FY07-09 proposal 200725000

Jump to Reviews and Recommendations

Section 1. Administrative

Proposal titleGenetic Evaluation of Chinook Salmon Supplementation in Idaho Rivers
Proposal ID200725000
OrganizationIdaho Department of Fish and Game / Nez Perce Tribe
Short descriptionWe intend to use DNA analyses to quantify the relative reproductive success of Chinook salmon of various origins in ISS study streams. This will help determine the effect of "de facto" supplementation by hatchery strays in treatment and control streams.
Information transferInformation will be transferred in a variety of means. Summarized data will be available annually in technical reports that should lead to peer reviewed publicatoin. Raw data will be stored on the centralized ISS web server where it will be available upon request. Data colleted by this program will also be provided as appropriate to regional databases such as STREAMNET, PSMFC, RMIS, and others.
Proposal contact person or principal investigator
Contacts
ContactOrganizationEmail
Form submitter
David Venditti Idaho Department of Fish and Game dvenditti@idfg.idaho.gov
All assigned contacts
Conan Chiu Idaho Department of Fish and Game cchiu@idfg.idaho.gov
Arleen Henry Nez Perce Tribe arleenh@nezperce.org
Jay Hesse Nez Perce Tribe jayh@nezperce.org
Jerald Lockhart Nez Perce Tribe jerryl@nezperce.org
Dan Schill Idaho Department of Fish and Game dschill@idfg.idaho.gov
David Venditti Idaho Department of Fish and Game dvenditti@idfg.idaho.gov

Section 2. Locations

Province / subbasin: Mountain Snake / Salmon

LatitudeLongitudeWaterbodyDescription
44 06 54.7 N 114 25 43.9 W East Fork Salmon River At and above the ISS weir and screw trap on the East Fork Salmon River
46 22 19.9 N 116 09 55.9 W Lolo Creek At and above the ISS weir and screw trap on Lolo Creek
45 49 55.7 N 115 36 45.1 W Newsome Creek At and above the ISS weir and screw trap on Newsome Creek
45 48 26.6 N 115 28 15.5 W Red River At and above the ISS weir and screw trap on the Red River
44 07 28.0 N 114 52 08.2 W Salmon River At and above the ISS weir and screw trap on the Salmon River above Sawtooth Hatchery
44 52 02.4 N 115 41 50.3 W South Fork Salmon River At and above the ISS weir and screw trap on the South Fork Salmon River
44 41 08.5 N 114 02 24.5 W Pahsimeroi River At and above the ISS weir and screw trap on the Pahsimeroi River

Section 3. Focal species

primary: Chinook Snake River Spring/Summer ESU

Section 4. Past accomplishments

YearAccomplishments

Section 5. Relationships to other projects

Funding sourceRelated IDRelated titleRelationship
BPA 198909800 Salmon Studies Id Rvrs IDFG This project will use IDFG ISS screw traps, weirs, and personnel to collect most of the adult and juvenile DNA samples for the project on the Red, South Fork Salmon, Pahsimeroi, and upper Salmon rivers. IDFG ISS personnel will administer this project on these streams as well as the East Fork Salmon River.
BPA 198335003 Nez Perce Tribal Hatchery M&E This project will use NPT hatchery screw traps, weirs, and personnel to collect most of the adult and juvenile DNA samples for the project on the Lolo and Newsome creeks.
BPA 198909802 Salmon Studies Id Rvrs NPT NPT ISS personnel will administer this project on Lolo and Newsome creeks.
BPA 198909803 Salmon Studies Id Rvrs SBT This project will use the SBT ISS screw trap and personnel on the East Fork Salmon River to collect Juvenile DNA samples for this project.
BPA 199700100 Idaho Chinook Salmon Captive R Personnel from the Captive Rearing project will collect most of the adult DNA samples for this project from the East Fork Salmon River.
Other: LSRCP 14110-0-J007 LSRCP Chinook Evaluation Studies in Idaho This LSRCP program can provide personnel to collect adult DNA samples on the South Fork Salmon River.
Other: LSRCP [no entry] LSRCP Migigation Hatcheries Hatchery personnel from Sawtooth, Pahsimeroi, McCall, and Clearwater hatcheries will operate weirs for adult collections
BPA 198909801 Salmon Studies Id Rvrs USFWS Cooperator

