FY 2002 Innovative proposal 34022

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
34022 Narrative	Narrative

Section 1. Administrative

Proposal title	Evaluate the population structure of chinook salmon by combining inferences from ecological, demographic, and molecular genetic analysis
Proposal ID	34022
Organization	USDA Forest Service Rocky Mountain Research Station (USFS)
Proposal contact person or principal investigator
Name	Russ Thurow/Jason Dunham
Mailing address	316 East Myrtle Boise, ID 83702
Phone / email	2083734377 / rthurow@fs.fed.us
Manager authorizing this project	Bruce Rieman
Review cycle	FY 2002 Innovative
Province / Subbasin	Mountain Snake / Salmon
Short description	Identify population structure of indigenous chinook salmon in the Middle Fork Salmon River from patterns of genetic variation indicated by microsatellite DNA markers and spatio-temporal patterns of spawning habitat utilization
Target species	Chinook salmon

Project location

Latitude	Longitude	Description
45.2972	-114.5914	Middle Fork Salmon River drainage, entire drainage centered on the listed Lat.-Long
		4th Code Hydrologic Units #17060205 (Upper Middle Fork Salmon) and #17060206 (Lower Middle Fork Salmon)

Reasonable and Prudent Alternatives (RPAs)

Sponsor-reported:

RPA

Relevant RPAs based on NMFS/BPA review:

Reviewing agency	Action #	BiOp Agency	Description
BPA	Action 180	NMFS	The Action Agencies and NMFS shall work within regional prioritization and congressional appropriation processes to establish and provide the level of FCRPS funding to develop and implement a basinwide hierarchical monitoring program. This program shall be developed collaboratively with appropriate regional agencies and shall determine population and environmental status (including assessment of performance measures and standards) and allow ground-truthing of regional databases. A draft program including protocols for specific data to be collected, frequency of samples, and sampling sites shall be developed by September 2001. Implementation should begin no later than the spring of 2002 and will be fully implemented no later than 2003.

Section 2. Past accomplishments

Year	Accomplishment

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 2002 cost	Subcontractor

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 2002 cost	Subcontractor
Objective 1. Apply molecular genetic markers to define spatial and temporal patterns of genetic variability among spawning aggregations of chinook salmon in tributaries of the MFSR.	Task 1. Inventory existing samples available for genetic analysis. Task 2. Collect additional tissue samples in 2002. Task 3. Determine the optimal set of microsatellite primers, and conduct laboratory assays of genetic variability.	12	$69,738	Yes
Objective 2. Analyze patterns of molecular genetic variation using standard and new maximum-likelihood methods to define patterns of population structure and dispersal (gene flow) between them.	Task 1. Assemble the database and conduct standard analysis of patterns of genetic variation. Task 2. Explore alternative data analysis approaches	12	$65,110	Yes
Objective 3. Apply new analytical methods to evaluate the potential for population bottlenecks (severe reductions in population size leading to loss of genetic variation) within populations.	Task 1. Test for equilibrium of genotype frequencies. Task 2. Identify the potential for relatively recent founder events or bottlenecks.	4	$16,277	Yes
Objective 4 & 5. Explore new applications of genetic assignment tests for analysis of dispersal among populations, and to identify individuals of unknown origin. Integrate results from demographic, ecological, and genetic analysis	Task 1 (Obj 4). Identify recent migrants and their source populations. Task 1 (Obj 5). Integrate demographic, ecological, and molecular genetic analysis.	8	$48,832	Yes

Outyear objectives-based budget

Objective	Starting FY	Ending FY	Estimated cost

Outyear budgets for Construction and Implementation phase

Section 6. Budget for Operations and Maintenance phase

Task-based budget

Objective	Task	Duration in FYs	Estimated 2002 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 2002 cost	Subcontractor

Outyear objectives-based budget

Objective	Starting FY	Ending FY	Estimated cost

Outyear budgets for Monitoring and Evaluation phase

Section 8. Estimated budget summary

Itemized budget

Item	Note	FY 2002 cost
Personnel		$0
Fringe		$0
Supplies		$0
Travel		$0
Indirect		$36,000
Capital		$0
PIT tags		$0
NEPA		$0
Subcontractor	University of Nevada-Reno	$163,957
		$199,957

