FY 2002 Mountain Snake proposal 199703800

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
199703800 Narrative	Narrative
199703800 Sponsor Response to the ISRP	Response
199703800 Powerpoint Presentation	Powerpoint Presentation
Mountain Snake: Salmon Subbasin Map with BPA Fish & Wildlife Projects	Subbasin Map
Mountain Snake: Salmon Subbasin Map with BPA Fish & Wildlife Projects	Subbasin Map

Section 1. Administrative

Proposal title	Preserve Salmonid Gametes and Establish a Regional Salmonid Germplasm Repository
Proposal ID	199703800
Organization	Nez Perce Tribe Department of Fisheries Resources Management (NPT)
Proposal contact person or principal investigator
Name	Bill Young
Mailing address	P. O. Box 1942 McCall, ID 83638
Phone / email	2086345290 / [email protected]
Manager authorizing this project	Jaime Pinkham
Review cycle	Mountain Snake
Province / Subbasin	Mountain Snake / Salmon
Short description	Preserve Salmonid Gametes through cryogenic techniques to maintain genetic diversity in populations with low levels of abundance and at high risk of extirpation. Establish a Regional Salmonid Germplasm Repository for populations listed under the ESA.
Target species	chinook salmon, (Snake River spring/summer chinook salmon ESU), steelhead, bull trout

Project location

Latitude	Longitude	Description
		Upper Salmon River sites are Marsh creek, Capehorn Creek and Sawtooth Hatchery.
		Pahsimeroi hatchery is on the Pahsimeroi River near Ellis, Idaho.
		Sites include South Fork and Middle Fork Salmon River and their tributaries.
44.4493	-115.2301	Marsh Creek
44.476	-115.185	Cape Horn Creek
44.1517	-114.8843	Sawtooth Hatchery
45.3783	-115.5122	South Fork Salmon River
45.2972	-114.5914	Middle Fork Salmon River

Reasonable and Prudent Alternatives (RPAs)

Sponsor-reported:

RPA
Hatchery RPA Action 176
RM&E RPA Action 184

Relevant RPAs based on NMFS/BPA review:

Reviewing agency	Action #	BiOp Agency	Description
NMFS	Action 176	NMFS	BPA shall, in coordination with NMFS, USFWS, and the relevant state and Tribal comanagers, fund the development of HGMPs for the Grande Ronde and Tucannon spring/summer chinook safety-net programs.
NMFS	Action 177	NMFS	In 2002, BPA shall begin to implement and sustain NMFS-approved, safety-net projects.
NMFS/BPA	Action 177	NMFS	In 2002, BPA shall begin to implement and sustain NMFS-approved, safety-net projects.

Section 2. Past accomplishments

Year	Accomplishment
1992	Cryopreserved 7 male chinook salmon samples
1993	Cryopreserved 10 male chinook salmon samples
1994	Cryopreserved 4 male chinook salmon samples
1995	Cryopreserved 1 male chinook salmon samples
1996	Cryopreserved 58 male chinook salmon samples
1997	Cryopreserved 189 male chinook salmon samples
1997	Cryopreserved 5 male steelhead samples
1998	Submitted 1997 annual report to BPA
1998	Cryopreserved 296 male chinook salmon samples
1998	Cryopreserved 25 male steelhead samples
1998	Cryopreserved 101 Grande Ronde basin captive broodstock male chinook salmon gametes
1998	Thawed 5 Grande Ronde basin captive broodstock male chinook salmon gametes and fertilized Grande Ronde chinook eggs
1998	Conducted fertilization trials with cryopreserved and fresh semen
1999	Submitted 1998 annual report to BPA
1999	Cryopreserved 340 male chinook salmon samples
1999	Cryopreserved 212 male steelhead samples
1999	Conducted fertilization trials with cryopreserved and fresh semen
1999	Completed genetic analysis on 1998 chinook and 1999 steelhead
1999	Visited the San Diego Zoo's Center for the Reproduction of Endangered Species Frozen Zoo
1999	Presented a poster about the project at the Western Division American Fisheries Society meeting
2000	Submitted 1999 annual report to BPA
2000	Cryopreserved 349 male chinook salmon samples
2000	Cryopreserved 283 male steelhead samples
2000	Conducted fertilization trials with cryopreserved and fresh semen
2000	Completed genetic analysis on 1999 chinook and 2000 steelhead
2000	Presented a poster about the project at the Native American Fish and Wildlife Society meeting
2000	Presented the project at the Western Division American Fisheries Society meeting
2001	Submitted 2000 annual report to BPA
2001	Cryopreserved 295 male steelhead samples
2001	Presented the project at the Idaho Chapter American Fisheries Society meeting

