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Susitna‐Watana Hydroelectric Project Document
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Title:
Genetic baseline study for selected fish species, Study plan Section 9.14,
2014 Study Implementation Report SuWa 289
Author(s) – Personal:
Author(s) – Corporate:
Gene Conservation Laboratory (Commercial Fisheries Division, Alaska Department of Fish and
Game)
AEA‐identified category, if specified:
November 2015; Study Completion and 2014/2015 Implementation Reports
AEA‐identified series, if specified:
Series (ARLIS‐assigned report number):
Susitna-Watana Hydroelectric Project document number 289
Existing numbers on document:
Published by:
[Anchorage : Alaska Energy Authority, 2015]
Date published:
October 2015
Published for:
Alaska Energy Authority
Date or date range of report:
Volume and/or Part numbers:
Study plan Section 9.14
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Document type:
Pagination:
iv, 55, 1 pages
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Notes:
All reports in the Susitna‐Watana Hydroelectric Project Document series include an ARLIS‐
produced cover page and an ARLIS‐assigned number for uniformity and citability. All reports
are posted online at http://www.arlis.org/resources/susitna‐watana/
Susitna-Watana Hydroelectric Project
(FERC No. 14241)
Genetic Baseline Study for Selected Fish Species
Study Plan Section 9.14
2014 Study Implementation Report
Prepared for
Alaska Energy Authority
Prepared by
Gene Conservation Laboratory
Commercial Fisheries Division
Alaska Department of Fish and Game
October 2015
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TABLE OF CONTENTS
1. Introduction ....................................................................................................................... 1
2. Study Objectives................................................................................................................ 2
3. Study Area ......................................................................................................................... 2
4. Methods and Variances .................................................................................................... 2
4.1. Sample Collection ................................................................................................... 3
4.1.1. Adult Chinook Salmon collections ................................................. 3
4.1.2. Other adult salmon collections ........................................................ 4
4.1.3. Juvenile Chinook Salmon collections ............................................. 5
4.1.4. Other species collections ................................................................. 7
4.1.5. Sampling coordination with other studies ....................................... 8
4.1.6. Collection trip documentation ......................................................... 8
4.2. Tissue Storage ......................................................................................................... 8
4.3. Laboratory Analysis ................................................................................................ 8
4.4. Data Retrieval and Quality Control ........................................................................ 9
4.5. Variances from Study Plan ..................................................................................... 9
5. Results .............................................................................................................................. 10
5.1. Sample Collection ................................................................................................. 10
5.1.1. Adult Chinook Salmon collections ............................................... 10
5.1.2. Other adult salmon collections ...................................................... 10
5.1.3. Juvenile Chinook Salmon collections ........................................... 11
5.1.4. Other species collections ............................................................... 12
5.1.5. Pacific salmon sampling coordination with other studies ............. 12
5.1.6. Collection trip documentation ....................................................... 12
5.2. Tissue Storage ....................................................................................................... 12
5.3. Laboratory Analysis .............................................................................................. 12
5.4. Data Retrieval and Quality Control ...................................................................... 13
6. Discussion......................................................................................................................... 13
6.1. Chinook Salmon Adults and Juveniles Above Devils Canyon ............................. 13
6.2. Chinook Salmon Adults in the Susitna River Below Devils Canyon ................... 14
6.3. Chinook Salmon Adults Outside of the Susitna Basin ......................................... 14
6.4. Other Fish Species ................................................................................................ 14
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7. Conclusion ....................................................................................................................... 15
8. Literature Cited .............................................................................................................. 16
9. Tables ............................................................................................................................... 18
10. Figures .............................................................................................................................. 49
LIST OF TABLES
Table 4-1. Area, location, and sublocation of baseline samples of adult and juvenile Chinook
Salmon spawning aggregates for genetic analysis. ....................................................................... 19
Table 4-2. Location and sublocation of baseline samples of adult Sockeye Salmon spawning
aggregates for genetic analysis. .................................................................................................... 23
Table 4-3. Location and sublocation of baseline samples of adult Chum Salmon spawning
aggregates for genetic analysis. .................................................................................................... 25
Table 4-4. Location and sublocation of baseline samples of adult Coho Salmon spawning
aggregates for genetic analysis. .................................................................................................... 27
Table 4-5. Location and sublocation of baseline samples of adult Pink Salmon spawning
aggregates for genetic analysis. .................................................................................................... 29
Table 4-6. Resident and non-salmon anadromous fish species targeted for genetic tissue
sampling in the Susitna River and samples sizes collected in 2013 and 2014. ............................ 31
Table 4-7. Summary of survey flights conducted during 2013 and 2014. .................................... 33
Table 4-8. Genetic sampling effort through time by river area for adult salmon species and
juvenile Chinook Salmon in 2013 and 2014. ................................................................................ 34
Table 4-9. Marker name and source for the microsatellite (µSAT), 48 single nucleotide
polymorphism (SNP), and 188 SNP marker sets. ......................................................................... 36
Table 4-10. Species clustering in scatter plots for each of the seven standard markers used for
discriminating among Pacific and Atlantic salmon at the Gene Conservation Laboratory. ......... 42
Table 4-11. Metadata and location of Chinook Salmon samples collected above Devils Canyon.
