Update on Genetic Monitoring throughout the Snake River Basin
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- Doreen Banks
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1 Update on Genetic Monitoring throughout the Snake River Basin Lance Hebdon and Matthew Campbell Idaho Department of Fish and Game 71st Pacific States Marine Fisheries Commission Annual Meeting August 21 st,
2 Eagle Fish Genetics Lab-2018 PSMFC staff = 13 full-time employees IDFG = 2 full-time employees 2
3 Talk Outline I. Background Why these projects were initiated What these genetic technologies are and how they work The major objectives achieved during proof-of-concept period Examples of current uses of Snake River genetic baselines II. III. Major recent achievements of these genetic technologies in the Snake and Columbia River Basins and beyond Tracking of family units to release site Increased PBT sampling throughout the CRB Decreased genotyping costs/increase in output SNPs under selection Increased GSI precision Identifying SNPs linked to specific traits Future? 3
4 Why were these genetic projects initiated? In 2008/2009 the Pacific Salmon Commission and the Independent Scientific Review Panel and Advisory Boards recommended large-scale evaluations of genetic technologies for salmon and steelhead management
5 Based on these recommendations and endorsements IDFG proposed two new projects to BPA for evaluating new genetic technologies in the Snake River Basin (awarded funding in July 2010): Collaborative projects between IDFG and CRITFC IDFG Eagle Fish Genetics Lab Eagle, ID Collaborative Center for Applied Fish Science Hagerman, ID
6 What these genetic technologies are and how they work Parentage-based genetic tagging - PBT (Hatchery Fish) Genetic-based fish tagging method that involves genotyping hatchery broodstock By genetically sampling the parents, all offspring are genetically tagged Tag recovery is non-lethal, and possible at all life stages 2 = 6,000!!!!
7 What these genetic technologies are and how they work Genetic Stock Identification- GSI (Wild fish) Uses genetic profiles from all contributing wild populations to identify the stock of origin of any unknown fish
8 Review of 2011 talk to PSMFC PBT achievements during proof-of-concept period: What we demonstrated: PBT accurate and matched CWT assignments (Steele et al 2014) PBT/GSI genetic marker panels combined (efficient), multiple labs = same data High Snake River genetic tagging annually for each species (>95%) (2009- present) ~9 million hatchery steelhead ~14 million hatchery Chinook Salmon
9 Review of 2011 talk to PSMFC GSI achievements during proof-of-concept period: What we demonstrated: Can monitor these species at the ESU and MPG level Stock abundance estimates using GSI baselines exhibit low bias (Powell et al 2018) and high precision (Steinhorst et al 2016) * * * * * * * * 928 * * * * * 795 GRROND * 822 LOSALM * IMNAHA 721 * 591 * SFSALM UPSALM MFSALM
10 Examples of research and monitoring programs using Snake River steelhead and Chinook Salmon GSI/PBT baselines
11 Chinook salmon Steelhead
12 A Columbia River Estuary: Predation NOAA is using these standardized genetic baselines to assess the genetic origin of salmon and steelhead eaten by sea lions and birds in the LCR Rub et al NOAA researchers concluded that about 68% of the fish tagged and sampled near Astoria were destined for the river and tributaries above Bonneville based on genetic testing Kuligowski et al 2014-NOAA researchers concluded that PBT analysis suggests Snake River steelhead and Chinook Salmon are a larger proportion of the birds diets
13 B Bonneville Dam: Stock proportion, run-timing CRITFC estimates stock proportion of hatchery and wild Chinook Salmon and steelhead over Bonneville Dam 47% of ad-clipped adults assigned to Snake River hatcheries Chinook salmon jacks from 8 0f 9 Snake River hatcheries show delayed run-timing compared to 4-year old fish