Section 6. Biological objectives

Biological objectivesFull descriptionAssociated subbasin planStrategy
Compare reproductive success between adult groups Determine if there are statistically significant differences in the reproductive contribution between natural, ISS supplementation, and GP hatchery adults when measured in the resulting progeny. Clearwater Problem 1.A.2 Problem 3.C.2,3 Problem 3.D.1,3,4,5 "ISRP 2003-8 pg 4" "NPPC memo dated 7/9/2003 M. Fritsch to F&W Comittee Members pg 1" "ISRP/ISAB 2005-15 pg 7, 9" "ISRP 2005-14 pg 85"
Compare reproductive success between adult groups Determine if there are statistically significant differences in the reproductive contribution between natural, ISS supplementation, and GP hatchery adults when measured in the resulting progeny. Salmon 1B4, 2A2&7, 3A2, 3C4
Determine relatedness between spawning populations Determine the level of relatedness/differentiationbetween spawning aggregates in ISS treatment and control streams as well as the hatcheries used as sources of treatment juveniles and compare this to relatedness/ differentiation levels observed in baseline ISS genetic samples. Clearwater Problem 1.A.2. Problem 3.C.2,3. Problem 3.D.1,3,4
Determine relatedness between spawning populations Determine the level of relatedness/differentiationbetween spawning aggregates in ISS treatment and control streams as well as the hatcheries used as sources of treatment juveniles and compare this to relatedness/ differentiation levels observed in baseline ISS genetic samples. Salmon 1B4, 2A1-2&4&7, 3C4
Effect of differences on long term viability Estimate the effects of reproductive differences between Chinook salmon of different origins on population growth, recovery, and genetic fitness in subsequent generations according to VSP criteria. Clearwater Problem 1.A.2 Problem 3.C.2,3 Problem 3.D.1,2,4
Effect of differences on long term viability Estimate the effects of reproductive differences between Chinook salmon of different origins on population growth, recovery, and genetic fitness in subsequent generations according to VSP criteria. Salmon 1.B.1&4, 2.A.1&2&4&7,
Persistence of reproductive differences Determine if F1 parental origin (natural, ISS supplementation, or GP hatchery) affects reproductive success in F2 progeny. Salmon 1.B.4, 2.A.2&4&7, 3.A.1, 3.C.4
Persistence of reproductive differences Determine if F1 parental origin (natural, ISS supplementation, or GP hatchery) affects reproductive success in F2 progeny. Clearwater Problem 1.A.2 Problem 3.C.2,3 Problem 3.D.1,3,4,5
Spawner to spawner contribution by origin Determine if F1 juveniles with different parental origin (natural, ISS supplementation, or GP hatchery) return at different rates as adults. Clearwater Problem 1.A.1,3 Problem 3.D.1,4
Spawner to spawner contribution by origin Determine if F1 juveniles with different parental origin (natural, ISS supplementation, or GP hatchery) return at different rates as adults. Salmon 1.A.1, 1.B.4.2.A.2&4&7, 3.A.1, 3.C.4

Section 7. Work elements (coming back to this)

