
Travel $10,334 $10,334 $10,334 $7,234
Prof. Meetings & Training $0 $0 $0 $0
Vehicles $0 $0 $0 $0
Facilities/Equipment (See explanation below) $0 $0 $0 $0
Rent/Utilities $0 $0 $0 $0
Capital Equipment $0 $0 $0 $0
Overhead/Indirect $110,550 $110,550 $110,550 $77,385
Other $26,398 $26,398 $26,398 $18,479
PIT Tags $0 $0 $0 $0
Total $534,112 $534,112 $534,112 $373,878
Major Facilities and Equipment explanation:
The Columbia River Research Laboratory (CRRL) and Idaho Fishery Resource Office (IFRO) are equipped with all of the resources necessary to carry out this project. Both offices provide computers and the necessary software to complete data reduction, storage, and complex statistical analyses. This project has all the boats, vehicles, and capital equipment necessary to collect data for field related tasks including: a selection of 25 boats up to 30' in length for use in all types of aquatic habitats; two 2700 square ft. storage facilities; 4000 square feet of wet lab facilities to conduct physiological experiments; an office and analytical laboratory in a 15,000 square foot facility; and a technical staff of 60-100 fishery biologists, ecologists, physiologists. Boats will be operated by Department of Interior certified boat operators who are trained in CPR and First Aid.

Back To Top

Cost Share

Source / Organization Fiscal Year Proposed Amount Type Description
Idaho Power 2012 $75,000 In-Kind Pays for 50% of the redd surveys and provide 1 mos labor for writing reports.
Idaho Power 2013 $75,000 In-Kind Pays for 50% of the redd surveys and provide 1 mos labor for writing reports.
Idaho Power 2014 $75,000 In-Kind Pays for 50% of the redd surveys and provide 1 mos labor for writing reports.
Washington Department of Fish and Wildlife (WDFW) 2012 $16,500 In-Kind Provide 1 mos labor for writing reports.
Washington Department of Fish and Wildlife (WDFW) 2013 $16,500 In-Kind Provide 1 mos labor for writing reports.
Washington Department of Fish and Wildlife (WDFW) 2014 $16,500 In-Kind Provide 1 mos labor for writing reports.
National Oceanic and Atmospheric Administration 2012 $20,500 In-Kind Covers travel costs for life cycle modeling and provides 1 mos labor for writing reports.
National Oceanic and Atmospheric Administration 2013 $20,500 In-Kind Covers travel costs for life cycle modeling and provides 1 mos labor for writing reports.
National Oceanic and Atmospheric Administration 2014 $20,500 In-Kind Covers travel costs for life cycle modeling and provides 1 mos labor for writing reports.
US Army Corps of Engineers (COE) 2012 $19,900 In-Kind Provide 500 12-mm PIT tags and 500 8.5-mm PIT tags.
US Army Corps of Engineers (COE) 2013 $19,900 In-Kind Provide 500 12-mm PIT tags and 500 8.5-mm PIT tags.
US Army Corps of Engineers (COE) 2014 $19,900 In-Kind Provide 500 12-mm PIT tags and 500 8.5-mm PIT tags.

