Alaska Sustainable Salmon Fund
Statement of Work
I.
Project Title: Chinook Salmon Growth and Survival
II.
Project Number: 44902
III.
Principal Investigator
Trent Sutton, Professor
University of Alaska Fairbanks (UAF)
School of Fisheries and Ocean Sciences (SFOS)
905 N. Koyukuk Drive
Fairbanks, AK 99775
Phone: (907) 474-7285
Email: tmsutton@alaska.edu
Co-Principal Investigators
Milo Adkison, Professor
UAF, SFOS
905 N. Koyukuk Drive
Fairbanks, AK 99775
Phone: (907) 474-1811
Email: mdadkison@alaska.edu
Philip Richards, Fishery Biologist III
Alaska Department of Fish and Game (ADF&G)
Division of Sport Fish (SF)
P.O. Box 110024
Douglas, AK 99811
Phone: (907) 465-8114
Email: philip.richards@alaska.gov
Troy Jaecks, Fishery Biologist II
ADF&G, SF
P.O. Box 110024
Douglas, AK 99811
Phone: (907) 465-4271
Email: troy.jaecks@alaska.gov
IV.
Project Period: 3/1/14 – 11/30/16
V.
AKSSF Objective: 2A-4
VI.
Project Description
1. Synopsis
Chinook Salmon Growth and Survival
44902
PCSRF Objective: RM&E
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Chinook salmon runs in the Chilkat and Stikine rivers support subsistence fisheries in
Southeast Alaska. This project will examine the importance of freshwater and marine
processes on Southeast Alaska female Chinook salmon recruitment to reproductive
age in these systems using a combination of long-term scale archive samples, adult
abundance estimates, and smolt data sets. These evaluations will allow for the
assessment of growth and survival on recruitment within individual stocks by
following cohorts from freshwater through marine residence until they return to their
natal river as reproductively mature adults. Project results will allow the
development of more accurate and reliable forecasts for making management
decisions on subsistence salmon Chinook salmon stock status and escapement goals
in Southeast Alaska.
2. Introduction
Chinook salmon support important and diverse subsistence, commercial, recreational,
and personal use fisheries throughout Alaska. Highly variable recruitment, coupled
with statewide declines in productivity and abundance, has created social and
economic hardships for many communities in rural and urban Alaska. As a result,
there is a clear need to more precisely characterize productivity and abundance trends
for Chinook salmon stocks, collect information to understand the causal mechanisms
for these widespread declines, and develop more accurate tracking and forecasting of
future population trends.
In Southeast Alaska, Chinook salmon abundance declined in the 1970s in many
tributaries, including transboundary rivers, relative to historical levels of production.
In response, the Alaska Department of Fish and Game (ADF&G) and the Canada
Department of Fisheries and Oceans (DFO) initiated concurrent programs to facilitate
stock recovery. Both programs were incorporated into an inclusive coast-wide
rebuilding program in 1985 via the U.S./Canada Pacific Salmon Treaty which
required the annual monitoring of escapement trends in 11 index tributaries. Two of
these tributaries, the Stikine River (a transboundary river) and the Chilkat River, are
glacial systems that annually produce the first or second and third or fourth largest
populations of Chinook salmon, respectively, in Southeast Alaska. These fish are
primarily caught in marine troll, commercial drift gillnet, and recreational fisheries as
well as subsistence fisheries in U.S. waters, and in in-river commercial, aboriginal
gillnet, and recreational fisheries in Canada. While Chinook salmon escapements
rebounded in the Stikine River post-1985, adult spawner returns continued to decline
in the Chilkat River. As a result, restrictive regulations for recreational and
commercial fisheries were implemented in 2007. While increases in marine harvest
contributed to both stock declines, the potential role of environmental factors on
Chinook salmon recruitment is not clear.
