Columbia Basin Fish and Wildlife Program Columbia Basin Fish and Wildlife Program
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Project Summary

Project 2010-031-00 - Snake River Chinook and Steelhead Parental Based Tagging
Project Number:
2010-031-00
Title:
Snake River Chinook and Steelhead Parental Based Tagging
Summary:
This project will evaluate a new, dynamic genetic technology that should be cheaper and more efficient than coded-wire tags for mass marking hatchery steelhead and Chinook salmon in the Snake River basin. This technology, called Parentage Based Tagging (PBT), should provide a better tool to meet Fish & Wildlife Program objectives associated with marking hatchery stocks, conducting hatchery evaluations and reform, and enforcing salmonid fishery management measures. This project will genotype approximately 16,500 samples annually to create the first PBT parental genetic baselines for hatchery steelhead and Chinook salmon in the Snake River basin. In doing so, it will effectively, permanently genetically mark ~12 million smolts, per species, per year. This project will work closely with an existing BPA funded project (2008-907-00) to ensure that future genetic marker sets used in the Columbia River basin are standardized, providing unprecedented genetic tools for managing wild and hatchery stocks in the basin: with Genetic Stock Identification techniques segregating adult wild runs by stock of origin, and Parentage Based Tagging technologies identifying the stock and age of sampled hatchery fish.


In the ISRP review of Proposal 201003100: Snake River Chinook and Steelhead Parental Based Tagging, they suggested that two items be addressed during contracting:

1.) They suggested that for objective 4, 157...SNP Genotyping (juveniles) - a number of non-hatchery wild juveniles originating from major population groups (MPGs) or reporting groups should be tested against the parents used to establish the PBT baseline. They should not assign to any of the hatcheries. It was not apparent from the objectives and methods that this testing was included.

While intuitively the screening of wild juveniles may seem necessary to test power of parentage assignments in terms of false-positive error rates (wild juveniles shouldn’t assign to the hatchery parental baseline), the highest likelihood for error will be within datasets that contain full siblings. We will have ample opportunities to test for this type of error through the screening of both adult and juvenile hatchery samples, where it is likely that full siblings of their parents will be within the dataset. In addition, since the SNP marker sets that will be run for PBT analyses will be the same marker sets used for wild GSI, there will be numerous wild samples whose genotypes could be tested against the hatchery parental baseline.

2.)They also expressed concern that the high throughput requirements for analysis of 16.5K samples per year plus any future samples from fisheries, etc., may quickly overwhelm the system. Given the genetic laboratory's other demands, proponents need to verify in contracting that results can be provided in accordance with proposed schedules.

With the acquisition of new SNP genotyping instruments and an automated pipetting robot prior to the development of these proposals, along with the request of additional Personnel and laboratory equipment as part of these new proposals, we are confident that we will be able to provide results in accordance to proposed schedules.
Proposer:
Proponent Orgs:
Idaho Department of Fish and Game (IDFG) (Govt - State)
Starting FY:
2010
Ending FY:
2022
BPA PM:
Stage:
Implementation - Project Status Report
Area:
Province Subbasin %
Blue Mountain Grande Ronde 20.00%
Imnaha 20.00%
Columbia Plateau Snake Lower 20.00%
Mountain Snake Clearwater 20.00%
Salmon 20.00%
Purpose:
Programmatic
Emphasis:
RM and E
Focal Species:
Chinook - Mid-Columbia River Spring ESU
Chinook - Snake River Fall ESU
Chinook - Snake River Spring/Summer
Chinook - Snake River Spring/Summer ESU
Sockeye - Snake River ESU
Steelhead - Snake River DPS
Species Benefit:
Anadromous: 100.0%   Resident: 0.0%   Wildlife: 0.0%
Special:
None

No photos have been uploaded yet for this Project.

