FY 2001 Ongoing proposal 198909600

Section 1. General administrative information
Section 2. Past accomplishments
Section 3. Relationships to other projects
Section 4. Budgets for planning/design phase
Section 5. Budgets for construction/implementation phase
Section 6. Budgets for operations/maintenance phase
Section 7. Budgets for monitoring/evaluation phase
Section 8. Budget summary

Reviews and Recommendations

Additional documents

Title	Type

Section 1. Administrative

Proposal title	Monitor and evaluate genetic characteristics of supplemented salmon and steelhead
Proposal ID	198909600
Organization	National Marine Fisheries Service, Conservation Biology Division (NMFS)
Proposal contact person or principal investigator
Name	Paul Moran And Robin S. Waples
Mailing address	2725 Montlake Boulevard East Seattle, WA 98112-2097
Phone / email	2068603245 / [email protected]
Manager authorizing this project	Robin Waples
Review cycle	FY 2001 Ongoing
Province / Subbasin	Systemwide / Systemwide
Short description	Monitor changes over time in genetic characteristics of hatchery, natural (supplemented), and wild (unsupplemented) populations of Snake River spring/summer chinook salmon and steelhead. Estimate reproductive success of hatchery and wild steelhead.
Target species

Project location

Latitude	Longitude	Description

Reasonable and Prudent Alternatives (RPAs)

Sponsor-reported:

RPA

Relevant RPAs based on NMFS/BPA review:

Reviewing agency	Action #	BiOp Agency	Description

Section 2. Past accomplishments

Year	Accomplishment
1993	High levels of genetic variability documented within and among Snake River chinook salmon and steelhead populations. This variability shown to be stable through time.
1993	Allozyme data supported distinctiveness of Dworshak Hatchery steelhead. Distinctiveness appeared to be ancestral. Provided an improved understanding of the genetic relationship between resident fish in the NF Clearwater and the hatchery population.
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).
1995	Interagency memorandum for USFW and IDFG summarizing genetic relationships among Snake River steelhead populations.
1996	Allozyme data played a critical role in the US v. Oregon dispute resolution. Data were provided to the Independent Scientific Review Panel for their own analyses.
1996	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.
1996	Summary of DNA data was requested by ODFW at the outset of the NE Oregon chinook salmon captive brood program to help evaluate the genetic distinctiveness of the populations putatively identified for induction into captivity.
1997	Multiplex sets used to collect data for multiple studies related to genetic monitoring. Substantial reductions in time effort and expense associated with genotyping. Multiplex sets are continually expanded and improved.
1997	Technological developments in the rapid assay of single nucleotide polymorphisms (SNPs). Results published in peer-reviewed literature (two papers, one republished as a book chapter, a third study nearing completion). Continued efforts ongoing.
1998	Developed an analytical solution for the Phelps/Allendorf effect, a common sampling problem associated with the collection of juveniles when population sizes are small. Published in peer-reviewed literature.