....................................................................................................................................................... 43
Table 4-12. Area, sampling location, sublocation, and number of samples successfully analyzed
at greater than or equal to 80% of markers for the 13 microsatellite (uSATs), 48 single nucleotide
polymorphism (SNP), and 188 SNP marker sets. ......................................................................... 44
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LIST OF FIGURES
Figure 2-1. A generalized flow chart to distinguish among hypotheses of population structure for
Chinook Salmon collected over spawning habitat above Devils Canyon in the Middle and Upper
Susitna River. ................................................................................................................................ 49
Figure 3-1. Collection strata for samples collected for genetic archive and/or analysis. ............. 50
Figure 4-1. Baseline sampling locations for adult Sockeye Salmon sampled through 2014. ...... 51
Figure 4-2. Baseline sampling locations for adult Chum Salmon sampled through 2014. ......... 52
Figure 4-3. Baseline sampling locations for adult Coho Salmon sampled through 2014. ........... 53
Figure 4-4. Baseline sampling locations for adult Pink Salmon sampled through 2014. ............ 54
Figure 4-5. Baseline sampling locations for adult and juvenile (inset) Chinook Salmon sampled
through 2014. ................................................................................................................................ 55
APPENDICES
Appendix A. Non-lethal juvenile finfish OmniSwab sampling for DNA analysis.
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LIST OF ACRONYMS, ABBREVIATIONS, AND DEFINITIONS
Abbreviation Definition
ADF&G Alaska Department of Fish and Game
AEA Alaska Energy Authority
CFR Code of Federal Regulations
CIRWG Cook Inlet Region Working Group
DNA deoxyribonucleic acid
FERC Federal Energy Regulatory Commission
GCL Gene Conservation Laboratory
GPS global positioning system
ILP Integrated Licensing Process
IP Implementation Plan
ISR Initial Study Report
ml milliliter
Mm Millimeter
MSA mixed-stock analysis
n/a not applicable/not available
NOAA National Oceanic and Atmospheric Administration
NMFS National Marine Fisheries Service
oz. ounce
PRM Project River Mile
Project Susitna-Watana Hydroelectric Project
RM River Mile(s) referencing those of the 1980s Project.
RSP Revised Study Plan
SPD Study Plan Determination
USFWS United States Fish and Wildlife Service
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1. INTRODUCTION
This Genetic Baseline Study for Selected Fish Species, Section 9.14 of the Revised Study Plan
(RSP) approved by the Federal Energy Regulatory Commission (FERC) for the Susitna-Watana
Hydroelectric Project, FERC Project No. 14241, focuses on understanding the genetic structure
of selected species within the Susitna River.
A summary of the development of this study, together with the Alaska Energy Authority’s
(AEA) implementation of it through the 2013 study season (September 2013), appears in Part A,
Section 1 of the Initial Study Report (ISR) filed with FERC in June 2014. As required under
FERC’s regulations for the Integrated Licensing Process (ILP), the ISR describes AEA’s
“overall progress in implementing the study plan and schedule and the data collected, including
an explanation of any variance from the study plan and schedule.” (18 CFR 5.15(c)(1)).
In accordance with the intent of the FERC February 1, 2013 SPD, AEA consulted with the
Services on March 12, 2014 and received comments on developing a draft 2014 Implementation
Plan for the Genetic Baseline Study for Selected Fish Species in the Susitna River, Alaska
(Genetics Implementation Plan [IP]. The final 2014 Genetics IP was filed on June 3, 2014 as ISR
Part B Attachment 1. The 2014 Genetics IP supersedes portions of the Revised Study Plan.
Since filing the ISR in June 2014, AEA has continued to implement the FERC-approved plan for
the Genetic Baseline Study. For example:
Collection of juvenile and adult Chinook Salmon from above Devils Canyon.
Collection of adult Chinook Salmon from upper Cook Inlet tributaries.
Opportunistic collection other salmon and non-salmon species from the Susitna River.
Genotyping of Chinook Salmon samples collected in the Middle and Upper Susitna River
for single nucleotide polymorphism (SNP) and microsatellite (µSAT) loci.
On October 15, 2014 AEA held an ISR meeting for the Genetic Baseline Study for
Selected Fish Species in the Susitna River.
In furtherance of the next round of ISR meetings and FERC’s SPD expected in 2016, this report
describes AEA’s overall progress in implementing the Genetic Baseline Study from September
2013 through December 2014. Rather than a comprehensive reporting of all field work, data
collection, and data analysis since the beginning of AEA’s study program, this report is intended
to supplement and update the information presented in Part A and Part B of the ISR for the
Genetic Baseline Study for Selected Fish Species in the Susitna River through the end of
calendar year 2014. It describes the methods and results of the 2014 effort, and includes a
discussion of the results achieved.
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2. STUDY OBJECTIVES
The goals of this study are to (1) acquire genetic material from samples of selected fish species
within the Susitna River drainage, (2) characterize the genetic structure of Chinook Salmon in the
Susitna River watershed and (3) assess the use of Lower and Middle River habitat by juvenile
Chinook Salmon originating in the Middle and Upper Susitna River.
As described in the 2013 Genetics IP Section 3, the objectives of this study are to:
1. Develop a repository of genetic samples for target resident fish species captured within the
Lower, Middle, and Upper Susitna River drainage.
2. Contribute to the development of genetic baselines for chum, coho, pink, and Sockeye
Salmon spawning in the Middle and Upper Susitna River drainage.
3. Characterize the genetic population structure of Chinook Salmon from Upper Cook Inlet,
with emphasis on spawning aggregates in the Middle and Upper Susitna River.
4. Examine the genetic variation among Chinook Salmon populations from the Susitna
River drainage, with emphasis on Middle and Upper River populations, for mixed-stock
analyses (MSA).
5. If sufficient genetic variation is found for MSA, estimate the annual percent of juvenile
Chinook Salmon in selected Lower River habitats that originated in the Middle and
Upper Susitna River in 2013 and 2014 (Figure 2-1).
AEA expects that each of these goals and objectives will be met through the complete
implementation of the study program. Data collection toward achieving these objectives during
the 2014 study season was limited to the activities described in the Introduction and further
detailed below.
3. STUDY AREA
As established in the 2013 and 2014 Genetics IP Section 2.2, the study area encompasses the
Susitna River and its tributaries from Cook Inlet upstream to the Oshetna River confluence
(PRM 235.1; Figure 3-1). For baseline data related to stock-specific sampling, there was an
emphasis on tributaries of the Middle and the Upper Susitna River. For assessing habitat use
(juveniles) of fish originating from the Middle (PRM 102.4 – 187.1) and Upper Susitna River
(above PRM 187.1 – 261.3), tissue from juvenile Chinook Salmon was collected in the Lower
River (below PRM 102.4).
