FY 2007 Solicitation Homepage

Project Proposal Request for FY 2007 - FY 2009 Funding

Proposal 198909600: Genetic Monitoring of Snake River Chinook Salmon and Steelhead

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Table of Contents
Part 1. Administration and Budgeting
Section 1: General Administrative
Section 2: Project Location
Section 3: Project Species
Section 4: Past Accomplishments
Section 5: Relationship to Other Projects
Section 6: Biological Objectives
Section 7: Work Elements
Section 8: Budget
Section 9: Project Future
Section 10: Documents
Part 2. Reviews
Part 1 of 2. Administration and Budgeting
Section 1: General Administrative Information
Process Information:
Date Proposal Submitted & Finalized Status Form Generator
January 10, 2006 Finalized Paul Moran

Proposal Type: Ongoing
Proposal Number: 198909600
Proposal Name: Genetic Monitoring of Snake River Chinook Salmon and Steelhead
BPA Project Manager: Sabrina Keen
Agency, Institution or Organization: Northwest Fisheries Science Center
Short Description: Direct and indirect estimates of reproductive success. Estimate selection gradients in hatchery and wild. Monitor changes in hatchery, natural (supplemented), and wild (unsupplemented) populations. Evaluate effectiveness of hatchery supplementation
Information Transfer: We are committed to actively distributing our results, and we continue to use a variety of methods to disseminate this information to comanagers. Examples of reports and peer-reviewed articles resulting from previous years of this project are listed elsewhere in this document. Results of various aspects of this study have been presented annually in public meetings throughout the region as well as nationally and internationally. In addition, we have provided many informal summaries of recent or unpublished results to fishery and hatchery managers in Washington, Idaho, and Oregon. These results have been used in an adaptive management framework to make real-time decisions about issues such as broodstock collection, mating protocols, and release strategies. In spite of our peer-reviewed contributions, we recognize previous criticisms of this project and seek to make our results more readily available to managers.
 
Project Proposal Contacts
Contact Organization Address Phone/Email Roles Notes
Form Submitter
Paul Moran Northwest Fisheries Science Center 2725 Montlake Blvd. E.
Seattle WA 98112-2097
Ph: 206.860.3245
Fax: 206.860.3335
Email: paul.moran@noaa.gov
Form Submitter
All Assigned Contacts
Melissa Baird NMFS-NOAA Fisheries 2725 Montlake Blvd. E
Seattle, WA 98112
Ph: 206-302-2430
Fax: 206-860-3335
Email: melissa.baird@noaa.gov
Technical Contact
Ewann Berntson NOAA NMFS NWFSC 2725 Montlake Blvd E
Seattle, WA 98112
Ph: 206-302-2429
Fax: 206-860-3335
Email: ewann.berntson@noaa.gov
Technical Contact
Paul Moran Northwest Fisheries Science Center 2725 Montlake Blvd. E.
Seattle WA 98112-2097
Ph: 206.860.3245
Fax: 206.860.3335
Email: paul.moran@noaa.gov
Project Lead

