FY07-09 proposal 200713300
Jump to Reviews and Recommendations
Section 1. Administrative
| Proposal title | Systemwide distribution of genetic variation within and among populations of the white sturgeon (Acipenser transmontanus) |
| Proposal ID | 200713300 |
| Organization | University of California at Davis |
| Short description | We will analyze microsatellite genetic variation within and among white sturgeon populations throughout their range to assess both the interrelationships of populations to one another and the genetic health of the populations within the Columbia basin. |
| Information transfer | Microsatellite genetic variation will be compiled, analyzed, and reported in progress and annual reports to BPA and USFWS ; in symposia, conferences and workshops (both general fisheries and sturgeon specific); in peer-reviewed scientific publications; to state, tribal, and federal management and research agencies; and to other stakeholder groups. |
| Proposal contact person or principal investigator | |
Contacts
| Contact | Organization | |
|---|---|---|
| Form submitter | ||
| Bernie May | University of California at Davis | bpmay@ucdavis.edu |
| All assigned contacts | ||
| Paul Anders | S.P. Cramer and Associates, UI | anders@spcramer.com |
| Paul Anders | S.P. Cramer and Associates, UI | anders@spcramer.com |
| Mary Curtis | U.S. Fish and Widlife Service | Mary_Curtis@fws.gov |
| Steven Fain | U.S. Fish and Wildlife Service - National Fish and Wildlife Forensic Laboratory | steve_fain@fws.gov |
| Bernie May | University of California at Davis | bpmay@ucdavis.edu |
| Bernie May | University of California at Davis | bpmay@ucdavis.edu |
| Jeff Rodzen | California Department of Fish and Game | jrodzen@dfg.ca.gov |
| Jeff Rodzen | California Department of Fish and Game | jrodzen@dfg.ca.gov |
Section 2. Locations
Province / subbasin: Mainstem/Systemwide / Systemwide
| Latitude | Longitude | Waterbody | Description |
|---|
Section 3. Focal species
primary: White Sturgeon All PopulationsSection 4. Past accomplishments
| Year | Accomplishments |
|---|
Section 5. Relationships to other projects
| Funding source | Related ID | Related title | Relationship |
|---|---|---|---|
| BPA | 198605001 | Experimental White Sturgeon Re | Defines population, diversity, gene flow, relatedness, and population structure to benefit design and management of existing and future project(s) |
| BPA | 198605000 | Evaluate Sturgeon Physical Hab | Proposed project will define relevant population(s), genetic diversity, gene flow, relatedness, and population structure to benefit design and management of existing and future project(s). |
| BPA | 198806400 | Kootenai R White Sturgeon | Defines population, diversity, gene flow, relatedness, and population structure to benefit design and management of existing and future project(s) |
| BPA | 199502700 | Lake Roosevelt Sturgeon | Proposed project will help assess white sturgeon stock and genetic status to assist in developing and implementing management actions for blocked area fisheries |
| BPA | 199700400 | Resident Fish Above Chief Joe | Proposed project will help assess white sturgeon stock and genetic status to assist in developing and implementing management actions for blocked area fisheries |
| BPA | 199700900 | Eval Sturgeon Pop - Snake R (L | Proposed project will define relevant population(s), genetic diversity, gene flow, relatedness, and population structure to benefit design and management of existing and future project(s). |
| BPA | 200302700 | White Sturgeon Oxbow/Hells Can | Proposed project will define relevant population(s), genetic diversity, gene flow, relatedness, and population structure to benefit broodstock source evaluations and choices for a put, grow, and take white sturgeon fishery in Oxbow and Hells Canyon reservoirs |
| BPA | 198806500 | Kootenai R White Sturgeon Inve | Proposed project will define relevant population(s), genetic diversity, gene flow, relatedness, and population structure to benefit design and management of existing and future project(s). |
Section 6. Biological objectives
| Biological objectives | Full description | Associated subbasin plan | Strategy |
|---|---|---|---|
| Determine genetic variation | Determine the genetic variation within and genetic relationships among white sturgeon populations by examining microsatellite loci. | None | This work involves populations from multiple subbasins: Columbia Gorge Intermountain, Kootenai, Lower Columbia, Mid Columbia, Lower Snake, Middle Snake, Snake-Hells canyon Upper MidColumbia, Upper Snake, and Fraser and Sacramento rivers (outgroups) |
Section 7. Work elements (coming back to this)
| Work element name | Work element title | Description | Start date | End date | Est budget |
|---|---|---|---|---|---|
| Collect/Generate/Validate Field and Lab Data | Acquire tissue samples | Work with field crews from other projects to acquire fin samples from sturgeon.Work to collect, create, generate, our capture source data. Includes initial entering of data into a computer spreadsheet/database, developing automated data capture programs/routines and related hardware/software (e.g., PDAs, data loggers, thermographs), preparing metadata, and quality assurance/quality control processes. Also includes taking samples for later analysis (e.g., fish tissues for DNA analysis, macroinvertebrate samples, etc.), and any preparations for collecting data if not covered by another work element. Also includes generating secondary/derived data when those data are stored in a database for access and use by other parties for analysis like primary data. Capturing data includes entering data into a computer from historical records, digitizing images, and other methods for converting information to digital format. | 10/1/2006 | 6/30/2009 | $45,000 |