Back To Top

Project References or Citations

Adams, S.M., R.B. McLean, and M.M. Huffman. 1982. Structuring of a predator community through temperature–mediated effects on prey availability. Canadian Journal of Fisheries and Aquatic Sciences 39:1175-1184. Akaike, H. 1973. Information theory and an extension of the maximum likelihood principle. Proceedings of the Second International Symposium on Information Theory. Arnsberg, B.D., W.P. Connor, and E. Connor. 1992. Mainstem Clearwater Study: Assessment for salmonid spawning, incubation, and rearing. Final Report to BPA. Bennett, D. H., W. P. Connor, and C. A. Eaton. 2003. Substrate composition and emergence success of fall Chinook salmon in the Snake River. Northwest Science 77:93-99. Beverton, R.J.H. and S.J. Holt. 1957. On the dynamics of exploited fish populations. Chapman and Hall London. Brigham, E. O. 1988. Fast Fourier Transform and Its Applications. Prentice-Hall, Upper Saddle River, NJ. Bugert, R. M., C. W. Hopley, C. A. Busack, and G. W. Mendel. 1995. Maintenance of stock integrity in Snake River fall Chinook salmon. American Fisheries Society Symposium 15:267 276. Burnham, K. P., and D. R. Anderson. 2002. Model selection and multimodel inference: a practical information-theoretic approach. Springer Science, New York. CBFWA (Columbia Basin Fish and Wildlife Authority). 1999. www.ptagis.org. Connor, W.P., H.L. Burge, and D.H. Bennett. 1998. Detection of subyearling Chinook salmon at a Snake River dam: Implications for summer flow augmentation. North American Journal of Fisheries Management 18:530-536. Connor, W.P., R.K. Steinhorst, and H.L. Burge. 2000. Forecasting survival and passage for migratory juvenile salmonids. North American Journal of Fisheries Management 20:650-659. Connor, W.P., and several coauthors. 2001a. Estimating the carrying capacity of the Snake River for fall Chinook salmon redds. Northwest Science 75:363-370. Connor, W.P. and several coauthors. 2001b. Early life history attributes and run composition and of wild subyearling Chinook salmon recaptured after migrating downstream past Lower Granite Dam. Northwest Science 75:254-261. Connor, W.P, A.R. Marshal, T.C. Bjornn, and H.L. Burge. 2001c. Growth and long-range dispersal by wild subyearling spring and summer Chinook salmon in the Snake River. Transactions of the American Fisheries Society 130:1070-1076. Connor, W.P., H.L. Burge, R. Waitt, and T.C. Bjornn. 2002. Juvenile life history of wild fall Chinook salmon in the Snake and Clearwater rivers. North American Journal of Fisheries 22:703-712. Connor, W.P., H.L. Burge, J.R. Yearsley, and T.C. Bjornn. 2003a. The influence of flow and temperature on survival of wild subyearling fall Chinook salmon in the Snake River. North American Journal of Fisheries Management 23:362-375. Connor, W.P., R.K. Steinhorst, and H.L. Burge. 2003b. Migrational behavior and seaward movement of wild subyearling fall Chinook salmon in the Snake River. North American Journal of Fisheries Management 23:414-430. Connor, W.P., and H.L. Burge. 2003. Growth of wild subyearling Chinook salmon in the Snake River. North American Journal of Fisheries Management 23:594-599. Connor, W.P., C.E. Piston, and A.P. Garcia. 2003c. Temperature during incubation as one factor affecting the distribution of Snake River fall Chinook salmon spawning areas. Transactions of the American Fisheries Society 132:1236-1243. Connor, W.P., S.G. Smith, T. Andersen, S.M. Bradbury, D.C. Burum, E.E. Hockersmith, M.L. Schuck, G.W. Mendel, and R.M. Bugert. 2004. Post-release performance of hatchery yearling and subyearling fall Chinook salmon released into the Snake River. North American Journal of Fisheries Management 24:545-560. Connor, W.P., J.G. Sneva, K.F. Tiffan, R.K. Steinhorst, and D. Ross. 2005. Two alternative juvenile life histories for fall Chinook salmon in the Snake River basin. Transactions of the American Fisheries 134:291-304. Connor, W. P., and A. P. Garcia. 2006. Pre-spawning movement of wild and hatchery fall Chinook salmon in the Snake River. Transactions of the American Fisheries Society 135:131-139. Culpin, P. 1963. Oxbow experimental incubation facility operation. Idaho Department of Fish and Game, Boise. Craig, G. 1965. Oxbow experimental incubation facility operation. Idaho Department of Fish and Game, Boise. Dauble, D. D., and D. G. Watson. 