Section 2: Project Location
Sponsor Province: None Selected ARG Province: Mainstem/Systemwide
Sponsor Subbasin: None Selected ARG Subbasin: Systemwide
Location(s) at which the action will be implemented
Latitude Longitude Waterbody Location Description County/State Subbasin Primary?
N46° 20.18’ W115° 20.99’ Clearwater Lochsa River (Fish Cr.) , Idaho Clearwater No
N46° 03.68’ W115° 18.90’ Clearwater Selway River (Gedney Cr.) , Idaho Clearwater No
N46° 30.21’ W116° 19.39’ Clearwater Dworshak facility , Idaho Clearwater No
N45° 18.34' W117° 51.99' Grande Ronde Catherine Creek (reproductive success study) , Oregon Grande Ronde No
N45° 43.90' W117° 51.78' Grande Ronde River Lookingglass Creek , Oregon Grande Ronde No
N45° 43.90' W117° 51.78' Grande Ronde River Lookingglass facility (formerly Rapid River stock, currently several locally derived stocks) , Oregon Grande Ronde No
N45° 59.02' W117° 23.34' Grande Ronde River Upper Grande Ronde River (reproductive success study) , Oregon Grande Ronde No
N45° 32.14' W117° 43.15' Grande Ronde River Minam River , Oregon Grande Ronde No
N45° 28.71' W117° 25.68' Grande Ronde River Lostine River (reproductive success study) , Oregon Grande Ronde No
N45° 06.81' W116° 59.41' Imnaha Imnaha River , Oregon Imnaha No
N45° 11.58' W116° 52.16' Imnaha Imnaha River facility , Oregon Imnaha No
N45° 28.95’ W116° 55.29’ Imnaha Little Sheep Creek (reproductive success study) , Oregon Imnaha No
N45° 10.57’ W117° 02.23’ Imnaha Lick Creek , Oregon Imnaha No
N45° 15.87’ W116° 55.25’ Imnaha Grouse Creek , Oregon Imnaha No
N45° 37.40’ W116° 56.24’ Imnaha Camp Creek , Oregon Imnaha No
N45° 21.23' W116° 23.78' Little Salmon River Rapid River Hatchery , Idaho Salmon No
N45° 21.23' W116° 23.78' Little Salmon River Rapid River , Idaho Salmon No
N44° 09.74' W114° 53.18' Mainstem Salmon River Sawtooth facility , Idaho Salmon No
N44° 14.16' W114° 59.62' Mainstem Salmon River Lower Valley Creek , Idaho Salmon No
N44° 16.11' W115° 00.41' Mainstem Salmon River Upper Valley Creek , Idaho Salmon No
N43° 50.71' W114° 45.20' Mainstem Salmon River Upper Salmon River , Idaho Salmon No
N45° 06.22' W114° 51.35' Middle Fork Salmon River Lower Big Creek , Idaho Salmon No
N45° 06.08' W115° 19.86' Middle Fork Salmon River Upper Big Creek , Idaho Salmon No
N44° 23.53' W115°09.75' Middle Fork Salmon River Marsh Creek , Idaho Salmon No
N44° 53.74' W116° 06.94' South Fork Salmon River McCall facility (production and conservation stocks) , Idaho Salmon No
N44° 35.93' W115° 41.20' South Fork Salmon River Stolle Meadows , Idaho Salmon No
N45° 13.97' W115° 48.72' South Fork Salmon River Secesh River , Idaho Salmon No
N44° 50.14' W115° 42.23' South Fork Salmon River Poverty Flat , Idaho Salmon No
N44° 39.52' W115° 42.17' South Fork Salmon River Knox Bridge , Idaho Salmon No
N44° 56.30' W115° 29.71' South Fork Salmon River Johnson Creek , Idaho Salmon No
N46° 35.48’ W118° 13.49’ Tucannon River Lyons Ferry facility , Idaho Tucannon No
N46° 13.06 W117° 42.82’ Tucannon River Upper Tucannon River , Idaho Tucannon No
N46° 32.72’ W118° 09.97’ Tucannon River Lower Tucannon River , Idaho Tucannon No
N45° 20.55’ W117° 14.15’ Upper Grande Ronde Wallowa facility , Oregon Grande Ronde No
N45° 42.82’ W117° 09.15’ Upper Grande Ronde Chesnimnus Creek , Oregon Grande Ronde No
N45° 37.17’ W117° 41.95’ Upper Grande Ronde Big Canyon Creek , Oregon Grande Ronde No
, Systemwide Yes

Section 3: Focal Species
Focal Species:
Primary Secondary Additional Species
Chinook Snake River Spring/Summer ESU
Steelhead Snake River ESU
Rainbow Trout