4. METHODS AND VARIANCES
AEA implemented the methods as described in the Study Plan with the exception of variances
explained below (Section 4.5).
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4.1. Sample Collection
For this study fish populations were defined using Waples and Gaggiotti’s (2006) definition: a
group of individuals of the same species living in close enough proximity that any member of the
group can potentially mate with any other member. Functionally, populations were represented
by single or pooled collections following the “Pooling Collections into Populations” methods
below.
Based on field sampling in previous years (Tables 4-1 to 4-5), information gathered from the
Catalog of Waters Important for the Spawning, Rearing or Migration of Anadromous Fishes,
ADF&G biologists selected possible sites where fish of each target Pacific salmon species might
be spawning and generated idealized sample sizes for each site (Tables 4-1 to 4-5). ADF&G and
AEA’s contractors made an intensive effort to collect these samples as outlined in the sections
below. However, AEA recognized at the inception of this project (2013 Genetics IP) that it was
unlikely to obtain the idealized sample size at all sites due to uncontrolled variables (i.e.,
numbers of fish at a spawning location, number of fish returning in 2013 and 2014, access
limitations, water conditions, and catchability of the fish). Therefore, a column was added to
Tables 4-1 to 4-5 labeled “Expected” that shows the number of fish that could reasonably be
sampled at each site (or group of sites) in two years.
AEA implemented the methods for sampling to achieve collection targets as described in the
2013 and 2014 Genetics IP Section 4.2, with no variances. Cumulative collection targets ranged
between 0 and 200 individuals per species per location depending on the number of archived
samples and prior knowledge about likely sample collection success (Tables 4-1 to 4-5).
Samples were acquired from field collections performed as a part of this Study Plan (Studies
9.14), and from each of four interrelated studies: Study of Fish Distribution and Abundance in
the Upper Susitna River (Study 9.5); Study of Fish Distribution and Abundance in the Middle
and Lower Susitna River (Study 9.6); Salmon Escapement Study (Study 9.7); and Eulachon Run
Timing, Distribution, and Spawning in the Susitna River Study (Study 9.16). All four
interrelated studies provided samples from resident fish species collected in the course of their
work (Table 4-6). Study 9.5 also provided samples of juvenile Chinook Salmon (Table 4-1), and
Study 9.7 provided samples from adult salmon from the Indian River and from the Middle River
at Curry (detailed in Section 4.1.5). Sampling methods for this Study Plan are described below.
Sampling methods for the four interrelated studies are described in those respective Initial Study
Reports (2013) and in the Study Implementation or Study Completion Reports (2014). Analysis
of all samples will be integrated and reported in the Updated Study Report.
4.1.1. Adult Chinook Salmon collections
To address Objectives 3 and 4, tissue samples were to be collected during the study period from
Chinook Salmon spawning in drainages within Knik Arm and northwestern Cook Inlet, and
within the Susitna River drainage. For drainages within Knik Arm and northwest Cook Inlet,
this study was to augment the existing baseline by adding collections of up to 200 Chinook
Salmon from two tributaries from each area. For the Susitna River drainage, this project was to
augment the existing baseline such that all tributaries were represented by at least 50 (and ideally
200) Chinook Salmon.
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Understanding the population structure of Chinook Salmon collected above and below Devils
Canyon will inform policymakers regarding the relatedness and isolation of spawning
aggregates. Population structure of Chinook Salmon will be measured at three different levels:
within the set of individuals spawning above the canyon; among the groups of individuals
spawning within the Susitna River watershed (with particular emphasis on the Middle River and
Upper River); and in relationship to populations from nearby drainages in Upper Cook Inlet.
These higher-level analyses will anchor the results and help provide a context for interpretation.
As in 2013, Chinook Salmon were captured using either hook-and-line, seines, or gillnets
depending on the size of the stream and where the fish were located. Upon capture, a single
axillary process was clipped from each Chinook Salmon and placed in a bottle of ethyl alcohol
for preservation. Fish were held in the water as much as possible while hooks were removed and
samples were collected, and released immediately after the sample was placed in the bottle. If
necessary, crews held the fish in the water to make sure they could swim before releasing them.
For Chinook Salmon sampled above Devils Canyon, additional paired samples/data were
collected including scales, length (mid-eye to fork, to nearest 5 mm), sex, and GPS information
(decimal degrees, to the nearest 0.001). Therefore, for these fish, an axillary process and five
scale samples were sampled into individually labeled vials. Scales were sampled at a point along
the diagonal line from the posterior insertion of the dorsal fin to the anterior insertion of the anal
fin, two rows above the lateral line. Length, sex and GPS information was recorded on Rite-in-
the-Rain® notebooks paired with the vial identifier.
The methods used in 2013 adult salmon sample collections are detailed in the Study 9.14 ISR
Part A Sections 4.1.1 and 4.1.2. In 2014, an ADF&G Gene Conservation Laboratory (GCL)
sampling crew of three people dedicated to collecting juvenile and adult Chinook Salmon from
above Devils Canyon was employed. Additional staff were added for a day or two at a time to
provide rest days for the dedicated crew or add an additional crew. During days when fish were
not present above Devils Canyon or weather prevented access, crews focused on collecting
Chinook Salmon in the following areas (in order of priority) 1) Middle River tributaries
(including Susitna River above Talkeetna, but below Devils Canyon, Talkeetna River, and
Chulitna River); 2) Lower River tributaries; 3) Yentna River tributaries; 4) other Upper Cook
Inlet tributaries (Table 4-1). Crews opportunistically collected other species of both Pacific
salmon and resident species within the Susitna River.