1997. Status of fall chinook salmon populations in the mid Columbia River, 1948B1992. North American Journal of Fisheries Management 17:283-300. Dauble D., R.L. Johnson, and A.P. Garcia. 1999. Fall Chinook salmon spawning in the tailraces of hydroelectric projects. Transactions of the American Fishery Society 128:672-679. Efron, B. and R.J. Tibshirani. 1998. An Introduction to the Bootstrap. Chapman and Hall/CRC, Boca Raton, Florida. Fulton, L. A. 1968. Spawning areas and abundance of Chinook salmon Oncorhynchus tshawytscha in the Columbia River basinCpast and present. U.S. Fish and Wildlife Service Special Scientific Report Fisheries No. 571. Garcia, A.P., W.P. Connor, D.J. Milks, S.J. Rocklage, and R.K. Steinhorst. 2004. Movement and spawner distribution of hatchery fall Chinook salmon adults acclimated and released as yearlings at three locations in the Snake River basin. North American Journal of Fisheries Management 24:1134-1144. Garland, R.D., K.F. Tiffan, D.W. Rondorf, and L.O. Clark. 2002. Comparison of subyearling fall Chinook salmon’s use of riprap revetments and unaltered habitats in Lake Wallula of the Columbia River. North American Journal of Fisheries Management 22:583-589. Graban, J.R. 1964. Evaluation of fish facilities at Brownlee and Oxbow dams. Idaho Department of Fish and Game, Boise. Groves, P. A., and A. P. Garcia. 1998. Two carriers used to suspend an underwater video camera from a boat. North American Journal of Fisheries Management 18:1004-1007. Groves, P. A., and J. A. Chandler. 1999. Spawning habitat used by fall chinook salmon in the Snake River. North American Journal of Fisheries Management 19:912-922.Groves et al. in preparation Haas, J. B. 1965. Fishery problems associated with Brownlee, Oxbow, and Hells Canyon Dams on the Middle Snake River. Fish Commission of Oregon, Portland. Haskell, C.A., K.F. Tiffan, and D.W. Rondorf. 2006a. Food habits of juvenile American shad and dynamics of zooplankton in the lower Columbia River. Northwest Science 80:47-64. Haskell, C.A., R.D. Baxter, and K.F. Tiffan. 2006b. Range expansion of an exotic Siberian prawn to the Lower Snake River. Northwest Science 80:311-316 Hansel, H.C., S.D. Duke, P.T. Lofy, and G.A. Gray. 1988. Use of diagnostic bones to identify and estimate original lengths of ingested prey fishes. Transactions of the American Fisheries Society 117:55-62. Interior Columbia Technical Recovery Team (ICTRT). 2003. www.nwfsc.noaa.gov/trt/col_docs/Independentpopchinsteelsock.pdf ICRT 2007 Interior Columbia Technical Recovery Team (ICTRT) and R. W. Zabel. 2007. www.nwfsc.noaa.gov/trt/col/trt_ic_viability_survival.cfm Independent Scientific Advisory Board (ISAB). 2007. www.nwcouncil.org/library/isab/isab2007-2.htm Kareiva, P., M. Marvier, and M. McClure. 2000. Recovery and management options for spring/summer Chinook salmon in the Columbia River Basin. Science 290: 977-979. Krcma, R. F. and R. F. Raleigh. 1970. Migration of juvenile salmon and trout into Brownlee Reservoir, 1962-65. Fishery Bulletin 68:203-217. Maceina, M.J. and D.L. Pereira. 2007. Recruitment. Pages121-186 in C.S. Guy and M.L. Brown, editors. Analysis and interpretation of freshwater fisheries data. American Fisheries Society, Bethesda Maryland. Mains, E. M. and J. M. Smith. 1964. The Distribution, size, time and current preferences of seaward migrant chinook salmon in the Columbia and Snake Rivers. Washington Department of Fisheries, Fisheries Research Papers 2(3):5-43. Marshall, A. R., H. L. Blankenship, and W. P. Connor. 2000. Genetic characterization of naturally spawned Snake River fall-run Chinook salmon. Transactions of the American Fisheries Society 129:680-698.Narum et. al. 2004 microsatellite DNA loci Naughton, G.P., D.H. Bennett, and K.B. Newman. 2004. Predation on juvenile salmonids by smallmouth bass in the Lower Granite Reservoir system, Snake River. North American Journal of Fisheries Management 24:534-544. Nelle, R.D. 1999. Smallmouth bass predation on juvenile fall Chinook salmon in the Hells Canyon Reach of the Snake River, Idaho. Master’s Thesis, University of Idaho, Moscow. NMFS (National Marine Fisheries Service). 