|
Biological objectives |
Metrics Primary R, M, and E Type: Project implementation Focal Area: Systemwide |
||||
| Collect/Generate/Validate Field and Lab Data | Collect genotypic data | Extract DNA, run PCRs, run and image amplifications, score genotypes -Work to collect, create, generate, our capture source data. Includes initial entering of data into a computer spreadsheet/database, developing automated data capture programs/routines and related hardware/software (e.g., PDAs, data loggers, thermographs), preparing metadata, and quality assurance/quality control processes. Also includes taking samples for later analysis (e.g., fish tissues for DNA analysis, macroinvertebrate samples, etc.), and any preparations for collecting data if not covered by another work element. Also includes generating secondary/derived data when those data are stored in a database for access and use by other parties for analysis like primary data. Capturing data includes entering data into a computer from historical records, digitizing images, and other methods for converting information to digital format. | 10/1/2006 | 7/30/2009 | $410,182 |
|
Biological objectives Determine genetic variation |
Metrics Focal Area: Systemwide Primary R, M, and E Type: uncertainties research |
||||
| Analyze/Interpret Data | Analyze data | Genotypic data will be analyzed for allelic frequencies, levels of variation within populations, relatednesss of individuals within populations, and relationships among populations. These activities apply analytical tools to render meaning from data for making better management decisions. They go beyond data summaries. Often involves tests of statistical significance and may include modeling, indices, and synthesis. Typically culminates in resource managment recommendations presented in a report of research/evaluation findings or analyses presented as formal publications. | 3/1/2007 | 7/30/2009 | $140,000 |
|
Biological objectives |
Metrics Primary R, M, and E Type: Uncertainties Research, Focal Area: Sytemwide |
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| Produce/Submit Scientific Findings Report | Report findings | This element includes all parts of transmission of finding including: progress reports, presentations at agency meetings and symposia, and scientific publishing. - This applies to two general types of scientific publications: 1) Manuscripts being submitted for publication in a scientific journal and 2) Final technical reports. The latter category includes research and evaluation reports, and higher-level programmatic reviews. Monitoring reports (e.g., updated annual escapement counts) are usually considered part of annual progress reports. "Analysis" typically involves hypothesis testing and/or tests of statistical significance in differences across groups/treatments or time that directly support decisions regarding resource or program/project management. This contrasts with reports that primarily present raw or summarized data (including means, variances, and trends). Preliminary analyses are reported as progress toward Final Scientific Findings reports and should be covered by WE# 132: Produce Annual Report. | 10/1/2006 | 9/30/2009 | $97,000 |
|
Biological objectives |
Metrics |
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| Coordination | Facilitate Columbia Basin Sturgeon Genetics Workgroup | Includes all work to coordinate with other parties involved in Coulmbia Basin white sturgeon projects. Project personnel will facilitate Columbia Basin White Sturgeon Genetics Workgroup, a clearinghouse and mechanism for information exchange among Basin white sturgeon researchers, managers, culturists, planners, and forensics and enforcement specialists. Annual meetings will be a part of the project agenda to address ISRP recommendation for collaboration and coordination, and information sharing among all Columbia Basin white sturgeon projects. | 5/1/2007 | 9/30/2009 | $105,000 |
|
Biological objectives |
Metrics |
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Section 8. Budgets
Itemized estimated budget
| Item | Note | FY07 | FY08 | FY09 |
|---|---|---|---|---|
| Personnel | B. May, 520 hrs. @$53/hr. ; P. Anders, 200 hrs. @ $95/hr.; J. Pedroia (or other tech), 700 hrs. @$19/hr.; graduate student $22,000 (1st year), $24,000 (2nd), $26,000 (3rd) | $81,860 | $83,860 | $85,860 |
| Fringe Benefits | @ 10% for graduate students and @ 35% for others | $23,151 | $23,351 | $23,551 |
| Supplies | biochemicals, glassware, plasticware, equipment maintenance, computing, publications, shipping | $29,000 | $27,000 | $23,000 |
| Travel | Professional meetings, travel between participant locations, to field sites sytemwide, yearly Columbia Basin Sturgeon Genetics Workgroup meetings | $22,000 | $22,000 | $22,000 |
| Capital Equipment | Rapidplate liquid handling workstation | $57,000 | $0 | $0 |
| Overhead | @ 52%, except capital equipment and tuition and fees | $81,126 | $81,230 | $80,293 |
| Other | graduate student tuition and fees | $9,600 | $10,300 | $11,000 |
| Totals | $303,737 | $247,741 | $245,704 | |