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

Decided Budget Transfers  (FY2019 - FY2021)

Acct FY Acct Type Amount Fund Budget Decision Date
FY2019 Expense $1,081,234 From: Fish Accord - Idaho Accord Extensions (State of Idaho) 10/1/2018 10/01/2018
FY2020 Expense $1,081,234 From: Fish Accord - Idaho Accord Extensions (State of Idaho) 10/1/2018 10/01/2018
FY2021 Expense $1,094,749 From: Fish Accord - Idaho Accord Extensions (State of Idaho) 10/1/2018 10/01/2018

Pending Budget Decision?  No


Actual Project Cost Share

Current Fiscal Year — 2020
Cost Share Partner Total Proposed Contribution Total Confirmed Contribution
Idaho Power $262,382
Total $0 $262,382
Previous Fiscal Years
Fiscal Year Total Contributions % of Budget
2019 $262,382 20%
2016 (Draft)
2015 $100,000 7%
2014 $100,000 9%
2013 $100,000 9%
2012 $310,916 23%
2011

Contracts

The table below contains contracts with the following statuses: Active, Complete, History, Issued.
* "Total Contracted Amount" column includes contracted amount from both capital and expense components of the contract.
Expense Contracts:
Number Contractor Name Title Status Total Contracted Amount Dates
82618 SOW Idaho Department of Fish and Game (IDFG) 2010-031-00 EXP SNAKE RIVER CHINOOK AND STEELHEAD Issued $1,081,234 7/1/2019 - 6/30/2020
85312 SOW Idaho Department of Fish and Game (IDFG) 2010-031-00 EXP SNAKE RIVER CHINOOK AND STEELHEAD Issued $1,081,234 7/1/2020 - 6/30/2021



Annual Progress Reports
Expected (since FY2004):10
Completed:10
On time:10
Status Reports
Completed:40
On time:36
Avg Days Early:5

Earliest Subsequent           Accepted Count of Contract Deliverables
Contract Contract(s) Title Contractor Start End Status Reports Complete Green Yellow Red Total % Green and Complete Canceled
48348 53238, 57342, 61801, 65500, 69574, 73195, 76552, 79587, 82618, 85312 2010-031-00 EXP IDF&G - SNAKE R CHINOOK AND STEELHEAD PARENT TAG Idaho Department of Fish and Game (IDFG) 07/2010 07/2010 Issued 40 215 0 0 0 215 100.00% 1
Project Totals 40 215 0 0 0 215 100.00% 1


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: Fast Track ISRP Review 2010

Independent Scientific Review Panel Assessment

Assessment Number: 2010-031-00-ISRP-20100623
Project: 2010-031-00 - Snake River Chinook and Steelhead Parental Based Tagging
Review: Fast Track ISRP Review 2010
Completed Date: None
First Round ISRP Date: 2/24/2010
First Round ISRP Rating: Meets Scientific Review Criteria (Qualified)
First Round ISRP Comment:
1. Technical Justification, Program Significance and Consistency, and Project Relationships
The need for the monitoring of hatchery salmon and steelhead performance once released is an essential feature of management obligations to evaluate the efficacy of the artificial production programs in terms of their yields to fisheries and impacts to natural population. The ISAB/ISRP, as well as the Pacific Salmon Commission technical team, recently concluded that Parental Based Tagging (PBT) has the potential to provide important data for cohort analysis of salmon and steelhead populations. The project proponents (IDFG) propose to genotype the entirety of Chinook salmon and steelhead broodstock from 14 Snake River hatcheries to empirically test and validate whether PBT can be used to replace coded-wire tags (CWT) for estimating stock contributions of Snake River steelhead and Chinook salmon to fisheries, run-timing, straying, etc., of adult salmon in the Snake/Columbia River basins.

The technical justification of using PBT as a replacement for CWT-based assessment of hatchery production in harvest, straying, and returns to hatcheries (life-cycle survival) is adequately described. The ISRP notes, however, that successful implementation of PBT will not eliminate all problems associated with CWTs, mass marking, and selective fisheries. For example, there will still be a need to handle and mass mark juvenile hatchery fish with an adipose fin clip or some other highly-visible mark for selective fisheries.

The technological development to bring PBT to pilot scale trial is consistent with the BiOp, Fish and Wildlife Program, and Lower Snake River Compensation Plan. Relationships with other projects in the Basin are sufficiently described, and evidence is provided that the proponents are familiar with other PBT trials in Puget Sound, Washington and the Sacramento River, California. The proposed project involves coordination with the Columbia River Intertribal Fish Commission (CRITFIC) and other Genetics Analysis of Pacific Salmon (GAPS) and Stevan Phelps Allele Nomenclature (SPAN) laboratories to develop a coastwide Single-Nucleotide Polymorphism (SNPS) baseline.

