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Contract 46273 REL 131: 1989-096-00 EXP GENETIC M&E PROG FOR SALMON/STEELHEAD
Project Number:
Title:
Genetic Monitoring and Evaluation (M&E) Program for Salmon and Steelhead
BPA PM:
Stage:
Implementation
Area:
Province Subbasin %
Basinwide - 100.00%
Contract Number:
46273 REL 131
Contract Title:
1989-096-00 EXP GENETIC M&E PROG FOR SALMON/STEELHEAD
Contract Continuation:
Previous: Next:
46273 REL 115: 1989-096-00 EXP GENETIC M&E PROG FOR SALMON/STEELHEAD
  • 46273 REL 148: 1989-096-00 EXP GENETIC M&E PROG FOR SALMON/STEELHEAD
Contract Status:
Closed
Contract Description:
Project:  198909600 -- Monitoring and evaluating the genetic characteristics of supplemented salmon and steelhead

Brief description:  
Initiated in 1989, this study monitors genetic changes associated with hatchery propagation in multiple Snake River sub-basins for Chinook salmon and steelhead.  We also derive estimates of reproductive success for individual families and groups of fish.  

The information obtained from this study directly addresses a critical knowledge gap identified by comanagers, which is: under what conditions does hatchery supplementation provide a sustained contribution to natural production?  Co-managers are ODFW, CTUIR, NPT, WDFW, IDFG, and SBT.  Specific representatives are: Richard Carmichael for ODFW,  Steve Boe for CTUIR, Jay Hesse for NPT,  Mark Schuck for WDFW, Sam Sharr for IDFG, and Doug Taki from SBT.

This type o... f monitoring work is now an essential part of hatchery reform and the goal of using widespread hatchery propagation in recovery of natural populations.  Tier 2 sites use changes in gene frequencies through time in hatchery, natural and wild Chinook salmon and steelhead populations to evaluate the genetic effects of hatchery supplementation on a broad geographic scale.  Tier 3 sites involve direct measures of the relative reproductive success of hatchery fish spawning in the wild by using parentage analysis to construct pedigrees (see study sites below).  These methods were explained in detail in the proposal recommended and approved by the ISRP, BPA, and the NWPPC.

This study has made important contributions to management and research in the Snake River basin:
- Provided genetic data for Chinook and steelhead NMFS status reviews
- Data contributed to US v. Oregon dispute resolution
- Best available estimates in salmon for important genetic parameters, Nm, Ne, and N to Nb ratios
- Individual-specific reproductive success estimates in steelhead and Chinook
- Quantitative genetic analysis of a mixed hatchery and natural steelhead and Chinook populations
- Development of marker systems and continued participation in interagency data standardization
- 41 papers, reports, book chapters, and abstracts (3/4 in peer-reviewed literature)

This project directly addresses RPA #182:  
- "Determine the reproductive success of hatchery fish relative to wild."  Our study has directly and indirectly measured the relative reproductive success of hatchery and natural fish spawning in the wild.  

This project also addresses RPA #184:
- "Determine whether hatchery reforms reduce the risk of extinction….and whether conservation hatcheries contribute to recovery."  Because our pedigree design provides family- and individual-specific information this study offers what is perhaps the most powerful method currently available to measure the efficacy of hatchery reforms, particularly in real time.
  
Account Type(s):
Expense
Contract Start Date:
04/15/2017
Contract End Date:
03/31/2018
Current Contract Value:
$374,167
Expenditures:
$374,167

