Genetic Monitoring of Snake River Chinook Salmon and Steelhead proposal 198909600

FY07-09 proposal 198909600

Section 1. Administrative

Proposal title	Genetic Monitoring of Snake River Chinook Salmon and Steelhead
Proposal ID	198909600
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 In addition, we have provided many informal summaries of recent or unpublished results to fishery and hatchery managers in Washington, Idaho, and Oregon.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.
Proposal contact person or principal investigator

Contacts

Contact	Organization	Email
Form submitter
Paul Moran	Northwest Fisheries Science Center	paul.moran@noaa.gov
All assigned contacts
Melissa Baird	NMFS-NOAA Fisheries	melissa.baird@noaa.gov
Ewann Berntson	NOAA NMFS NWFSC	ewann.berntson@noaa.gov
Paul Moran	Northwest Fisheries Science Center	paul.moran@noaa.gov

Section 2. Locations

Province / subbasin: None Selected / None Selected

Latitude	Longitude	Waterbody	Description
N46° 20.18’	W115° 20.99’	Clearwater	Lochsa River (Fish Cr.)
N46° 03.68’	W115° 18.90’	Clearwater	Selway River (Gedney Cr.)
N46° 30.21’	W116° 19.39’	Clearwater	Dworshak facility
N45° 18.34'	W117° 51.99'	Grande Ronde	Catherine Creek (reproductive success study)
N45° 43.90'	W117° 51.78'	Grande Ronde River	Lookingglass Creek
N45° 43.90'	W117° 51.78'	Grande Ronde River	Lookingglass facility (formerly Rapid River stock, currently several locally derived stocks)
N45° 59.02'	W117° 23.34'	Grande Ronde River	Upper Grande Ronde River (reproductive success study)
N45° 32.14'	W117° 43.15'	Grande Ronde River	Minam River
N45° 28.71'	W117° 25.68'	Grande Ronde River	Lostine River (reproductive success study)
N45° 06.81'	W116° 59.41'	Imnaha	Imnaha River
N45° 11.58'	W116° 52.16'	Imnaha	Imnaha River facility
N45° 28.95’	W116° 55.29’	Imnaha	Little Sheep Creek (reproductive success study)
N45° 10.57’	W117° 02.23’	Imnaha	Lick Creek
N45° 15.87’	W116° 55.25’	Imnaha	Grouse Creek
N45° 37.40’	W116° 56.24’	Imnaha	Camp Creek
N45° 21.23'	W116° 23.78'	Little Salmon River	Rapid River Hatchery
N45° 21.23'	W116° 23.78'	Little Salmon River	Rapid River
N44° 09.74'	W114° 53.18'	Mainstem Salmon River	Sawtooth facility
N44° 14.16'	W114° 59.62'	Mainstem Salmon River	Lower Valley Creek
N44° 16.11'	W115° 00.41'	Mainstem Salmon River	Upper Valley Creek
N43° 50.71'	W114° 45.20'	Mainstem Salmon River	Upper Salmon River
N45° 06.22'	W114° 51.35'	Middle Fork Salmon River	Lower Big Creek
N45° 06.08'	W115° 19.86'	Middle Fork Salmon River	Upper Big Creek
N44° 23.53'	W115°09.75'	Middle Fork Salmon River	Marsh Creek
N44° 53.74'	W116° 06.94'	South Fork Salmon River	McCall facility (production and conservation stocks)
N44° 35.93'	W115° 41.20'	South Fork Salmon River	Stolle Meadows
N45° 13.97'	W115° 48.72'	South Fork Salmon River	Secesh River
N44° 50.14'	W115° 42.23'	South Fork Salmon River	Poverty Flat
N44° 39.52'	W115° 42.17'	South Fork Salmon River	Knox Bridge
N44° 56.30'	W115° 29.71'	South Fork Salmon River	Johnson Creek
N46° 35.48’	W118° 13.49’	Tucannon River	Lyons Ferry facility
N46° 13.06	W117° 42.82’	Tucannon River	Upper Tucannon River
N46° 32.72’	W118° 09.97’	Tucannon River	Lower Tucannon River
N45° 20.55’	W117° 14.15’	Upper Grande Ronde	Wallowa facility
N45° 42.82’	W117° 09.15’	Upper Grande Ronde	Chesnimnus Creek
N45° 37.17’	W117° 41.95’	Upper Grande Ronde	Big Canyon Creek

Section 3. Focal species

primary: Chinook Snake River Spring/Summer ESU
primary: Steelhead Snake River ESU
secondary: Rainbow Trout

Section 4. Past accomplishments

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

Funding source	Related ID	Related title	Relationship
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	198909800	Salmon Studies ID Rvrs IDFG	We coordinate genetic sampling with sampling from this study.
BPA	199107300	Idaho Natural Production Monit	We coordinate genetic sampling with sampling from this study.
BPA	199005500	ID Steelhead M&E Studies	We coordinate genetic sampling with collections for this program.
BPA	199801001	Grande Ronde Captive Brood O&M	We coordinate genetic sampling with collections for 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	198712700	Smolt Monitoring By Non-Feder	Sampling is coordinated with this program.
BPA	199606700	Manchester Spring Chinook Capt	We coordinate genetic sampling with 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	199800702	Gd Ronde Supp Lostine O&M/M&E	Adult sampling is coordinated with this project

Section 6. Biological objectives

Biological objectives	Full description	Associated subbasin plan	Strategy
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.
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.
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]
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.
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).
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.”
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).
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
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
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.
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.
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)
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.
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.
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.
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.
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
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) .
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.
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.
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.
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.
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.
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.
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.

Section 7. Work elements (coming back to this)

Work element name	Work element title	Description	Start date	End date	Est 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
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 1. Describe genetics, 3. Measure change 2. Reproductive success 4. Standardized marker development			Metrics
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
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
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
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 1. Describe genetics, 3. Measure change 2. Reproductive success 4. Standardized marker development 5. Evaluate genetic monitoring			Metrics
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 1. Describe genetics, 3. Measure change 2. Reproductive success 4. Standardized marker development 5. Evaluate genetic monitoring			Metrics
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 1. Describe genetics, 3. Measure change 2. Reproductive success 4. Standardized marker development			Metrics
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 1. Describe genetics, 3. Measure change 2. Reproductive success 4. Standardized marker development 5. Evaluate genetic monitoring			Metrics

Section 8. Budgets

Itemized estimated budget

Item	Note	FY07	FY08	FY09
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/org	Item or service provided	FY 07 est value ($)	FY 08 est value ($)	FY 09 est value ($)	Cash or in-kind?	Status
Totals		$0	$0	$0

Section 9. Project future

FY 2010 estimated budget: $557,050
FY 2011 estimated budget: $557,050

Comments: Assuming 3% per year increase in costs to keep constant effort.

Future O&M 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: 10/31/12
Comments: 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 and other documents

Reviews and recommendations

FY07 budget	FY08 budget	FY09 budget	Total budget	Type	Category	Recommendation
NPCC FINAL FUNDING RECOMMENDATIONS (Oct 23, 2006) [full Council recs]
$483,525	$483,525	$483,525	$1,450,575	Expense	Basinwide	Fund
NPCC DRAFT FUNDING RECOMMENDATIONS (Sep 15, 2006) [full Council recs]
$483,525	$483,525	$483,525	$0		Basinwide

ISRP PRELIMINARY REVIEW (Jun 2, 2006)

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.

ISRP FINAL REVIEW (Aug 31, 2006)

Recommendation: Fundable