One concern is that the ISRP could not determine whether this proposed project unnecessarily duplicates work already being performed or proposed by other BPA-funded projects. For example, the proposed work is contingent upon the success (efficiency, precision, and accuracy) of efforts associated with BPA Project #200890700, “Genetic Assessment of Columbia River Stocks.” Moreover, the project will "identify SNP loci" for Chinook salmon and steelhead. Presumably, BPA Project #200890700 should be far enough along to inform these choices now without significant new work. Finally, the proposed project will not analyze future harvested or escaped (from fishery) Snake River salmon and steelhead except as a test (objective 5). The ISRP does not understand why BPA Proposal No. 201002600: “Chinook and steelhead genotyping for genetic stock identification (GSI) at Lower Granite Dam,” which is contingent on the results of this proposed project, was submitted as a separate proposal. As a result, is there unnecessary overlap or duplication of some work elements between the two proposals?


2. Project History and Results
The proposed project is new, but efforts to begin collecting tissue for genetic analysis are already underway, e.g., samples from broodstock at most Snake River hatcheries were obtained in 2008 and 2009. Since this project is closely linked with the CRITFC project developing SNP assays for Columbia River salmon ESUs (BPA Project #200890700), a more detailed description of the number of SNPs identified to date and how many of those have been polymorphic in the populations of interest would have been useful.

3. Objectives, Work Elements, and Methods
The objectives are relatively straightforward. The overall work plan and strategy to collect tissue samples; develop SNPs; identify a SNP panel for both genetic stock identification (GSI) and PBT; and then test that panel using progeny from known populations; and finally cross check with harvested fish that carry CWTs is sound. One difficulty for ISRP reviewers not expert in the field of salmon genetics was that proponents used lots of technical jargon without defining their terminology. In addition, publications and computer software packages were frequently cited for methods without providing a concise summary or explanation of these methods in the proposal.

The ISRP suggests that for objective 4, 157...SNP Genotyping (juveniles) - a number of non-hatchery wild juveniles originating from major population groups (MPGs) or reporting groups should be tested against the parents used to establish the PBT baseline. They should not assign to any of the hatcheries. It was not apparent from the objectives and methods that this testing was included.

One final concern is that the high throughput requirements for analysis of 16.5K samples per year plus any future samples from fisheries, etc., may quickly overwhelm the system. Given the genetic laboratory's other demands, proponents need to verify in contracting that results can be provided in accordance with proposed schedules.
Documentation Links:
Review: RME / AP Category Review

Council Recommendation

Assessment Number: 2010-031-00-NPCC-20110624
Project: 2010-031-00 - Snake River Chinook and Steelhead Parental Based Tagging
Review: RME / AP Category Review
Proposal: RMECAT-2010-031-00
Proposal State: Pending BPA Response
Approved Date: 6/10/2011
Recommendation: Fund (Qualified)
Comments: Fund through 2016 per April-May 2010 decision for Fast Track projects. Implementation subject to regional hatchery effects evaluation process described in programmatic recommendation #4.
Conditions:
Council Condition #1 Per April-May 2010 Council decision for Fast Track project - Prior to contracting, BPA and sponsors to address ISRP qualifications. In addition, BPA and Council will consider integration and coordination of similar genetic projects through the larger RM&E/Artificial production Categorical Review.
Council Condition #2 Programmatic Issue: RMECAT #4 Hatchery Effectiveness—.

2008 FCRPS BiOp Workgroup Assessment

Assessment Number: 2010-031-00-BIOP-20101105
Project Number: 2010-031-00
Review: RME / AP Category Review
Proposal Number: RMECAT-2010-031-00
Completed Date: None
2008 FCRPS BiOp Workgroup Rating: Response Requested
Comments: BiOp Workgroup Comments: For compliance with RPA 50.7: This RPA action is for hatchery fish marking only. Confirm that the scope of work proposed is for 100% marking of fish (visible or non visible) from the hatchery supported. If this project is marking fish for the hatchery, please specify the hatchery name and populations affected. If marking is conducted under another project or program, please let us know the name of that project/program.