1998	>95 PCR primer pairs have been made for marker development in introns, 3' & 5' untranslated regions, random clones, and other noncoding sequences (microsatellite primers not included, see below).
1998	Markers and genetic results published in peer-reviewed literature (4 papers). Continued efforts ongoing. Primers distributed to other laboratories, including other researchers funded by BPA (e.g., Matt Powell's group at U of Idaho)
1998	Collection of microsatellite and RFLP data (five and five loci, respectively) for over 800 individual chinook salmon from nine populations in NE Oregon across 2 years (1994 and 1995).
1998	The geographic distribution of genetic variation revealed in this study was used extensively in the status reviews for both of these species (Busby et al. 1996, NOAA Tech Memo. NMFS-NWFSC-27; Myers et al. 1998, NOAA Tech Memo. NMFS-NWFSC-35).
1998	DNA data helped evaluate potential genetic distinctiveness of marked and unmarked fish returning to the trap at the Rapid River Hatchery. Interagency memo provided to Sharon Kiefer and Rick Lowell, IDFG with copies distributed to other comanagers.
1999	Periodically updated allozyme data shared widely among comanagers (e.g., CRITFC, Nez Perce, USFWS, Warm Springs, ISRP).
1999	Groups of six to twelve microsatellite markers (multiplex sets) developed and implemented in both chinook salmon and steelhead, permitting rapid and efficient genotyping. >90 microsatellite primer pairs made.
1999	Non-lethal allozyme genotyping of frozen adult fin clips (peer-reviewed publication)
1999	New restriction site markers developed for nuclear DNA loci. Used to describe genetic structure of selected Snake River populations.
1999	Collection, DNA extraction, and genotyping (nine loci) of 80 adult steelhead passed over the Little Sheep Creek weir.
1999	Collection of 300 juvenile steelhead from dispersed sites above the Little Sheep Creek weir. DNA extraction and genotyping of 24 juvenile steelhead (smaller sized fish likely to be age 0+) for nine loci.
1999	Little Sheep microsatellite data used for preliminary power analyses for parentage identification and evaluation of reproductive success. A second multiplex set of eight loci is being added in FY2000.
1999	Development of DNA extraction and genotyping of historic scale samples. Methodological experiments completed. Manuscript submitted.
2000	Collection of microsatellite and RFLP data (17 and 8 loci, respectively) for over 800 individual chinook salmon from nine populations in NE Oregon across 2 additional years (1992 and 1993).
2000	Collection, DNA extraction, and genotyping of microsatellite and RFLP loci (nine and five, respectively) for ~48 steelhead individuals from each of 13 Snake River populations representing four major river drainages.
2000	Tissue samples taken for genetic monitoring since 1989 and logged into the archive at NWFSC represent a major component of the largest tissue repository available for Pacific salmon (>20,000 samples).
2000	Essentially all samples collected through 1998 have been analyzed for allozyme variation. Over 6500 samples have been DNA-extracted and genotyped, and a variety of tissue samples have been made available to collaborators and comanaging agencies.

