I. Project Title: Northern Cook Inlet Chinook Salmon Marine Harvest. II. Project Number: 44908

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1 Alaska Sustainable Salmon Fund Statement of Work Revision #1: Revise budget to account for FY15 change to ADF&G indirect base of line 100 only at 21%; change PI I. Project Title: Northern Cook Inlet Chinook Salmon Marine Harvest II. Project Number: III. Principal Investigator Adam St. Saviour, Fishery Biologist III Alaska Department of Fish and Game (ADF&G) Division of Sport Fish (SF) 333 Raspberry Road Anchorage, Alaska Jack Erickson, ADF&G, former PI Co-Principal Investigators Timothy R. McKinley Fishery Biologist III ADF&G SF Kalifonsky Beach Road, Suite B Soldotna, AK timothy.mckinley@alaska.gov Andy Barclay Fisheries Biologist III ADF&G, Division of Commercial Fisheries (CF) Gene Conservation Laboratory (GCL) 333 Raspberry Road Anchorage, AK andy.barclay@alaska.gov Davin Holen, ADF&G Division of Subsistence, former Co-PI IV. Project Period: 4/1/14 11/30/16 V. AKSSF Objective: 2A-5 PCSRF Objective: RM&E VI. Project Description 1. Synopsis NCI Chinook Salmon Marine Harvest Page 1 of 11

2 Cook Inlet Chinook salmon comprise an important subsistence resource for the residents of Tyonek. This project will collect and analyze Chinook salmon tissue samples from the Tyonek subsistence fishery and the Northern District commercial set gillnet fishery to estimate the stock-specific harvests of Chinook salmon in each fishery and to improve understanding of stock productivity. This information will help ensure that escapement goals are met and will assist in the management of the Chinook runs that support the Tyonek subsistence fishery. 2. Introduction Chinook salmon returning to the Susitna River and west Cook Inlet streams are harvested in the mixed stock marine fisheries of upper Cook Inlet (UCI), primarily the Tyonek Subdistrict subsistence set gillnet fishery and the Northern District commercial set gillnet fishery. Recent low Chinook salmon runs throughout Southcentral Alaska, especially to UCI, have heightened concerns about stockspecific harvest of Chinook salmon in these fisheries. There are now six Chinook salmon stocks in the Northern District of Cook Inlet that are designated as stocks of concern by the Alaska Board of Fisheries (BOF). Three of these stocks of concern (Theodore, Lewis, and Chuitna rivers) likely comprise the majority of the Chinook salmon harvested in the Tyonek Subdistrict subsistence fishery. These three streams are the most productive Chinook salmon rivers flowing into the West Cook Inlet management area and are adjacent to the community of Tyonek. However, little, if any, information regarding stock-specific harvests of Chinook salmon in these mixed-stock marine fisheries is currently available. Tyonek residents have stated that they believe most Chinook salmon harvested in the subsistence fishery in marine waters are headed for the Chuitna River; however, it is likely some Chinook harvested in the subsistence fishery are headed further up Cook Inlet to the Susitna River system. This project will sample Chinook salmon from the two marine fisheries, and genetic stock identification (GSI) techniques will be used to estimate the contribution of the known reporting groups to each fishery. A baseline suitable for genetic mixed stock analysis (MSA) of Chinook salmon captured in UCI is capable of discrimination among at least ten reporting groups useful for fishery management. 3. Location Site: Community of Tyonek Latitude: N Longitude: W NCI Chinook Salmon Marine Harvest Page 2 of 11