Section 4: Past Accomplishments
Past Accomplishments for Each Fiscal Year of This Project
Fiscal Year Accomplishments
2005 Added 10 microsatellite loci to FY04 Salmon R Chinook study (standardized CTC loci). Completed draft manuscript on expand Snake R steelhead data, including hatchery stocks and all remaining samples from the Conservation Biology Division Tissue Archive.
2004 Completed a microsatellite study of spatial and temporal variation in Salmon R Chinook populations. Initiated a comprehensive microsatellite study of Snake R steelhead hatchery stocks. Collaborative manuscript (CRITFC) on Grande Ronde steelhead.
2003 Completion of a broad and comprehensive microsatellte survey of Snake R steelhead. Used to infer hatchery effects and gene flow among wild populations. Data provided to Technical Recovery Team and comanagers.
2002 Developed "allele ladders" for both chinook and steelhead to facilitate the interlaboratory standardization of microsatellite data. Selection gradients for Little Sheep Creek hatchery and wild steelhead. Resident/anadromous matings.
2001 Completed microsatellite and SNP survey of 13 Snake R steelhead populations (peer-reviewed publication). Over 6,500 samples have been DNA-extracted and genotyped. A variety of tissue samples have been made available to collaborators and co-managers.
2000 New SNP markers developed and screened. DNA extraction from scales (peer-reviewed publication). Initiated steelhead pedigree study in Little Sheep Cr for estimation of hatchery/wild reproductive success (9 loci initially, 8 added).
1999 Genetic results used extensively in the status reviews for both of these species (Busby et al. 1996, Myers et al. 1998). DNA data compared marked and unmarked Chinook returning to Rapid R. Hatchery. Results distributed among comanagers.
1998 Solution for the Phelps/Allendorf effect published in peer-reviewed literature. >95 PCR primer pairs developed for SNP discovery in noncoding sequences. Markers and genetic results published in peer-reviewed literature (4 papers).
1997 Multiplex sets of microsatellite loci used to collect data for multiple studies related to genetic monitoring. Substantial reductions in time, effort, and expense associated with genotyping these highly informative markers.
1996 Allozyme data played a critical role in the US v. Oregon dispute resolution. Data were provided to the Independent Scientific Review Panel. Panel concluded that endemic gene pools remained despite hatchery straying. DNA results provided to comanagers..
1995 DNA markers (nonlethally analyzed) provided information on the relative distinctiveness of NE Oregon spring chinook salmon captive brood stock collections as compared to the Rapid River stock spawned at Lookingglass hatchery.
1994 Interagency memorandum for USFW and IDFG summarizing genetic relationships among Snake River steelhead populations. Implemented DNA markers in genetic monitoring for both Chinook and steelhead.
1993 Estimation of Nm and the critical ratio of Nb/N. Results from this study provide the most comprehensive data available for salmon for these important parameter estimates (updated periodically). Hosted workshop on DNA technology, published proceedings.
1992 High levels of temporally stable genetic variability documented within and among populations. Ancestral distinctiveness in Dworshak steelhead hatchery stock shared by resident O. mykiss above the dam suggesting residualization. Began DNA work.
1991 Refined study design, continued collections and allozyme genotyping. Preliminary characterization of spatial and temporal genetic diversity and relationships among samples.
1990 Expanded tissue sampling for both Chinook and steelhead, continued allozyme genotyping, began population genetic analyses.
1989 Developed study design and initiated tissue collections for allozyme genotyping.

Section 5: Relationships to Other Projects
Other Current Projects Related to this Project (any funding source)
Funding Source Related ID Related Project Title Relationship
BPA 198712700 Smolt Monitoring By Non-Feder Sampling is coordinated with this program.
BPA 198805301 NE OR Hatchery Master Plan - N Sampling is coordinated with this program.
BPA 198805305 NE OR Outplntg Facilities Mst Sampling is coordinated with this program.
BPA 198909800 Salmon Studies ID Rvrs IDFG We coordinate genetic sampling with sampling from this study.
BPA 199005200 Perf/Stock Prod Impacts of Hat We have shared steelhead samples from this study and we provide NBS results of our genetic analyses for some of their study streams.
BPA 199005500 ID Steelhead M&E Studies We coordinate genetic sampling with collections for this program.
BPA 199009300 Genetic Analyses of Oncorhynch We have traded DNA samples and PCR primers with this project, as well as carrying on an ongoing dialog regarding methods and marker classes.
BPA 199107300 Idaho Natural Production Monit We coordinate genetic sampling with sampling from this study.
BPA 199606700 Manchester Spring Chinook Capt We coordinate genetic sampling with this program.
BPA 199800702 Gd Ronde Supp Lostine O&M/M&E Adult sampling is coordinated with this project
BPA 199801001 Grande Ronde Captive Brood O&M We coordinate genetic sampling with collections for this program.

