Within-Year Modification Request Form for FY 2008

 
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Table of Contents
Part 1. Administration and Budgeting
Section 1: General Administrative Information
Section 2: Description
Section 3: Related Projects
Section 4: Planning and Design
Section 5: Construction/Implementation
Section 6: Operations and Maintenance
Section 7: Monitoring and Evaluation
Section 8: Total Budget
Section 9: Project Documents
Part 2. Current Status of Modification Request
Part 3. Comments on this Modification Request


Part 1 of 3. Administration and Budgeting
Section 1: General Administrative Information
Process Information:
Date Proposal Submitted & Finalized Status BOG Meeting Date
September 30, 2008 Finalized October 8, 2008

Modification Type: FY 2008 Within-Year Ongoing
BPA Project Number: 198909600
BPA Project Name: Genetic M&E Program for Salmon and Steelhead
COTR/BPA Project Manager: Wynn Avocette
Agency, Institution or Organization Requesting Rescheduling: National Marine Fisheries Service
Funding Type: expense
Project Leader: Dr. Ewann Berntson
Province: Mainstem/Systemwide
Subbasin: Systemwide
 
Contact Person
First Name: Ewann
Last Name Berntson
Address: 7305 Beach Dr. East
City, State Zip: Port Orchard, WA 98366
Phone: 360-871-8333
Fax: 206-842-8364
Email: ewann.berntson@noaa.gov

Administrative Contacts
Primary Administrative Contact Secondary Administrative Contact:
Name Helen Brandling-Bennett Name Paul Aebersold
Address: 2725 Montlake Blvd. E. Address: 2725 Montlake Blvd. E.
City, State Zip: Seattle, WA 98112 City, State Zip: Seattle, WA 98112
Phone: 206-860-3232 Phone: 206-860-3247
Fax: Fax: 206-860-3335
Email: helen.brandling-bennett@noaa.gov Email: paul.aebersold@noaa.gov
Note: Note:

Section 2a: Description (Species Information)
Target Species fish
Oncorhynchus mykiss (rainbow trout)
Oncorhynchus mykiss (steelhead)
Oncorhynchus mykiss gairdnerii (redband trout)
Oncorhynchus tshawytscha (chinook)

Provide explanations as to why the following alternative funding solutions are not feasible and will jeopardize the project:
Reduction in existing scope of project: Reduction in scope to accommodate the current (FY2009) reduction in funding would not meet the expressed needs of the Snake Basin comanagers. In order to maintain the temporal integrity that is essential to this study, we must cut genotyping and analysis disproportionately in order to maintain sampling effort and keep that temporal continuity. This means that, although we can defer genotyping, comanagers will not have the results in a timely manner.
Deferral of existing work elements to later date: Uncertainty about the relative reproductive success of hatchery fish spawning in the wild is a critical gap in our knowledge, and comanagers continue to express the need for the information provided by our monitoring program. Our data are needed in real time to evaluate the genetic effects of different art prop protocols and hatchery reforms, including, for example, transition from captive brood stock to conventional stocks in northeast Oregon.

Section 2b: Description (Location Information)
Location(s) at which the action will be implemented
Latitude Longitude Location Description
Scores of study sites throughout the Snake R basin, including hatchery programs, natural populations influenced by art prop, and wild populations

Is this/Are these the same study location(s) that was/were identified in the original proposal? Yes

Condition/situation creating the need for the modification:
Is the situation the result of a catastrophic event that occurred within the existing location? No
Has a habitat/population/mechanical/structural dilemma developed in the proposed study location since the contract was signed with BPA? No

Section 2c: Description (Work Element Information)
What work elements in the existing proposal does the proposed modification address?
Work Element Work Element Title
157. Collect/Generate/Validate Field and Lab Data Salmon and steelhead tissue sampling and data collection

Proposed action to achieve the objective(s) Without restoration of the $69,075 cut from this project in FY2009, we must reduce
our genotyping, analysis, and reporting goals by approximately 1,727 fish. Although
we will continue to collect samples consistent with our original design and guidance
from the comanagers, we will not be able to provide analysis of those samples in time
to provide results to managers until those samples can be analyzed, either in our lab
or another.

