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Columbia Basin Fish and Wildlife Program Columbia Basin Fish and Wildlife Program
SOW Report
Contract 84042 REL 71: 2010-033-00 EXP STUDY REPRODUCTIVE SUCCESS
Project Number:
Title:
Study Reproductive Success of Hatchery and Natural Origin Steelhead in the Methow
Stage:
Implementation
Area:
Province Subbasin %
Columbia Cascade Methow 100.00%
Contract Number:
84042 REL 71
Contract Title:
2010-033-00 EXP STUDY REPRODUCTIVE SUCCESS
Contract Continuation:
Previous: Next:
84042 REL 37: 2010-033-00 EXP STUDY REPRODUCTIVE SUCCESS IN THE METHOW
  • CR-375644: 2010-033-00 EXP STUDY REPRODUCTIVE SUCCESS
Contract Status:
Issued
Contract Description:
During the August-2024 to July 2025 contract cycle, we will trap, sample, and collect the necessary tissue samples from the 2025 brood of returning adult steelhead at the Twisp River weir, and will collect and sample juvenile progeny in the Twisp River.  All sampling data will be entered in local databases, and the genetic material collected will be transferred to the WDFW Molecular Genetics Lab in Olympia WA, for archiving.

In 2023, we released 64 wild adult steelhead and 24 hatchery adult steelhead upstream of the Twisp River weir. Wild adult steelhead returning to the Twisp weir were generally larger, had a higher fat content, arrived at the Twisp weir earlier, and spawned earlier than hatchery steelhead. However, hatchery females returning to the weir had greater fecundity than wild females. Wild and hatchery steelhead were similar in terms of migration speed, spawn timing and distribution throughout the study years. Preliminary g... enotyping results from all progeny that have been genotyped suggest that hatchery steelhead had a lower relative reproductive success (RRS) rate than wild steelhead across all years and life stages for which parentage assignments were complete. At the age-1 parr stage, female hatchery steelhead from the 2009-2018 broods were about 74% as productive as wild females, and hatchery males were about 57% as productive as wild males.  

Background on project:

We propose to quantitatively evaluate the relative reproductive success of naturally spawning hatchery and natural origin steelhead in the Twisp River, a tributary to the Methow River in the upper Columbia River Basin.  Hatcheries are one of the main tools that have been used to mitigate for salmon losses caused by the construction and operation of the Columbia River hydropower system.  In addition to harvest augmentation, hatcheries have recently been used in attempts to protect stocks from extinction (e.g., captive breeding) and attempts to enhance natural production (supplementation).  Surprisingly, little is known about how much the investment in hatcheries benefits or harms natural production.  We propose to take advantage of recent technological advances in genetics to empirically monitor the reproductive success of hatchery and natural steelhead using a DNA-based pedigree approach.  For this contract period, we will continue to trap and collect DNA and biological data from all steelhead released upstream of the weir, conduct spawning ground surveys and collect DNA samples from progeny (i.e., parr and smolts) of previous brood years.  Specifically, we will (1) directly measure the relative reproductive success of hatchery- and natural-origin steelhead  in a the natural environment, (2) determine the degree to which any differences in reproductive success between hatchery and natural steelhead can be explained by measurable biological characteristics such as run timing, morphology, or behavior, and (3) estimate the relative fitness of hatchery-lineage steelhead after they have experienced an entire generation in the natural environment.
  
Account Type(s):
Expense
Contract Start Date:
08/01/2024
Contract End Date:
07/31/2025
Current Contract Value:
$246,266
Expenditures:
$75,776