Section 3. Relationships to other projects

Project ID	Title	Description
199604300	Johnson Creek Artificial Propagation Enhancement Project	Cryopreserve semen from Johnson Creek fish for future artifical propagation options
199800770	Lostine River Monitoring and Evaluation Project	Cryopreserve semen from Lostine River fish for future artifical propagation options
	Nez Perce Tribe Lower Snake River Compensation Plan Hatchery Evaluation	Cryopreserve semen from salmonids at LSRCP hatcheries for future artifical propagation options
199801001	Grande Ronde Captive Brood O&M/M&E	Coordination
199800702	Grande Ronde Spring Chinook Captive Broodstock Project	Coordination
19980077	Grande Ronde Supplementation - Lostine River Monitoring and Evaluation Project	Cryopreserve semen from Lostine River salmonids for future artifical propagation options
14666	Steelhead supplementation in Idaho	Coordination and cryopreserved semen from Fish Creek steelhead for future artificial propagation options
9107200	Redfish Lake Sockeye Salmon Captive Broodstock Program	Storing cryopreserved semen from endangered sockeye salmon in project tanks
198806400	Kootenai River white sturgeon studies and conservation aquaculture	Storing cryopreserved semen from endangered white sturgeon in project tanks

Section 4. Budget for Planning and Design phase

Task-based budget

Objective	Task	Duration in FYs	Estimated 2002 cost	Subcontractor
1. Coordinate project activities and Regional Repository with agencies.	a. Coordinate planned salmonid gamete preservation activities with management and other agencies.	ongoing	$8,000
	b. Refine the selection of salmonid spawning aggregates for cryopreservation.	3	$2,000
	c. Consult with NMFS and USFWS (Section 10 research permits) to ensure consistency with recovery planning efforts under the Endangered Species Act.	ongoing	$4,000
2. Obtain necessary environmental reviews, permits and evaluations for construction activities for facility.	a. NEPA	1	$4,000
	b. Other permits	.5	$2,000
3. Design Regional Salmonid Germplasm Repository.	a. Preliminary design.	1	$88,000	Yes
	b. Final engineering design.	1	$50,000	Yes

Outyear objectives-based budget

Objective	Starting FY	Ending FY	Estimated cost
1. Coordinate project activities and Regional Repository with agencies.	2003	2006	$146,000
2. Obtain necessary environmental reviews, permits and evaluations for construction activities for facility.	2003	2003	$24,000
3. Design Regional Salmonid Germplasm Repository.	2003	2003	$280,000

Outyear budgets for Planning and Design phase

FY 2003	FY 2004	FY 2005	FY 2006
$270,000	$65,000	$60,000	$55,000

Section 5. Budget for Construction and Implementation phase

Task-based budget

Objective	Task	Duration in FYs	Estimated 2002 cost	Subcontractor
4. Establish a regional salmonid germplasm repository.	a. Acquire land for the facility.	1	$95,000
	b. Construct a regional salmonid germplasm repository.	2	$200,000	Yes
	c. Purchase equipment for cold room and storage facilities.	1	$50,000
	d. Maintain storage facilities for preservation of genetic material.	ongoing	$28,000	Yes

Outyear objectives-based budget

Objective	Starting FY	Ending FY	Estimated cost
4. Establish a regional salmonid germplasm repository.	2003	2006	$1,909,000