Section 6: Biological Objectives
Biological Objectives of this Proposed Project
Biological Objective Full Description Associated Subbasin Plan Strategy Page Nos
1. Describe genetics We now recognize the necessity of considering the genetic relationship between resident and anadromous components of O. mykiss populations in order to fully understand steelhead genetics. Clearwater 4. Proposed Research: Assess population status, limiting factors, and genetics of redband rainbow trout in the Clearwater subbasin. 72-73
1. Describe genetics The proposed study design will continue to provide basic descriptive population genetic data that is recommended in the Subbasin Plan. Imnaha 4) Genetics Research: The collection of genetics data is defined as a research need for each focal species. This information will allow for the differentiation of populations and sub-populations, and provide for more effective management of the focal spp. 119
1. Describe genetics The proposed study offers the further population-level characterization that is called for in both spring/summer Chinook and summer steelhead. Imnaha 6.3.1.2 Species-Level Recommendations: Collection of genetic information at the population level is recommended for both species. [spring/summer Chinook, summer steelhead] 119-120
1. Describe genetics Our study elucidates resident/anadromous relationships at multiple scales. The pedigree work in Little Sheep Creek provides a fine-scale view for this single river system, whereas our conventional allele frequency monitoring provides information from more systems at a broader geographic scale . Tucannon Critical uncertainties...understanding the relationship between resident and anadromous O. mykiss subpopulations. App M, 3
1. Describe genetics The cornerstone of our study design is a broad characteriztion of native, and wild populations, at least to the extent that is possible. Salmon “…carry out focused activities designed to improve our understanding of wild populations” (Table 5). 18
1. Describe genetics, 3. Measure change The study design proposed here is exactly concordant with RM&E recommendations for genetic characterization and monitoring of effective population size. Tucannon Table 1, RME opportunities, specifically lists “assessment of genetic characteristics for all supplemented, reintroduced, and listed species,” "assessment of reproductive success," and "standardized monitoring of effective population size.” App M, 12
1. Describe genetics, 3. Measure change This study design provides information about both short- and long-term changes in genetic diversity and structure. Salmon “Minimize short- and long-term genetic, ecological and life history effects on wild populations.” (Table 5). 18
1. Describe genetics, 3. Measure change This study design characterizes stock-specific genetic changes through time. Clearwater C 2 Research stock specific interactions between wild and hatchery fish in areas influenced by hatcheries in the Clearwater 55
1. Describe genetics, 3. Measure change The need for genetic characterization and evaluation of effects of artificial propagation are identified in the Tucannon River Subbasin Plan, Appendix M, p. 2-3. Tucannon Focus RM&E efforts on critical data needs. Four critical areas were identified under NOAA’s Viable Salmonid Population (VSP) treatise. Diversity--Genetic characterization, life history pathways (juvenile and adult), artificial propagation effects (hatche App M, 2-3
1. Describe genetics, 3. Measure change The design proposed here will refine stock structure and population boundary information and will monitor genetic relationships and characteristics through time. Clearwater "2. Proposed Research: Profile anadromous salmonid genetics. Collect relevant genetic data on spring and fall chinook. Conduct genetic profiling to define steelhead sub-populations within the subbasin to determine geographic structure and gene flow. 75
1. Describe genetics, 3. Measure change Our experimental design explicitly compares “natural” populations that are the target of supplementation to “wild” populations that are not expected to be impacted by hatchery propagation. We then monitor these different classes of salmon populations for changes in genetic characteristics over time. Imnaha 3A1: Preserve Genetic Integrity: Preserve the genetic integrity of existing wild stocks in the Imnaha Subbasin. Protect and monitor wild stocks in wilderness and other portions of the subbasin that have not been influenced by hatchery or mixed stocks. 22
1. Describe genetics, 3. Measure change M&E Objective 3a supports our basic descriptive population genetics efforts. The hypotheses to be tested reflect the temporal aspects of our study design, measuring genetic drift and gene flow (a function of the reproductive success of natural strays and hatchery fish). Imnaha Monitoring and Evaluation Objective 3a. Determine and compare genetic characteristics of hatchery and natural fish in the Imnaha subbasin (2B1, 2B2, 3A, 4E, 4E1, 5A, 5A1, 5A3, 5A4, 5B3; all salmonid focal species) 81
1. Describe genetics, 3. Measure change Our genetic monitoring experimental design is consistent with the rigorous scientific standard that is called for in the Subbasin plan (6.3.1.1 Subbasin-Level Recommendations, p. 118 – 119). We also explicitly commit to further coordination and facilitation of interagency genetic research throughout the Columbia River basin. Imnaha 3) A Regionally Coordinated RM&E Effort. Paired comparisons should be tested at multiple life stages and involve treatment vs. natural, treatment vs. reference, and treatment vs. treatment analysis. 118
