Guidelines for Formatting a Statement of Work For

Alaska Sustainable Salmon Fund

Statement of Work

1. Project Title: Yukon River Juvenile Chum Stock Analysis

1. Project Number: 44619PCSRF Objective: RM&E

III. Principal Investigator

Jeffrey R. Guyon, PhD, Genetics Program

National Marine Fisheries Service (NMFS)

Auke Bay Laboratories (ABL)

Ted Stevens Marine Research Institute (TSMRI)

17109 Point Lena Loop Road

Juneau, AK 99801

Phone: (907) 789-6079

E-mail:

Co-Principal Investigator

Christine Kondzela, PhD, Genetics Program

National Marine Fisheries Service (NMFS)

Auke Bay Laboratories (ABL)

Ted Stevens Marine Research Institute (TSMRI)

17109 Point Lena Loop Road

Juneau, AK 99801

Phone: (907) 789-6084

E-mail:

IV. Project Period: 7/1/11 – 5/31/14

V. Project Description

1. Synopsis

This project will use genetic analysis to investigate the stock composition of juvenile chum salmon collected on the northeastern Bering Sea shelf. The results will be used to determine the stock contribution of juvenile chum salmon, compare the distribution across years, determine the relative percentage of juvenile summer and fall Yukon River chum salmon in the northeastern Bering Sea, and relate the relative estimated proportions of summer- and fall-run juveniles to adult Yukon River returns. Information gathered through this project is vital to understanding chum salmon ocean life history, whether juvenile relative abundance indices can be developed for understanding ocean and river mortality and in developing future forecasting models. These models will assist with management of the Yukon River chum stocks to help aid subsistence fishing opportunities.

1. Introduction

The Yukon River has two distinct runs of chum salmon: an earlier and typically more abundant summer chum run and a later fall run. Both runs are managed by ADF&G to provide for escapement and maximize harvest opportunity. Summer chum salmon generally spawn in the lower to middle reaches of the Yukon drainage while fall chum salmon are typically larger and generally spawn in spring-fed regions of the middle to upper reaches in Alaska and Canada. Returns of fall chum salmon average between 400 thousand and 1.4 million fish. Concern about fall chum salmon abundance in some years has resulted in reduced subsistence fishing opportunities and has created challenges in fulfilling treaty obligations with Canada which must also meet aboriginal needs. To date, there is very little information regarding the survival of Yukon River chum salmon in their fresh or saltwater environments.

Juvenile chum salmon have been collected as part of annual Bering-Aleutian Salmon International Surveys (BASIS) in the northeastern Bering Sea since 2002. While a genetic stock composition of the 2002 juvenile chum salmon was completed, all other years remain unanalyzed. The analysis of the 2002 sample set included 1,302 juvenile chum salmon and was performed using allozyme markers. The 2002 year samples were collected in the Bering Sea from 55°N to 65°N, an area ranging from south of the Kuskokwim River to Norton Sound. Genetic analysis showed that Yukon River fall run stocks were predominantly located north of 60°N latitude; their relative contribution diminished toward the south. Given the genetic similarity between coastal Bering Sea chum salmon populations (summer stocks) and the difficulty of genetically distinguishing lower river Yukon and Kuskokwim chum salmon summer runs, this project will focus on the genetic analysis of samples between 60° and 65° N, an area for which juvenile chum salmon are likely to be from the Yukon River and for which relative abundances between summer- and fall-run juvenile indices are more likely to correlate with adult Yukon River returns.

There is significant scientific experience and genetic information available for performing the study of the stock composition of juvenile chum salmon. Available information about adult returns will be gathered from collaborations with scientists from ADF&G and annual reports from the Yukon River Joint Technical Committee (JTC). Juvenile chum salmon outmigrate from the Yukon River in the spring and are found in the pelagic waters on the eastern Bering Sea shelf during summer and fall months. Previous work determined that a substantial proportion of juvenile chum salmon samples collected in this area from the 2002 year BASIS cruise were from the Yukon River, but the extent of contribution across years is still unknown. This project will perform a genetic stock composition analysis of the juvenile chum salmon collected in the northeastern Bering Sea off the mouth of the Yukon River during the 2003-2007 BASIS cruises by using DNA-based genetic markers. Estimates of the relative proportions of juvenile summer- and fall-run chum salmon will be compared across years and, if possible, correlated to subsequent Yukon River adult returns.

