FY07-09 proposal 200732300

Jump to Reviews and Recommendations

Section 1. Administrative

Proposal titleInvestigate genetic parentage analysis techniques to estimate spawner abundance in ESA-listed steelhead populations
Proposal ID200732300
OrganizationIdaho Department of Fish & Game
Short descriptionInvestigate the feasibility of sampling juvenile steelhead and using parentage analysis techniques to estimate the number of steelhead spawners in rivers.
Information transfer1. Peer reviewed journal articles 2. IDFG databases 3. BPA annual reports
Proposal contact person or principal investigator
Contacts
ContactOrganizationEmail
Form submitter
Alan Byrne IDFG abyrne@idfg.idaho.gov
All assigned contacts
Alan Byrne IDFG abyrne@idfg.idaho.gov
Conan Chiu Idaho Department of Fish and Game cchiu@idfg.idaho.gov
Dan Schill Idaho Department of Fish and Game dschill@idfg.idaho.gov

Section 2. Locations

Province / subbasin: Mountain Snake / Clearwater

LatitudeLongitudeWaterbodyDescription
115° 20' 42 46° 19' 60 Fish Creek Fish Creek
116° 21' 17" 45° 22' 28" Rapid River Rapid River

Section 3. Focal species

primary: Steelhead Snake River ESU

Section 4. Past accomplishments

YearAccomplishments

Section 5. Relationships to other projects

Funding sourceRelated IDRelated titleRelationship
BPA 199005500 Id Steelhead M&E Studies The Idaho Steelhead Monitoring and Evaluation Studies (ISMES) operates the weir in Fish Creek and works with the staff of Rapid River Hatchery to collect adult data from the weir in Rapid River. Project personnel have collected tissue samples from all adult steelhead trapped at each weir since 1998 and will collect tissue samples in the future. ISMES field crews will collect most of tissue samples from fry and juvenile steelhead in Fish Creek and Rapid River. The IDFG steelhead genetics database, consisting of 74 wild populations and five hatchery stocks, was developed from work done by ISMES.

Section 6. Biological objectives

Biological objectivesFull descriptionAssociated subbasin planStrategy
Objective 1 Examine the literature for genetic methodologies used in analysis of fish and wildlife populations and determine their applicability to estimate steelhead spawner abundance and the contribution of resident O. mykiss Clearwater A2, VIII.1, VIII.3. Also relevant to strategy 1A2, and 2A3 in the Salmon Subbasin Plan (p 20 and 24).
Objective 2 Investigate genetic parentage analysis methodologies to measure reproductive skewness and resident O. mykiss contribution to progeny arrays Clearwater A2, VIII.1, VIII.3. Also relevant to strategy 1A2, and 2A3 in the Salmon Subbasin Plan (p 20 and 24).
Objective 3 Investigate the utility of monitoring Ne in steelhead populations as a method to estimate the number of spawners Clearwater A2, VIII.1, VIII.3. Also relevant to strategy 1A2, and 2A3 in the Salmon Subbasin Plan (p 20 and 24).
Objective 4 Investigate genetic parentage analysis methodologies to estimate steelhead spawner abundance in streams Clearwater A2, VIII.1, VIII.3. Also relevant to strategy 1A2, and 2A3 in the Salmon Subbasin Plan (p 20 and 24).

Section 7. Work elements (coming back to this)

Work element nameWork element titleDescriptionStart dateEnd dateEst budget
Produce/Submit Scientific Findings Report data transfer Produce article for scientific journal 1/1/2007 12/31/2009 $43,834
Biological objectives
Objective 2
Metrics
Produce/Submit Scientific Findings Report data transfer prepare results for publication in scientific journal 1/1/2007 12/31/2009 $43,834
Biological objectives
Objective 3
Metrics
Produce/Submit Scientific Findings Report data transfer prepare results for publication in scientific journal 1/1/2007 12/31/2009 $43,834
Biological objectives
Objective 4
Metrics
Analyze/Interpret Data analyze data use samples from Objective 2. Add additional samples if sample size is too small. Identify relationships of individuals. 1/1/2007 12/31/2009 $269,874
Biological objectives
Objective 4
Metrics
Focal Area: Tributaries,
Analyze/Interpret Data Analyze data Use the microsatillite analysis of progeny samples done in Objective 2. Determine Ne from a subset of the samples. 1/1/2007 12/31/2009 $100,854
Biological objectives
Objective 3
Metrics
Analyze/Interpret Data Analyze data Microsatillite analysis of adult and progeny samples. Conduct parentage analysis. 1/1/2007 12/31/2009 $501,233
Biological objectives
Objective 2
Metrics
Focal Area: Tributaries,
Collect/Generate/Validate Field and Lab Data Collect data Sample adults at Fish Creek and rapid River wier. Sample 1,000 progeny per stream for case 1. Sample 50 emergent fry per redd ffrom 20 redds for case 2. 1/1/2007 1/1/2009 $40,944
Biological objectives
Objective 2
Metrics
Focal Area: Tributaries
Collect/Generate/Validate Field and Lab Data collect data Sample collected for Objective 2 can also be used for this Objective 1/1/2007 12/31/2009 $23,884
Biological objectives
Objective 3
Metrics
Focal Area: Tributaries,
Collect/Generate/Validate Field and Lab Data collect data Collect samples from progeny. Collect additional samples if the sample size obtained for Objective 2 is not adequate. 1/1/2007 12/31/2009 $47,768
Biological objectives
Objective 4
Metrics
Focal Area: Tributaries
Create/Manage/Maintain Database manage database add data to database 1/1/2007 12/31/2009 $23,240
Biological objectives
Objective 4
Metrics
Create/Manage/Maintain Database manage database add database to database 1/1/2007 12/31/2009 $23,240
Biological objectives
Objective 3
Metrics
Create/Manage/Maintain Database manage database put data into databases 1/1/2007 1/1/2009 $23,240
Biological objectives
Objective 2
Metrics
Develop RM&E Methods and Designs develop methodlogy computer simulation studies to analyze samples where no information was obtained from the parents and progeny arrays were not sampled. 1/1/2007 12/31/2009 $43,834
Biological objectives
Objective 4
Metrics
Develop RM&E Methods and Designs literature search Conduct a literature search and contact researchers working in this field to find and adapt methodologies for steelhead studies 1/1/2007 12/31/2009 $37,572
Biological objectives
Objective 1
Metrics

