Columbia Basin Fish and Wildlife Program Columbia Basin Fish and Wildlife Program
SOW Report
Contract 53239: 2010-026-00 EXP CHINOOK AND STEELHEAD GENOTYPING
Project Number:
Title:
Chinook and Steelhead Genotyping for Genetic Stock Identification (GSI) at Lower Granite Dam
BPA PM:
Stage:
Implementation
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%
Contract Number:
53239
Contract Title:
2010-026-00 EXP CHINOOK AND STEELHEAD GENOTYPING
Contract Continuation:
Previous: Next:
48347: 2010-026-00 EXP IDF&G CHINOOK AND STEELHEAD GENOTYPING
  • 57343: 2010-026-00 EXP CHINOOK AND STEELHEAD GENOTYPING
Contract Status:
Closed
Contract Description:
This project will develop and implement GSI methodologies within the Snake River basin for wild Chinook salmon and steelhead passing Lower Granite Dam. Project leads will ensure that all SNP genotype data generated from this project will be standardized and available for Columbia River genetic baseline expansions (CRITFC 200890700-objective 2).  In addition, side by side comparisons of Parentage Based Tagging datasets (BPA project #201003100) and GSI datasets, will allow the identification of a single set of SNPs that can be used for both technologies.  This will allow the integration of sampling programs at Bonneville and Lower Granite Dam and in Columbia River and Snake River mainstem fisheries such that any sampled wild adult can be included in mixture analyses to determine stock composition and any sampled Snake River hatchery adult can be assigned to a stock and cohort. Once standardized SNP marker sets have been developed and tested, this project will genotype 2000 adults and 2000 juveniles (for each species) annually as they migrate past Lower Granite Dam on the Snake River.  An additional 1000 samples (for each species) will be genotyped annually as part of generational genetic baseline development and maintenance.  This sampling and genotyping will provide a robust baseline from which GSI mixture analyses can be performed, and will also provide temporal monitoring of genetic diversity/structure across the basin allowing estimation of gene flow and effective population size. Incorporating age and sex information collected simultaneously from migrating adults and juveniles will provide data on abundance and biodiversity of Snake River Chinook salmon and steelhead that have previously been unavailable for managing wild stocks in the basin.

In the ISRP review of Proposal 201002600: Chinook and Steelhead Genotyping for Genetic Stock Identification (GSI) at Lower Granite Dam, they suggested that three items be addressed in contracting and future proposals:

1.) They suggested that while the GSI methodology was established in the proposal that the analytical framework for including this information in status and trends analysis and reporting for steelhead and Chinook salmon was not provided.  

Specifically this project will provide managers working on population viability assessments and recovery efforts for Snake River steelhead and Chinook salmon (e.g.  NOAA Fisheries Service salmon recovery team):
a. More detailed descriptions of genetic population structure for steelhead and Chinook salmon in the Snake River basin than what has been previously available.  This will allow better information for delineating extant populations of listed Chinook salmon and steelhead within the Snake River ESU.  Currently, independent populations are defined for VSP purposes using a definition that is equivalent to Ricker’s (1972) characterization of a stock, that is, “an independent population is a group of fish of the same species that spawns in a particular lake or stream (or portion thereof) at a particular season and which, to a substantial degree, does not interbreed with fish from any other group”.
b. Annual, stock specific estimates of adult and juvenile abundance in the Snake River basin above Lower Granite Dam.  This will allow estimates of abundance and productivity statistics including:  Number of natural origin spawners and natural origin recruits, lambda (median annual population growth rate based on four-year running), Number of recruits per spawner.
c. Diversity estimates on a stock specific basis including life history traits (run-timing, size and age at return, sex ratios, etc.), estimates of effective population size, and measures of genetic differentiation/similarity of hatchery populations to wild populations.

2.) They suggested that the rationale for sampling 2000 individuals at LGD needs to be justified.  

Sampling of juveniles and subsequent stock specific estimates of juvenile abundance will be required to estimate the statistics described above (mean of natural origin recruits, mean of recruits per spawner, etc.).  The sample size of 2000 was selected because this sample size should allow us to partition the run by sex and most abundant age classes, while maintaining sample sizes needed for mixture analyses between 400-600.  These sample sizes should be adequate to ensure that stock proportion estimates are within ±5 percentage points of the true values 90-95% of the time (Thompson 1987).

