Fast Track FCRPS BiOp Project Review
Section 10. Narrative
This last section of your project form is for text responses, explanations, and justifications that support the previous nine sections of the online form.
To complete and return the Narrative Form (Section 10):
- See the Narrative Instructions document (bullet #3 of online form Section 10)
- Provide as much detail as you need in the spaces marked “(Replace this text with your response in paragraph form).” Although there is no limit to the number of pages for the narrative section, most projects can provide sufficient detail to adequately cover items A-G in 10 pages, complex projects in no more than 25 pages.
- You can insert tables, graphics, or maps into this document.
- This document will be viewed on the Internet. If you refer to online documents, include web addresses and use Word’s hyperlink tool to make those addresses active links in the document.
- Use Word’s spell-check tool before submitting this document.
- Upload your completed narrative using Section 10 of the online form.
Fast Track FCRPS BiOp Project Review - Narrative Form 3
PROJECT TITLE:
Parentage Based Tagging of Snake River hatchery steelhead and Chinook salmon
A. Abstract
This project will genotype approximately 16,500 samples annually to create the first parental genetic baselines for hatchery steelhead and Chinook salmon in the Snake River basin. In doing so, it will effectively, permanently genetically mark ~12 million smolts, per species, per year. Parentage Based Tagging (PBT) should provide a better tool than coded-wire tags to meet specific Fish and Wildlife Program objectives associated with marking hatchery stocks, conducting hatchery effectiveness evaluations and hatchery reform, and estimating harvest contributions of specific stocks to various fisheries. State, tribal and federal agencies in the Snake River basin are uniquely positioned to perform PBT studies for both steelhead and Chinook salmon because most hatchery steelhead and Chinook salmon broodstock spawned in the Snake River for the past two years have been genetically sampled (WA, OR, and ID); significant resources have been dedicated to the development of powerful and cost-efficient genetic markers for both species (SNPs); and there are sampling programs in place at Bonneville Dam, at Lower Granite Dam, and in tribal and non-tribal fisheries in the mainstem Columbia River and in the Salmon and Clearwater Rivers, to sample returning hatchery adults and verify the accuracy and utility of PBT technology. This project will work closely with an existing BPA funded project (2008-907-00) to ensure that future genetic marker sets used in the Columbia River basin are standardized, providing unprecedented genetic tools for managing wild and hatchery stocks in the basin. Genetic Stock Identification techniques will allow the segregation of adult wild runs by origin (major group population or finer scale), and PBT technologies will identify the stock and age of sampled hatchery fish.
B. Problem statement: technical and/or scientific background
For over forty years, researchers and managers in the Columbia River basin have used coded-wire tags (CWTs) to monitor and assess the harvest patterns and survival rates of salmon and steelhead in the Columbia River basin (Johnson 2004). In the Snake River basin, CWT recoveries are one of the primary tools used by managers in Oregon, Washington, and Idaho to:
· Estimate the number of hatchery salmon and steelhead contributing to fisheries in the Columbia River basin
· Estimate run-timing and harvest of individual hatchery stocks
Despite its’ predominance in addressing the above management concerns, CWT technology has several limitations. The process of physically tagging tens of thousands of juveniles from different hatchery stocks is logistically difficult, labor intensive, cost prohibitive, and potentially increases physiological stress to the juveniles just prior to their release for downstream migration. All of these restrictions ultimately limit the total number of juveniles that get tagged each year, which in turn limits the number of CWT recoveries. The resulting small sample sizes greatly reduce statistical power to estimate stock contributions since the precision of these estimates are directly related to the number of CWTs recovered in fisheries or escapements (Hankin et al. 2005).
One technological alternative to CWT management, which would eliminate the problem of small sample sizes, is parentage-based genetic tagging (Anderson and Garza 2005). Parentage-based tagging (PBT) involves annual sampling and genotyping of all broodstock at each hatchery, creating a parental genotype database. Progeny from any of these parents (either collected as juveniles or returning adults), if genotyped, could be assigned back to their parents, thus identifying the hatchery they originated from and their exact brood year. Essentially this technology is very similar to human parentage testing (i.e. “who’s the father?”). The advantage PBT has over CWT technology is increased sample size. By genotyping all parental broodstock, every juvenile and adult is genetically “tagged”. Additional advantages of PBT technology have been summarized by Anderson and Garza (2005) and include:
· The higher proportion of tagged fish may eliminate the need for a secondary, electronic tag detection method in sampling of harvest or in escapement;
· The collection of genetic tissue samples from returning adults at the hatchery requires much less effort than physically tagging the much more numerous offspring;
· While CWT technology requires the sacrifice of fish to recover the tag, only a small, non-lethal fin clip must be collected for PBT genetic analysis;
· Tag loss, which affects CWT to an uncertain but substantial degree (Johnson 2004), is not an issue for PBT;
· A parental PBT genotype database could easily be integrated into a genetic stock identification (GSI) database that shares molecular markers, allowing wild and hatchery adults sampled in the same fishery/migration to be genetically sampled and genotyped with wild adults identified to origin (e.g. DPS/ESU, major population group, population, etc.) and PBT hatchery adults identified to stock and cohort.