Does not implementing this modification jeopardize the ability to achieve existing biological objectives of this project, as well as other projects? Yes

Explain: We've worked with comanagers and collaborators to maintain the integrity of this
project despite level funding since 2005--a period of time that have seen at least
a 20% increase in our costs. Again, the net effect is to delay the availability of
critically important information on the reproductive success of hatchery fish spawning
in the wild and the general effects of hatchery propagation over time and under
different management regimes. Other BPA projects such as Idaho supplementation have
been declined funding for genetics and referred to this project for support. With
continued loss of funding for our genetic monitoring project, we're increasingly
unable to meet that obligation.

Section 2d: Description (BiOp Information)
NMFS and/or FWS Biological Opinion that this funding request addresses Strategy
NMFS &/or USFWS
How proposed actions will address the BiOp
(i.e., substrategy / limiting factor / metric to be achieved)
NMFS 2004 RM&E Substrategy 2.3 Action Effectiveness Research hatchery Project 198909600 seeks to determine whether safety-net and other hatchery programs contribute to recovery. Specifically, we characterize ecological genetic impacts of hatchery stocks on wild populations, and we've developed a framework for genetic M&E.
NMFS 2004 RM&E Strategy 3: Critical Uncertainties Research hatchery The central focus of our project is on relative reproductive success of hatchery fish spawning in the wild and the associated genetic effects of art prop over time.
NMFS 2004 RM&E Strategy 5: Data Management System hatchery Our primary responsibility is to share results with comanagers in real time, both raw data for reanalysis and summary narratives. We are principal facilitators for regional and international, shared, genetic databases that broadly support BPA goals and help leverage research efforts across projects and applications.
NMFS 2004 RM&E Strategy 6: REgional Coordination hatchery This project is tightly coordinated with other BPA-funded genetics laboratories (CRITFC, IDFG, USFWS, and WDFW). We collaborate with those groups to share tissue samples and genetic data (please see above).