1. Describe genetics, 3. Measure change Our study maps neutral and potentially selected genetic diversity against life history characteristics and compares those relationships among hatchery, natural (supplemented), and wild (unsupplemented). Grande Ronde Management Objective 3. Assess “life history characteristics and genetic diversity in supplemented and unsupplemented focal populations.” Monitoring and Evaluation Objective 3a. Determine and compare genetic characteristics of hatchery and natural fish. 280-282
1. Describe genetics, 3. Measure change Our study of pedigrees in natural populations offers a very powerful tool for evaluating specific hatchery reform measures. For example, DNA-typing broodstock parents in different treatment groups provides essentially 100% marking of their offspring. Grande Ronde To mitigate some of the concerns with hatchery fish, hatchery reform [has been implemented] with increased use of local broodstock, and hatchery releases away from areas of natural production. 65
2. Reproductive success Comanagers in the Grande Ronde have entrusted to our lab the task of monitoring and evaluating the effects of hatchery propagation (conventional and captive) and the effects of hatchery reform. M&E Objective 2b presents a series of testable hypotheses, the text of which was drawn from an earlier version of this proposal. Grande Ronde Monitoring and Evaluation Objective 2b: Determine and compare relative reproductive success of hatchery and naturally produced focal species. 279
2. Reproductive success We test the assumptions outlined in Management Objective 2: Assess, maintain, and enhance natural populations, e.g., B. Natural reproductive success of endemic hatchery-origin fish must be similar to that of natural-origin fish. C. Spatial distribution of endemic hatchery-origin spawners in nature is similar to that of natural-origin fish. Imnaha MANAGEMENT OBJECTIVE 2: ASSESS, MAINTAIN, AND ENHANCE NATURAL PRODUCTION AND SURVIVAL OF FOCAL SALMONID POPULATIONS IN SUPPLEMENTED STREAMS WITHIN THE IMNAHA 71
2. Reproductive success M&E Objective 2b is exactly concordant with our primary focus to estimate reproductive success. Imnaha Monitoring and Evaluation Objective 2b: Determine and compare relative reproductive success of hatchery and naturally produced focal species (3A, 5A4, 4E4; all salmonid focal species) . 79
4. Standardized marker development Our study seeks to standardize genetic data collection and analysis with all other Columbia River laboratories. This includes data and sample sharing, standardized genotyping for common sets of genetic markers, and coordination of marker development (SNPs and EST-linked microsatellite loci). Imnaha Problem 23: Insufficient coordination and integration limit the benefits of aquatic and terrestrial protection and restoration. Discussion: Coordination of programs and plans in the subbasin will achieve benefits beyond the value of an individual prog. 55
4. Standardized marker development This study has included close coordination with research activities throughout the Snake River basin. We’ve always spent a small fraction of our effort on development of new markers and standardizing genetic data collection with other laboratories. All our Chinook work under this contract now employs the coast-wide standardized CTC microsatellite loci. We will continue ongoing standardization activities for Columbia River steelhead. Clearwater Coordination Potential: Coordinate with ongoing genetics research efforts and/or other population status M&E programs. 75
4. Standardized marker development The plan indicates the importance of data management and coordination that is built into our study in the standardization of current and future genetic data collection. Tucannon 7.5.1 Aquatic Habitats and Species. Following are the guiding principles and priorities outlined in the plan: • Data management and coordination are crucial to meet regional data accessibility needs. 176-177
4. Standardized marker development Research activities are closely coordinated with other BPA-funded laboratories. A small fraction of our research budget has consistently gone for standardizing new genetic markers as technologies evolve. Salmon Problem 66: Better coordination is necessary to focus funding. Discussion: Coordination of programs and projects in the subbasin will achieve benefits beyond the value of any individual program or project. 105-106
4. Standardized marker development Use of standardized markers and genotyping conventions allows independent validation and verification by multiple interested parties (CRITFC, WDFW, etc.). Grande Ronde 3. Data Information Archive, 9. Independent validation and verification. Coordination of data management will be most successful if standard RM&E protocols are adhered to by planners. 288-289
4. Standardized marker development Coordination and standardization facilitates collaboration, reduces redundancy and maximizes efficiency in addresssing a wide range of genetic questions. Grande Ronde 4. Coordination and Implementation, coordinate between project-specific and regional RM&E efforts to establish the most effective system design and application needed to accomplish objectives at both levels. 289
5. Evaluate genetic monitoring An integral part of this study is evaluation of the utility of our results and the effectiveness of our M&E methods. None The ISRP/ISAB give a general call for M&E of recovery actions and we extend that philosophy to evaluation of our M&E methods themselves. Consistent with the adaptive framework of recovery efforts and the desire to maximize efficiency of M&E research. 10