1. Location

Latitude: 62.627372 NLongitude: 165.415649 W

1. AKSSF Objective

AYK: 1C-1

1. Objectives
2. Project Objectives
3. Determine the extent of stock contribution of juvenile chum salmon on the eastern Bering Sea shelf off the mouth of the Yukon River and compare the distribution across years
4. Develop a relative abundance index of Yukon River summer- and fall-run for juvenile chum salmon on the eastern Bering Sea shelf
5. Examine the potential to correlate juvenile relative abundances with adult returns for summer and fall Yukon River chum salmon runs
6. Methods

Sample Analysis

A total of 2,874 juvenile chum salmon genetic samples have already been collected between 60° and 65°N from the 2003, 2004, 2006, and 2007 Bering Sea BASIS cruises. Stock composition estimates for time and spatial strata will be compared to identify spatial differences in juvenile stock composition in the northeastern Bering Sea, which may provide information on where specific stocks occur.

Genotyping

Either the microsatellite or SNP baseline would be suitable for mixed-stock analyses in this study because both baselines can accurately identify summer- and fall-run chum salmon. The NMFS ABL genetics laboratory has extensive experience using both types of markers; however, the Department of Fisheries and Oceans Canada (DFO) chum salmon microsatellite baseline has already been used for the chum salmon bycatch analysis, and will likely be used for this study, although results may be supplemented with highly informative SNPs identified through the collaborations.

Microsatellite allele conversion to SPAM and BAYES mixture format and stock composition analysis

The NMFS ABL laboratory has developed conversion tables to ensure that microsatellite allele calls performed in the ABL genetics laboratory match the allele designations in the DFO microsatellite baseline. Compatibility of the NMFS allele designations to the DFO baseline was confirmed with a set of samples from the DFO Molecular Genetics Lab that were analyzed on the ABL’s Applied Biosystems 3130xl Genetic Analyzer. Genotypes from converted mixtures will be exported from Excel as text files; C programs have been written to format both microsatellite and SNP data into SPAM and BAYES mixture files. Stock composition analysis will be performed with both the SPAM and BAYES software by using previously published procedures.

Determine the extent of stock contribution of juvenile Yukon River summer- and fall-run chum salmon on the eastern Bering Sea shelf off the mouth of the Yukon River and compare the distributions across years

Stock composition estimates will be prepared with similar spatial strata used previously for the 2002 juvenile sample set, although samples may be ultimately aggregated to offshore and inshore sample sets given the variability in the sample distributions. Stock composition across years for these spatial strata will be compared to determine if Yukon River summer and fall chum salmon stocks annually inhabit the same areas of the northeastern Bering Sea. As stocks of coastal western Alaska (summer runs) are difficult to distinguish genetically, it is possible that the relative juvenile index may be for summer western Alaska fish and Yukon River fall run fish. To minimize the impact from non-Yukon River juvenile chum salmon, the sample area has been limited to an area most proximal to the mouth of the Yukon River, an area known from previous analysis to contain a high concentration of Yukon River juvenile chum salmon.

Develop a relative abundance index of Yukon River summer- and fall-run for juvenile chum salmon on the eastern Bering Sea shelf

A relative abundance index for Yukon River summer- and fall-run juvenile chum salmon will be completed by dividing the overall stock composition of fall-run juvenile chum salmon by the stock composition of summer-run chum salmon. Relative indices will be developed for the entire survey area (60° to 65°N) and for the inshore area that is more likely to have highly concentrated Yukon River fish.

Examine the potential to correlate juvenile relative abundances with adult returns for summer and fall Yukon River chum salmon runs

In addition to understanding the ocean distribution of juvenile Yukon River chum salmon, this study will examine the potential to correlate juvenile indices with adult returns and identify the complexities associated with this task. Participants anticipate comparing relative juvenile indices with (1) the brood stock that produced the juveniles, and (2) available information regarding the returning adults.

Prior to commencement of project activity, PI will obtain ADF&G Fish Collection, Fish Resource, Fish Transport, and/or other required permits, as appropriate.

1. Benefits

Yukon River chum salmon serve as a critical subsistence resource for communities along the Yukon River in Alaska and Canada; however, stocks of fall-run Yukon River chum salmon have had low abundances in some years, falling to levels at which subsistence fishing opportunities have been limited. This project will use genetic analysis to identify the origin of juvenile chum salmon collected in the northeastern Bering Sea near the mouth of the Yukon River and attempt to correlate the relative abundances of summer- and fall-run Yukon River chum salmon with adult returns. Identifying the limiting factors that may need to be addressed will assist in developing future models for predicting adult returns that will help ensure sustainable subsistence fisheries.