4.1.2. Other adult salmon collections
To address Objective 2, tissue samples were to be collected from 100 individuals (total archived
and samples collected during the study period) from at least three spawning aggregates of Pink,
Sockeye, Chum, and Coho Salmon from each of the following drainages: 1) the Susitna River
upstream of the Three Rivers Confluence (Middle Susitna River), 2) the Talkeetna River, and 3)
the Chulitna River (Tables 4-2 to 4-5; Figures 4-1 to 4-4). Capture and sampling of salmon
followed the methods used for adult Chinook Salmon.
Previously documented spawning time periods for each species in the Middle Susitna River,
indicated below, were used as the general time periods for sampling trips (Thompson et al.
1986).
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Pink Salmon – last week of July to third week of August
Chum Salmon – late-August to mid-September
Sockeye Salmon – late-August to mid-September
Coho Salmon – late-August to late-September
Details regarding adult salmon sample collection in 2013 are reported in the Study 9.14 ISR Part
A Section 4.1.2. In 2014, collections from adult pink and Sockeye Salmon were conducted
during the week of August 4. Collections from Coho Salmon were conducted in an unrelated
project for the weeks of September 22 and 29 and October 13 (Table 4-8). Samples from these
other salmon species were collected opportunistically by the Susitna River crews.
4.1.3. Juvenile Chinook Salmon collections
4.1.3.1. Above and within Devils Canyon
To address Objectives 3 and 4, tissue samples were to be collected from an ideal target of 200
juvenile Chinook Salmon during the study period at the Oshetna River and in each of Kosina,
Fog, and Cheechako creeks as described in the 2013 and 2014 IP Section 4.2.1 (Table 4-1). The
expected sample size from all tributaries above Devils Canyon from all years combined was a
total of 70 fish (2013 and 2014 IP Table 4-1) Methods for capturing juvenile Chinook Salmon
in minnow traps followed Magnus et al. (2006). Cured salmon roe was used as bait and several
minnow traps were set at each location. Minnow traps were checked at least once per day.
Collections occurred at the same time as adult salmon collection trips.
In 2013, caudal fin tissue was collected as detailed in ISR Part A Section 4.1.3.1. Caudal fin
sampling is lethal to the fish. As described in the 2014 Implementation Plan (ISR Part B), buccal
swab samples were collected in 2014 instead of caudal fin tissue to allow for non-lethal sampling
(see Appendix A for sampling methods).
4.1.3.2. Lower River collections
No juvenile sampling occurred in the Lower Susitna River in 2014.
4.1.3.3. Species identification of juvenile collections
Species identification was performed in the field using phenotypic characteristics (i.e. Pollard
et al. 1997). Juvenile Pacific salmon samples were collected in the Susitna River from 2012 to
2014 by the ADF&G GCL and by contractors to AEA which were provided to GCL. Field
species determinations were provided for each sample.
Confirmation of species identification of juvenile samples was provided by genetic analysis of
tissue samples. Samples from 20 adult fish from each of the five Pacific salmon species native to
North America were used as positive controls (100 known fish). Positive controls were selected
from fish collected in the Cook Inlet region. In this report, we provide results from juvenile
Pacific salmon captured within and above Devils Canyon because these samples will be used to
investigate population structure.
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Genomic DNA was isolated from the samples using a DNeasy® 96 Blood and Tissue Kit by
QIAGEN® (Valencia, CA).
Laboratory analysis for species determination was accomplished using one of two methods: 1)
microsatellites screened for the population structure project were used to positively identify
Chinook Salmon and 2) SNP markers were used to discriminate among all species of Pacific
salmon. Results from these analyses for samples taken in related studies were distributed to
project leads. Fish-specific species identification results will be included in the associated
projects reports.
4.1.3.3.1. Microsatellites
This method was employed because GCL had already genotyped many juvenile Pacific salmon
samples collected above Devils Canyon for the population structure analysis of Chinook Salmon.
This method provides positive identification that a sample is a Chinook Salmon if the sample has
adequate quality and quantity of DNA. However, this method cannot discriminate between a
sample with poor quality DNA of Chinook Salmon or among other Pacific salmon species.
Thirteen microsatellites that are commonly used for Chinook Salmon were genotyped (Table 4-
9). Samples were assayed for DNA loci developed for use in U.S-Canada Treaty fisheries (Seeb
et al. 2007). Polymerase chain reaction (PCR) was carried out in 10 ul reaction volumes (10 mM
Tris-HCl, 50 mM KCl, 0.2 mM each dNTP, 0.5 units Taq DNA polymerase [Promega, Madison,
WI]) using an Applied Biosystems (AB, Foster City, CA) thermocycler. Primer concentrations,
MgCl2 concentrations and the corresponding annealing temperature for each primer are available
in Seeb et al. (2007). PCR fragment analysis was done on an AB 3730 capillary DNA sequencer.
A 96-well reaction plate was loaded with 0.5 ul PCR product along with 0.5 ul of GS500LIZ
(AB) internal lane size standard and 9.0 ul of Hi-Di (AB). PCR bands were visualized and
separated into bin sets using AB GeneMapper software v4.0.
Genetic data were collected as individual multilocus genotypes for the 13 microsatellite loci.
Genotype data were stored as GeneMapper (*.fsa) files on a network drive that was backed up
nightly. Long-term storage of the data was in an Oracle database (LOKI) on a network drive
maintained by ADF&G computer services.
If at least 10 of the 13 microsatellite markers amplified, we designated the sample as a Chinook
Salmon. If not, the sample was designated as “undetermined” and further analyzed using the
SNP method. Undetermined samples were either not a Chinook Salmon or had inadequate
quantity or quality DNA for consistent amplification using these methods.