3 VII. Objectives This project will estimate the harvest composition, by reporting group, of Chinook salmon harvests in the Tyonek Subdistrict subsistence and Northern District commercial set gillnet fisheries for the 2014, 2015, and 2016 seasons. VIII. Methods A Chinook salmon genetic baseline that includes representative Pacific-wide populations is now available for MSA applications. An additional Chinook salmon genetic baseline that includes extensive sampling of populations within Cook Inlet is nearing completion. Using the existing Cook Inlet baseline, at least nine reporting groups can be identified within Cook Inlet. The genetic structure of populations from throughout the Pacific Rim indicates that reporting groups outside of Cook Inlet can also be identified. A single reporting group will be used for these populations when analyzing Cook Inlet marine harvest samples because most of the fish in the sampled harvests are expected to originate in Cook Inlet. This project will sample Chinook salmon from the Tyonek subsistence set gillnet fishery and the Northern District commercial set gillnet fishery for three years and use the existing genetic baseline to estimate the contribution of the known reporting groups to each fishery. This will be the second time marine harvests of Cook Inlet Chinook salmon have been assessed in this way. Project staff will visit as many fish processors and buyers as possible in Anchorage and Nikiski to collect samples from the Northern District commercial set gillnet fishery after each fishing period from late May through early July each year of the project. The fishing periods start on the first Monday on or after May 25 and continue through June 24 from 7:00 a.m. to 7:00 p.m. on Mondays unless altered by emergency order. Subsistence fishing is open during two seasons per year. The early season, May 15 through June 15, is open for three periods per week (Tuesday, Thursday, and Friday) for 16 hours per period (4:00 a.m. to 8:00 p.m.). The late season, June 16 through October 15, is open for one period per week (Saturday) for 12 hours (6:00 a.m. to 6:00 p.m.). Tyonek subsistence fishery samplers will collect samples at the beach during the subsistence fishery. Samplers will obtain the date and location of harvest, measure the mid eye to tail fork (METF) length, collect a scale for age determination, assess sex, and collect a tissue sample from Chinook salmon in the harvest. Tissue samples will be stored in uniquelynumbered vials (one vial per fish). All tissue samples will be the distal 1 cm of the left axillary process and will be preserved in denatured ethanol. At the end of the fishing seasons, the data and tissue samples will be delivered to the ADF&G Gene Conservation Laboratory (GCL) in Anchorage. DNA from the harvest samples will be extracted from axillary processes using DNeasy 96 tissue kits (Qiagen, Valencia, California). The DNA samples will be analyzed for at NCI Chinook Salmon Marine Harvest Page 3 of 11

4 least 52 SNP markers using Fluidigm Dynamic Arrays ( The Dynamic Arrays will be read on a BioMark TM Real- Time PCR System (Fluidigm) after amplification and scored using Fluidigm SNP Genotyping Analysis software. For some SNP markers, genotyping will be performed in 384-well reaction plates. These plates will be scanned on an Applied Biosystems Prism 7900HT Sequence Detection System after amplification and scored using Applied Biosystems Sequence Detection Software (SDS) version 2.2. All genotypes collected will be entered into the GCL Oracle database, LOKI. Quality control measures include re-extraction and re-analysis of 8% of each collection for all markers to ensure that genotypes are reproducible and to identify laboratory errors and rates of inconsistencies. Genotypes will be assigned to individuals using a doublescoring system. A minimum sample of 400 fish in each stand-alone stratum is required to estimate the stock proportion within 5% (simultaneous internal) of the true proportion 90% of the time. Smaller samples sizes (200 fish minimum) will be analyzed as part of associated strata analyses (i.e., early, middle, and late within a fishery). Genotypic data will be retrieved from LOKI and imported into R (R Development Core Team 2010) and allele frequencies will be calculated for each locus. All subsequent analyses will be performed in R unless otherwise noted. Prior to statistical analysis, two analyses will be performed to ensure the quality of the data. These analyses remove individuals with low-quality DNA and duplicate genotypes. Reporting group composition of harvest mixtures will be estimated with the program BAYES. Protocols for the BAYES analysis will follow those reported in Barclay et al. (2010). The reporting groups used in the analysis of the harvest mixtures will include: 1) West Cook Inlet streams/yentna River; 2) Susitna River; 3) Deshka River; 4) Knik and Turnagain Arm streams; 5) Kenai River tributaries; 6) Kenai River mainstem; 7) Kasilof River mainstem; 8) Crooked Creek (Kasilof River tributary); 9) South Kenai Peninsula streams; and 10) outside of Cook Inlet. During estimation of reporting group composition, populations will be maintained separately within these reporting groups. Reporting group estimates will be calculated by summing population estimates. After estimating the reporting group composition of each mixture, these proportions will be applied to the overall harvest within a given stratum to estimate the number of fish harvested from each reporting group. All harvests are expected to be known or estimated during the grant period. Methods for applying reporting group proportions to harvest will be the same as reported in Barclay et al. (2010). IX. Benefits This project will provide stock composition estimates for the Northern District commercial and the Tyonek subsistence set gillnet fisheries. This information will be used to help ensure that escapement goals are met and to assist with management of the Chinook salmon fishery near Tyonek. NCI Chinook Salmon Marine Harvest Page 4 of 11