Section 7: Work Elements
Work Elements and Associated Biological Objectives
Work Element Name Work Element Title Description Start Date End Date Estimated Budget
Produce Environmental Compliance Documentation ESA permitting and reporting Because 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. 11/1/2006 8/5/2009 $8,675
Biological Objectives Metrics
No Metrics for this Work Element

Coordination Sample design, collection planning, and state permitting Discussion and consultation takes place each year in planning for summer field sampling. Comanagers must agree that adult abundance the previous year was sufficient to make genetic sampling appropriate and desirable. The "adaptive design" of this study requires this feedback from comangers to help establish sampling priorities in a given year. This work element also includes state permitting activities (not NEPA), including permit application and reporting. 5/1/2007 8/5/2009 $27,013
Biological Objectives Metrics
1. Describe genetics, 3. Measure change
2. Reproductive success
4. Standardized marker development
No Metrics for this Work Element

Manage and Administer Projects Contracting, billing and administrative logistics This Work Element covers all aspects of contract management and administration, both BPA and NOAA administrative requirements. Much of the labor for this contract requires third-party subcontracting. These contracts require one or more renewals each year. Throughout the Work Elements of this contract indications are provided regarding the prortions of any Work Elements carried out by subcontractors. Project mangement also includes preparing a statement of work for the coming fiscal year, as well as June and September accrual estimates. 11/1/2006 10/31/2009 $32,261
Biological Objectives Metrics
No Metrics for this Work Element

Produce Annual Report Annual report on genetic monitoring of hatchery supplementation An 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 20-30% of the total reporting effort. 11/15/2006 12/15/2009 $30,100
Biological Objectives Metrics
No Metrics for this Work Element

Produce Pisces Status Report Produce quarterly BPA Pisces status reports Reporting on milestones and general project status is provided from the project leader to the COTR on a quarterly basis. Non-NOAA staff doing work under subcontract provide periodic summary reports of their activities that contribute to the quarterly reports to BPA. These reporting activities for subcontractors themselves might represent 30-40% of the total reporting effort. 1/1/2007 10/31/2009 $12,194
Biological Objectives Metrics
No Metrics for this Work Element

Produce/Submit Scientific Findings Report Publication of peer-reviewed scientific publications This work element covers the preparation of manuscript(s) for publication in peer-reviewed scientific literature. Approximately 20% of the specific effort toward publication is contributed by subcontractors (i.e., not data collection, but only writing, editing, conducting specialized analyses, prepartion of figures and tables, communicating with editors, etc.). 11/1/2006 5/31/2009 $114,412
Biological Objectives Metrics
1. Describe genetics, 3. Measure change
2. Reproductive success
4. Standardized marker development
5. Evaluate genetic monitoring
No Metrics for this Work Element

Analyze/Interpret Data Data analysis and interpretation Data 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. Experimental design at 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 genetyping and sharing of new genetic markers developed in our lab. A small amount of this work (~5%) is carried out through labor sub-contracts. 11/1/2006 10/31/2009 $109,225
Biological Objectives Metrics
1. Describe genetics, 3. Measure change
2. Reproductive success
4. Standardized marker development
5. Evaluate genetic monitoring
No Metrics for this Work Element

Collect/Generate/Validate Field and Lab Data Salmon and steelhead ampling and data collection Sampling involves the collection of tissues for genetic analysis. Data collection includes microsatellite genotyping, DNA sequencing and other methods for the examination and characterization of genetic variation within and among groups of salmon and steelhead. Much of this work (~50%) is carried out through labor sub-contracts. 11/1/2006 10/31/2009 $1,216,970
Biological Objectives Metrics
1. Describe genetics, 3. Measure change
2. Reproductive success
4. Standardized marker development
No Metrics for this Work Element

Disseminate Raw/Summary Data and Results Distribution of results among comanagers of results from genetic research on hatchery supplementation Results of genetic monitoring research are made available to comanagers throughout the preformance 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. A small amount of this work (~5%) is carried out through labor sub-contracts. 11/1/2006 10/31/2009 $33,620
Biological Objectives Metrics
1. Describe genetics, 3. Measure change
2. Reproductive success
4. Standardized marker development
5. Evaluate genetic monitoring
No Metrics for this Work Element