Section 2e: Description (Objectives)
Objectives of this proposed project
Objective
(abbreviation)
Full Description
1. Describe gentics Clearwater Sub-Basin Plan, Strategy 4. Proposed Research: Assess population status, limiting factors, and genetics of redband rainbow trout in the Clearwater subbasin (pp 72 - 73). 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.
1. Describe genetics Imnaha Sub-basin Plan, Strategy 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 (p 119). The proposed study design will continue to provide basic descriptive population genetic data that is recommended in the Subbasin Plan.
1. Describe genetics Imnaha Sub-Basin PLan, Strategy 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] (pp 119 - 120). The proposed study offers the further population-level characterization that is called for in both spring/summer Chinook and summer steelhead.
1. Describe genetics Tucannon Sub-basin Plan, Strategy Critical uncertainties...understanding the relationship between resident and anadromous O. mykiss subpopulations (App M, 3). 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
1. Describe genetics Salmon River Sub-basin Plan, Strategy “…carry out focused activities designed to improve our understanding of wild populations” (Table 5, p 18). The cornerstone of our study design is a broad characteriztion of native, and wild populations, at least to the extent that is possible.
1/3 Desc/measure gene change Tucannon Sub-basin Plan, Strategy 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” (App M, 12). The study design proposed here is exactly concordant with RM&E recommendations for genetic characterization and monitoring of effective population size.
1/3 Desc/measure gene change Salmon Sub-basin Plan, Strategy “Minimize short- and long-term genetic, ecological and life history effects on wild populations.” (Table 5, p 18). This study design provides information about both short- and long-term changes in genetic diversity and structure.
1/3 Desc/measure gene change Clearwater Sub-basin Plan, Strategy C 2 Research stock specific interactions between wild and hatchery fish in areas influenced by hatcheries in the Clearwater (p 55). This study design characterizes stock-specific genetic changes through time.
1/3 Desc/measure gene changes Tucannon Sub-basoin Plan, Strategy 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 (App M, 2-3). 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.
1/3 Desc/measure gene changes Clearwater Sub-basin Plan, Strategy 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 (p 75). The design proposed here will refine stock structure and population boundary information and will monitor genetic relationships and characteristics through time.
1/3 Desc/measure gene change Imnaha Sub-basin Plan, Strategy 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 (p 22). 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 differentclasses of salmon populations for changes in genetic characteristics over time.
1/3 Desc/measure gene change Imnaha Sub-basin Plan, Strategy 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) (p 81). 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).
1/3 Desc/measure gene change Imnaha Sub-basin Plan, Strategy 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 (p 118). 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 furthercoordination and facilitation of interagency genetic research throughout the Columbia River basin.
1/3 Desc/measure gene change Grande Ronde Sub-basin Plan, Strategy 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 (p 280 - 282). Our study maps neutral and potentially selected genetic diversity against life history characteristics and compares those relationships among hatchery, natural (supplemented), and wild (unsupplemented).
1/3 Desc/measure gene change Grande Ronde Sub-basin Plan, Strategy 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 (p 65). 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.
2. Reproductive success Grande Ronde Sub-basin Plan, Strategy Monitoring and Evaluation Objective 2b: Determine and compare relative reproductive success of hatchery and naturally produced focal species (p 279). 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.
2. Reproductinve success Imnaha Sub-basin Plan, Strategy MANAGEMENT OBJECTIVE 2: ASSESS, MAINTAIN, AND ENHANCE NATURAL PRODUCTION AND SURVIVAL OF FOCAL SALMONID POPULATIONS IN SUPPLEMENTED STREAMS WITHIN THE IMNAHA (p 71). 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.
2. Reproductive success Imnaha Sub-basin Plan, Strategy 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) (p 79). M&E Objective 2b is exactly concordant with our primary focus to estimate reproductive success.
4. Standardized marker develop Imnaha Sub-basin Plan, Strategy 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 (p 55). 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).
4. Standardized marker develop Clearwater Sub-basin Plan, Strategy Coordination Potential: Coordinate with ongoing genetics research efforts and/or other population status M&E programs (p 75). 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.
4. Standardized marker develop Tucannon Sub-basin Plan, Strategy 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 (p176 - 177). 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.
4. Standardized marker develop Salmon Sub-basin Plan, Strategy 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 (p 105 - 106). 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.
4. Standardized marker develop Grande Ronde Sub-basin Plan, Strategy 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 (288 - 289). Use of standardized markers and genotyping conventions allows independent validation and verification by multiple interested parties (CRITFC, WDFW, etc.).
4. Standardized marker develop Grande Ronde Sub-basin Plan, Strategy 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 (p 289). Coordination and standardization facilitates collaboration, reduces redundancy and maximizes efficiency in addressing a wide range of genetic questions.
5. Evaluate genetic monitoring (No associated sub-basin plan) 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 (p 10). An integral part of this study is evaluation of the utility of our results and the effectiveness of our M&E methods.

Section 3: Is This Funding Request Related to Other Projects in the Basin?

Other projects that are related to this request
Project # Project Title/Description Nature of Relationship
198712700 Smolt Monitoring by Federal and Non-Federal Agencies Sampling and information exchange is coordinated with this program.
198805301 NE OR Hatchery Master Plan Sampling and information exchange is coordinated with this program.
198805305 Northeast Oregon Hatcheries Implementation Sampling and information exchange is coordinated with this program.
198909800 Idaho Supplementation Studies Sampling and information exchange is coordinated with this program.
199005200 Performance/Stock Productivity Impacts of Hatchery Supplementation Sampling and information exchange is coordinated with this program.
199005500 Steelhead Supplementation Studies in Idaho Rivers Sampling and information exchange is coordinated with this program.
199009300 Analysis Of Oncorhynchus Nerka (Modified To Include Chinook Salmon) Sampling and information exchange is coordinated with this program.
199107300 Idaho Natural Production Monitoring And Evaluation Sampling and information exchange is coordinated with this program.
199606700 Manchester Spring Chinook Broodstock Project Sampling and information exchange is coordinated with this program.
199800702 Grande Ronde Supplementation: Lostine River O&M and M&E Sampling and information exchange is coordinated with this program.
199801001 Grande Ronde Basin Spring Chinook Captive Broodstock Program Sampling and information exchange is coordinated with this program.

Section 4: Estimated Budget for Planning & Design phase for this request (request amount only)

Work element-based estimated budget
Planning & Design
Objective Work Element Work Element Title Work Element Description Description of Metrics Task Duration
in FYs
Estimated Budget Subcontractor?