3.) They suggested that it may be useful to consider ways to integrate and coordinate projects 201002600, 201003100 and 200890700 under an umbrella proposal that clearly identifies the  responsibilities of the individual projects.

Due to the size of these projects, the fact that project 200890700 was initiated in 2008, and the fact that each project has very specific goals and objectives, we do not feel that it would be efficient or practical to attempt to combine these projects under one umbrella proposal.  These projects will be highly integrated and coordinated however.  Not just among themselves but with other genetic labs and projects throughout the Columbia River basin.  Both IDFG and CRITFC scientists have substantial experience collaborating with other coastwide genetic labs to standardize microsatellite loci for both steelhead and Chinook salmon (GAPS-Seeb et al. 2007; SPAN-Stephenson et al. 2008).  Both IDFG and CRITFC scientists are already involved in coordination efforts to sample baseline populations and standardize SNP loci for both species (SNP Workshop III, March 22-24, 2010 and Coastwide Salmonid Genetics Meeting Jun 2-4, 2010).
Account Type(s):
Expense
Contract Start Date:
07/01/2011
Contract End Date:
06/30/2012
Current Contract Value:
$669,448
Expenditures:
$669,448

* Expenditures data includes accruals and are based on data through 31-Aug-2021.

Env. Compliance Lead:
Work Order Task(s):
Contract Type:
Contract (IGC)
Pricing Method:
Cost Reimbursement (CNF)
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Full Name Organization Write Permission Contact Role Email Work Phone
Mike (PSMFC) Ackerman Pacific States Marine Fisheries Commission Yes Technical Contact mike.ackerman@idfg.idaho.gov (208) 939-6713
Matthew Campbell Idaho Department of Fish and Game (IDFG) Yes Contract Manager matthew.campbell@idfg.idaho.gov (208) 939-6713
Conan Chiu Idaho Department of Fish and Game (IDFG) No Administrative Contact conan.chiu@idfg.idaho.gov (208) 287-2813
Jeff Dillon Idaho Department of Fish and Game (IDFG) No Supervisor jeff.dillon@idfg.idaho.gov (208) 287-2777
Israel Duran Bonneville Power Administration Yes Env. Compliance Lead induran@bpa.gov (503) 230-3967
Eric Grau Idaho Department of Fish and Game (IDFG) No Interested Party ericdgrau@gmail.com (206) 979-7506
Jon Hess Columbia River Inter-Tribal Fish Commission (CRITFC) No Interested Party hesj@critfc.org (208) 837-9096x1107
Maureen (CRITFC) Hess Columbia River Inter-Tribal Fish Commission (CRITFC) No Interested Party hesm@critfc.org (503) 731-1318
Paul Krueger Bonneville Power Administration Yes F&W Approver pqkrueger@bpa.gov (503) 230-5723
Jesse McCane Idaho Department of Fish and Game (IDFG) No Technical Contact jesse.mccane@idfg.idaho.gov (208) 939-6713
Shawn Narum Columbia River Inter-Tribal Fish Commission (CRITFC) No Interested Party nars@critfc.org (208) 837-9096x1120
William Schrader Idaho Department of Fish and Game (IDFG) No Interested Party bill.schrader@idfg.idaho.gov (208) 465-8404x235
Barbara Shields Bonneville Power Administration Yes COTR bashields@bpa.gov (503) 230-4748
Susan Smith Idaho Department of Fish and Game (IDFG) No Administrative Contact susan.smith@idfg.idaho.gov (208) 287-2803
Craig Steele Pacific States Marine Fisheries Commission Yes Technical Contact craig.steele@idfg.idaho.gov (208) 939-6713
Kristi Van Leuven Bonneville Power Administration No Contracting Officer kjvleuven@bpa.gov (503) 230-3605