Section 8: Budget

Itemized Estimated Budget
Item Note FY 2007 Cost FY 2008 Cost FY 2009 Cost
Personnel 55 total pay periods distributed among four NOAA employees $114,810 $119,400 $124,180
Fringe Benefits Leave and Benefits surcharge $57,290 $59,580 $61,970
Supplies Reagents and laboratory supplies, collection materials $73,300 $73,300 $73,300
Travel Collection trips, planning/reporting meetings, national and international society meetings, BPA workshops $5,650 $5,760 $5,880
Overhead Combined overhead (GSA, NOAA, NMFS, NWFSC) $90,160 $93,770 $97,520
Other Transportation (GSA vehicle lease fees and shipping $2,000 $2,020 $2,040
Other Contract, labor $58,800 $60,270 $61,780
Other Contract, instrument service $7,500 $7,650 $7,800
Other Contract, waste disposal $1,200 $1,200 $1,200
Other Contract, smolt trapping by ODFW $101,000 $103,530 $106,110
Other Printing, page charges $1,500 $1,500 $1,500
Totals $513,210 $527,980 $543,280

Total Estimated FY 2007-2009 Budgets
Total Itemized Budget$1,584,470
Total Work Element budget$1,584,470

Cost sharing
Funding Source or Organization Item or Service Provided FY 2007 Est Value ($) FY 2008 Est Value ($) FY 2009 Est Value ($) Cash or in-kind? Status

Section 9: Project Future
Project Future Costs and/or Termination
FY 2010 Est Budget FY 2011 Est Budget Comments
$557,050 $573,760 Assuming 3% per year increase in costs to keep constant effort.
Future Operations & Maintenance Costs
This study requires no long-term committment to O&M beyond its usfulness to comanagers. Thus, when genetic monitoring data are no longer needed associated with artificial propagation, this study can be terminated at no further cost.
 
Termination Date Comments
10/31/12 This study has been developed in increments with periodic evaluation of utility. When comanagers indicate that genetic data are no longer needed to help facilitate and evaluate the efficacy of supplementation, then no additional work will be proposed. If the next solicitation cycle is accompanied by the same calls for genetic data in the Subbasin Plans, then some extension may be proposed, otherwise the study would conclude after FY2009.
 
Final Deliverables
Relative reproductive success estimates for naturally spawning hatchery and wild Chinook salmon and steelhead. Detailed characterization of genetic effects of artificial propagation on hatchery brood stocks and natural populations. Specific recommendations of effective genetic M&E methods. Results published in peer-reviewed scientific literature.

Section 10: Narrative
Document Type Size Date

Part 2 of 2. Reviews of Proposal
Administrative Review Group (ARG) Results
Account Type:
Expense
Location:
Province: Mainstem/Systemwide
Subbasin: Systemwide
Primary Focal Species
No Change
ARG Comments: [none]


NPCC Final Funding Recommendations (October 23, 2006) [Full NPCC Council Recs]

FY 2007 Budget
$483,525
FY 2008 Budget
$483,525
FY 2009 Budget
$483,525
Total NPCC Rec
$1,450,575
Budget Type:Expense
Budget Category:Basinwide
Recommendation:Fund
Comments:


NPCC Draft Funding Recommendations (September 15, 2006) [Full NPCC Council Recs]

FY 2007 Budget
$483,525
FY 2008 Budget
$483,525
FY 2009 Budget
$483,525
Total NPCC Rec
$1,450,575
FY 2007 MSRT Rec
$483,525
FY 2008 MSRT Rec
$483,525
FY 2009 MSRT Rec
$483,525
Total MSRT Rec
$1,450,575
Budget Category:Basinwide
Comments:

Local or MSRT Comments: Due to the limited funding environment, the MSRT recommends sequencing the work within this project to meet FY 2006 funding levels (plus a 5% increase for increased costs) for the next three years.


Independent Scientific Review Panel Final Review (August 31, 2006) [Download full document]

Recommendation: Fundable
NPCC Comments: Although the proposal is fundable, the ISRP emphasizes that the results need to be used in regional analytical forums; e.g., NOAA’s Technical Recovery Teams (TRTs). The proposal could be improved by showing how the data from this project have guided adaptive management of recovery and implementation strategies.