Outyear budgets for Construction and Implementation phase

FY 2003	FY 2004	FY 2005	FY 2006
$1,374,000	$470,000	$30,000	$35,000

Section 6. Budget for Operations and Maintenance phase

Task-based budget

Objective	Task	Duration in FYs	Estimated 2002 cost	Subcontractor
5. Preserve the genetic diversity of Snake River salmonid populations at high risk of extirpation through application of cryogenic techniques.	a. Identify salmonid spawning aggregates that are at high risk of extirpation in the Snake River basin for germplasm sampling. Determine the number of spawning aggregates and/or subbasin from which to cryopreserve materials	3	$30,000
	b. Determine sample sizes required per spawning aggregate to preserve a representative sample of the genetic diversity within the population.	5	$5,000
	c. Collect male chinook salmon gamete samples.	ongoing	$90,000
	d. Collect male steelhead gamete samples.	ongoing	$90,000
	e. Collect male resident fish gamete samples.	ongoing	$70,000
	f. Set up state-of-the-art cryogenic laboratory.	3	$220,000
	g. Conduct fertilization experiments to evaluate the ability of the thawed germplasm to fertilize eggs.	ongoing	$5,000
	h. Determine the period of time (years) for gamete collections and cryopreservation to occur	4	$7,000
6. Identify salmonid populations at critically low levels of abundance in the Columbia River basin and initiate germplasm collections for cryopreservation.	a. Identify salmonid spawning aggregates that are at high risk of extirpation in the Columbia River basin for germplasm sampling.	ongoing	$20,000
	b. Determine sample sizes required per spawning aggregate to preserve a representative sample of the genetic diversity within the population.	5	$5,000
	c. Collect male chinook salmon gamete samples.	ongoing	$0
	d. Collect male steelhead gamete samples.	ongoing	$0
	e. Collect male resident fish gamete samples.	ongoing	$0
	f. Conduct fertilization experiments to evaluate the ability of the thawed germplasm to fertilize eggs.	ongoing	$0
	g. Determine the period of time (years) for gamete collections and cryopreservation to occur.	3	$6,000
7. Manage the physical salmonid germplasm inventory.	a. Develop an aquatic species genetic resource cryopreservation management plan.	2	$20,000	Yes
	b. Manage germplasm inventory.	10	$30,000
8. Cryopreservation research.	a. Explore and find the ideal freezing curve for 5 mL straws.	2	$15,000	Yes
	b. Determine how many eggs you can fertilize with .5 and 5 mL straws respectively.	1	$8,000	Yes
	c. Experiment with using a buffer in the freezing solution to improve post-thaw motility.	1	$4,000	Yes
	d. Determine probability of pathogen cross-contamination among straws in the germplasm repository.	3	$8,000	Yes
	e. Test for disease/ pathogen cryogenic viability capabilities.	2	$6,000	Yes
	f. Refine the thawing and fertilizing of eggs with cryopreserved sperm methodology.	2	$5,000	Yes
9. Transfer of technology.	a. Facilitate data dissemination within the region.	ongoing	$8,000
	b. Prepare and provide annual reports	ongoing	$10,000
	c. Prepare and provide quarterly reports	ongoing	$2,000
	d. Prepare annual ESA summary reports for NMFS and USFWS.	ongoing	$4,000

Outyear objectives-based budget

Objective	Starting FY	Ending FY	Estimated cost
5. Preserve the genetic diversity of Snake River salmonid populations at high risk of extirpation through application of cryogenic techniques.	2003	2006	$1,156,000
6. Identify salmonid populations at critically low levels of abundance in the Columbia River basin and initiate germplasm collections for cryopreservation.	2003	2006	$803,000
7. Manage the physical salmonid germplasm inventory.	2003	2006	$150,000
8. Cryopreservation research.	2003	2006	$24,000
9. Transfer of technology.	2003	2006	$50,000