Total estimated FY 2007-2009 budgets
| Total itemized budget: | $797,182 |
| Total work element budget: | $797,182 |
Cost sharing
| Funding source/org | Item or service provided | FY 07 est value ($) | FY 08 est value ($) | FY 09 est value ($) | Cash or in-kind? | Status |
|---|---|---|---|---|---|---|
| Calif. DFG Forensics Lab | forensics assistance | $4,039 | $4,241 | $4,453 | In-Kind | Confirmed |
| U.S. Fish and Wildlife Service | Forensics assistance | $5,960 | $5,960 | $2,960 | In-Kind | Confirmed |
| Totals | $9,999 | $10,201 | $7,413 | |||
Section 9. Project future
|
FY 2010 estimated budget: $200,000 FY 2011 estimated budget: $200,000 |
Comments: Other entities within subbasins may wish to address component white sturgeon populations with more detailed genetic studies. Additionally, any enhancement projects will want to follow up with genetic monitoring programs. |
Future O&M costs: This particular project will not incur future costs beyond the three year time-line. Any future costs (e.g., 2010 and beyond) will be generated by interest among agency biologists working within specific subbasins.
Termination date:
Comments:
Final deliverables:
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 | Basinwide | Do Not Fund |
| 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 project sponsors propose genotyping white sturgeon from various (all) locations in the Columbia basin at a minimum of 15 microsatellite loci. The purpose of the genotyping is to provide a better understanding of the population structure of white sturgeon. The background section fails to provide a sufficient summary of the current consensus opinion on the metapopulation structure of white sturgeon - both with the Columbia basin and across the species range - to establish the need and basis for the proposed genotyping. The recruitment problem facing white sturgeon is presented, but the management options for addressing it, and how the data from this project would be used to decide among alternative management choices are not presented. The case that this data will be used to decide among the options available for improving the condition of white sturgeon is not compelling. Although the key geneticists on the west coast are on board, nothing in this proposal has emanated from managers. It needs to have compelling endorsement by the managers who might actually need this information. It is not clear how the results of the genetic analyses would (or should) be interpreted. Sponsors assert (page 12) - "Systemwide population genetic data and derived management recommendations generated from this project will provide meaningful guidelines and quantitative benchmarks for the recovery and preservation of native white sturgeon throughout the Columbia basin." This assertion is not supported by a presentation of the types of guidelines and quantitative benchmarks the data could be used to generate. Page 15: "For example, if recruitment failure is confirmed in a particular population, this project can provide valuable information about whether the native remnant population provides sufficient genetic variability to legitimately act as a re-founding stock." Is there a credible empirical basis for this assertion? How would the sponsors decide what the threshold level of genetic variation should be to determine that a remnant stock is unlikely to provide viable re-founding? Page 15: "Data from this proposed study can also be used to estimate minimum number of breeders contributing to a naturally produced year class, the degree of representation of wild alleles into a conservation aquaculture program, or can be used to assign unknown juvenile fish collected in the wild to hatchery or wild spawned parents." This is true. The important issue is whether or not this information is actually needed by managers to decide between management options they have available to them. Sponsors do not establish this. The ISRP had specific comments on the "description of proposed project benefit" as follows (numbers are from the proposal): 5. Assess historic gene flow patterns to assist with various aspects of sturgeon management. Comment: This would be an important contribution -- the question being whether there was really more than a single population in the anadromous portion of the Columbia basin. The sponsors need to demonstrate that the data they generate could actually accomplish this task, beyond the usual calculation of Nm from Fst. 7. Assess relative genetic health and associated demographic conditions of the extant and remnant white sturgeon populations. Comment: How do the sponsors propose to arrive at these conclusions from there data? Is there an established method to make these decisions? 12. Provide valuable new empirical population genetic data for systemwide white sturgeon management and viability and persistence modeling. Comment: How do the sponsors propose to incorporate genetic data into modeling population viability and persistence? 13. Evaluate individual or systemwide population and species status to help determine the urgency and magnitude of management or conservation intervention. Comment: How do the sponsors propose to use genetic data to make these decisions? The sponsors have been involved with sturgeon genetics in other geographic regions. They could provide more compelling evidence that the data they produced are actually employed to help select among alternative management choices to initiate management options.