For this research, the importance of freshwater and marine processes on Chinook
salmon recruitment to spawning age will be examined in the Stikine and Chilkat
rivers using long-term scale archive samples, adult abundance estimates, and smolt
data sets collected by ADF&G. Analyses will be conducted at the system scale which
will allow assessment of pre-smolt, smolt, and post-smolt growth and survival on
recruitment within individual stocks by following cohorts (i.e., broods) from
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freshwater through marine residence until they return to their natal river as
reproductively mature adults. Examining rate-dynamic functions separately in
freshwater and marine systems, and coupling these findings within the context of
large-scale environmental drivers, should lend insights into the factors that limit
recruitment. This evaluation will allow the development of more accurate and
reliable forecasts for making management decisions on Chinook salmon stock status
and escapement goals in these rivers. Further, this research will augment similar
analyses being conducted by the investigators on the role of freshwater and marine
processes on Chinook salmon growth, survival, and recruitment in the Taku and Unuk
rivers in Southeast Alaska.
3. Location
Site: Chilkat River
Latitude: 59.2659 N Longitude: 135.608196 W
Site: Stikine River
Latitude: 56.747440 Longitude: -131.785469
VII.
Objectives
 Objective 1: Using archived scale samples, conduct a retrospective analysis of the
relationships of freshwater and marine growth to survival to the age of reproduction
for female Chinook salmon by brood year
 Objective 2: Evaluate past and current influences of biological and environmental
factors on Chinook salmon smolt migration run timing by brood year
 Objective 3: Assess the relationship between Chinook salmon smolt biological
attributes, smolt migration run timing characteristics, and environmental factors on
female survival to the age of reproductive maturity by brood year
VIII. Methods
Archived Scale Growth Analysis (Objective 1)
A time series of freshwater and marine growth patterns for Chinook salmon from the
Stikine River (1996-2012) and the Chilkat River (1991-2012) will be constructed using
archived scales previously collected by ADF&G. Scale acetate impressions for female
Chinook salmon will be digitized and an image analysis routine will be used that follows
ADF&G methods. A sample size of at least 25 females per age class per year for each
river will be chosen for this study. Scale circuli increment widths will be measured to
allow assessment of the importance of freshwater (pre-smolt and smolt) and marine (postsmolt) processes on survival and recruitment for each brood year in both rivers. Scale
measurements will include the length of the freshwater zone (freshwater increment
width) and measurement of intercirculi pair spacing of the marine zone from the end of
the freshwater zone to the margin of the scale (marine increment width). Post-smolt
growth will be characterized by the number of circuli pairs laid down during the first and
post-smolt stage, which will be divided by the months at sea before the first winter.
Estimates of river-specific sex ratio, age structure, size-at-age, smolt body size,
freshwater and marine survival, and recruitment and data on size-fecundity relationships
will be obtained and used to estimate the number of female spawners and the number of
eggs spawned in each brood year for each river. Freshwater and marine growth
Chinook Salmon Growth and Survival
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increments, along with proportional monthly marine growth indices, will be correlated to
the aforementioned series of recruitment benchmarks. To examine the relationship
between smolt body size and female survival to the age of reproductive maturity, lengthfrequency distributions will be examined for each brood year. Female brood return will
be estimated and used to determine if correlations exist separately between freshwater
and marine growth and the number of female Chinook salmon returning to spawn.
Correlations will be examined between freshwater growth and female spawner size-atage to determine if different age classes display different freshwater growth values.
Female brood returns will be used to determine if a correlation exists between the size
and number of females and the freshwater and marine growth of their offspring.
Smolt Run Timing (Objective 2)
An evaluation will be conducted for Chinook salmon from the Stikine and Chilkat rivers
in Southeast Alaska using a time series of smolt downstream migration (Stikine River:
1998-2007; Chilkat River: 1998-2007) and adult female spawner return data (Stikine
River: 1996-2012; Chilkat River: 1991-2012) collected by ADF&G. The mean duration
of the downstream smolt migration and range of Julian dates, as well as Chinook salmon
smolt body size, condition, and age, and the mean and range of water temperature, water
depth/water level, and discharge for each river, will be determined from previously
collected data for each year. The role of biological and environmental variables on the
timing and rate of the smolt run will be examined using multivariate analyses for each
river. In a second set of multiple regression analyses, daily smolt catch will be replaced
by the total cumulative smolt catch.