5 X. Products, Milestones, and Timelines April-May 2014: Write operational plan; purchase sampling equipment; hire and train samplers May-August 2014: Sample harvests; complete ethnographic field work November-December 2014: Genotype 2014 tissue samples March-May 2015: Purchase sampling equipment; hire and train samplers May-August 2015: Sample harvests November-December 2015: Genotype 2015 tissue samples March-May 2016: Purchase sampling equipment; hire and train samplers May-August 2016: Sample harvests October 2016: Provide project results to Tyonek area residents at a community meeting November, 2016: Genotype 2016 tissue samples; analyze data from all years; draft peer-reviewed journal article; submit final report to AKSSF XI. Budget Revision #1 revises the budgets to account for the FY15 change to ADF&G s indirect base of line 100 only at 21%. The original budget tables are retained in this document as Appendix A. REV1 Summary Budget Total 100 Personnel $454, Travel $28, Contractual $18, Supplies $54, Equipment $8,000 Subtotal $564, Indirect $94,858 Total $659,282 This project funds the following three ADF&G divisions: Subsistence: $61,374 Commercial Fisheries GCL: $114,659 Sport Fish Region II: $483,249 ADF&G SUB Budget: Revision #1 ADF&G SUB Budget Total 100 Personnel $44, Travel $9, Contractual $0 400 Supplies $0 500 Equipment $0 Subtotal $53, Indirect $8,214 NCI Chinook Salmon Marine Harvest Page 5 of 11

6 Total $61,374 ADF&G Division of Subsistence Budget Narrative: Line 100: Personnel (not updated with Revision #1) The State of Alaska salary calculator was used to estimate personnel costs. Davin Holen, Subsistence Program Manager, will be responsible for project implementation, communications, and logistics: FY14: 0.5 $10,984/month = $5,492 FY15: 1 $11,314/month = $11,314 FY16: 0.5 $11,653/month = $5, FY17: 0.5 $12,003/month = $6,001 Bronwyn Jones, Subsistence Resource Specialist I, will assist with sampling the Tyonek subsistence fishery and with project logistics: FY14: 0.5 $6,216/month = $3,108 FY15: 1 $6,402/month = $6,402 FY16: 0.5 $6,595/month = $3, FY17: 0.5 $6,792/month = $3,396 Line 200: Travel ($9,000; not changed with Revision #1) Davin Holen will travel from Anchorage to Tyonek for community scoping meetings and sampling: Airfare: 15 $180/ticket = $2,700 Per diem: 18 $60/day = $1,080 Bronwyn Jones will travel from Anchorage to Tyonek for field work and project oversight: Airfare: 15 $180/ticket = $2,700 Per diem: 42 $60/day = $2,520 Line 600: Indirect (updated with Revision #1) ADF&G s federally negotiated indirect rate through June 30, 2014, was 14.93% excluding equipment and pass-through funds; however, indirect was recovered at a reduced rate of 14% for this project ($3, of indirect was collected through FY14). The indirect rate effective July 1, 2014, is 21% on line 100 only (estimated indirect from July 1, 2014, through the remainder of the project is $4,285.19). ADF&G CF Budget: Revision #1 ADF&G CF GCL Budget Total 100 Personnel $57, Travel $0 300 Contractual $0 400 Supplies $45,000 NCI Chinook Salmon Marine Harvest Page 6 of 11