Work element nameWork element titleDescriptionStart dateEnd dateEst budget
Analyze/Interpret Data Effect of Supplementation and/or Straying on Long-term Population Viability Estimate the effects of reproductive differences between Chinook salmon of different origins on population growth, recovery, and genetic fitness in subsequent generations according to VSP criteria. 1/1/2010 8/31/2010 $30,000
Biological objectives
Effect of differences on long term viability
Metrics
Focal Area: Systemwide
Primary R, M, and E Type: Action Effectiveness Research
Analyze/Interpret Data Produce Reports and Publications Biologist time to analyze and interpret data for inclusion in contract reports and peer reviewed publications 1/1/2007 8/31/2010 $85,430
Biological objectives
Compare reproductive success between adult groups
Metrics
Focal Area: Tributaries
Primary R, M, and E Type: Uncertainties Research
Secondary R, M, and E Type: Action Effectiveness Research
Collect/Generate/Validate Field and Lab Data Carcass Surveys on Study Streams Conduct carcass surveys on study streams approximately every other day to collect carcasses of fish not sampled at weirs. Budget includes personnel cost for 12 month temporary technician as well as 3 month temporary technician for field collections. 7/1/2007 8/31/2010 $224,700
Biological objectives
Compare reproductive success between adult groups
Metrics
Focal Area: Tributaries,
Collect/Generate/Validate Field and Lab Data Collect DNA from juvenile Chinook salmon at ISS screw traps Collect tissue samples for DNA analyses from juvenile Chinook salmon emigrating from ISS study reaches above traps for. Juvenile DNA will be removed for various reasons and studies (e.g., parental analysis, baseline comparisons with historic stocks). The number of samples collected will vary between streams (and years) based on the projected number of migrants each year and to compensate for incomplete adult sampling at some locations. Sample collection at the South Fork Salmon, Red, Pahsimeroi, and upper Salmon river weirs will be provided by BPA Project 198909800; Lolo Creek weir, Newsome Creek weir BPA Project 198335003; and East Fork Salmon River BPA Project 198909803. 3/15/2007 8/31/2010 $35,000
Biological objectives
Compare reproductive success between adult groups
Metrics
Focal Area: Tributaries,
Collect/Generate/Validate Field and Lab Data Collect DNA Samples from Adult Chinook Salmon at ISS Weirs Collect tissue samples for DNA analyses from all adult Chinook salmon released to spawn naturally upstream of ISS escapement weirs. DNA samples will be used to quantify reproductive success of adults by origin type. Sample collection at the South Fork Salmon, Red, Pahsimeroi, and upper Salmon river weirs will be provided by BPA Project Number 198909800 East Fork Salmon River weir will be provided by BPA Project 199700100; Lolo Creek weir, Newsome Creek weir BPA project 198335003. 6/1/2007 8/31/2010 $25,000
Biological objectives
Compare reproductive success between adult groups
Metrics
Focal Area: Tributaries
Collect/Generate/Validate Field and Lab Data Effect of F1 Parental Origin on F2 Reproductive Contribution Conduct parentage analyses on F2 adults with known parentage to determine if (assumed) differences in observed contribution in F1 origin adults persist. 1/1/2007 8/31/2010 $35,000
Biological objectives
Persistence of reproductive differences
Metrics
Focal Area: Tributaries
Primary R, M, and E Type: Uncertainties Research
Collect/Generate/Validate Field and Lab Data F2 Adult Returns by F1 Parental Origin Conduct parentage analyses on F2 adults (by brood year) to determine if returns by parental origin differ from what was observed in emigrating juveniles. 1/1/2007 8/31/2010 $35,000
Biological objectives
Spawner to spawner contribution by origin
Metrics
Focal Area: Systemwide
Primary R, M, and E Type: Uncertainties Research
Collect/Generate/Validate Field and Lab Data Locate and Re-analyze ISS Baseline Samples Locate as many of the original ISS baseline genetics samples as possible and re-analyze them using the suite of CTC microsatellite loci to more accurately describe relatedness/differentiation between spawning aggregates in ISS streams prior to inception of the program. 1/1/2007 12/31/2008 $86,400
Biological objectives
Determine relatedness between spawning populations
Metrics
Focal Area: Tributaries
Primary R, M, and E Type: Uncertainties Research
Collect/Generate/Validate Field and Lab Data Parentage Analysis for Fish Sampled During 2007 - 2009 (Adult to Juvenile) Extract and perform parental exclusion tests on adult and juvenile DNA samples collected from weirs and screw traps on study streams collected during 2007 – 2009. Analysis will include a summary report from the subcontracting lab including information on allele frequency, heterozygosity, allelic composition, and relatedness of fish (samples) analyzed. 4/1/2007 8/31/2010 $2,004,660
Biological objectives
Compare reproductive success between adult groups
Metrics
Focal Area: Tributaries
Primary R, M, and E Type: Uncertainties Research
Collect/Generate/Validate Field and Lab Data Parentage Analysis for Samples Currently in Inventory (Adult to Juvenile) Extract and perform parental exclusion tests on adult and juvenile DNA samples collected from weirs and screw traps on study streams collected since 2002. Analysis will include a summary report from the subcontracting lab including information on allele frequency, heterozygosity, allelic composition, and relatedness of fish (samples) analyzed. 1/1/2007 12/31/2008 $330,000
Biological objectives
Compare reproductive success between adult groups
Metrics
Focal Area: Tributaries
Primary R, M, and E Type: Uncertainties Research
Collect/Generate/Validate Field and Lab Data Relatedness Through Time in ISS Streams Annually perform microsatellite genotyping on a subset of approximately 60 DNA samples collected from ISS treatment and control streams and hatchery populations used in ISS broodstocks to quantify relatedness changes over time. 3/1/2007 8/31/2010 $172,800
Biological objectives
Determine relatedness between spawning populations
Metrics
Focal Area: Tributaries,
Primary R, M, and E Type: Action Effectiveness Research
Create/Manage/Maintain Database Develop Data Handling / Database Needs Develop, manage, maintain, organize, provide access to, develop analysis protocols for, and provide security for the immense amount of raw data that will be generated by this program from multiple sampling sites and from laboratories around the Pacific Northwest. 1/1/2007 8/31/2010 $150,000
Biological objectives
Compare reproductive success between adult groups
Metrics