Technical and scientific background: There is good explanation of the need to use this data to assess the natural spawning by hatchery salmon and steelhead in the Grande Ronde and Imnaha subbasins. Testable hypotheses are included. It is less clear how more genetic data can serve to guide TRTs and others in the broader survey of populations.

Rationale and significance to subbasin plans and regional programs: Five uncertainties from the Fish and Wildlife Program are identified in the narrative as being addressed by this proposal. The uncertainty over relative fitness of hatchery fish spawning in the wild (point 1) is well presented by the proposal. The remainder of the uncertainties are either questionably justified (point 2), partially covered (3 and 5), or not clear (4). The project could be strengthened by integration between this project and the monitoring and evaluation it supports for other agencies and tribes and by clarifying these applications of the data.

Project history: The history of the project is well described, and the milestones properly identified. The sponsors have a good track record of publications in the peer reviewed scientific literature. Less compelling is the evidence that the information being developed is making its way to guiding management decisions.

Objectives: It is not clear from the bulleted list below biological objective 1 (Describe demographic, evolutionary, and population genetic relationships) what demographic relationships mean or how they will be assessed. Evolutionary and population genetic relationships are clear, however.

Information transfer: The sponsors publish peer-reviewed work on salmon genes and lead development of standardized protocols for cross validating genetic data. There is little evidence however, that management decisions have been guided by the work to date. For example, has the captive broodstock work in the Grande Ronde been thought about differently, or the use of captive broodstock justified or reinforced as a result of the data collected by this project? The sponsors themselves note that more effort has been requested by cooperators to assist with information transfer. Data from this project have been used extensively by the Interior Columbia Technical Recovery Teams (TRT) to develop the independent populations and ESU boundaries for the Snake system. The ISAB was critical of the depth to which that data was analyzed in the TRT work. The sponsors only cite Myers (1998) and Busby (1996) as status reviews that used data from the project. Those references are now outdated, and new status reviews have been performed. It would be useful for the sponsors to identify how the recent NOAA hatchery review and status review update used data from this project.


Independent Scientific Review Panel Preliminary Review (June 2, 2006) [Download full document]

Recommendation: Fundable
NPCC Comments: Although the proposal is fundable, the ISRP emphasizes that the results need to be used in regional analytical forums; e.g., NOAA’s Technical Recovery Teams (TRTs). The proposal could be improved by showing how the data from this project have guided adaptive management of recovery and implementation strategies.

Technical and scientific background: There is good explanation of the need to use this data to assess the natural spawning by hatchery salmon and steelhead in the Grande Ronde and Imnaha subbasins. Testable hypotheses are included. It is less clear how more genetic data can serve to guide TRTs and others in the broader survey of populations.

Rationale and significance to subbasin plans and regional programs: Five uncertainties from the Fish and Wildlife Program are identified in the narrative as being addressed by this proposal. The uncertainty over relative fitness of hatchery fish spawning in the wild (point 1) is well presented by the proposal. The remainder of the uncertainties are either questionably justified (point 2), partially covered (3 and 5), or not clear (4). The project could be strengthened by integration between this project and the monitoring and evaluation it supports for other agencies and tribes and by clarifying these applications of the data.

Project history: The history of the project is well described, and the milestones properly identified. The sponsors have a good track record of publications in the peer reviewed scientific literature. Less compelling is the evidence that the information being developed is making its way to guiding management decisions.

Objectives: It is not clear from the bulleted list below biological objective 1 (Describe demographic, evolutionary, and population genetic relationships) what demographic relationships mean or how they will be assessed. Evolutionary and population genetic relationships are clear, however.

Information transfer: The sponsors publish peer-reviewed work on salmon genes and lead development of standardized protocols for cross validating genetic data. There is little evidence however, that management decisions have been guided by the work to date. For example, has the captive broodstock work in the Grande Ronde been thought about differently, or the use of captive broodstock justified or reinforced as a result of the data collected by this project? The sponsors themselves note that more effort has been requested by cooperators to assist with information transfer. Data from this project have been used extensively by the Interior Columbia Technical Recovery Teams (TRT) to develop the independent populations and ESU boundaries for the Snake system. The ISAB was critical of the depth to which that data was analyzed in the TRT work. The sponsors only cite Myers (1998) and Busby (1996) as status reviews that used data from the project. Those references are now outdated, and new status reviews have been performed. It would be useful for the sponsors to identify how the recent NOAA hatchery review and status review update used data from this project.

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