7 500 Equipment $0 Subtotal $102, Indirect $12,090 Total $114,659 ADF&G Division of Commercial Fisheries GCL Budget Narrative: Line 100: Personnel (not updated with Revision #1) The State of Alaska salary calculator was used to estimate personnel costs. A Fish and Wildlife Technician (FWT) IV (TBD) will perform DNA extraction and processing of baseline samples: FY15: 1 $5,112/month = $5,112 FY16: 1 $5,265/month = $5,265 FY17: 1 $5,423/month = $5,423 An FWT III (TBD) will perform DNA extraction and processing of baseline samples: FY15: 0.5 $5,727/month = $2,864 FY16: 0.5 $5,899/month = $2,950 FY17: 0.5 $6,076/month = $3,037 A Fishery Biologist (FB) III (TBD) will perform quality control analysis of genetic data and analysis of the baseline for reporting group performance in mixture analyses; statistical analysis; and report writing: FY15: 1 $7,449/month = $7,449 FY16: 1 $7,672/month = $7,672 FY17: 2 $7,903/month = $15,806 Line 400: Supplies ($45,000; not changed with Revision #1) Genotyping chips: 50 $460/chip = $23,000 Quality control analysis supplies and biochemical and plastic disposables (e.g., Taq, loading buffer, 96-well plates, pipette tips, plate-sealing tape, plate mats, bottles): $12,846 Quiagen kits for extracting DNA from tissue samples: 46 $199/ kit = $9,154 Line 600: Indirect (updated with Revision #1) ADF&G s federally negotiated indirect rate through June 30, 2014, was 14.93% excluding equipment and pass-through funds; however, no indirect was recovered during this period. The indirect rate effective July 1, 2014, is 21% on line 100 only (estimated indirect from July 1, 2014, through the remainder of the project is $12,090). ADF&G SF Budget: Revision #1 ADF&G SF Region II Budget Total 100 Personnel $352,995 NCI Chinook Salmon Marine Harvest Page 7 of 11

8 200 Travel $19, Contractual $18, Supplies $9, Equipment $8,000 Subtotal $408, Indirect $74,554 Total $483,249 ADF&G Division of Sport Fish Region II Budget Narrative: Line 100: Personnel (not updated with Revision #1) The State of Alaska salary calculator was used to estimate personnel costs. An FB I (TBD) will supervise overall project operation: FY14: 4 $6,686/month = $26,744 FY15: 12 $6,887/month = $82,644 FY16: 12 $7,093/month = $85,116 FY17: 5 $7,306/month = $36,530 An FWT III (TBD) will perform crew leader duties and sample the Northern District set gillnet fishery (rate includes 10 hours overtime per month): FY14: 3 $5,871/month = $17,613 FY15: 3 $6,047/month = $18,141 FY16: 3 $6,229/month = $18,687 An FWT II (TBD) will sample the Northern District set gillnet fishery (rate includes 10 hours overtime per month): FY14: 3 $5,366/month = $16,098 FY15: 3 $5,527/month = $16,581 FY16: 3 $5,693/month = $17,079 An FWT III (TBD) will perform crew leader duties in Tyonek and sample the Tyonek subsistence set gillnet fishery: FY14: 2 $5,493/month = $10,985 FY15: 2 $5,658/month = $11,311 FY16: 2 $5,828/month = $11,656 Line 200: Travel ($19,800; not changed with Revision #1) An FWT III will travel from Anchorage to Tyonek for project planning and sample collection: Airfare: 30 $180/ticket = $5,400 Per diem: 60 $60/day = $3,600 An FWT III will travel from Anchorage to Nikiski for project planning and sample collection: NCI Chinook Salmon Marine Harvest Page 8 of 11