Viewing of Work Statement Elements

Deliverable Title WSE Sort Letter, Number, Title Start End Complete
Environmental Compliance A: 165. Environmental Complicance Documentation 07/01/2011 07/01/2011
Funding Package - Submit draft to COTR B: 119. OBJ 1-3: Project Management 05/31/2012 05/31/2012
Attach Progress Report in Pisces D: 132. OBJ 1-3: Submit Progress Report for the period 7/1/2011 to 6/30/2012 06/30/2012 06/29/2012
Tables ranking informativeness of SNP loci for GSI E: 162. OBJ 1: Evaluate and maintain SNPs 01/02/2012 01/02/2012
Attend GAPS/SPAN meetings and maintain SNP assay and baseline data F: 189. OBJ 1: Evaluate and maintain SNPs 06/30/2012 06/26/2012
SNP assay information spreadsheet G: 161. OBJ 1: Evaluate and maintain SNPs 01/02/2012 01/02/2012
List of SNPs and populations H: 156. OBJ 2: Baseline maintenance and expansion 06/29/2012 06/26/2012
Analyze Genetic Data I: 162. OBJ 2: Baseline maintenance and expansion 04/02/2012 04/02/2012
Report/Present Genetic Data J: 161. OBJ 2: Baseline maintenance and expansion 01/02/2012 01/02/2012
Valid Sample Lists K: 156. OBJ 3. Sampling and logistics 01/02/2012 01/02/2012
Inventory all tissue samples L: 157. OBJ 3: Inventory and label all tissue samples 04/15/2012 04/15/2012
Multi-locus genotype data will be uploaded into Progeny genetic database M: 157. OBJ 2-3: Genotyping 06/15/2012 06/15/2012
Estimate Stock Compositions N: 162. OBJ 3. Stock composition estimates 06/15/2012 06/15/2012
Report Stock Composition O: 161. OBJ 3. Stock composition estimates 06/30/2012 06/28/2012

Viewing of Implementation Metrics
Viewing of Environmental Metrics Customize

Primary Focal Species Work Statement Elements
Chinook (O. tshawytscha) - Snake River Spring/Summer ESU (Threatened)
  • 2 instances of WE 157 Collect/Generate/Validate Field and Lab Data
  • 3 instances of WE 161 Disseminate Raw/Summary Data and Results
  • 3 instances of WE 162 Analyze/Interpret Data
Chinook (O. tshawytscha) - Snake River Spring/Summer (not listed)
  • 2 instances of WE 157 Collect/Generate/Validate Field and Lab Data
  • 3 instances of WE 161 Disseminate Raw/Summary Data and Results
  • 3 instances of WE 162 Analyze/Interpret Data
Steelhead (O. mykiss) - Snake River DPS (Threatened)
  • 2 instances of WE 157 Collect/Generate/Validate Field and Lab Data
  • 3 instances of WE 161 Disseminate Raw/Summary Data and Results
  • 3 instances of WE 162 Analyze/Interpret Data

Sort WE ID WE Title NEPA NOAA USFWS NHPA Has Provisions Inadvertent Discovery Completed
A 165 Environmental Complicance Documentation 07/01/2011
B 119 OBJ 1-3: Project Management 07/01/2011
C 185 OBJ 1-3: Periodic Status Reports to BPA 07/01/2011
D 132 OBJ 1-3: Submit Progress Report for the period 7/1/2011 to 6/30/2012 07/01/2011
E 162 OBJ 1: Evaluate and maintain SNPs 07/01/2011
F 189 OBJ 1: Evaluate and maintain SNPs 07/01/2011
G 161 OBJ 1: Evaluate and maintain SNPs 07/01/2011
H 156 OBJ 2: Baseline maintenance and expansion 07/01/2011
I 162 OBJ 2: Baseline maintenance and expansion 07/01/2011
J 161 OBJ 2: Baseline maintenance and expansion 07/01/2011
K 156 OBJ 3. Sampling and logistics 07/01/2011
L 157 OBJ 3: Inventory and label all tissue samples 07/01/2011
M 157 OBJ 2-3: Genotyping 07/01/2011
N 162 OBJ 3. Stock composition estimates 07/01/2011
O 161 OBJ 3. Stock composition estimates 07/01/2011