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: (50.5 50.7 62.5 64.2)
All Questionable RPA Associations (50.7) and
All Deleted RPA Associations ( 55.8 63.2 64.1 )
Proponent Response:

The RME Workgroup comments agreed with three project BiOp RPA associations (50.5, 62.5 and 64.2), questioned one (50.7) and suggested that three be deleted (55.8, 63.2, 64.1).  For 50.7 that asked to confirm that the scope of work proposed is for 100% marking of fish (visible or non visible) and that if the project involved marking fish for the hatchery, that we specify the hatchery name and populations affected.  The hatchery stocks are listed below for both spring/summer Chinook salmon and steelhead.  Responses to the three RPAs suggested for deletion are also provided below. 

 50.7- Fund marking of hatchery releases from Action Agencies funded facilities to enable monitoring of hatchery-origin fish in natural spawning areas and the assessment of status of wild populations. (Annually) 

Response:  BPA project will permanently genetically mark all hatchery spring/summer Chinook salmon and steelhead in the Snake River basin (Idaho, Oregon and Washington).  These populations are summarized in Table 1 and 2 along with the number of broodstock spawned in 2008 and 2009. 

Steelhead

Spawn Year

Spawn Year

Snake River Hatcheries

2008

2009

 

LSRCP/IDFG Sawtooth (IDFG)

556

519

 

LSRCP/IDFG Sawtooth (SBT)

502

462

 

LSRCP/IDFG Sawtooth (EFSR)

119

132

 

LSRCP/IDFG Sawtooth (USB/Squaw)

35

53

 

Idaho Power/IDFG,Oxbow F.H.

927

600

 

Idaho Power/IDFG, Pahsimeroi F.H.

1530

968

 

Idaho Power/IDFG, Pahsimeroi F.H. (SBT)

300

336

 

LSRCP/IDFG/USFWS Dworshak/C.W.

1420*

1880

 

LSRCP/ODFW-Wallowa F.H.

0**

460

 

LSRCP/WDFW-Lyons Ferry

0*

215

 

LSRCP/WDFW-L.F. (Tucannon)

0*

25

 

LSRCP/WDFW-L.F. (Touchet)

0*

29

 

LSRCP/WDFW-L.F. (G.R. cottonwood)

169

100

 

Total

5558

5674

 

         

 Table 1.  Total number of Snake River steelhead hatchery broodstock sampled in 2008 and 2009.  *Early egg-takes were missed.  **ODFW hatcheries were not sampled in 2008.

 

Chinook Salmon

Spawn Year

Spawn Year

Snake River Hatcheries

2008

2009

Idaho Power/IDFG, Rapid River

2902

2098

LSRCP/USFWS, Dworshak

1216

908

LSRCP/IDFG, Clearwater (powell)

1074

871

LSRCP/IDFG, Clearwater (SF)

1220

872

LSRCP/IDFG, Sawtooth

1200

1010

Idaho Power/IDFG, Pahsimeroi

714

628

LSRCP/WDFW-L.F. (Tucannon)

131

175

LSRCP/IDFG, McCall (SFSR)

1920

946

LSRCP/ODFW, Imnaha

248

226

LSRCP/ODFW/NPT, Lostine

108

109

LSRCP/ODFW, Catherine Creek

57

81

LSRCP/ODFW, Grande Ronde

27

116

LSRCP/ODFW, Lookingglass Creek

150

65

Nez Perce Tribal Hatchery (NPTH)

193

350

Total

11160

8455

 Table 2.  Total number of Snake River Chinook salmon hatchery broodstock sampled in 2008 and 2009. 

 55.8-Evaluate new tagging technologies for use in improving the accuracy and assessing delayed or indirect hydro effects on juvenile or adult fish.