Outyear work element-based estimated 2009 - 2012 budget for this proposal
Planning & Design
Work Element Work Element Outyear Description Starting FY
numbers only
Ending FY
numbers only
Estimated cost

Outyear totals
Planning & Design

Section 5: Estimated Budget for Contruction/Implementation phase for this request (request amount only)

Work element-based estimated budget
Contruction/Implementation
Objective Work Element Work Element Title Work Element Description Description of Metrics Task Duration
in FYs
Estimated Budget Subcontractor?

Outyear work element-based estimated 2009 - 2012 budget for this proposal
Contruction/Implementation
Work Element Work Element Outyear Description Starting FY
numbers only
Ending FY
numbers only
Estimated cost

Outyear totals
Contruction/Implementation

Section 6: Estimated Budget for Operations & Maintenance phase for this request (request amount only)

Work element-based estimated budget
Operations & Maintenance
Objective Work Element Work Element Title Work Element Description Description of Metrics Task Duration
in FYs
Estimated Budget Subcontractor?
1. Describe genetics Collect/Generate/Validate Field and Lab Data 157: Salmon and steelhead tissue sampling 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. Primary R, M, and E Focal Area : Hatchery; Primary R, M, and E Type : Uncertainties Research; Secondary R, M, and E Type : Action Effectiveness Research; Secondary R, M, and E Focal Area : Population Status 1 $69,075 No

Outyear work element-based estimated 2009 - 2012 budget for this proposal
Operations & Maintenance
Work Element Work Element Outyear Description Starting FY
numbers only
Ending FY
numbers only
Estimated cost

Outyear totals
Operations & Maintenance

Section 7: Estimated Budget for Monitoring & Evaluation phase for this request (request amount only)

Work element-based estimated budget
Monitoring & Evaluation
Objective Work Element Work Element Title Work Element Description Description of Metrics Task Duration
in FYs
Estimated Budget Subcontractor?

Outyear work element-based estimated 2009 - 2012 budget for this proposal
Monitoring & Evaluation
Work Element Work Element Outyear Description Starting FY
numbers only
Ending FY
numbers only
Estimated cost

Outyear totals
Monitoring & Evaluation

Section 8: Total Budget Modification Request

Itemized Estimated Budget
Item Note FY 2008 Cost
Personnel [blank] $22,388
Fringe Benefits [blank] $11,731
Supplies [blank] $15,650
Travel [blank] $ 0
Capital Equipment [blank] $ 0
Overhead [blank] $17,973
Other Contract, instrument service $1,230
Other Contract, waste disposal $103

Total Estimated Budget Modification
Total FY 2008 budget modification $69,075
Total FY 2008 budget for this project, including modification request $460,500

Outyear Budget Totals
Not applicable

Cost sharing associated with this modification
Organization Item or Service Provided Amount ($) Cash or in-kind?
Pacific Salmon Commission Support for coast-wide database $23,025 In-Kind
NOAA-Fisheries Population genetics of Snake R. steelhead $27,630 In-Kind
NOAA-Fisheries Coordination of marker development $4,605 In-Kind
US Army Corps of Engineers Migration and habitat use by Snake R Chinook in the Columbia R estuary $4,605 In-Kind

Section 9: Narrative, Maps and Project Documents
Document Type Size Date

Part 2 of 3. Current Status of Modification Request
Meeting Date Status Record Entry Date Decision Group Adjustment Category Urgency Status Budget Impact Reconsider Date
10/8/2008  9/30/2008  NA      Submitted  $69,075   
Decision Comments Next Steps
   
10/8/2008  10/8/2008  BOG  Budget  CAT-3b2: Loss of Monitoring and Evaluation Data  Under BOG Review  $69,075  2/15/2009 
Decision Comments Next Steps
This request is part of BPA 15% reduction.  This request will be pooled for the 1st Quarter Review with a February decision. 
10/8/2008  2/11/2009  BPA  Budget    BPA Denied  $ 0   
Decision Comments Next Steps
Per letter from Bill Maslen to Tony Grover on 1/6/09, FY09 budgets were increased to FY08 levels. Therefore, no additional funds will be added via this BOG request.   

Part 3 of 3. Comments on this Modification Request
Comment Date Commentor Agency Comment
9/30/2008 Paul Moran National Marine Fisheries Service Please note that this budget modification request seeks to restore funding cut from the *FY2009* budget for project 198909600.