14 C - E Mainstem Columbia River: CRITFC monitors Chinook Salmon harvest Adipose clipped Fishery during summer mgmt period 100% 90% 80% 70% 60% 50% 40% 30% 20% 10% 0% PBT Snake PBT Columbia OT ST LC Unassigned 100% 90% 80% 70% 60% 50% 40% 30% 20% 10% 0% PBT Snake PBT Columbia OT ST LC Unassigned
15 C - G Columbia and Snake Rivers: IDFG (and others) monitors steelhead harvest Data courtesy of Alan Byrne Idaho Department of Fish and Game (*all data for SY2015 and considered preliminary)
16 H Deschutes River: Straying and Reproductive Success USFWS/ODFW/CRITFC used baseline to determine the origin of stray hatchery steelhead collected in mainstem Deschutes and tributaries (Bakeoven and Buck Hollow Creeks) /FABER_SteelheadMgrs_Faber _primary.pdf ODFW-Derrek Faber, Wayne Wilson, James Ruzycki, USFWS-Matt Smith Hess et al Assessed the origin of hatchery steelhead taking thermal refuge during migration Stock-specific migration time coincident with use of refuge during time of warm main-stem temperatures
17 I Lower Granite Dam: Wild and hatchery abundance by stock Lower Granite Dam What genetic stock am I from? Our goal with this sampling is to partition the returning wild run over LGR into their genetic stocks
18 Wild versus Hatchery Determination Am I hatchery or wild? Some hatchery fish are unclipped/marked: Intentionally released Miss-clipped CWT/PIT shed CWT/PIT undetected NOAA Requires accurate estimates of wild abundance!!!!!
19 Wild versus Hatchery Determination LGR Trap wild fish Adult Trapping Facility Hatchery PBT Match? NO YES WILD unmarked hatchery
20 Only now can we get accurate estimates of wild abundance back to the Snake River!!! Removing unclipped hatchery fish critical! PBT makes the difference!!!!!! Steelhead Chinook Salmon Species Without PBT With PBT Difference % Steelhead 19,592 15,576 4, % Chinook 9,049 5,793 3, %
21 Wild Escapement - Genetic Stock Steelhead Annual estimates of wild abundance needed to determine recovery status are now available annually!!!! Same estimates available for Snake River Chinook ESU Available by age, sex, etc. Escapement above Lower Granite Dam of STHD by stock from spawn years 2009 to 2016
22 K Meanwhile..Back at the hatchery Since all broodstock are sampled and genotyped each year, PBT also allows precise estimates of broodstock effective population size of, inter-hatchery stray rates, and demographic characteristics of individual broodstocks and release groups. Combined with sampling of wild fish above weirs allows monitoring of integrated/segregated management goals. Integrated/Segregated
23 Chinook salmon Steelhead
24 Major achievements in PBT/GSI in the Snake and Columbia River Basins and beyond.. (since last presentation to PSMFC)
25 Achievements: Hatchery and management staff at IDFG developed protocols and procedures for tracking families from spawn to release High PBT tagging rates have been realized at the hatchery stock, rearing stock, and release site levels Vat-A Raceway-A Raceway-B Raceway-C Release Group A Egg Trays Vat- B Raceway-D Raceway-E Raceway-F Release Group B Vat-C Raceway-G Raceway-H Raceway-I Release Group C Huge thanks to Carl Stiefel for his vision and leadership for developing family tracking protocols for LSRCP hatcheries!!!!! 25
26 PBT tagging rates at the hatchery stock level: Average: 96.9% 26
27 PBT tagging rates at the rearing stock level: Average: 96.9% 27
28 PBT tagging rates at the release group level: Average: 91.8% 28
29 Achievements: FishGen All PBT/GSI baselines available on FishGen ~500,000 Chinook Salmon ~150,000 Steelhead Standardized genetic marker panels Publicly available 29
30 Achievements: PBT expansion throughout the Columbia River Basin Dr. Shawn Narum and Maureen Hess Columbia Inter-Tribal Fish Commission
31 PBT expansion in the Columbia River Basin Star = Bonneville Dam, Gray = broodstock NOT sampled % released smolts tagged estimated from Fish Passage Center, migration year 2015
32 PBT expansion in the Columbia River Basin
33 PBT expansion in the Columbia River Basin 33
34 PBT expansion in the Columbia River Basin 34
35 Achievements: New genetic platforms and techniques have greatly increased power and throughput while decreasing costs CRITFC!