Section 3. Relationships to other projects

Project ID	Title	Description

Section 4. Budget for Planning and Design phase

Task-based budget

Objective	Task	Duration in FYs	Estimated 2001 cost	Subcontractor
Major Planning and Design completed in FY1989		0.5	$0

Outyear objectives-based budget

Objective	Starting FY	Ending FY	Estimated cost

Outyear budgets for Planning and Design phase

Section 5. Budget for Construction and Implementation phase

Task-based budget

Objective	Task	Duration in FYs	Estimated 2001 cost
1. Collect samples	a. Consult comanagers and conduct preseason evaluations of previous year escapements to identify optimal sampling strategy	Annually ongoing	$2,200
	b. Obtain appropriate collection permits and complete collection reports	Annually ongoing	$7,300
	c. Coordinate sampling efforts to maximum extent possible with other ongoing projects	Annually ongoing	$2,100
	d. Collect samples from hatchery, natural, wild, and captive populations	Annually ongoing	$12,400
2. Conduct genetic analyses	a. Perform allozyme and DNA genotyping	Annually ongoing	$114,000
	b. Perform quality control tests on preliminary data	Annually ongoing	$8,300
	c. Cooperate with other laboratories in data set standardization	Ongoing	$5,800
3. Measure levels of genetic variation in each population	a. Quantify percent polymorphic loci, heterozygosity, number of alleles per locus	Ongoing	$2,100
	b. Compare values in hatchery, natural, and wild populations	Ongoing	$2,100
	c. Evaluate pattern of change in genetic variability over time	Ongoing	$2,100
4. Estimate effective population size (Ne) and the ratio Ne/N for each population	a. Compute F, a measure of temporal change in allele frequency	Ongoing	$2,100
	b. Compute r2, a measure of gametic disequilibrium	Ongoing	$2,100
	c. Use temporal and disequilibrium methods to obtain a combined estimate of Ne for each population	Ongoing	$4,200
	d. Estimate total population size (N) based on redd counts, spawner surveys, or population enumeration	Ongoing	$2,100
	e. Compute ratio Ne/N	Ongoing	$2,100
5. Describe population genetic structure of natural and wild populations	a. Compute indices of genetic differentiation among natural and wild populations	Ongoing	$2,100
	b. Perform hierarchical gene diversity analyses to partition genetic differences into various components (e.g., spatial and temporal)	Ongoing	$4,350
	c. Estimate levels of gene flow among populations based on genetic data	Ongoing	$2,800
6. Quantify relative reproductive success of naturally-spawning hatchery and wild steelhead	a. Identify parents of juvenile steelhead collected above the Little Sheep Cr. weir (Imnaha R.) from the pool of potential parents passed over the weir in the 1999 and 2000	Annually ongoing	$36,200
	b. Compare results with theoretical expectations derived using both probabilistic and deterministic models	Annually ongoing	$2,000
	c. Estimate the relative reproductive success of hatchery and wild fish	Annually ongoing	$2,640
7. Document genetic effects of supplementation on target and non-target populations	a. Compare indices of genetic differentiation between hatchery, natural, and wild populations	Ongoing	$2,100
	b. Compare patterns of genetic change over time in hatchery populations with those in natural and wild populations	Ongoing	$2,200
	c. Prepare and submit results for distribution/publication and presentation at national and international scientific meetings	Periodic ongoing	$9,300

Outyear objectives-based budget

Objective	Starting FY	Ending FY	Estimated cost

Outyear budgets for Construction and Implementation phase

FY 2004	FY 2005	FY 2002	FY 2003
$263,000	$273,000	$244,000	$253,000

Section 6. Budget for Operations and Maintenance phase

Task-based budget

Objective	Task	Duration in FYs	Estimated 2001 cost	Subcontractor

Outyear objectives-based budget

Objective	Starting FY	Ending FY	Estimated cost

Outyear budgets for Operations and Maintenance phase

Section 7. Budget for Monitoring and Evaluation phase

Task-based budget

Objective	Task	Duration in FYs	Estimated 2001 cost
1. Evaluate effectiveness of genetic monitoring	a. Describe genetic differences between hatchery, natural, and wild populations	Ongoing	$2,300
	b. Quantify sources of noise in analysis (sampling error, genetic drift)	Ongoing	$2,430
	c. In light of a) and b), evaluate combined power of genetic markers (allozymes + DNA) to provide monitoring and evaluation information that is useful for an adaptive management approach to supplementation.	Periodic ongoing	$4,650
2. Evaluate power and utility of reproductive success studies as they pertain to characterizing genetic change through time	a. Describe strengths and limitations of deterministic and probabilistic approaches to parentage assignment	Periodic ongoing	$2,500
	b. Explore sources of variation and establish confidence limits on parentage assignment (e.g., number of loci, level of polymorphism, genotyping error rates, percentage of missing parents, etc.)	Periodic ongoing	$2,630
3. Generate specific guidelines for effective genetic monitoring research with consideration of statistical power and capability to provide practical management information	a. Publish characterization of spatial and temporal genetic differences between hatchery and natural populations, including consideration of accuracy and precision	Ongoing	$0
	d. Provide recommendations (in peer-reviewed literature) regarding alternative analytical methods for the measurement of geneflow/detection of migrants	Ongoing	$0
	b. Final presentation of information obtained framed in the context of specific recovery and management issues	0.2	$0