* 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:
Release
Pricing Method:
Cost Reimbursement (CNF)
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100 km
100 mi
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Viewing 11 of 11 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
A163295185Produce CBFish Status ReportPeriodic Status Reports for BPAThe Contractor shall report on the status of milestones and deliverables in Pisces. Reports shall be completed either monthly or quarterly as determined by the BPA COTR. 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 COTR.$7,0001.87%07/01/201703/31/2018
B163296119Manage and Administer ProjectsContracting, billing and administrative logisticsThis Work Element covers all aspects of BPA contract management. Project management also includes preparing a statement of work package for the coming fiscal year, as well as the September accrual estimate. Includes SOW package, as well as general administrative functions of the contract, including administrative issues such as accrual estimate, bookkeeping and accounting, accurate invoices, contracting and purchasing, as well as addressing concerns/ unforeseen opportunities and issues.$17,0004.54%04/15/201703/31/2018
C163297165Produce Environmental Compliance DocumentationESA permitting and reportingBecause this study involves handling of salmonid species protected under the US Endangered Species Act, all field activities require permitting/consultation under ESA Section 10 or Section 7. Take reports must be filed each year with NMFS (Chinook salmon and steelhead) and with USFWS (bull trout) for the previous year's sampling activities. Periodically the permit/consultation must be renewed. This WE also includes state permitting and reporting. Although it is not possible to have all collection permits in place before the performance period begins, no field collections are scheduled until all permits are in hand.$5,0001.34%04/15/201703/01/2018
D163298157Collect/Generate/Validate Field and Lab DataSalmon and steelhead tissue sampling and data collection, Tier 2Sampling involves the collection of tissues for genetic analysis. Data collection includes microsatellite genotyping, SNP genotyping, DNA sequencing and other methods for the examination and characterization of genetic variation within and among groups of salmon and steelhead. Some of this work (~5%) may be carried out through labor sub-contracts. These contracts require one or more renewals each year. STUDY SITES Snake River genetic monitoring study sites for Chinook salmon and steelhead. All locations represent gene frequency monitoring sites (tier 2). Lat/long are listed followed by the site name. River system names are in caps. These represent the core study sites of the project, however substitutions and additional sites are sampled in some years in response to co-manager (tribal and state) requests. CHINOOK SALMON IMNAHA RIVER (sum) N45° 11.58' W116° 52.16' Imnaha River facility N45° 06.81' W116° 59.41' Imnaha River GRANDE RONDE RIVER (spr) N45° 18.34' W117° 51.99' Catherine Creek (also for RRS study) N45° 28.71, W117° 25.68' Lostine River (also for RRS study) N45° 32.14' W117° 43.15' Minam River N45° 59.02' W117° 23.34' Upper Grande Ronde River N45° 56.74' W117° 30.11' Wenaha River N45° 43.90' W117° 51.78' Lookingglass facility (formerly Rapid River stock, currently several locally derived stocks) N45° 43.90' W117° 51.78' Lookingglass Creek SOUTH FORK SALMON RIVER (sum) N44° 56.30' W115° 29.71' Johnson Creek N44° 39.52' W115° 42.17' Knox Bridge N44° 50.14' W115° 42.23' Poverty Flat N45° 13.97' W115° 48.72' Secesh River N44° 35.93' W115° 41.20' Stolle Meadows N44° 53.74' W116° 06.94' McCall facility (production and conservation stocks) MIDDLE FORK SALMON RIVER N44° 23.53' W115°09.75' Marsh Creek N45° 06.08' W115° 19.86' Upper Big Creek N45° 06.22' W114° 51.35' Lower Big Creek MAINSTEM SALMON RIVER N43° 50.71' W114° 45.20' Upper Salmon River N44° 16.11' W115° 00.41' Upper Valley Creek N44° 14.16' W114° 59.62' Lower Valley Creek N44° 09.74' W114° 53.18' Sawtooth facility LITTLE SALMON RIVER N45° 21.23' W116° 23.78' Rapid River N45° 21.23' W116° 23.78' Rapid River Hatchery STEELHEAD IMNAHA RIVER N45° 37.40' W116° 56.24' Camp Creek N45° 15.87' W116° 55.25' Grouse Creek N45° 10.57' W117° 02.23' Lick Creek N45° 28.595', W116° 56.088' Little Sheep Creek (also RRS study) GRANDE RONDE RIVER N45° 37.17' W117° 41.95' Big Canyon Creek N45° 42.82' W117° 09.15' Chesnimnus Creek N45° 20.55' W117° 14.15' Wallowa facility TUCANNON RIVER N46° 32.72' W118° 09.97' Lower Tucannon River N46° 13.06 W117° 42.82' Upper Tucannon River N46° 35.48' W118° 13.49' Lyons Ferry facility CLEARWATER RIVER N46° 20.18' W115° 20.99' Lochsa River (Fish Cr.) N46° 03.68' W115° 18.90' Selway River (Gedney Cr.) N46° 30.21' W116° 19.39' Dworshak facility$23,0006.15%04/15/201703/31/2018