ISRP FINAL REVIEW (Aug 31, 2006)
Recommendation: Not fundable
NPCC comments: The project sponsors propose genotyping white sturgeon from various (all) locations in the Columbia basin at a minimum of 15 microsatellite loci. The purpose of the genotyping is to provide a better understanding of the population structure of white sturgeon. The background section fails to provide a sufficient summary of the current consensus opinion on the metapopulation structure of white sturgeon - both with the Columbia basin and across the species range - to establish the need and basis for the proposed genotyping. The recruitment problem facing white sturgeon is presented, but the management options for addressing it, and how the data from this project would be used to decide among alternative management choices are not presented. The case that this data will be used to decide among the options available for improving the condition of white sturgeon is not compelling. Although the key geneticists on the west coast are on board, nothing in this proposal has emanated from managers. It needs to have compelling endorsement by the managers who might actually need this information. It is not clear how the results of the genetic analyses would (or should) be interpreted. Sponsors assert (page 12) - "Systemwide population genetic data and derived management recommendations generated from this project will provide meaningful guidelines and quantitative benchmarks for the recovery and preservation of native white sturgeon throughout the Columbia basin." This assertion is not supported by a presentation of the types of guidelines and quantitative benchmarks the data could be used to generate. Page 15: "For example, if recruitment failure is confirmed in a particular population, this project can provide valuable information about whether the native remnant population provides sufficient genetic variability to legitimately act as a re-founding stock." Is there a credible empirical basis for this assertion? How would the sponsors decide what the threshold level of genetic variation should be to determine that a remnant stock is unlikely to provide viable re-founding? Page 15: "Data from this proposed study can also be used to estimate minimum number of breeders contributing to a naturally produced year class, the degree of representation of wild alleles into a conservation aquaculture program, or can be used to assign unknown juvenile fish collected in the wild to hatchery or wild spawned parents." This is true. The important issue is whether or not this information is actually needed by managers to decide between management options they have available to them. Sponsors do not establish this. The ISRP had specific comments on the "description of proposed project benefit" as follows (numbers are from the proposal): 5. Assess historic gene flow patterns to assist with various aspects of sturgeon management. Comment: This would be an important contribution -- the question being whether there was really more than a single population in the anadromous portion of the Columbia basin. The sponsors need to demonstrate that the data they generate could actually accomplish this task, beyond the usual calculation of Nm from Fst. 7. Assess relative genetic health and associated demographic conditions of the extant and remnant white sturgeon populations. Comment: How do the sponsors propose to arrive at these conclusions from there data? Is there an established method to make these decisions? 12. Provide valuable new empirical population genetic data for systemwide white sturgeon management and viability and persistence modeling. Comment: How do the sponsors propose to incorporate genetic data into modeling population viability and persistence? 13. Evaluate individual or systemwide population and species status to help determine the urgency and magnitude of management or conservation intervention. Comment: How do the sponsors propose to use genetic data to make these decisions? The sponsors have been involved with sturgeon genetics in other geographic regions. They could provide more compelling evidence that the data they produced are actually employed to help select among alternative management choices to initiate management options.