1992. Threatened status for Snake River spring/summer chinook salmon, threatened status for Snake River fall chinook salmon. Federal Register 57:78(22 April 1992): 14,653-14,663. NMFS (National Marine Fisheries Service). 2005a. Threatened and Endangered Species: Final Listing Determinations for 16 ESUs of West Coast Salmon, and Final 4(d) Protective Regulations for Threatened Salmonid ESUs. Federal Register (June 28, 2005) 70(123): 37,160- 37,204. Northwest Power and Conservation Council (NPCC). 2009. www.nwcouncil.org/library/2009/2009-09.pdf Plumb, J. M., C. M. Moffitt1, W. P. Connor, K. F. Tiffan, R. W. Perry, N. S. Adams, and D. W. Rondorf. In preparation a. Modeling detection probability of juvenile salmon at a dam to improve abundance and run-timing estimation. Will be in BPA annual report August 2010. Expected submission to Transactions of the American Fisheries Society fall 2010. Plumb, J. M., C. M. Moffitt1, W. P. Connor, and K. F. Tiffan. In preparation b. Evidence for a density dependent effect on migration rate, migrant size, and migration timing in subyearling Chinook salmon. Will be in BPA annual report August 2010. Expected submission to Transactions of the American Fisheries Society spring 2011. Prentice, E. F., T. A. Flagg, and C. S. McCutcheon. 1990a. Feasibility of using implantable passive integrated transponder (PIT) tags in salmonids. American Fisheries Society Symposium 7:317 322. PTAGIS (Columbia Basin PIT Tag Information System). 2009. www.ptagis.org. Rasmussen, C. R., C. O. Ostberg, D. R. Clifton, J. L. Holloway, and R. J. Rodriguez. 2003. Identification of a genetic marker that discriminates ocean-type and stream-type Chinook salmon in the Columbia River basin. Transactions of the American Fisheries Society 132:131-142. Ricker, W.E. 1954. Stock and recruitment. Journal of the Fisheries Research Board of Canada 11:559-623. Rieman, B.E., R.C. Beamsderfer, S. Vigg, and T.P. Poe. 1991. Estimated loss of juvenile salmonids to predation by northern squawfish, walleyes, and smallmouth bass in John Day Reservoir, Columbia River. Transactions of the American Fisheries Society 120:448-458. Rogers, J.B., and C.C. Burley. 1991. A sigmoid model to predict gastric evacuation rates of smallmouth bass (Micropterus dolomieu) fed juvenile salmon. Canadian Journal of Fisheries and Aquatic Sciences 48:933-937. Rosenberger, S. J., W. P. Connor, M. L. Schuck, D. Milks, J. Hesse, anc C. A. Peery. In preparation. A comparison of acclimated and direct releases of hatchery fall Chinook salmon subyearlingsinto the Snake River. Will be in BPA annual report August 2010. Expected submission date to Transactions of the American Fisheries Society of spring 2011. Sandford, B.P., and S.G. Smith. 2002. Estimation of Smolt-to-Adult Return Percentages for Snake River Basin Anadromous Salmonids, 1990-1997. Journal of Agricultural, Biological, and Environmental Statistics 7:243-263. Scheuerell, M. D., R. Hilborn, M. H. Ruckelshaus, K. K. Bartz, K.M. Lagueux, A.D. Haas, and K. Rawson. 2006. The Shiraz model: a tool for incorporating anthropogenic effects and fish–habitat relationships in conservation planning. Canadian. Journal of Fisheries and Aquatic. Sciences 63: 1596–1607. Seaburg, K.G. 1957. A stomach sampler for live fish. The Progressive Fish Culturist 19:137-139.Rosenberger et al. in preparation Smith, S.G., W.D. Muir, E.E. Hockersmith, R.W. Zabel, R.J. Graves, C.V. Ross, W.P. Connor, and B.D. Arnsberg. 2003. Influence of river conditions on survival and travel time of Snake River subyearling fall Chinook salmon. North American Journal of Fisheries Management 23:939-961. Steinhorst, K., D. Milks, G. Naughton, M. Schuck, and B. Arnsberg (in review) Use of statistical bootstrapping to calculate confidence intervals for the fall Chinook salmon run reconstruction to Lower Granite Dam. Resubmitted after revision in June 2010 to Transactions of the American Fisheries Society. Tiffan, K.F., D.W. Rondorf, and P.G. Wagner. 2000. Physiological development and migratory behavior of subyearling fall Chinook salmon in the Columbia River. North American Journal of Fisheries Management 20:28-40. Tiffan, K.F., D.W. Rondorf, R.D. Garland, and P.A. Verhey. 