Outyear budgets for Operations and Maintenance phase

FY 2003	FY 2004	FY 2005	FY 2006
$380,000	$400,000	$680,000	$723,000

Section 7. Budget for Monitoring and Evaluation phase

Task-based budget

Objective	Task	Duration in FYs	Estimated 2002 cost	Subcontractor
10. Analyze the genetic material to assess the diversity contained within.	a. Conduct genetic analysis of salmonid genetic material cryopreserved.	ongoing	$30,000	Yes
	b. Analyze scales of fish whose germplasm has been cryopreserved to determine age structure of fish sampled.	ongoing	$10,000	Yes
11. Test the gamete samples for viral and bacterial infections.	a. Send each milt sample for viral and bacterial contamination testing.	ongoing	$40,000	Yes

Outyear objectives-based budget

Objective	Starting FY	Ending FY	Estimated cost
10. Analyze the genetic material to assess the diversity contained within.	2003	2006	$140,000
11. Test the gamete samples for viral and bacterial infections.	2003	2006	$170,000

Outyear budgets for Monitoring and Evaluation phase

FY 2003	FY 2004	FY 2005	FY 2006
$70,000	$75,000	$80,000	$85,000

Section 8. Estimated budget summary

Itemized budget

Item	Note	FY 2002 cost
Personnel	FTE: 2 FTE Biologists, 6 FTE Technician, 0.5 FTE Admin Support, 0.5 FTE Office Manager	$203,000
Fringe	40%	$81,000
Supplies	field supplies, office services, telephone, rent, training, computers,	$85,000
Travel	airline, vehicles, per diem	$8,000
Indirect	20.9 %	$80,000
Capital	land, equipment	$300,000
NEPA		$4,000
Subcontractor	University of Idaho, Dr. Cloud	$20,000
Subcontractor	WSU, Thorgaard lab assistance	$20,000
Subcontractor	Architect/Planning	$88,000
Subcontractor	Cryo flights	$16,000
Subcontractor	liquid nitrogen	$24,000
Subcontractor	CRITFC genetic analsysis	$22,000
Subcontractor	engineer	$50,000
Subcontractor	general contractor	$28,000
Subcontractor	USFWS Disease testing	$40,000
Subcontractor	CRITFC scale analysis	$10,000
Other	construction	$200,000
		$1,279,000

Total estimated budget

Total FY 2002 cost	$1,279,000
Amount anticipated from previously committed BPA funds	$0
Total FY 2002 budget request	$1,279,000
FY 2002 forecast from 2001	$420,000
% change from forecast	204.5%

Reason for change in estimated budget

Scope increased from ongoing project due to the addition of establishing Regional Germplasm Repository. Preserving genetic diversity for future conservation action (captive broodstock and conventional hatchery) warrants a regional ecosystem approach to gene conservation.

Reason for change in scope

Scope increased from ongoing project due to establishing Regional Germplasm Repository.

Cost sharing

Organization	Item or service provided	Amount	Cash or in-kind
Idaho Department of Fish and Game	personnel, services	$2,000	in-kind
Oregon Department of Fish and Wildlife	personnel, services	$2,000	in-kind

Other budget explanation

Construction of the Regional Germplasm Repository in 2003 and 2004 accounts for the increase for those years. The expansion of the field collections into the Columbia River basin account for the costs in 2005 and 2006.

Reviews and recommendations

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

REVIEW:
ISRP Preliminary Review (ISRP 2001-9)

Recommendation:
Fundable only if response is adequate

Date:
Sep 28, 2001

Comment:

Response is needed. To date, the project has cryopreserved male gametes from over 2,700 chinook salmon and steelhead. The proposal would continue and expand that program roughly four-fold after construction of a new building, evaluating additional basins for gamete collections from salmonids (resident and anadromous), other fishes such as lamprey and burbot, and amphibians.

Sponsors need to provide a convincing argument that use of cryopreservation as a tool of conservation for Columbia River salmonids continues to be logical, in part, by responding to the following statements.

Generally, measures such as cryopreservation are taken in an attempt to protect a species for a very short time while emergency actions are taken to restore lost habitat. A concern is that the gametes retained do not represent the population, and their contribution to a breeding program may not be random. Sampling from the population is only from males. The population is already in a potential genetic bottleneck before the original samples are taken and repeated sampling only exacerbates that problem. Because trials generally show relatively low viability of cryopreserved sperm, is a random sample of the genetic material passed to subsequent generations?