Total estimated budget

Total FY 2002 cost	$199,957
Total FY 2002 budget request	$199,957

Cost sharing

Organization	Item or service provided	Amount	Cash or in-kind
RMRS	Salary for R. Thurow (4 ppd), J. Dunham (8 ppd), and D. Isaak (6 ppd)	$52,500	cash
Idaho Department of Fish and Game	Salary for C. Petrosky	$1,400	cash
RMRS	Computer hardware, software, maint.	$10,250	in-kind
RMRS	Office space and administrative support	$13,400	in-kind
RMRS	Temporary field crew's salaries for collection of additonal tissue samples related to projects #199902000 and #28001 (4 ppd x 6 positions)	$24,000	cash

Reviews and recommendations

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

REVIEW:
ISRP Review (ISRP 2002-8)

Recommendation:
Fund - Rank 1

Date:
May 24, 2002

Comment:

This number one ranked proposal is fundable, innovative, technically sound, and of high priority. This excellent proposal offers an innovative use of recent developments in analysis of molecular genetic markers (microsatellites) to define spatial and temporal patterns of genetic variability among spawning aggregations of chinook salmon. Results from this project could provide greater detail and improve resolution of patterns of population structure and dispersal (gene flow), and determine occurrence of possible population bottlenecks or founder events within populations. It would also provide analysis of dispersal among populations, and make use of existing data on spatial and temporal patterns of spawning activity to produce combined inferences about population structure and metapopulation dynamics.

The proposal brings together a very capable group of scientists, leaders in the field, to test fine-scale patterns of genetic variation among chinook salmon with spatial and temporal ecological data. Some of the techniques proposed are new and rapidly developing. The approach is innovative in that it leads on from work conducted elsewhere (see references in proposal) and within the Columbia-Snake. Microsatellite techniques and the accompanying statistical analyses have been progressing rapidly and this work will combine many of the latest techniques for field application and population management. It offers a logical step in the study of molecular genetic markers. Preliminary data from other systems (Lahontan cutthroat trout) suggest that the project will yield new insights appropriate to management of depressed endangered fish.

The proposed work is essential and critical for chinook in the study area. The proposal would have been appropriately funded as part of the Provincial Review process under stock assessment methods. The information to be gained from this project will contribute to analyses under related projects such as the Idaho Supplementation Studies and project 199902000 (www.cbfwa.org/files/province/mtnsnake/projects/199902000.htm). The proposal will explore the possible alteration of genetic structure that might arise from supplementation and small numbers of brood fish (i.e., human-induced bottlenecks).

The proposal includes good cost share and relationships to ongoing projects. The bulk of the budget is going to the subcontractor (University of Nevada-Reno) for the genetics work.

Task 2 of Objective 1, collect additional tissue samples in 2002, should include a probabilistic sampling plan for collection of additional tissue samples.

REVIEW:
CBFWA Funding Recommendation

Recommendation:
High Priority

Date:
Jun 28, 2002

Comment:

The project sponsors should coordinate closely with Fred Utter, the Interior Columbia Basin Technical Recovery Team geneticist, in order to maximize benefits from this project.

REVIEW:
NMFS Review

Recommendation:

Date:
Jul 12, 2002

Comment:

Statement of Potential Biological Benefit
Indirect benefit. Use molecular genetic markers to look at various characteristics of a population. An important aspect of the study will be the integration of genetic inferences with existing research describing ecological and demographic patterns, and the potential to interpret genetic structure over generations.

Comments
This proposal would use genetic data from microsatellite loci data to describe the population structure of chinook salmon in the middle fork of the Salmon River. This is the sort of basic research needed to manage this region. The molecular and statistical methods proposed have successfully been used in many similar studies, so this proposal is not particularly innovative, but it has a high probability of success.

Already ESA Required?
No

Biop?
No

REVIEW:
NMFS Review

Recommendation:

Date:
Jul 12, 2002

Comment:

Statement of Potential Biological Benefit to ESU
Indirect benefit. Use molecular genetic markers to look at various characteristics of a population. An important aspect of the study will be the integration of genetic inferences with existing research describing ecological and demographic patterns, and the potential to interpret genetic structure over generations.

Already ESA Req? No

Biop? No

REVIEW:
BPA Funding Recommendation

Recommendation:
A- w/cond.

Date:
Aug 2, 2002

Comment:

Recommend, contingent on coordination with NMFS and others to ensure that it does not duplicate work currently underway. The development of this technique could lead toward achieving population status monitoring objectives in the Biological Opinion. The funding responsibility for population status monitoring is still being discussed by BPA, NMFS and USFWS, however, the development of the specific techniques to be used could be appropriate for BPA funding under the Innovative Project solicitation.