Section 8. Budgets

Itemized estimated budget
ItemNoteFY07FY08FY09
Supplies IDFG Contract $11,700 $11,900 $12,100
Travel IDFGContract $3,500 $3,700 $3,900
Other IDFG Contract Database development and maintenance $50,000 $50,000 $50,000
Other IDFG Contract Genetic and statistical consulting $10,000 $5,000 $5,000
Personnel IDFG Personnel $54,062 $55,684 $57,354
Fringe Benefits IDFG Personnel $24,436 $25,169 $25,924
Overhead IDFG Overhead (21%) $32,277 $31,805 $32,398
Personnel NPT Contract $32,781 $34,747 $36,832
Fringe Benefits NPT Contract $9,277 $9,833 $10,423
Supplies NPT Contract $6,491 $7,231 $7,396
Travel NPT Contract $6,226 $6,413 $6,605
Overhead NPT Contract $16,241 $17,263 $18,162
Other NPT subcontract genetic analysis archived samples $330,000 $0 $0
Other SBT subcontract genetic analyses FY07-09 $668,220 $668,220 $668,220
Other SBT subcontract genetic analyses relatedness $32,500 $32,500 $32,500
Totals $1,287,711 $959,465 $966,814
Total estimated FY 2007-2009 budgets
Total itemized budget: $3,213,990
Total work element budget: $3,213,990
Cost sharing
Funding source/orgItem or service providedFY 07 est value ($)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: $1,015,155
FY 2011 estimated budget: $1,015,155
Comments: Assumes a 5% annual budget increase

Future O&M costs: Little additional O&M would be necessary because juvenile collections would end along with ISS collections, and hatchery personnel will continue to operate weirs for broodstock collection.