E169832157Collect/Generate/Validate Field and Lab DataSalmon and steelhead tissue sampling and data collection, Tier 3Sampling involves the collection of tissues for genetic analysis. Data collection includes microsatellite genotyping, SNP genotyping, DNA sequencing and other methods for the examination and characterization of genetic variation within and among groups of salmon and steelhead. Some of this work (~5%) may be carried out through labor sub-contracts. These contracts require one or more renewals each year. STUDY SITES Snake River genetic monitoring study sites for Chinook salmon and steelhead. All locations represent reproductive success studies (tier 3). Lat/long are listed followed by the site name. River system names are in caps. CHINOOK SALMON GRANDE RONDE RIVER (spr) N45° 18.34' W117° 51.99' Catherine Creek N45° 28.71', W117° 25.68' Lostine River STEELHEAD IMNAHA RIVER N45° 28.595', W116° 56.088' Little Sheep Creek$162,16743.34%04/15/201703/31/2018
F163299162Analyze/Interpret DataAnalysis and interpretation of genetic, phenotypic, ecological, life-history, and other data, Tier 2Data analysis includes descriptive population genetic characterization for tier 2 sites (gene-frequency monitoring), especially levels of variability, relative relationships among hatchery and wild populations, and changes in those parameters over time. Coordination among genetics labs has become an essential element of effective comanagement. Our interaction includes exchange and sharing of tissue samples, exchange of reference samples for standardization of genotyping and sharing of new genetic markers developed in our lab.$8,7002.33%04/15/201703/31/2018
G169833162Analyze/Interpret DataAnalysis and interpretation of genetic, phenotypic, ecological, life-history, and other data, tier 3Data analysis includes descriptive population genetic characterization for tier 3 sites involves parentage analysis to document differences in reproductive success among hatchery fish, wild fish, and progeny of captive parents. Coordination among genetics labs has become an essential element of effective comanagement. Our interaction includes exchange and sharing of tissue samples, exchange of reference samples for standardization of genotyping and sharing of new genetic markers developed in our lab.$61,30016.38%04/15/201703/31/2018
H163300161Disseminate Raw/Summary Data and ResultsData Distribution among comanagersResults of genetic monitoring research are made available to comanagers throughout the performance period . All classes of data are made available, including raw data, analyzed data, summaries, written reports, oral reports, and presentation at regional, national and international meetings. These materials and presentations are made periodically as requested and as opportunities arise.$10,0002.67%04/15/201703/31/2018
I163301183Produce Journal ArticlePublication of peer-reviewed scientific publicationsThis work element covers the preparation of manuscript(s) for publication in peer-reviewed scientific literature. Less than 1% of the specific effort toward publication is contributed by subcontractors (i.e., not data collection, but only writing, editing, conducting specialized analyses, preparation of figures and tables, communicating with editors, etc.).$60,00016.04%04/15/201703/31/2018
J163303132Produce Progress (Annual) ReportSubmit Progress Report for the period 1/1/2017-12/31/2017An annual report is provided associated with each BPA contract performance period. The report provides a summary of biological results in a technical report format. Because of the long-term study design, the technical report will only produce cursory reports in some years, however they will include all data and analysis identified in each SOW. More comprehensive results in the form of higher level syntheses and results accumulated over multiple years will be submitted for publication in peer-reviewed scientific literature (see WE 183). Non-NOAA staff doing work under subcontract provide periodic summary reports of their activities that contribute to the annual report to BPA. These reporting activities for subcontractors themselves represent perhaps 5% of the total reporting effort.$13,0003.47%08/01/201703/31/2018
K163304202Produce BiOp RPA ReportBiOp RPA Report for CY 2017Projects that have claimed that they support one or more RM&E RPAs (i.e., RPAs 50-73) under the FCRPS BiOp are required to report their results. To facilitate the summary of these results across the entire Columbia River Basin, and to provide more clarity as to the format required under the BiOp, these reports are required to be completed online. If desired, the required information can be prepared in MS Word, and pasted into Taurus. For more guidance see https://www.cbfish.org/Content/tutorials/Reporting_Guidance_BiOp_2013.pdf. This contract addresses BiOp RPAs 62, 63, and 64.$7,0001.87%07/01/201703/15/2018
      