Outyear objectives-based budget

Objective	Starting FY	Ending FY	Estimated cost

Outyear budgets for Monitoring and Evaluation phase

FY 2004	FY 2005	FY 2002	FY 2003
$17,000	$17,700	$15,600	$16,300

Section 8. Estimated budget summary

Itemized budget

Item	Note	FY 2001 cost
Personnel	FTE: 2.23	$99,050
Fringe	23.24% of personnel	$23,020
Supplies		$50,160
Travel		$4,800
Indirect	45.6% of personnel + fringe benefits	$55,660
Subcontractor	Laboratory service contracts, waste disposal	$2,000
Personnel	FTE: 0.12	$6,970
Fringe		$1,620
Travel		$2,000
Indirect		$3,920
		$249,200

Total estimated budget

Total FY 2001 cost	$249,200
Amount anticipated from previously committed BPA funds	$0
Total FY 2001 budget request	$249,200
FY 2001 forecast from 2000	$250,000
% change from forecast	-0.3%

Reason for change in estimated budget

This project has been funded at $250K in the past but was reduced in FY2000 by 30%. Major budget reductions at this point are a significant concern for two reasons. First, in order to maintain the continuity of this unique and powerful data set it essential to continue the regular collection and genotyping of samples using the same genetic markers that comprise this very large data set (i.e., 23K fish genotyped for >70 allozyme loci). In spite of significant strides in the development and implementation of nonlethal DNA markers, these new markers simply can not replace the large body of existing allozyme data. Second, the interrelated nature of research objectives makes it impossible to simply omit specific tasks. Without complete funding, this study is at risk of significant compromise.

Reason for change in scope

The central objective of this study, the characterization of genetic change through time, has remained unchanged since its inception in 1989. Workplan changes reflect a natural evolution toward nonlethal sampling and the implementation of new technologies. Continued allozyme analysis provides continuity with previous data while DNA markers permit nonlethal sampling and access to historic scale samples. Further, highly polymorphic microsatellite markers are now used to establish parentage and quantify reproductive success of hatchery and wild fish providing a powerful new tool for monitoring genetic change in real time in natural populations.

Cost sharing

Organization	Item or service provided	Amount	Cash or in-kind

Reviews and recommendations

This information was not provided on the original proposals, but was generated during the review process.

REVIEW:
CBFWA Funding Recommendation

Recommendation:
Ongoing Funding: yes; New Funding: no

Date:
Jul 14, 2000

Comment:

This project has been funded at $250,000 in the past but was reduced in FY 2000 by 30%. Major budget reductions at this point are a significant concern for two reasons. First, in order to maintain the continuity of this unique and powerful data set it essential to continue the regular collection and genotyping of samples using the same genetic markers that comprise this very large data set (i.e., 23,000 fish genotyped for >70 allozyme loci). In spite of significant strides in the development and implementation of nonlethal DNA markers, these new markers simply can not replace the large body of existing allozyme data. Second, the interrelated nature of research objectives makes it impossible to simply omit specific tasks. Without complete funding, this study is at risk of significant compromise.

The central objective of this study, the characterization of genetic change through time, has remained unchanged since its inception in 1989. The workplan changes reflect a natural evolution toward nonlethal sampling and the implementation of new technologies. Continued allozyme analysis provides continuity with previous data while DNA markers permit nonlethal sampling and access to historic scale samples. Further, highly polymorphic microsatellite markers are now used to establish parentage and quantify reproductive success of hatchery and wild fish providing a powerful new tool for monitoring genetic change in real time in natural populations.

The NEOSEW SRT commented that aspects of this project are not well coordinated with the local managers and results are not being reported in a manner that can be easily accessed by the local managers.

REVIEW:
NWPPC Funding Recommendation

Recommendation:
Fund

Date:
Sep 13, 2000

Comment:

Rationale: Budget increase inappropriate in this review.

REVIEW:
NW Power and Conservation Council's FY 2006 Project Funding Review

Funding category:
expense

Date:
May 2005

FY05 NPCC start of year:	FY06 NPCC staff preliminary:	FY06 NPCC July draft start of year:
$460,500	$460,500	$460,500

Sponsor comments: See comment at Council's website