4.1.3.3.2. Single nucleotide polymorphisms
Preamplification of the extracted DNA was conducted using unlabeled primers from Integrated
DNA Technologies prior to genotyping. All primers were hydrated with TE and combined in a
10x primer mix. A Master Mix of the 10x unlabeled primers and a Multiplex PCR MMix by
QIAGEN® was plated onto a 384-well plate along with the extracted DNA and loaded onto an
Applied Biosystems 9700 thermocycler for preamplification. The preamplified DNA was then
diluted with TE and plated into Axygen raised-well plates.
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Applied BioSystems’ SNP Taqman assay analysis methods were used. Preamplified DNA was
diluted to a 1:10 concentration prior to genotyping and plated onto a 384-well plate along with a
10mM Tris water solution. Seven markers were used to discriminate among Pacific salmon
species (Tables 4-10). Each marker was plated onto a single 384-well plate and all plates were
loaded onto Applied Biosystems 9700. After PCR was complete, the plates were scanned using
an Applied Biosystems Quant Studio and analyzed using the 12K Flex Software v1.2.2.
Species determination was performed by examining the clustering of positive controls and
juvenile samples collected for this study (Table 4-10). Species were identified if the sample was
consistent with a single species determination across all markers successfully screened and at
least two markers amplified. Samples that did not amplify for at least two diagnostic markers
were designated as “Failed”. Samples that amplified but did not locate to a consistent species
were designated as “undetermined”. Samples that were not analyzed by error were designated as
“N/A”. Determinations were reviewed by two staff.
4.1.3.3.3. Quality control measures
Several measures were implemented to insure the quality of data produced regardless of marker
type. First, each individual tissue sample was assigned a unique accession identifier. At the time
DNA was extracted or analyzed from each sample, a sample sheet was created that linked each
individual sample’s code to a specific well number in a uniquely numbered 96-well plate. This
sample sheet then followed the sample through all phases of the project, minimizing the risk of
misidentification of samples through human-induced errors. Second, genotypes were assigned to
individuals using a system in which two individuals score the genotype data independently.
Discrepancies between the two sets of scores were then resolved with one of two possible
outcomes: (1) one score was accepted and the other rejected, or (2) both scores were rejected and
the score was blanked. Third, approximately 8 percent of the individuals, eight samples from
each 96-well DNA extraction plate, were reanalyzed for all loci. This insured that the data were
reproducible, and any errors created from the processing of individual plates were corrected.
4.1.4. Other species collections
To address Objective 1, tissue samples were to be collected from up to 50 representative
individuals during the study period from each of the resident fish species listed in Table 4-6, with
an emphasis on fish collected in the Lower, Middle and Upper Susitna River. Samples of
resident fish species were collected opportunistically while crews were collecting adult and
juvenile salmon samples. Resident fish were identified to genus or species with a field key. A
small piece of fin tissue was sampled from each fish and placed into a bottle or vial of ethyl
alcohol for preservation. Samplers recorded on each bottle, or on datasheets for vial collections,
the areas from which the samples were collected: 1) Chulitna River, 2) Talkeetna River, 3)
Upper Susitna River, 4) Middle Susitna River below Devils Canyon, 5) Middle Susitna River
above Devils Canyon, or 6) Lower River. Tissues were placed in separate bottles for each
species and area where they were collected.
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4.1.5. Sampling coordination with other studies
Methods used in 2013 adult salmon sample collections are reported in the Study 9.14 ISR Part A
Section 4.1.5. In 2014, project leads met biweekly starting on July 17 to coordinate field work. In
addition, Salmon Escapement Study (Study 9.7) field crews released seven spawning survey
results summarizing Chinook Salmon observations soon after the surveys were completed
between July 14 and August 19, 2014. As in 2013, there was also frequent direct communication
among ADF&G, the contractor liaison, and study leads designated for each interrelated study.
Samples were delivered to the GCL and were entered into ADF&G’s LOKI database. Most of
these samples were resident fish (Table 4-6) or juvenile Chinook Salmon from above Devils
Canyon (Table 4-1) collected as part of Study 9.5. As part of the Salmon Escapement Study
(Study 9.7), AEA also collected samples from salmon radio-tagged at Curry (PRM 124-126), and
salmon radio-tagged in the Lower River near the confluence with the Yentna River (PRM 33-
34), and in the Yentna River (RM 6). Sampling methods for all fish tissue samples provided
from the interrelated studies are described in the respective ISRs and Study Implementation
Reports.
4.1.6. Collection trip documentation
As in 2013, detailed notes were kept during each collection trip and then entered into the trip
report database in the GCL Oracle database, LOKI, when crews returned to Anchorage (ISR Part
A Appendix A). The following information was recorded for each trip: 1) trip logistical
information, 2) GPS waypoints where fish were collected, 3) number of fish and species
collected at each location, 4) notes on other fish species present, 5) life stage of observed fish, 6)
fish habitat information, and 7) recommendations for future collection trips. Collection trip
records were used post-season to submit Anadromous Waters Catalog nomination forms.
4.2. Tissue Storage
AEA implemented the methods for tissue storage of samples collected in ethanol as described in
Section 4.3 of the 2013 and 2014 Genetics Implementation Plans, with no variances. While in
the field, tissue samples were preserved in ethyl alcohol in either a 125–500 ml (4.2-16.9 oz)
bulk sample bottle for each location or individual 2 ml (0.07 oz) vials. After samples were
received by the GCL, collection information was recorded in LOKI. For long-term storage,
samples were preserved as follows: 1) vials were pierced, ethanol removed, and sample vacuum-
dried; 2) once dry, tissue samples were stored at room temperature.
Storage for tissue samples collected on buccal swabs (Appendix A) was similar: tissues were
stored dry at room temperature. The only difference is that these samples were desiccated in the
field (by placing the samples in desiccant beads within individual 2ml vials) rather than after
they arrived at the lab.
4.3. Laboratory Analysis
Laboratory analysis began during the fourth quarter of 2013 and is continuing without variances
(Figure 7.1). Methods were described in detail in the 2013 and 2014 Genetics IP Section 4.4.