$374,167
   

Deliverable Title WSE Sort Letter, Number, Title Start End Concluded
FY18 SOW package signed by 2/1/18, accrual estimate, accurate invoices, general management B: 119. Contracting, billing and administrative logistics 03/01/2018
ESA permitting and reporting C: 165. ESA permitting and reporting 03/01/2018 03/20/2018
Tissue sampling, data collection, sub-contract management D: 157. Salmon and steelhead tissue sampling and data collection, Tier 2 03/31/2018 03/20/2018
Tissue sampling, data collection, sub-contract management E: 157. Salmon and steelhead tissue sampling and data collection, Tier 3 03/31/2018 03/20/2018
Coordinate, analyze, and interpret research F: 162. Analysis and interpretation of genetic, phenotypic, ecological, life-history, and other data, Tier 2 03/31/2018 03/20/2018
Coordinate, analyze, and interpret research G: 162. Analysis and interpretation of genetic, phenotypic, ecological, life-history, and other data, tier 3 03/31/2018 03/20/2018
2-3 presentations H: 161. Data Distribution among comanagers 03/31/2018
1 manuscript in progress I: 183. Publication of peer-reviewed scientific publications 03/31/2018
Final progress report for calendar year 2017, attached in Pisces J: 132. Submit Progress Report for the period 1/1/2017-12/31/2017 03/31/2018 03/20/2018
Submit BiOp RPA Report in Taurus K: 202. BiOp RPA Report for CY 2017 03/15/2018 03/15/2018

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Primary Focal Species Work Statement Elements
Chinook (O. tshawytscha) - Snake River Spring/Summer ESU (Threatened)
  • 1 instance of WE 183 Produce Journal Article
  • 2 instances of WE 157 Collect/Generate/Validate Field and Lab Data
  • 1 instance of WE 161 Disseminate Raw/Summary Data and Results
  • 2 instances of WE 162 Analyze/Interpret Data
Steelhead (O. mykiss) - Snake River DPS (Threatened)
  • 1 instance of WE 183 Produce Journal Article
  • 2 instances of WE 157 Collect/Generate/Validate Field and Lab Data
  • 1 instance of WE 161 Disseminate Raw/Summary Data and Results
  • 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 04/01/2017
B 119 Contracting, billing and administrative logistics 04/01/2017
C 165 ESA permitting and reporting 04/01/2017
D 157 Salmon and steelhead tissue sampling and data collection, Tier 2 04/01/2017
E 157 Salmon and steelhead tissue sampling and data collection, Tier 3 04/01/2017
F 162 Analysis and interpretation of genetic, phenotypic, ecological, life-history, and other data, Tier 2 04/01/2017
G 162 Analysis and interpretation of genetic, phenotypic, ecological, life-history, and other data, tier 3 04/01/2017
H 161 Data Distribution among comanagers 04/01/2017
I 183 Publication of peer-reviewed scientific publications 04/01/2017
J 132 Submit Progress Report for the period 1/1/2017-12/31/2017 04/01/2017
K 202 BiOp RPA Report for CY 2017