2001. Identification of juvenile fall versus spring Chinook salmon migrating through the lower Snake River based on body morphology. Transactions of the American Fisheries Society 129:1389-1395. Tiffan, K.F., R.D. Garland, and D.W. Rondorf. 2002. Quantifying flow-dependent changes in subyearling fall Chinook rearing habitat and stranding area using two-dimensional spatially-explicit modeling. North American Journal of Fisheries Management 22:713-726. Tiffan, K.F., C.A. Haskell, and D.W. Rondorf. 2003. Thermal exposure of juvenile fall Chinook salmon migrating through a lower Snake River Reservoir. Northwest Science 77:100-109. Tiffan, K.F., L.O. Clark, R.D. Garland, and D.W. Rondorf. 2006. Variables influencing the presence of subyearling fall Chinook salmon in shoreline habitats of the Hanford Reach, Columbia River. North American Journal of Fisheries Management 26:351-360. Tiffan, K.F., T.J. Kock, C.A. Haskell, W.P. Connor, and R.K. Steinhorst. 2009a. Water velocity, turbulence, and migration rate of subyearling fall Chinook salmon in the free-flowing and impounded Snake River. Transactions of the American Fisheries Society 138:373-384. Tiffan, K.F., T.J. Kock, W.P. Connor, R.K. Steinhorst, and D.W. Rondorf. 2009b. Behavioural thermoregulation by subyearling fall (autumn) Chinook salmon Oncorhynchus tshawytscha in a reservoir. Journal of Fish Biology 74:1562-1579. Tiffan, K. F., and W. P. Connor. In review. Distinguishing between natural and hatchery Snake River fall Chinook salmon subyearlings in the field using body morphology. Recommended for publication in Transactions of the American Fisheries Society, July 2010. Venditti, D.A., D.W. Rondorf, J.M. Kraut. 2000. Migratory behavior and forebay delay of radio-tagged juvenile fall Chinook salmon in a lower Snake River impoundment. North American Journal of Fisheries Management 20:41-52. Vigg, S., T.P. Poe, L.A. Prendergast, and H.C. Hansel. 1991. Rates of consumption of juvenile salmonids and alternative prey fish by northern squawfish, walleyes, smallmouth bass, and channel catfish in John Day Reservoir, Columbia River. Transactions of the American Fisheries Society 120:421-438. Ward, D.L., J.H. Petersen, and J.J. Loch. 1995. Index of predation on juvenile salmonids by northern squawfish in the lower and middle Columbia River and in the lower Snake River. Transactions of the American Fisheries Society 124:321-334. White, G.C., and K.P. Burnham. 1999. Program MARK: survival estimation from populations of marked animals. Bird Study 46(Supplement):120-138. Williams, J. G., R. W. Zabel, R. S. Waples, J. A. Hutchings and W. P. Connor. 2008. Potential for anthropogenic disturbances to influence evolutionary change in the life history of a threatened salmonid. Evolutionary Applications 1: 271–285. Wolter, K., and M.S. Timlin, 1993: Monitoring ENSO in COADS with a seasonally adjusted principal component index. Proc. of the 17th Climate Diagnostics Workshop, Norman, OK, NOAA/NMC/CAC, NSSL, Oklahoma Clim. Survey, CIMMS and the School of Meteor., Univ. of Oklahoma, 52-57. . Wolter, K., and M. S. Timlin, 1998: Measuring the strength of ENSO events - how does 1997/98 rank? Weather, 53, 315-324. Yanke, J. A., C M. Moffitt, J. A. Congleton, and W. P. Connor. In review. Growth, survival, and physiology of subyearling fall Chinook salmon PIT-Tagged and then reared at elevated water temperatures. Submitted to the North American of Journal of Fisheries Management July 2010. Zabel, R.W., J. Faulkner, S.G. Smith, J.J. Anderson, C. Van Holmes, N. Beer, S. Iltis, J. Krinke, G. Fredricks, B. Bellerud, J. Sweet, A. Giorgi. 2008. Comprehensive Passage (COMPASS) Model: a model of downstream migration and survival of juvenile salmonids through a hydropower system. Hydrobiologia 609: 289-300. Zabel, R. W., M. D. Scheuerell, M. M. McClure, and J. G. Williams. 2006. The interplay between climate variability and density dependence in the population viability of Chinook salmon. Conservation Biology 20(1):190-200. Zimmerman, M.P. 1999. Food habits of smallmouth bass, walleyes, and northern pikeminnow in the lower Columbia River Basin during outmigration of juvenile anadromous salmonids. Transactions of the American Fisheries Society 128:1036-1054.