1. Products, Milestones, and Timelines

• July 2011: Isolate DNA from 2,876 juvenile chum salmon samples collected in the northeastern Bering Sea near the mouth of the Yukon River as part of the 2003-2007 BASIS cruises
• Fall 2011: Start genotyping the 2003 and 2004 juvenile chum salmon samples
• Spring 2012: Finish genotyping the 2003 and 2004 juvenile chum samples, perform stock composition analysis to determine the percentage of summer and fall run chum salmon, and compare results to that from the 2002 juvenile chum allozyme study; report results to the ADF&G and USFWS
• Summer 2012: Start genotyping the 2006 and 2007 juvenile chum salmon samples
• Winter 2012: Finish genotyping the 2006 and 2007 juvenile chum samples, perform stock composition analysis to determine the percentage of summer- and fall-run chum salmon, and compare results to that from the 2002-2004 juvenile chum studies; report results to the Yukon River JTC, ADF&G, and USFWS
• Spring 2013: In collaboration with ADF&G, collect escapement information for summer- and fall-run Yukon River chum salmon for years 2002 (broodstock for the 2003 juveniles) through 2012 (when 2006 juveniles would return as 6 year olds and 2007 juveniles would return as 5 year olds); evaluate potential correlations between relative juvenile indices and adult returns (brood and returning adults)
• Fall 2013 – Spring 2014: Finish the statistical analyses and begin writing the final report and preparing manuscripts for peer-reviewed publication; attend Yukon River JTC meeting to present final results
• Spring 2014: Submit final report documenting results

PI will submit PCSRF performance metrics, semiannual, and project completion reports according to the AKSSF schedule, as well as copies of any other report/product/ deliverable produced with this funding.

All invoices will be submitted for payment within 30 days of the project end date in accordance with the current AKSSF invoicing P&P. Invoices will be sent to:

Alaska Department of Fish and Game

Alaska Sustainable Salmon Fund

Box 115526

Juneau, AK 99811-5526

Any report or product distributed as a result of this funding will include the following language:

This [report/video/website] was prepared by [recipient/author name] under award NA10NMF4380428 from the National Oceanic and Atmospheric Administration, U.S. Department of Commerce, administered by the Alaska Department of Fish and Game. The statements, findings, conclusions, and recommendations are those of the author(s) and do not necessarily reflect the views of the National Oceanic and Atmospheric Administration, the U.S. Department of Commerce, or the Alaska Department of Fish and Game.

Any displays produced (e.g., signs, interpretive displays, posters) must include logos from both the National Oceanic and Atmospheric Administration and the Alaska Department of Fish and Game (please contact AKSSF staff for graphics and relevant language).

1. Partners

ADF&G

X. Project Budget

FY12

FY13

Budget Narrative:

Line 200: Travel ($3,900)

FY13

Chris Kondzela and Jim Murphy will travel to Fairbanks to attend the Yukon River JTC meeting and to discuss progress reports: $1,100 airfare ($550/ticket x 2 tickets) + $588 per diem ($98/day x 3 days x 2 people) + $510 lodging ($85/night x 3 nights x 2 people) + $300 ground transportation ($100/day x 3 days) + $102 parking = $2,600

FY14

Jeff Guyon will travel to Fairbanks to attend the Yukon River JTC meeting and to discuss progress reports: $550 airfare + $294 per diem ($98/day x 3 days) + $255 lodging ($85/night x 3 nights) + $201 ground transportation/parking = $1,300

Line 300: Contractual ($46,000)

Laboratory technician contact (cost based on base salary for a ZT-2 @ $40,425/year which equates to a salary of $3,369/month, COLA of $809/month, and benefits of $944/month):

• FY12: 2.54 months x $5,122/month = $13,000
• FY13: 2.54 months x $5,122/month = $13,000

Laboratory equipment maintenance contract prorated for this project (including maintenance on the Perkin-Elmer Janus Robot and the Applied Biosystems 3130xl Genetic Analyzer):

• FY12: $10,000
• FY13: $10,000

Total FY12 Contractual: $23,000

Total FY13 Contractual: $23,000

Line 400: Supplies ($40,000)

Lab supplies for DNA purification and genotyping (including all necessary primers, probes, DNA purification kits, tips, tubes, plates, and reagents):

• FY12: 100 fish @ $25/fish = $2,500
• FY13: 1,500 fish @ $25/fish = $37,500

Line 500: Equipment ($10,100)

FY13

Applied Biosystems 9700 thermocycler: $10,100

Budget adjustments between line items are allowed for amounts equal to or less than 10% of the total award without prior AKSSF approval; any amount above 10% requires prior AKSSF approval. All costs in lines 100-500 must represent actual cash expenditures.

All direct and match expenses shall be adequately documented and filed.

All invoices will be submitted for payment within 30 days of the project end date in accordance with the current AKSSF invoicing P&P. Invoices submitted after that deadline will not be reimbursed. Expenses incurred after the project end date will not be reimbursed.

1. Match Budget

FY12

FY13

Total required NMFS match (35%): $35,000

Match Budget Narrative:

Non-federal matching funds are provided by the Arctic-Yukon-Kuskokwim Sustainable Salmon Initiative.

Line 400: Supplies ($35,000)

FY12

Lab supplies for DNA purification and genotyping (including all necessary primers, probes, DNA purification kits, tips, tubes, plates, and reagents): 1,400 fish @ $25/fish = $35,000

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