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The methods in the 2014 IP (ISR Part B Attachment 1) differed from those in the 2013 IP as a
result of consultation with USFWS and NMFS in March 2014. The 2014 plan includes 190 SNP
markers and 12 microsatellite markers to be analyzed for all adult and juvenile Chinook Salmon
captured in the Middle and Upper River to test among hypotheses for fish spawning above
Devils Canyon. Sets of markers to be screened in selected samples are in Table 4-9.
4.4. Data Retrieval and Quality Control
Data retrieval and quality control is ongoing with no variances. The Section 4.5 of both the 2013
IP and 2014 IP (ISR Part B Attachment 1) contain detailed descriptions of data retrieval and
quality control methods.
4.5. Variances from Study Plan
As described in ISR Part A Section 4.5, there were no variances from the collection, storage and
analysis methods described in the Genetic Baseline Study Plan in 2013. However, full access to
all of the sampling sites in the 2013 Genetics IP was not available in 2013. The Study Plan for
2013 included sampling on streams that required access to Cook Inlet Regional Working Group
(CIRWG) lands. Access was not granted to CIRWG lands in 2013, thereby fully or partially
restricting sampling on some streams. Lack of access to CIRWG lands above or near Dev ils
Canyon prevented potential sampling of Chinook Salmon on Cheechako, Devil, Fog, Tsusena,
and Watana creeks. Lack of access to CIRWG lands also prevented potential sampling at
Portage and Prairie creeks for Coho Salmon, and reduced sampling at Prairie Creek for Sockeye
Salmon. The study was designed to collect the target number of samples over multiple years. In
2014, full access to the CIRWG lands was granted. Analysis of 2013 and 2014 collections will
provide insight into whether there is a loss in power to test for stability in allele frequencies
across years for Chinook Salmon (testing between hypotheses 1a, 1b; Figure 2-1) and, if there is,
the magnitude of this loss in power.
There was one variance from the collection methods described in the Genetic Baseline Study
Plan as outlined in the 2014 Implementation Plan: Associated data (latitude/longitude, length,
sex) were not recorded for each individual and scales were not sampled for the 12 adult Chinook
Salmon captured and sampled for genetic tissues in Fog Creek due to an oversight in the field.
All the other adult Chinook Salmon captured within and above Devils Canyon were taken from
within Devils Canyon where these paired data were not required. However, latitude/longitude
data were recorded for the general area were the fish were collected. Lack of these data will
reduce the ability to determine correlations between location and genetic relatedness and could
reduce the precision of the estimation of effective population size (sex ratios affect effective
population size). Lack of these data will have minimal effect on the ability to test among
hypotheses for population structure.
Methods for tissue samples from Chinook Salmon juveniles collected from tributaries above
Devils Canyon differed between the 2013 IP and the 2014 IP. In the 2013 ISR Part A Section
4.1.3.1, methods describe sampling caudal fin tissue. Caudal fin sampling is lethal to the fish.
In the 2014 Implementation Plan (ISR Part B), methods describe sampling using buccal swabs to
allow for non-lethal sampling (see Appendix A for sampling methods). Within each year,
methods followed those described in their respective implementation plans.
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Finally, the laboratory methods in the 2014 IP (ISR Part B Attachment 1) differed from those in
the 2013 IP as a result of consultation with USFWS and NMFS in March 2014. The 2014 plan
includes 190 SNP markers and 12 microsatellite markers to be analyzed for all adult and juvenile
Chinook Salmon captured in the Middle and Upper River to test among hypotheses for fish
spawning above Devils Canyon.
5. RESULTS
5.1. Sample Collection
Details regarding sample collection through September 15, 2013 are reported in ISR Part A
Section 5.1. The sections below provide details regarding the 2014 sampling effort as well as a
cumulative summary of all collections delivered to the GCL each year since inception of the
Study, as presented in Tables 4-1 through 4-6. The genetic sampling effort through time by river
area for adult salmon species and juvenile Chinook Salmon during 2013 and 2014 is provided in
Table 4-8.
5.1.1. Adult Chinook Salmon collections
5.1.1.1. 2013
Details regarding the 2013 adult Chinook Salmon collections through September 15, 2013 are
reported in the 9.14 ISR Section 5.1.1. Full counts for sites visited and samples collected
through the end of the 2013 are reported here. AEA captured and sampled Chinook Salmon at
32 of the 35 sites surveyed. (Table 4-1). Samples from 1,405 adult Chinook Salmon were
collected. Most of these samples were taken from the Susitna River drainage (1,342). Three of
these samples were from above Devils Canyon (Tables 4-1 and 4-11). The remaining samples
came from other drainages within upper Cook Inlet.
5.1.1.1.1. 2014
A dedicated survey flight to determine distribution and availability of Chinook Salmon for
sampling occurred the week of July 1 (Table 4-8). Only the Knik Arm area was surveyed from
the air. However, many of the collection flights incorporated surveys. AEA captured and
sampled Chinook Salmon at 26 of the 27 sites surveyed (Table 4-1). Samples from 1,045 adult
Chinook Salmon were collected. Most of these samples were taken from the Susitna River
drainage (1,005). Thirteen of these samples were from above Devils Canyon (Fog and Devil
creeks) and 64 were sampled within Devils Canyon from Chinook Creek and Cheechako Creek.
The remaining samples came from other drainages within upper Cook Inlet.
5.1.2. Other adult salmon collections
Details regarding the collection of other adult salmon species through September 15, 2013 are
provided in ISR Part A Section 5.1.2. No dedicated surveys were performed for adult salmon
species other than Chinook Salmon in 2014, but samples were collected incidentally or during
other ADF&G sampling efforts unrelated to the this Study.