Section 8. Budgets

Itemized estimated budget
ItemNoteFY07FY08FY09
Personnel [blank] $155,610 $160,278 $165,086
Fringe Benefits [blank] $54,463 $56,097 $57,780
Supplies [blank] $105,367 $110,635 $116,167
Travel [blank] $8,831 $9,272 $9,736
Capital Equipment [blank] $12,000 $12,600 $13,230
Overhead [blank] $70,693 $73,309 $76,031
Totals $406,964 $422,191 $438,030
Total estimated FY 2007-2009 budgets
Total itemized budget: $1,267,185
Total work element budget: $1,267,185
Cost sharing
Funding source/orgItem or service providedFY 07 est value ($)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: $100,000
FY 2011 estimated budget: $100,000
Comments: If results are favorable then budget could increase as methods are used in other steelhead population units. This estimate includes continuing Objective 3 only, and publishing results from the work done in FY07-09.

Future O&M costs: dependent upon scope of work

Termination date: unknown
Comments: If the methodolgies this project develops prove successful to monitor adult steelhead abundance then, this project or other(s) can apply the methods to other ESA-listed steelehead population units. Methods could be used on fish species other than steelhead.

Final deliverables: 1. Methodolgies for field use to estimate adult steelhead spawners using genetic analysis of progeny. 2. Peer reviewed journal articles.

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]
$0 $0 $0 $0 Expense ProvinceExpense Do Not Fund
NPCC DRAFT FUNDING RECOMMENDATIONS (Sep 15, 2006) [full Council recs]
$0 $0 $0 $0 ProvinceExpense
Comments: Also reviewed by MSRT
NPCC DRAFT FUNDING RECOMMENDATIONS (Sep 15, 2006) [full Council recs]
$0 $0 $0 $0 Basinwide

ISRP PRELIMINARY REVIEW (Jun 2, 2006)

Recommendation: Not fundable

NPCC comments: The proposal and project are premature and undeveloped. The technical and scientific background on this exploratory research proposal is weak. Much of the first two objectives should be done as part of the project conceptualization and development process. While the technical background on the molecular methods is explained, there is a fair bit of listing computational techniques without much muscle to backup that this approach will provide answers. It is not clear what is actually being proposed other than research for an appropriate technique for estimation of spawner abundance based on genetic sampling of progeny. It is likely that a mathematical derivation is possible, but none is presented, or at least not understandably. The proposal is therefore premature and needs considerable development before reconsideration. The proposed method, once researched and developed, is placed in the context of the Clearwater and Salmon subbasin plans and steelhead monitoring. The rationale lacks a compelling case for its need. The Idaho Steelhead Monitoring and Evaluation Studies are noted as related to this work, but in fact there are many more studies that could be related, across the basin. Collaboration with other geneticists and studies in the basin overall would benefit the developmental work. The first two objectives are to explore the literature and talk with experts. These should have been undertaken as part of the conceptualization process. The third and fourth objectives have a little more meat but lack clarity as to what will be produced except lots of genotypes. No real hypotheses are articulated. Laboratory genetic methods are sound, but lack direction. This is a research project that can potentially lead to M&E tools; however it needs much greater detail and development than is described in the present proposal. The proponents expect benefits for Snake River steelhead, but the outcome is uncertain and therefore benefit horizon is also uncertain. The project should not affect non-focal species. The characteristics of the information to be delivered are unclear.


ISRP FINAL REVIEW (Aug 31, 2006)

Recommendation: Not fundable

NPCC comments: The proposal and project are premature and undeveloped. The technical and scientific background on this exploratory research proposal is weak. Much of the first two objectives should be done as part of the project conceptualization and development process. While the technical background on the molecular methods is explained, there is a fair bit of listing computational techniques without much muscle to backup that this approach will provide answers. It is not clear what is actually being proposed other than research for an appropriate technique for estimation of spawner abundance based on genetic sampling of progeny. It is likely that a mathematical derivation is possible, but none is presented, or at least not understandably. The proposal is therefore premature and needs considerable development before reconsideration. The proposed method, once researched and developed, is placed in the context of the Clearwater and Salmon subbasin plans and steelhead monitoring. The rationale lacks a compelling case for its need. The Idaho Steelhead Monitoring and Evaluation Studies are noted as related to this work, but in fact there are many more studies that could be related, across the basin. Collaboration with other geneticists and studies in the basin overall would benefit the developmental work. The first two objectives are to explore the literature and talk with experts. These should have been undertaken as part of the conceptualization process. The third and fourth objectives have a little more meat but lack clarity as to what will be produced except lots of genotypes. No real hypotheses are articulated. Laboratory genetic methods are sound, but lack direction. This is a research project that can potentially lead to M&E tools; however it needs much greater detail and development than is described in the present proposal. The proponents expect benefits for Snake River steelhead, but the outcome is uncertain and therefore benefit horizon is also uncertain. The project should not affect non-focal species. The characteristics of the information to be delivered are unclear.