While theoretically appealing (Anderson and Garza 2005; 2006), PBT technology still needs to be empirically tested and validated, and over the last three years, several committees and science review groups have recommended that two or more large-scale evaluations of the technology be performed (PFMC 2008; PSC 2008; ISAB/ISRP 2009). Although a number of studies have been completed or are in the process of examining the reproductive success of hatchery and wild salmon and steelhead adults using parentage analysis (Araki et al. 2007, 2008; Baumsteiger et al 2008; Murdoch et al. 2006; ISRP 2003), there have only been two PBT hatchery studies initiated on the west coast (both of limited scale). A project initiated by the Washington Department of Fish and Wildlife is attempting to assign real and theoretical progeny genotypes (using 13 standardized microsatellite loci; Seeb et al. 2007) to hatchery adults from two fall Chinook salmon hatcheries (Voights Creek and George Adams). That project has been hampered by flooding at the Voight Creek hatchery, although hatchery broodstock genotyping and parentage analysis is ongoing (Sewall Young, personal communication). Parentage Based Tagging is also currently being tested on Chinook salmon at the Feather River Hatchery, although closures of ocean and in-river fisheries have greatly limited the recovery of PBT tagged offspring (http://www.csgc.ucsd.edu/EDUCATION/CALFED/CALFEDpdf/ProgressReports/2006/Clemento_Year1.pdf).
While the two projects described above are of relatively small-scale, State, tribal and federal agencies in the Snake River basin are positioned to implement PBT studies for both steelhead and Chinook salmon at the Snake River basin scale. Most hatchery steelhead and Chinook salmon broodstock spawned in the Snake River for the past two years have been genetically sampled (WA, OR, and ID). Significant resources have been dedicated to the development of powerful and cost-efficient genetic markers for both species (SNPs). There are sampling programs in place at Bonneville Dam, at Lower Granite Dam, in tribal and non-tribal fisheries in the mainstem Columbia River and in the Salmon and Clearwater Rivers that can sample returning hatchery adults. Those sampling programs currently in place can facilitate the implementation of PBT technology and verify its accuracy and utility.
Given these recent advancements, we propose to construct the first PBT genetic baselines for Chinook salmon and steelhead hatcheries in the Snake River basin. This project can directly address concerns that have been raised over the feasibility of sampling thousands of hatchery broodstock each year and recording accurate biological information for every fish sampled (objective 1). In addition, we also recognize that although modeling indicates that as few as 60–100 SNPs may allow accurate pedigree reconstruction (Anderson and Garza 2006), this number has been met with skepticism (PSC 2008) and has not been demonstrated empirically. This project can identify a set of SNP markers that can achieve high parental assignment accuracy even when tens of thousands of potential parents are involved and when parentage involves hatchery populations that are very similar genetically due to shared ancestry or in situations where the broodstock contains closely related individuals (ISRP/ISAB 2009) (objective 2). Over the last several years, our lab has participated in coastwide efforts to standardize microsatellite loci for both steelhead and Chinook salmon (GAPS-Seeb et al. 2007; SPAN-Stephenson et al. 2008) and we strongly support the identification and standardization of coastwide SNP marker sets. As such, we plan to coordinate closely with the Columbia River Intertribal Fish Commission (project # 2008-907-00) and other GAPS and SPAN labs to identify SNP marker sets that will afford sufficient resolution to address both GSI needs in the Columbia River basin and PBT needs in the Snake River basin (objective 3). Finally, following identification of SNP marker sets, 100% sampling of hatchery broodstocks, and construction of parental genotype databases for both species (objective 4), we intend to demonstrate the applications of this technology through three “backend” sampling/genotype projects that will provide evaluations of both the accuracy and relative costs of PBT technology in providing equivalent CWT recovery data (objective 5). This will include: 1.) an assessment of the stock composition of Snake River salmon and steelhead passing Bonneville Dam and harvested in mainstem Columbia River fisheries; 2.) a paired CWT and PBT recovery experiment as part of existing LSRCP hatchery evaluations in Idaho; and 3.) an assessment of the origin of straying hatchery steelhead in the Salmon River basin.