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A total of 376 Sockeye Salmon adult samples have been collected. Samples from 336 Sockeye
Salmon were collected from 11 streams and 2 sloughs (Table 4-2) in 2013. During 2014,
Sockeye Salmon were sampled from Spink Creek (n=19) and Larson Lake - outlet stream (n=21;
Table 4-2). Samples from 659 Chum Salmon were collected from 13 streams and several
sloughs above the Three Rivers Confluence (Table 4-3) in 2013; no additional Chum Salmon
samples have been collected. A total of 1,101 Coho Salmon samples have been collected, with
541 collected from 10 streams in 2013 and another 560 sampled during 2014 for another
ADF&G study from 12 locations within this study area (Table 4-4). Odd-year Pink Salmon were
collected from 11 streams and 1 slough during 2013 (n=1,049; Table 4-5) and even-year Pink
Salmon were sampled in 2014 from Spink Creek (n=116; Table 4-5).
5.1.3. Juvenile Chinook Salmon collections
5.1.3.1. Above Devils Canyon
A total of 134 juvenile Chinook Salmon have been collected from tributaries within Devils
Canyon, below the uppermost impediment to fish migration (i.e., Impediment 3; Table 4-1).
Archived tissues collected in 2012 are available from Cheechako Creek, a tributary within Devils
Canyon (n=35). In 2014, samples from 120 juvenile Chinook Salmon were collected in 2014
from two tributaries within Devils Canyon (Cheechako Creek n=58; Chinook Creek n=62).
A total of 226 juvenile Chinook Salmon have been collected from above Devils Canyon
Impediment 3 (Table 4-1). Samples from 189 juvenile Chinook Salmon were collected in 2013
from 2 tributaries above Devils Canyon (Kosina Creek n=130; Oshetna River n=59). In 2014,
samples from 54 juvenile Chinook Salmon were collected from five tributaries and the mainstem
above Devils Canyon (Devil Creek n=14; Unnamed Tributary 184 n=1; Tsusena Creek n=1;
Kosina Creek n=3; Oshetna River n=3; Susitna River mainstem n= 32).
5.1.3.2. Lower River collections
No sampling of the Lower River occurred in 2014. As described in ISR Part A Section 5.1.3.2,
sampling during 2013 resulted in the collection of eight juvenile Chinook Salmon from the
Lower River (Table 4-1).
5.1.3.3. Species identification of juvenile collections
A total of 797 juvenile Pacific salmon samples from this and other studies collected in the
Susitna River from 2012 to 2014 were analyzed in the lab to determine species. Samples were
collected throughout the Susitna River but most came from the Middle and Upper River. Results
for species identification for collections made by AEA contractors below Devils Canyon will be
reported by Study 9.5 and 9.6. Of the 398 juveniles captured within and above Devils Canyon,
species were determined on 386 fish (96.5%). Unsuccessful analysis was determined to be due
to 1) no DNA amplification (3 fish), loss of the sample, paired data discrepancies, or lab error
(10 fish), or 3) equivocal results likely due to low amplification (1 fish). All successfully
analyzed samples collected within and above Devils Canyon were identified as Chinook Salmon.
Among these samples, there were no discrepancies in species identification between field
identification and DNA analysis.
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5.1.4. Other species collections
Results through 9/15/2013 were reported in the 9.14 ISR Section 5.1.4. Full counts for sites
visited and samples collected through all of 2013 and 2014 are reported here. In total, samples
were collected from 2,402 fish (1,652 in 2013 and 750 during 2014), with sampling sites further
broken into one of six potential strata (Table 4-6). The target sample size of 50 total fish per
species was reached for nine species (Burbot, Dolly Varden, Eulachon, Arctic Grayling, Slimy
Sculpin, Three-spine Stickleback, Longnose Sucker, Rainbow Trout, and Round Whitefish). No
samples were collected for six species (Alaska Blackfish, Pacific Lamprey, Coastrange Sculpin,
Pacific Staghorn Sculpin, Prickly Sculpin, and Lake Whitefish).
5.1.5. Pacific salmon sampling coordination with other studies
As part of the Salmon Escapement Study (Study 9.7) effort, Pacific salmon genetic samples were
collected by AEA from salmon radio-tagged at Curry and at Lower Susitna River and Yentna
River fish wheel sites administered by the ADF&G Division of Sport Fish. A total of 3,361
Chinook, 394 Chum, 445 Coho, 400 Pink, 335 Sockeye Salmon, and 230 non-salmon species
were sampled.
The samples from radio-tagged fish were intended to be used to supplement the data in areas
where genetic sample targets were not achieved and final spawning destination could be
confirmed. Final spawning locations have now been determined from telemetry and 12 Chinook
Salmon with final spawning locations above or within Devils Canyon will be used in this study
(Table 4-1). In 2013, seven radio-tagged Chinook Salmon were confirmed as spawning in two
tributaries within the Devils Canyon below Impediment 3 (Chinook Creek n=1; and Cheechako
Creek n=6) and another four were confirmed spawning in Cheechako Creek in 2014. One fish
radio-tagged in 2013 with a final spawning destination above Devils Canyon Impediment 3 (i.e.,
Devil Creek) will also be included in the analysis.
5.1.6. Collection trip documentation
In 2014, one entry was made into the GCL Oracle database to document a survey trip and 15
entries were made to document Chinook Salmon collection trips.
5.2. Tissue Storage
As in 2013, the 2014 samples were placed into bottles (multiple fish per container) for most of
the collections (75 percent) and for the remaining collections, samples were placed into vials
(one fish per container).
5.3. Laboratory Analysis
Laboratory and statistical analyses are ongoing. Laboratory analysis progress is presented for
three sets of markers in Table 4-13. Laboratory analyses of SNP markers to augment the
microsatellite data have been screened on all juvenile and adult Chinook Salmon collected within
and above Devils Canyon. For most of the adults, the 188 SNP panel has been successfully
screened. However low DNA amplification in juvenile fish have yielded unreliable results for
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many samples. The small initial tissue quantity resulted in low concentration DNA yields.