36 Achievements: High Genotyping Capacity 2017 White sturgeon 774 Coho Salmon 1, P. lamprey 10,439 Chinook salmon 33,456 Sockeye salmon 13,676 Steelhead 36,051 Sockeye salmon 20,539 Chinook salmon 104,807 Total: 151,884 Steelhead 20,850 Total: 112,340 Coho salmon 3,718 Brook Trout 11,513 Burbot 264 CRITFC IDFG
37 Achievements: CRITFC Narum et al. Cost per sample (one lane) Improved Cost Efficiency GT-seq Genotyping-in-thousands by sequencing $10.00 $9.00 Cost per sample sequencing: GT-seq $8.00 Total cost: GT-seq genotyping $7.00 Total cost: 5' exonuclease $6.00 $5.00 $4.00 $3.00 $2.00 $1.00 $16.50/fish $4.00/fish $160,000 $140,000 $120,000 $100,000 $80,000 $60,000 $40,000 $20,000 Total cost of genotyping $0.00 $ Individual Samples Campbell and Narum 2015, Mol. Ecol. Res
38 Powerful scans across the genome allows the identification of highly informative snps (often linked to traits under selection). Allows identification of more powerful markers for GSI Chen et al. Narum (2018)
39 CRITFC: Hasselman, Micheletti et al (BPA report) Accuracy of Steelhead GSI Difficult stocks to resolve Additional outliers improve accuracy
40 PBT programs are not limited to the Columbia River Basin: California PBT developed by Carlos Garza & Eric Anderson NOAA Image taken from slide prepared by Carlos Garza. Full presentation available:
41 PBT programs are not limited to the Columbia River Basin: Washington Coast-WDFW WDFW sampling started in hatcheries Samples collected, but not analyzed yet
42 PBT programs are not limited to the Columbia River Basin: Chinook Salmon: Sampling started in SNP loci 10 hatcheries British Columbia-DFO Coho Salmon: Sampling started in 2012 All hatchery populations sampled in 2014 and 2015 ~20,000 samples 490 SNP loci The overall accuracy of assignment for 1,939 coho salmon to the correct population was 100%, and to correct brood year within population was also 100%. With 23 regions defined by the coded-wire tag (CWT) program, mean regional assignment accuracy of individuals via GSI was 98.4% over all 23 regions. Demonstrated that a PBT GSI system of identification could provide an alternative to CWT program for assessment and management of Canadian-origin coho salmon.
43 Other Recommendations: Pacific Salmon Commission Chinook Technical Committee 2015: A reassessment of the relative costs and merits of the PBT-based or hybrid PBT/CWT systems should be undertaken again in five years or possibly sooner if technological changes or significant reductions in cost warrant it. Review.11August2015.pdf Northwest Power and Conservation Council Tagging Forum Funding should continue for developing and evaluating GSI and PBT throughout the basin and be re-evaluated in 5-10 years. Council-Decision-letter-August pdf
44 Other Recommendations: Senate Appropriations Committee 2015: The Committee supports continued research and testing of genetic stock identification [GSI] management techniques in the Pacific salmon fishery to meet the dual purpose of protecting weak and the Endangered Species Act listed stocks, while allowing for sustainable commercial and recreational access to healthy stocks in the wild. NMFS shall continue to support GSI research, including the collection, analysis, and testing of methods that rely on genetics-based data to identify and track the location of federally protected stocks in the wild. PSMFC Resolution Supports further efforts to fund necessary work to make these data available for salmon management, as long as such funds done come at the expense of current federal fisheries research and management.
45 Other Recommendations: Technical Report number 23, Vancouver British Columbia Pacific Salmon Commission 2008 For various historical, logistical, and financial reasons, the U.S. West Coast fishery harvest management community has generally resisted genetic methods
46 Future: Genetic Technology works- management and ancillary benefits IDFG and CRITFC committed to using this technology throughout the Columbia/Snake Rivers Broader Adoption? Expansion relies on funding, design and development of database system similar to RMIS/CWT data Coast-wide sampling system and design Databases for data compilation, validation, managing releases, recoveries, and dissemination of data and reports Staff and committees to oversee program
47
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