Back To Top

Notes

None

Back To Top

RME / AP Category Review Assessments

Review: RME / AP Category Review

Independent Scientific Review Panel Assessment

Assessment Number: 1991-029-00-ISRP-20101015
Project: 1991-029-00 - Snake River Fall Chinook Research & Monitoring
Review: RME / AP Category Review
Proposal Number: RMECAT-1991-029-00
Completed Date: 12/17/2010
Final Round ISRP Date: 12/17/2010
Final Round ISRP Rating: Meets Scientific Review Criteria
Final Round ISRP Comment:
This ongoing project has collected field data on Snake River fall Chinook salmon spawning activity, juvenile recruitment, survival, and growth for almost two decades, and proposes to continue these studies. The project also manages a very ambitious PIT-tagging program, with almost 400,000 hatchery fall Chinook PIT tagged annually. This project has provided a large portion of the available data on the Snake River fall Chinook Salmon ESU. The data have been used for development of the recovery plan, for planning of the Lyons Ferry hatchery program, and for design of the summer flow augmentation program. The study documented overwintering of juvenile fall Chinook salmon in the hydropower system reservoirs, and contributed to the decision to extend the operation of the juvenile bypass system at Lower Granite Dam later into the fall. This project is a collaborative effort between the USFWS and the USGS, and will provide information essential to NOAA life-cycle modeling efforts. A number of additional Federal and State agencies are involved in data collecting and reporting. The activities funded by this proposal would not duplicate other efforts.

This project is well integrated with other regional RM&E efforts relating to Snake River fall Chinook, as would be expected of a project with a nearly 20-year history. The proposal addresses RPAs in the BiOp, the AMIP, and Council’s draft MERR plan. The 2008 BiOp calls for (continuing) investigations of the early life history of Snake River fall Chinook salmon and of the effects of the hatchery program on natural productivity. The NPCC’s Fish and Wildlife Program calls for research on the effects of predation in the mainstem on juvenile salmonids, as does the Adaptive Management Implementation Plan (AMIP). The AMIP also calls for the development of improved life-cycle and passage models for ESA-listed salmonid stocks. The proposal has easily identifiable objectives and tasks related to these needs.

This was a well-written proposal for a project with an excellent track record of success and accomplishment (e.g., 32 peer-reviewed journal articles) over its long history. Project proponents have made a number of presentations to the ISAB and ISRP over the years in which major findings have been analyzed and discussed. The project has clearly benefited Snake River fall Chinook salmon over the years and will likely continue to do so. In particular, this proposal seems to be especially good at describing how data collection and data analysis/modeling will work together. It is more than a monitoring project. It is truly a combination monitoring and research/modeling effort. Their proposal is thus a well-synthesized effort at data collection and high-level analyses with clear applicability to management. The itemized list of management changes that have resulted from the findings of this study constitutes strong evidence of adaptive management. Their general approach could (and should) be applied to other programs in the Basin.

Some limitations on the extent and reliability of data collected by this project have been resolved (differentiating between natural-origin Fall and Spring Chinook subyearlings and between natural-origin Fall Chinook and hatchery-origin subyearlings), while others have not (inability to tag subyearlings <49 mm, uncertainty about effects of flow on beach-seining efficiency, lack of data on passage of juveniles during winter months).

One of the highlights of the project’s discoveries has been the recognition of a reservoir overwintering life history attribute in some Snake River fall Chinook, and extension of operation of the juvenile bypass systems at the lower Snake dams reflects this new understanding of year-round movement patterns. The research questions have been refined and focused over the years, and are addressing some of the most critical data gaps concerning this ESU.