Besides providing stock of origin and cohort information, PBT has the potential of contributing to a number of additional evaluations, including: hatchery versus wild reproductive success, ecological and quantitative genetic questions, such as the heritability of age at reproduction
and disease resistance/susceptibility, and estimation of effective population size.
C. Rationale and significance to regional programs
Parentage based Tagging technology addresses recommended Research, Monitoring and Evaluation (RM&E) Strategies called for under NOAA’s Fisheries Federal Columbia River Power System Biological Opinion (BiOp) (http://www.salmonrecovery.gov/Files/ResearchReportsPublications/RME%20RPA%20Assessment%20Report%20June%202009%20Draft%20_4_.pdf). This includes:
§ RPA 55.8-Evaluate new tagging technologies for use in improving the accuracy and assessing delayed or indirect hydro effects on juvenile or adult fish.
§ RPA 50.5- Provide additional status monitoring to ensure a majority of Snake River B-Run steelhead populations are being monitored for population productivity and abundance: “Obtain DNA fingerprint of each hatchery stock so that they can be detected passing through the fisheries and into the spawning grounds”…
§ RPA 50.7-Fund marking of hatchery releases from Action Agencies’ funded facilities to enable monitoring of hatchery origin fish in natural spawning areas and the assessment of status of wild populations.
§ RPA 62.5-Investigate the feasibility of genetic stock identification monitoring techniques.
Parentage Based Tagging addresses objectives and strategies that are outlined in Snake/Hells Canyon, Clearwater, and Salmon sub-basin plans (http://www.nwcouncil.org/fw/program/2008amend/uploadedfiles/111/2_Recommendation.pdf):
§ "Increase hatchery effectiveness for restoration and mitigation" ("explore and implement innovative hatchery actions to achieve both restoration and mitigation objectives").
§ "Monitor status and trends of focal species and populations" ("Gather and analyze harvest data to aid in run reconstruction to evaluate status and action effectiveness")
§ “Monitor and evaluate effectiveness of actions taken to implement measures" ("Monitor effectiveness of hatchery and natural production measures, Gather and analyze harvest data to aid in run reconstruction to evaluate status and action effectiveness.").
Support for this type of tagging project can be found in Basinwide Provisions:
§ Strategies D. 5. Harvest: “Monitor inriver and ocean fisheries and routinely estimate stock composition and stock-specific abundance, escapement, catch, and age distribution. Expand monitoring programs as necessary to reduce critical uncertainties. Manage data so that it can be easily integrated and readily available in real time.”
§ Strategies D. 6. Hydrosystem: “…evaluation of escapement numbers to spawning grounds and hatcheries, research into water temperature effects on fish passage, and the connection between fish passage design and fish behavior.”Monitor and evaluate effectiveness of actions taken to implement measures. Explore and implement innovative hatchery actions to achieve both restoration and mitigation objectives.
Additional support for this type of tagging program are found in recommendations to amend the Columbia River Basin Fish and Wildlife Program to address Population Traits in the Salmon and Clearwater Basins include (http://www.nwcouncil.org/fw/program/2008amend/recs.asp):
§ Quantify salmon stray rates and potential genetic consequences
§ Develop genetic methods to assist management
§ Determine the reproductive contribution of hatchery fish
§ Determine the contribution of adult hatchery on spawning grounds
§ Implement and evaluate supplementation strategies
Similar to CRITFC’s Accord project (Genetic Assessment of Columbia River Stocks) this proposal addresses needs for distinguishing specific stocks, determining genetic diversity, stock specific run timing, and estimating stock composition for improved fisheries management and harvest. These needs have been identified in multiple “Reasonable and Prudent Alternatives” (RPA) in the BiOp:
§ page 57, RPA No. 41, Preserve genetic resources
§ page 69, RPA No. 50, Fish population status monitoring
§ page 77, RPA No. 53, Monitor adult salmonids passing through FCRPS
§ page 89, RPA No. 63, Monitor hatchery effectiveness
§ page 89, RPA no. 64, Investigate hatchery critical uncertainties (i.e., Estimate relative reproductive success with genetic markers)
Finally, evaluations of PBT genetic tagging technology have been recommended by both the Pacific Salmon Commission and the Independent Scientific Review Panel and Advisory Boards