The daily recorded smolt catch over the outmigration period in each river, as well as
smolt body size, condition, and age and changes in river temperature, depth, and
discharge will be modeled to characterize smolt run timing. For this evaluation, it is
likely that a polynomial model or models will be used; however, the exact type of model
will not be determined until a more thorough examination of the predictor variables is
completed. The probability estimated from the model will represent the predicted
probability of outmigration for smolts that remain in the river, which will be transformed
into the population fraction predicted to migrate each day. Predictions will be compared
to the estimated ratio of the number of smolts captured on a given day to the number of
smolts captured that season. The association between post-smolt survival to reproductive
age and the age at reproductive maturity, and adult spawning run characteristics to annual
smolt attributes, smolt migration run timing characteristics, and environmental conditions
will also be examined annually using a series of linear regression analyses.
Smolt and Environmental Characteristic Influences on Female Survival (Objective 3)
The synergistic role of biological and environmental variables on the marine survival of
post-smolt Chinook salmon will also be examined for the Stikine and Chilkat rivers.
Multiple linear regression models will be used to examine relationships between postsmolt marine survival and the aforementioned biological and environmental variables.
IX.
Benefits
Chinook Salmon Growth and Survival
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This project will examine the importance of freshwater and marine processes on Chinook
salmon recruitment to reproductive age in the Stikine and the Chilkat rivers, both of
which support important subsistence fisheries. This information will have practical value
both in improving forecasts of Chinook salmon returns and in providing insight into the
causes of past fluctuations in productivity. Further, identifying the impact of freshwater
and marine environmental factors on recruitment variation will allow for the
identification of crucial phases in the life history of these Chinook salmon.
X.
Products, Milestones, and Timelines
 March – May 2014: Convene annual project planning meeting with ADF&G
personnel; obtain scale samples from ADF&G; compile adult spawner return and
smolt data
 May – June 2014: Assist ADF&G personnel with adult spawner and smolt sampling
and data collections at the Stikine and Chilkat field sites (graduate student)
 May – December 2014: Prepare and digitize ADF&G scale samples
 May 2014 – February 2015: Analyze adult spawner return and smolt data
 January – December 2015: Analyze ADF&G scale data
 May 2015: Attend annual project planning meeting with ADF&G personnel;
present and discuss analyses and results to date
 October 2015: Present preliminary study results at the annual meeting of the Alaska
Chapter of the American Fisheries Society (AK-AFS; PI and graduate student
registration and travel costs separately funded)
 January 2016: Present preliminary study results at the annual meeting of the Alaska
Marine Science Symposium (AMSS)
 January – September 2016: Complete data analyses and thesis writing
 May 2016: Attend annual project planning meeting with ADF&G personnel;
present and discuss analyses and results to date
 September 2016: Present final study results at the national annual meeting of the
American Fisheries Society (AFS)
 October 2016: Defend and revise graduate student thesis; present final study results
at the annual meeting of the AK-AFS (PI and graduate student registration and
travel costs separately funded)
 November 2016: Prepare and submit manuscripts to journals for peer review;
submit final formal project report and other publications to AKSSF
XI.
Budget
UAF Budget
100 Personnel
200 Travel
300 Contractual
400 Supplies
500 Equipment
Subtotal
Expenses subject to indirect
Chinook Salmon Growth and Survival
44902
Total
$126,332
$11,345
$27,650
$0
$0
$165,327
$138,677
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600 Indirect @ 25%
Total
$34,669
$199,996
UAF Budget Narrative:
Line 100: Personnel ($126,332)
 Dr. Trent Sutton, Professor, UAF School of Fisheries and Ocean Sciences, will
mentor the graduate student; directly supervise the research technician; assist with
sample processing, data analyses, and research presentations; and review project
progress reports, the graduate student's thesis, the final project completion report,
and peer-reviewed manuscripts:
 Salary: 217.5 hours @ $60.42/hour base rate plus leave reserve = $14,046
 Fringe benefits: $4,382

Dr. Milo Adkison, Professor, UAF School of Fisheries and Ocean Sciences, will
serve on the graduate student's committee, assist with data analyses, and review
project progress reports, the graduate student thesis, the final project completion
report, and peer-reviewed manuscripts:
 Salary: 217.5 hours @ $58.50/hour base rate plus leave reserve = $13,600
 Fringe benefits: $4,244

Nicholas Smith, Technician, will oversee all activities associated with Objectives
2 and 3 including data analyses, paper and poster presentations, and project report
and peer-reviewed manuscript writing:
 Salary: 582.8 hours @ $22.01/hour base rate plus leave reserve = $15,948
 Fringe benefits: $8,037

An M.S. graduate student (to be determined) will conduct research associated
with Objective 1. The graduate student will also be responsible for data analysis,
paper and poster presentations, and project report and peer-reviewed manuscript
writing associated with Objective 1 as well as field work in the first year of the
project including assisting ADF&G with adult spawner and smolt sampling and
data collections at the Stikine and Chilkat rivers.