9 Per diem: 90 $60/day = $5,400 An FWT II will travel from Anchorage to Nikiski for sample collection: Per diem: 90 $60/day = $5,400 Line 300: Contractual ($18,900; not changed with Revision #1) DOT lease for two vehicles for travel to Nikiski: $10,500 First aid training: $900 Field-use cell phone service: $1,000 Fuel for vehicles: $3,250 Equipment maintenance and repair (vehicles, project computers, handheld field computers): $3,250 Line 400: Supplies ($9,000; not changed with Revision #1) Allegro CT handheld field computers: 2 $2,500/computer = $5,000 Field data collection supplies (clipboards, Rite in the Rain paper, tapes, tweezers, docking stations, ethanol, etc.): $1,500 Field gear and supplies (boots, raingear, gloves, day packs, binoculars, digital camera with batteries and charger): $1,600 Small tools and equipment (hammers, wrenches, cables with locks, etc.): $900 Line 500: Equipment ($8,000; not changed with Revision #1) 4-wheel drive ATV to be used for collection of fish samples at fish camps: $8,000 Line 600: Indirect (updated with Revision #1) ADF&G s federally negotiated indirect rate through June 30, 2014, was 14.93% excluding equipment and pass-through funds; however, indirect was recovered at a reduced rate of 14% for this project ($1, of indirect was collected through FY14). The indirect rate effective July 1, 2014, is 21% on line 100 only (estimated indirect from July 1, 2014, through the remainder of the project is $73,438). XII. Match Budget (not changed with Revision #1) ADF&G SF Match Budget Total 100 Personnel $230, Travel $0 300 Contractual $0 400 Supplies $0 500 Equipment $0 Total $230,749 ADF&G Division of Sport Fish Match Budget Narrative: The State of Alaska salary calculator was used to estimate personnel costs. NCI Chinook Salmon Marine Harvest Page 9 of 11

10 Line 100: Personnel ($230,749) An FB II (TBD) will determine the inriver abundance of Susitna River Chinook salmon necessary to quantify, in conjunction with this project, total production of the stock: FY14: 2.88 $8,644/month = $24,087 FY15: 9 $8,977/month = $80,791 FY16: 8 $9,316/month. $74,529 FY17: 3 $9,670/month = $29,010 An FB II will estimate the spawning distribution of Susitna River Chinook salmon necessary to quantify, in conjunction with this project, total production of the stock: FY14: 3 $7,444/month = $22,332 XII. References Barclay, A. W., C. Habicht, W. D. Templin, H. A. Hoyt, T. Tobias, and T. M. Willette Genetic stock identification of Upper Cook Inlet sockeye salmon harvest, Alaska Department of Fish and Game, Fishery Manuscript No , Anchorage. NCI Chinook Salmon Marine Harvest Page 10 of 11

11 Appendix A: Original Project Budget Tables Original Project Summary Budget Total 100 Personnel $469, Travel $28, Contractual $18, Supplies $54, Equipment $8,000 Subtotal $579,300 Expenses subject to indirect $571, Indirect $79,982 Total $659,282 Original ADF&G SUB Budget Total 100 Personnel $44, Travel $9, Contractual $0 400 Supplies $0 500 Equipment $0 Subtotal $53, % $7,537 Total $61,374 Original ADF&G CF GCL Budget Total 100 Personnel $55, Travel $0 300 Contractual $0 400 Supplies $45, Equipment $0 Subtotal $100, % $14,081 Total $114,659 Original ADF&G SF Region II Budget Total 100 Personnel $369, Travel $19, Contractual $18, Supplies $9, Equipment $8,000 Subtotal $424,885 Expenses subject to indirect $416, % $58,364 Total $483,249 NCI Chinook Salmon Marine Harvest Page 11 of 11