Response:  It appears that the new tagging technology that RPA 55.8 references primarily involves acoustic tags.  The Pacific Ocean Shelf Tracking (POST) program is a BPA funded project (2003-114-00) that is developing electronic tagging technology and methods to determine delayed or indirect effects of hydro passage by tracking salmon and steelhead in the estuary below Bonneville Dam and the ocean environment off the Pacific coast.  While our current project goals do not include sampling hatchery salmon and steelhead in these areas, it easy to see how PBT technology ultimately could be used to address many of the same types of questions that acoustic tag technology is attempting to address.  These questions are outlined on the POST website (http://www.coml.org/projects/pacific-ocean-shelf-tracking-project-post) and includes:

  • ·         Do different salmon stocks form stock-specific aggregations at sea, or do they share common migration pathways and foraging areas? If such aggregations or pathways occur, where are the boundaries and how long do salmon remain in these areas?
  • ·         Do distributions and migration patterns fluctuate with annual and long-term changes in ocean productivity, such as spring bloom cycles and El Niño/La Niña conditions?
  • ·         How do different salmon species respond to changes in ocean conditions?
  • ·         What are the winter movements and habitat usage of juvenile salmon?
  • ·         What differences exist between the movement patterns and habitat use of wild and hatchery salmon?
  • ·         Do shelf migration behaviors correlate with changes in annual stock success?
  • ·         How do distribution and habitat use differ among species and stocks?
  • ·         Is there stock-specific, life-stage specific or location-specific mortality in the ocean?

The hatchery offspring that are genetically tagged as part of our project represents all of the Snake River hatchery steelhead and spring/summer Chinook salmon produced each year and  roughly 50% of the entire production of hatchery steelhead and spring/summer Chinook salmon that migrate out of the Columbia River basin annually. 

 63.2- Determine the effect that implemented hatchery reform actions have on the recovery of targeted salmon and steelhead populations.

Response:  The effectiveness of hatchery reform measures will require monitoring genetic divergence between hatchery and wild stocks and making assessments of hatchery straying.

For integrated hatchery programs, actions will be implemented to minimize genetic divergence between the hatchery broodstock and the wild population and to maximize the proportion of natural influence (PNI).  This project can provide annual estimates of the degree of genetic divergence between every hatchery stock within the Snake River basin and associated wild stocks.  Successfully managing segregated hatchery programs will require enhancing harvest opportunities and minimizing straying between hatchery and wild populations.  Parentage Based tagging (PBT) of hatchery stocks in the Snake River basin will allow managers to more efficiently evaluate the effects of different release strategies (where and when fish are released, size and age at release, etc.) on increasing harvest and minimizing straying.  We will demonstrate through a paired coded-wire tag (CWT) and PBT recovery experiment, as part of existing hatchery evaluations in Idaho, that PBT technology can provide the same information as CWT (information on stock and age) for harvest evaluations.  This project’s initial goals are also to demonstrate that any hatchery adult that has found to have strayed into natural production areas (either collected alive or as a carcass) could be sampled and its sex, stock and exact age be determined.  For hatchery steelhead in the upper Salmon River basin, we also intend to determine whether straying adults were from an on-site versus off-site juvenile release.  In the near future, with the completion of a collaborative hatchery rearing and release database module, we should also be able to identify the release location of any hatchery steelhead collected/sampled in a wild production area in the upper Salmon River basin.

 55.8-Continue to estimate the relative reproductive success (RSS) of hatchery-origin salmon and steelhead compared to reproductive success of their natural-origin counterparts.

 Response:  Throughout the Snake River basin Chinook salmon and steelhead hatcheries will be implementing hatchery reform measures to support sustainable fisheries while conserving natural spawning populations.  For stocks designated to be part of integrated programs, effectiveness monitoring will be necessary to assess the reproductive contribution of hatchery fish spawning in the wild and the number of adult recruits produced per hatchery spawner.  In coordination with this project (2010-031-00), IDFG, Tribal and federal co-managers in the Snake River basin are currently collecting genetic samples from all natural and hatchery fish passed above weirs associated with specific hatchery programs.   Because single, standardized SNP genetic marker sets are being developed to address genetic issues for both wild and hatchery stocks, this program will be able to contribute hatchery parental genotypes to any RRS study throughout the Snake River basin.


Project Relationships: None

Name Role Organization
Israel Duran Env. Compliance Lead Bonneville Power Administration
Matthew Campbell Project Lead Idaho Department of Fish and Game (IDFG)
Jeff Dillon Supervisor Idaho Department of Fish and Game (IDFG)
Craig Steele Interested Party Pacific States Marine Fisheries Commission
Martin Allen Project Manager Bonneville Power Administration
Brady (USGS) Allen Project SME US Geological Survey (USGS)