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

BPA CO:
BPA COR:
Env. Compliance Lead:
Work Order Task(s):
Contract Type:
Coop
Pricing Method:
Cost Reimbursement (CNF)
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Viewing 12 of 12 Work Statement Elements
Sort Order
WSEV ID
WE ID
Work Element Name
Title
Description
WSE Effective Budget
% of Total WSE Effective Budget
WSE Start
WSE End
A242781185Produce CBFish Status ReportPeriodic Status Reports for BPAThe Contractor shall report on the status of milestones and deliverables in CBFish. Reports shall be completed either monthly or quarterly as determined by the BPA COR. Additionally, when indicating a deliverable milestone as COMPLETE, the contractor shall provide metrics and the final location (latitude and longitude) prior to submitting the report to the BPA COR.$1,2310.50%10/01/202407/31/2025
B242782165Produce Environmental Compliance DocumentationProduce environmental compliance documentation for BPAProvide BPA with required EC documentation$820.03%08/01/202407/31/2025
C242783119Manage and Administer ProjectsOverall project administrationOverall project management to include BPA SOW and budget development and submittal as well as WDFW contracting and budget development.$4,6121.87%08/01/202407/31/2025
D242784157Collect/Generate/Validate Field and Lab DataCollect adult DNA samples from steelheadOperate Twisp weir as river conditions allow beginning no later than March 20. Trap and collect biological data (sex, length, origin, scales) and a tissue sample for DNA analysis from all wild fish and hatchery fish released to spawn naturally. Only returning naturally produced adults from the 2nd generation will need to be sampled between 2019 and 2025. In 2023, operation of the Twisp weir resulted in the capture of 100 adult steelhead, including 74 wild fish and 26 hatchery fish. Some of the wild fish (N=10) were retained for a local broodstock program, and some hatchery fish (N=2) were removed to control the proportion of hatchery fish on the spawning grounds or retained for hatchery broodstock, resulting in an approximate 0.35:1 hatchery:wild ratio in the spawning population upstream of the weir.$5,2552.13%08/01/202407/31/2025
E242785157Collect/Generate/Validate Field and Lab DataConduct steelhead spawning ground surveysConduct spawning grounds surveys in the Twisp River to identify spawning locations of floy-tagged adult steelhead. Identify spawning sites and mark with flagging and hand held GPS. Spawning ground surveys in 2023 documented 37 redds in the Twisp River. Significant differences were found in hatchery and wild female spawning locations when all years were examined (2009 - 2023).$1,2310.50%08/01/202407/31/2025
F242786157Collect/Generate/Validate Field and Lab DataCollect DNA from age-1 steelhead parrTissue samples of steelhead parr will be collected during routine surveys conducted in the Twisp River. Sampling is scheduled to occur between August and November using a combination of angling, electrofishing, snorkel/seining (i.e., snerding), or night netting capture techniques. Parr will be collected from throughout the spawning area and sampling effort will be spatially randomized, but with greater effort in known spawning areas of parents. In addition, all potential resident O. mykiss parents (i.e., wild rainbow trout or hatchery residual steelhead) captured during the summer parr collection will also be DNA sampled and included as potential parents in the analysis. Sampling during 2023 resulted in 2,839 steelhead parr collected via angling (N = 1,163), electrofishing (N = 737), and smolt trapping (N = 939).$21,0218.54%08/01/202407/31/2025
G242787158Mark/Tag AnimalsPIT tag age-1 steelhead parrJuvenile steelhead captured as part of WE F (Collect DNA from age 1- steelhead parr) will be PIT tagged to prevent double sampling during future DNA sampling and sampling events. The location of each tagging event will be geo-referenced using hand held GPS devices.$5,2582.14%08/01/202407/31/2025
H242788157Collect/Generate/Validate Field and Lab DataCollect DNA from steelhead smolts at smolt trapTissue samples of steelhead smolts will be collected from rotary smolts trap operated in the lower Twisp River between 1 March and 1 July. At the beginning of the study only steelhead smolt from the corresponding brood years (determined from scale samples) will be included in the analysis. In subsequent years, all steelhead smolts captured and the smolt trap will be included in the analysis. Previously PIT tagged parr will be included in the smolt sample, but not previously PIT tagged smolts (i.e., double sampled). During the 2023 smolt trapping period, we captured and sampled 939 steelhead parr and smolts at the Twisp River smolt trap. Peak monthly capture (N = 606) occurred during April, 2023.$1,2310.50%08/01/202407/31/2025
I242789162Analyze/Interpret DataGenotype Juvenile Steelhead and Conduct Parentage AnalysisTissue samples will be dissected to the appropriate size and DNA extracted using Machery-Nagel silica membrane-based kits following the manufacturer’s standard protocol. We will use the standard set of 13 SPAN microsatellite loci, plus an additional 2 microsatellite loci to construct multi-locus genotypes. The 15 microsatellite loci will be assembled into six multiplex PCR reactions. We will conduct PCR amplification using fluorescently end-labeled primers or vector tails and either AB 9700 or MJ-200 thermal cyclers. We will visualize microsatellites using an ABI 3730 automated DNA Analyzer, and alleles will be sized to numbers of basepairs and binned using an internal lane size standard (GS500Liz from Applied Biosystems) and GeneMapper software (Applied Biosystems). Parentage Analysis: We will use one of several programs available to calculate probabilities of parent-pairs and/or trios. The probabilities will be used first to exclude either adults or adult-pairs, and then will be used with simulations to test for the most likely parent-offspring pair or trio. Relative reproductive success: We will continue to calculate RRS at three different life stages (parr, smolt, and adult) for individuals of four ancestral types (i.e., Hf Hm, Hf Nm, Nf Hm, and Nf Nm) within the F1 generations.$132,77053.91%08/01/202407/31/2025
J242790157Collect/Generate/Validate Field and Lab DataCollect Ecological and Redd Morphology Data on the Spawning GroundsDuring spawning grounds surveys we will attempt to identify the origin of fish on as many redds as possible using colored floy tags or PIT tags that were deposited in redds. Data on life history traits to be collected will include, but not limited to: Run timing at the Twisp weir (Julian date) • Spawn timing (Julian date) • Redd location (river kilometer) • Spawner density • Redd morphology and location ­ Dimensions (bowl and tailspill) ­ Water depth (multiple locations) ­ Water velocity (multiple locations) ­ Substrate composition (visual estimation) • Habitat type (pool, riffle glide) • Channel type (single or multiple) • Location in channel (distance to bank in meters) Wild female steelhead generally spawned farther upstream and slightly earlier than hatchery steelhead and the differences were significant when all years were compared (2009-2023).$21,0218.54%08/01/202407/31/2025
K242791162Analyze/Interpret DataAnalyze ecological data from spawning groundsDetermine if differences in measured traits exist between hatchery and wild steelhead. After obtaining initial estimates of relative reproductive success, we will address Objective 2 by conducting a multiple regression analysis adding the traits such as run timing, length, weight and morphology to the analysis in order to determine to what degree variation in these traits can explain any observed difference in fitness between hatchery and natural fish. This analysis will be conducted separately for the juvenile and adult samples.$21,0218.54%08/01/202407/31/2025
L242792132Produce Progress (Annual) ReportSubmit Progress Report for Calendar Year 2024Develop technical report for 2024 calendar year. Reports describes field work and results that occurred in 2024. Activities to include adult trapping and DNA sampling, spawning grounds surveys, juvenile DNA sampling and parentage analysis.$31,53312.80%08/01/202405/20/2025
      