The technical background and objectives were clearly organized and explained. For each objective, detailed methods are provided. The project relies on standard field sampling methods. Deliverables, work elements, metrics and methods are well described in the proposal. The discussions of population modeling and the approaches to fitting stock-recruitment curves were especially thorough. Project proponents appear well equipped to carry out the work.

Of particular value in this proposed work are their analyses of abundance and growth data with stock recruitment relationships to address the idea of density dependence in supplementation programs. Post supplementation, there has been a significant decrease in smolt size. Hatchery supplementation has been associated with large increases in redd counts, followed by a leveling off/slight decline of natural fish. There are some indications that density dependent factors might be acting as stock size rebuilds. Whether or not density-dependence or other hatchery-wild interactions are occurring may be a contentious issue, but regardless of the outcome, addressing these questions with their long-term data sets is a highly important use of the data, and an appropriate approach for evaluating and shaping other supplementation projects in the basin as well. Results of the analysis should provide a biological basis for recovery goals. The proponents also have a riverine bass predation element to their project that will provide information related to survival. This project is exemplary in that it is making the attempt to truly assess a supplementation program not just through intermediate steps such as more smolts or more redds, but in terms of its ultimate impact on recovery, the wild stock, density effects, and other higher level population dynamics.
First Round ISRP Date: 10/18/2010
First Round ISRP Rating: Meets Scientific Review Criteria
First Round ISRP Comment:

This ongoing project has collected field data on Snake River fall Chinook salmon spawning activity, juvenile recruitment, survival, and growth for almost two decades, and proposes to continue these studies. The project also manages a very ambitious PIT-tagging program, with almost 400,000 hatchery fall Chinook PIT tagged annually. This project has provided a large portion of the available data on the Snake River fall Chinook Salmon ESU. The data have been used for development of the recovery plan, for planning of the Lyons Ferry hatchery program, and for design of the summer flow augmentation program. The study documented overwintering of juvenile fall Chinook salmon in the hydropower system reservoirs, and contributed to the decision to extend the operation of the juvenile bypass system at Lower Granite Dam later into the fall. This project is a collaborative effort between the USFWS and the USGS, and will provide information essential to NOAA life-cycle modeling efforts. A number of additional Federal and State agencies are involved in data collecting and reporting. The activities funded by this proposal would not duplicate other efforts. This project is well integrated with other regional RM&E efforts relating to Snake River fall Chinook, as would be expected of a project with a nearly 20-year history. The proposal addresses RPAs in the BiOp, the AMIP, and Council’s draft MERR plan. The 2008 BiOp calls for (continuing) investigations of the early life history of Snake River fall Chinook salmon and of the effects of the hatchery program on natural productivity. The NPCC’s Fish and Wildlife Program calls for research on the effects of predation in the mainstem on juvenile salmonids, as does the Adaptive Management Implementation Plan (AMIP). The AMIP also calls for the development of improved life-cycle and passage models for ESA-listed salmonid stocks. The proposal has easily identifiable objectives and tasks related to these needs. This was a well-written proposal for a project with an excellent track record of success and accomplishment (e.g., 32 peer-reviewed journal articles) over its long history. Project proponents have made a number of presentations to the ISAB and ISRP over the years in which major findings have been analyzed and discussed. The project has clearly benefited Snake River fall Chinook salmon over the years and will likely continue to do so. In particular, this proposal seems to be especially good at describing how data collection and data analysis/modeling will work together. It is more than a monitoring project. It is truly a combination monitoring and research/modeling effort. Their proposal is thus a well-synthesized effort at data collection and high-level analyses with clear applicability to management. The itemized list of management changes that have resulted from the findings of this study constitutes strong evidence of adaptive management. Their general approach could (and should) be applied to other programs in the Basin. Some limitations on the extent and reliability of data collected by this project have been resolved (differentiating between natural-origin Fall and Spring Chinook subyearlings and between natural-origin Fall Chinook and hatchery-origin subyearlings), while others have not (inability to tag subyearlings <49 mm, uncertainty about effects of flow on beach-seining efficiency, lack of data on passage of juveniles during winter months). One of the highlights of the project’s discoveries has been the recognition of a reservoir overwintering life history attribute in some Snake River fall Chinook, and extension of operation of the juvenile bypass systems at the lower Snake dams reflects this new understanding of year-round movement patterns. The research questions have been refined and focused over the years, and are addressing some of the most critical data gaps concerning this ESU. The technical background and objectives were clearly organized and explained. For each objective, detailed methods are provided. The project relies on standard field sampling methods. Deliverables, work elements, metrics and methods are well described in the proposal. The discussions of population modeling and the approaches to fitting stock-recruitment curves were especially thorough. Project proponents appear well equipped to carry out the work. Of particular value in this proposed work are their analyses of abundance and growth data with stock recruitment relationships to address the idea of density dependence in supplementation programs. Post supplementation, there has been a significant decrease in smolt size. Hatchery supplementation has been associated with large increases in redd counts, followed by a leveling off/slight decline of natural fish. There are some indications that density dependent factors might be acting as stock size rebuilds. Whether or not density-dependence or other hatchery-wild interactions are occurring may be a contentious issue, but regardless of the outcome, addressing these questions with their long-term data sets is a highly important use of the data, and an appropriate approach for evaluating and shaping other supplementation projects in the basin as well. Results of the analysis should provide a biological basis for recovery goals. The proponents also have a riverine bass predation element to their project that will provide information related to survival. This project is exemplary in that it is making the attempt to truly assess a supplementation program not just through intermediate steps such as more smolts or more redds, but in terms of its ultimate impact on recovery, the wild stock, density effects, and other higher level population dynamics.
Documentation Links:
Proponent Response:

2008 FCRPS BiOp Workgroup Assessment

2008 FCRPS BiOp Workgroup Assessment Rating:  Response Requested
BiOp Workgroup Comments: This project needs to work closely with the development of the regional PIT plan and regional assessments of tagging needs and priorities. This project seems like it could be developed further to support life cycle modeling for climate change assessments.

The BiOp RM&E Workgroups made the following determinations regarding the proposal's ability or need to support BiOp Research, Monitoring and Evaluation (RME) RPAs. If you have questions regarding these RPA association conclusions, please contact your BPA COTR and they will help clarify, or they will arrange further discussion with the appropriate RM&E Workgroup Leads. BiOp RPA associations for the proposed work are: (50.3 53.1 53.2 55.4 65.1 65.2 65.3)
All Questionable RPA Associations ( ) and
All Deleted RPA Associations ( )
Proponent Response:

We are willing to work closely with the development of the regional PIT plan and regional assessements of tagging needs and priorities.

With respect to support for life cycle modeling for climate change assessments, the proposal included the following under the emerging issues section.

Climate change will likely result in: (1) early peak flows, (2) a decrease in peak flows, and (3) an increase in water temperature (ISAB 2007).  The ISAB proposed that climate change will have the most significant impacts on the early life stages of fall Chinook salmon, which rear in mainstem habitats.  In summary, the ISAB hypothesized that climate change will lead to: (1) earlier fry emergence, (2) a smaller size at emergence, (3) earlier departure from protective rearing habitat, (4) reduced survival due to changes in rearing behavior due to predation, (5) increased metabolism and decreased growth if food resources are limited in less optimal habitat in down-river reaches, (6) forebay delay, (7) decreased smolt survival, and (8) a reduction in life history diversity if late summer temperatures become lethal and kill that later summer migrants and those fish destined to become fall migrants or to overwinter in reservoirs.  This proposal takes climate change and predation into account by fitting stock recruitment functions to predict changes in adult and juvenile abundance from covariates derived from empirical data collected on stream flow, temperature, and ocean conditions.

Project leader Connor is a member and researcher on the AMIP steering comittee and has already attended the opening coordination meeting where state of the art climate change models were presented and discussed in detail.  We did not fully develop a climate section in our proposal because we knew in advance we would be participants in AMIP and that AMIP would take the lead on the climate change issue.  We will continue to participate in AMIP and provide our knowledge and fish data to the true experts on climate change to avoid duplication of effort and provide the best product for the region. 

 


Back To Top