 Salary:
o Year 1: 696 hours @ $19.67/hour base rate plus leave reserve =
$13,690
o Year 2: 1,392 hours @ $21.34/hour base rate plus leave reserve =
$29,706
o Year 3: 696 hours @ $21.34/hour base rate plus leave reserve =
$14,852
 Fringe benefits: $7,827
Line 200: Travel ($11,345)
This project includes domestic travel to field sites, to meetings with ADF&G project
partners, and for AFS (national) and AMSS conference travel for dissemination and
discussion of project findings.
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The graduate student will travel from Fairbanks to Juneau in the first, second, and third
years of the project for project planning, discussion of data analyses and research
findings, and for data collection with ADF&G partners (first year only); Dr. Sutton will
join the graduate student in the third year of the project:
 Airfare: $600 + $660 + 2 tickets @ $726/ticket = $2,712
 Local Transportation: $100 + $110 + $242 = $452
 Lodging: 12 nights @ $149/night = $1,788
 Per diem: 16 days @ $60/day = $960
The graduate student will travel from Fairbanks to Anchorage in the third year of the
project to present research/project results at the 2016 AMSS conference:
 Airfare: $363
 Local transportation: $121
 Lodging: 1 night at $99/night = $99
 Per diem: 1 day @ $60/day = $60
The graduate student and Dr. Sutton will travel from Fairbanks to Kansas City, Missouri,
in the third year of the project to present project research and results at the 2016 AFS
national annual meeting:
 Airfare: 2 tickets @ $1,573/ticket = $3,146
 Local transportation: $242
 Lodging: 4 nights @ $99/night x 2 persons = $792
 Per diem: 5 days @ $61/day x 2 persons = $610
Line 300: Contractual ($27,650)
 Conference registration fee (AFS 2016 Kansas City national annual meeting): 2
fees @ $500/fee = $1,000
 Graduate student tuition: $26,650
Line 600: Indirect ($34,669)
UAF’s federally negotiated indirect rates through June 30, 2014, range from 35% to
49.5% excluding (among other costs) equipment, tuition, and subgrants and contracts
over the first $25,000; however, indirect will be recovered at a reduced rate of 25% for
this project.
XII.
Match Budget
UAF Match Budget (35%)
100 Personnel
200 Travel
300 Contractual
400 Supplies
500 Equipment
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Total
$55,999
$0
$0
$0
$0
2/8/2016
Subtotal
Expenses subject to indirect
600 Indirect @ 25%
Total
$55,999
$55,999
$14,000
$69,999
UAF Match Budget Narrative:
Line 100: Personnel ($55,999)
 Dr. Trent Sutton, Professor, UAF School of Fisheries and Ocean Sciences, will
mentor the graduate student; directly supervise the research technician; assist with
sample processing, data analyses, and research presentations; and review project
progress reports, the graduate student's thesis, the final project completion report,
and peer-reviewed manuscripts:
 Salary: 217.5 hours @ $60.42/hour base rate plus leave reserve = $14,047
 Fringe benefits: $4,382

Dr. Milo Adkison, Professor, UAF School of Fisheries and Ocean Sciences, will
serve on the graduate student's committee, assist with data analyses, and review
project progress reports, the graduate student thesis, the final project completion
report, and peer-reviewed manuscripts.
 Salary: 217.5 hours @ $58.50/hour base rate plus leave reserve = $13,600
 Fringe benefits: $4,244

Nicholas Smith, Technician, will conduct scale compilation and preparation for
Objective 1 and data compilation for Objectives 1-3.
 Salary: 464 hours @ $22.01/hour base rate plus leave reserve = $13,116
 Fringe benefits: $6,610
Line 600: Indirect ($14,000)
UAF’s federally negotiated indirect rates through June 30, 2014, range from 35% to
49.5% excluding (among other costs) equipment, tuition, and subgrants and contracts
over the first $25,000; however, indirect will be recovered at a reduced rate of 25% for
this project.
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