The ISRP also had specific questions concerning the following:

Why do the sponsors feel that it is "... logical that BPA fund this proposal because of its past investment in the ongoing Snake River Salmonid Gamete Preservation Project"? Shouldn't a Regional Center be a collaborative effort? Why is a new (vs renovated) building needed? Why build on the opposite side of Moscow (the Alturas location) from the university? Why isn't it better to place this in very close proximity to either UI or WSU to maximize interaction and (presumably) minimize cost?

Reviewers questioned why gametes would be collected from cutthroat trout for the repository when their population status has been judged healthy enough to preclude ESA listing.

Please clarify the relationship of the proposed regional repository in this proposal and that proposed for Hagerman.

REVIEW:
CBFWA Funding Recommendation

Recommendation:
High Priority

Date:
Nov 30, 2001

Comment:

Academic, management, and regulatory agencies have discussed and conferred the merits of a regional program such as what is proposed in this work. This project addresses RPA 177. The significant increase in budget is due to capital construction of a regional germ plasm repository facility.

REVIEW:
ISRP Final Review (ISRP 2001-12A)

Recommendation:
Fund

Date:
Dec 21, 2001

Comment:

Fundable in part, continuing sperm preservation at a level similar to current efforts, but not to expand and elevate this to a Regional Center without strong evidence that it truly is scientifically sound and broadly supported by a number of groups and agencies. This needs a high level scientific review such as by the ISAB that focuses on the state of the science of this strategy and its application in the FWP. It is time for a thoughtful analysis of what the FWP wants to accomplish in gene conservation, whether or not cryopreservation continues to be a useful tool, and whether an ever-increasing commitment to this program is consistent with that goal.

To date, the project has cryopreserved male gametes from over 2,700 chinook salmon and steelhead. The proposal would continue and expand that program roughly four-fold after construction of a new building, evaluating additional basins for gamete collections from salmonids (resident and anadromous), other fishes such as lamprey and burbot, and amphibians.

REVIEW:
NMFS Review

Recommendation:

Date:
Feb 1, 2002

Comment:

Statement of Potential Biological Benefit to ESU
Maintain genetic diversity in ESA-listed chinook salmon, steelhead, bull trout and other rare salmonids in the Columbia River basin by establishing a Regional Salmonid Germplasm Repository to preserve salmonid gametes through cryogenic techniques.

Comments
The project proposes to preserve salmonid gametes through cryogenic techniques in order to maintain genetic diversity in populations with low levels of abundance and at high risk of extirpation and to establish a regional salmonid germplasm repository for ESA-listed populations. Target species include chinook salmon, (Snake River spring/summer chinook salmon ESU), steelhead, and bull trout. Generally, measures such as cryopreservation are taken in an attempt to protect a species for a very short time while emergency actions are taken to restore lost habitat. NMFS has not yet determined the suitability of the use of cryopreservation as a tool of conservation for, or recovery of, Columbia River salmonids.

Already ESA Req? No

Biop? Yes

REVIEW:
BPA Funding Recommendation

Recommendation:
A Conditional

Date:
Feb 11, 2002

Comment:

Recommend funding at current project level only for implementation of RPA 177. Project should be evaluated for integration with SNAPP.

BPA RPA RPM:
177

NMFS RPA/USFWS RPM:
177

REVIEW:
NWPPC Funding Recommendation

Recommendation:
Fund

Date:
Apr 19, 2002

Comment:

REVIEW:
BPA Funding Decision

Recommendation:
Fund

Date:
Jun 13, 2002

Comment:

Funding at current project level only for implementation of RPA 177. Project should be evaluated for integration with SNAPP. Proposed project expansion to a regional level needs scientific and policy review by affected regional parties.

REVIEW:
NWPPC Funding Recommendation

Recommendation:
Fund

Date:
Sep 20, 2003

Comment:

On track. 05 increase of 3.4%

REVIEW:
Project Sponsor Request for FY04-05

Recommendation:

Date:
Sep 20, 2003

Comment:

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:
$308,447	$308,447	$308,447

Sponsor comments: See comment at Council's website