Termination date: 12/31/2019
Comments: This date would allow the collection of the last F2 generation adults in late 2017 and then approximately one and a half years for final analyses and publication of peer reviewed articles

Final deliverables: Completion report and one or more peer reviewed publications

Section 10. Narrative and other documents

200725000 Responses Jul 2006

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 Basinwide
NPCC DRAFT FUNDING RECOMMENDATIONS (Sep 15, 2006) [full Council recs]
$0 $0 $0 $0 ProvinceExpense
Comments: Also reviewed by MSRT

ISRP PRELIMINARY REVIEW (Jun 2, 2006)

Recommendation: Response requested

NPCC comments: This proposal was generated in response to the ISRP's recommendation on the ISS to use parentage analysis to partition juvenile Chinook production in ISS streams by natural, supplementation, and general production hatchery parents. Recognizing that the ISRP recommended a parentage analysis for the ISS, this new project should be justified within the context of the larger genetic network in the Columbia River Basin. The response should include evidence of discussion and coordination with ongoing efforts in the Basin. Are the proposed streams sites the best place to do this parentage analysis? Please include in response why these sites were chosen and what advantages they have over other sites? See programmatic comment and provide clear evidence that there is a regional statistical design for this work taking advantage of economies of scale for collection and testing of samples. In response, please include more details of the methods for genetic testing and collection. The Lutch report previously reviewed by the ISRP describes some of the methods, but the methods need to be summarized in the current proposal. If selected for funding, this project should be demonstrated and funded in phases; e.g., this project can be allocated funding based on demonstration of the ability to perform the parentage analysis, and expanded to genotype the full suite of individuals as justified by evidence that the uncertainties can be resolved. For analyses of population change objective see Pearse, D. E. and K. A. Crandall. 2004. Beyond Fst: Analysis of population genetic data for conservation. Conservation Genetics 5:585-602. For both analysis of population change and parentage analysis, the critical element at this point is to collect tissues. This should be recommended at the full-scale project to estimate mating behavior, not just single parent assignments. After a reasonable number of individuals are genotyped, preliminary analyses can be performed to inform the decision as to whether or not to complete genotyping for the entire set of individuals. The project has yet to identify a lab to genotype the fish but that should not be a problem. At this time a lead geneticist is not identified. This needs to happen before the genotyping begins. The budget for the genetics work, about 1 million per year, seems very high. The percentage of funding for the genetic work appears higher than in other similar proposals. Over the past few years, the cost per specimen has been going down. In response, please provide additional justification for the anticipated costs per specimen and for equipment. If the budget includes sot of equipment, what opportunities exist for reducing costs by subcontracting to other labs?


ISRP FINAL REVIEW (Aug 31, 2006)

Recommendation: Fundable

NPCC comments: The sponsor provides a complete reply to the questions raised by the ISRP. The ISRP requested evidence and justifications that the sites selected for an analysis of the relative reproductive performance of general production (hatchery), supplementation (hatchery), and natural-origin salmon were suitable. This response is thorough. The ISRP also requested additional information on the type of analysis the sponsor was going to pursue. The sponsor provided information on the type of genetic marker they intend to employ (the coastwide standard Chinook microsatellite panel) and that either assignment or exclusion methods would be used to identify parents. Sponsor provided a thorough discussion of sample sizes and statistical tests to evaluate assortative mating. The response to the ISRP questions were less satisfying regarding 1) beginning with an initial analysis followed by expanding the investigation to archived and contemporary samples, and 2) identifying a lead geneticist, a genetics lab to perform the genotyping, and an apparently high cost per sample. In response to the ISRP suggestion that the analysis begin with a subset of individual and demonstrate the ability to reasonably make an assessment of relative reproductive success, the sponsors noted that they have been associated with successful studies with Chinook salmon in the Pahsimeroi River and with sockeye salmon in Redfish Lake. The ISRP does not question the feasibility of the methodology working or the ability of the sponsor to execute the work. The query was about whether in this specific instance the estimates of reproductive success will be reasonable and statistically justified. In coho salmon studies in Minter Creek, Washington and steelhead studies in Hood River, Oregon there are an appreciable number of individuals that cannot be assigned to parents. It is unknown whether this represents individuals produced by resident fish or migrants. If this were the case in the ISS streams, extensive effort would not be justified. Nonetheless, the ISRP considers the examples provided sufficient evidence of proof of concept. Finally while the ISRP would prefer that in a project of this magnitude and importance the lead geneticist and lab would have been established before the proposal was accepted, we are satisfied they have a framework for identifying an appropriate lead geneticist and lab.