$246,266
   

Deliverable Title WSE Sort Letter, Number, Title Start End Concluded
EC documentation provided. B: 165. Produce environmental compliance documentation for BPA 07/31/2025
Effective implementation management and timely contract administration C: 119. Overall project administration 07/31/2025
Produce accessible, error-checked datasets D: 157. Collect adult DNA samples from steelhead 07/31/2025
Produce accessible, error-checked datasets E: 157. Conduct steelhead spawning ground surveys 07/31/2025
Produce accessible, error-checked datasets F: 157. Collect DNA from age-1 steelhead parr 11/30/2024 11/30/2024
PIT tagged age-1 steelhead parr uploaded G: 158. PIT tag age-1 steelhead parr 11/30/2024 11/30/2024
Produce accessible, error-checked datasets H: 157. Collect DNA from steelhead smolts at smolt trap 07/31/2025
Deliverable: An accessible, error-checked data set with metadata I: 162. Genotype Juvenile Steelhead and Conduct Parentage Analysis 07/31/2025
Produce accessible, error-checked datasets J: 157. Collect Ecological and Redd Morphology Data on the Spawning Grounds 05/31/2025
Deliverable: An accessible, error-checked data set with metadata K: 162. Analyze ecological data from spawning grounds 07/31/2025
Completed Annual Report L: 132. Submit Progress Report for Calendar Year 2024 05/20/2025

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Primary Focal Species Work Statement Elements
Steelhead (O. mykiss) - Upper Columbia River DPS (Threatened)
  • 5 instances of WE 157 Collect/Generate/Validate Field and Lab Data
  • 1 instance of WE 158 Mark/Tag Animals
  • 2 instances of WE 162 Analyze/Interpret Data

Sort WE ID WE Title NEPA NOAA USFWS NHPA Has Provisions Inadvertent Discovery Completed
A 185 Periodic Status Reports for BPA
B 165 Produce environmental compliance documentation for BPA
C 119 Overall project administration
D 157 Collect adult DNA samples from steelhead
E 157 Conduct steelhead spawning ground surveys
F 157 Collect DNA from age-1 steelhead parr
G 158 PIT tag age-1 steelhead parr
H 157 Collect DNA from steelhead smolts at smolt trap
I 162 Genotype Juvenile Steelhead and Conduct Parentage Analysis
J 157 Collect Ecological and Redd Morphology Data on the Spawning Grounds
K 162 Analyze ecological data from spawning grounds
L 132 Submit Progress Report for Calendar Year 2024