Methods to concentrate DNA of remaining samples are being investigated, but remaining
volumes are low and some samples have been exhausted. Analysis of SNP markers for Chinook
Salmon collected from Susitna River drainages below Devils Canyon (Objective 3) is largely
complete for 48 markers (Table 4-13). On the outset of this study, 30 locations were identified
as location groupings to collect samples that might represent individual populations. This study
has SNP data collected from at least 50 fish from 38 locations and from at least 100 fish from 24
locations.
The panel of 48 SNP markers has been successfully screened on at least 100 fish from three
locations and at least 50 fish in four locations within West Side of Cook Inlet and from at least
100 fish from three locations and at least 50 fish from 5 collections within Knik Arm (Table 4-
13). These samples will also be used to accomplish Objective 3.
5.4. Data Retrieval and Quality Control
Data retrieval and quality control are ongoing and no results are available for inclusion in this
Study Implementation Report.
6. DISCUSSION
The study was designed to achieve the target number of samples over the course of multiple
years. With a few exceptions, sample collections of Pacific salmon species delivered to GCL
were sufficient to maintain progress toward study objectives (“Expected” columns in Tables 4-1
to 4-5).
6.1. Chinook Salmon Adults and Juveniles Above Devils Canyon
Section 4.2 of the 2013 Genetics IP outlined sample collection in locations across the Susitna
River basin. In 2013, Alaska Energy Authority was not granted access to Cook Inlet Regional
Working Group (CIRWG) lands to collect samples associated with this study. As a result AEA
did not collect samples of adult salmon where they were observed on CIRWG lands from the air
or through radio-tag tracking. For adult Chinook Salmon, tributaries not accessed included
Watana, Tsusena, Fog, Devil, and Cheechako creeks (all above or within Devils Canyon on the
Susitna River). In addition, Portage Creek (below Devils Canyon on the Susitna River) and
Prairie Creek (a Talkeetna River tributary) received a reduced sampling intensity due to lack of
land access.
Access to these lands was obtained for the 2014 field season and progress was made in collecting
samples from these areas. AEA now has exceeded sampling expectations for both adult and
juvenile Chinook Salmon within and above Devils Canyon (Table 4-1). However, the lack of
large numbers of samples from the same locations over multiple years may provide challenges in
testing among hypotheses that explain population structure. Samples collected by AEA in field
studies 9.5 and 9.6 in additional years may mitigate for this shortcoming.
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Laboratory analyses is complete for microsatellites but incomplete for SNPs for these collections
and for adult collections within the Middle River below Devils Canyon (Table 4-13). Of the 395
juvenile Chinook Salmon screened for microsatellites, 392 individuals have genotypes for at
least 11 of the 13 markers. All 107 adults have genotypes for at least 11 of 13 markers. In
addition, 93 and 98 adult samples from Portage Creek and Indian River (all adult samples in the
Middle River of the Susitna River below Devils Canyon), respectively, have genotypes from at
least 11 of 13 markers. Of all the marker types, microsatellites offer the most useful information
to satisfy Objective 3 for collections within and above Devils Canyon. These markers have large
numbers of alleles providing information that will be useful in testing hypotheses about
population structure as outlined in Figure 2-1.
6.2. Chinook Salmon Adults in the Susitna River Below Devils
Canyon
Total number of fish collected in 2013 and 2014 (2,252 fish from 27 sites; Table 4-1) exceeded
expected numbers for the full project (1,032 fish from 20 to 29 sites), although the geographic
distribution of these collections differs from the anticipated distribution. In the Yentna River,
249 fish were collected from 5 sites (project expected 390 fish from 9 sites). In the Chulitna
River, 776 fish were collected from 9 sites; (project expected 218 fish from 2 to 8 sites). In the
Middle River, below Devils Canyon, 151 fish were collected from 3 sites (project expected 134
fish from 2 to 6 sites). In Talkeetna River, 410 fish were collected from 6 sites (project expected
196 fish from 3 to 7 sites). Finally, from the Lower River, 666 fish were collected from 4 sites
(project expected 159 fish from 5 to 9 sites). Nevertheless, the collections should provide
adequate representation of Chinook Salmon populations to meet objective 3: “Characterize the
genetic population structure of Chinook Salmon from Upper Cook Inlet, with emphasis on
spawning aggregates in the Middle and Upper Susitna River.” Despite exceeding the expected
numbers of samples collected in the study area, ideal sample sizes were only met for 6 of the 45
sites originally targeted. Statistical analyses of these data are in progress and should provide
adequate resolution to accomplish Objective 3.
6.3. Chinook Salmon Adults Outside of the Susitna Basin
Progress was made toward collecting Chinook Salmon in the other drainages from Upper Cook
Inlet in 2013 and 2014. In the western side of Cook Inlet, 47 fish were collected from one site
(study expected 235 fish from 4 sites). In the Knik Arm, 56 fish were collected from 3 sites
(study expected 181 fish from 5 to 6 sites). Ideal sample sizes have been met for one of the 11
sites originally targeted. Nonetheless, by including collections already in archive, there should
be adequate representation of Chinook Salmon populations to meet Objective 3. Statistical
analyses of these data are in progress and should provide adequate resolution to accomplish
Objective 3.
6.4. Other Fish Species
Sample collections were sufficient to attain or make progress towards study objectives for some
resident species (Objective 1). Although the target sample size in the 2013 and 2014 IPs for each
species was 50 fish for the entire Susitna River drainage, ADF&G also wanted to know roughly
what part of the drainage the samples came from, and so asked field crews to reference each
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collection to one of six location “strata” in the drainage (Table 4-6). Because crews worked
concurrently in different strata, this meant 50 samples were able to be collected in multiple
places for some species, and caused the drainage-wide target to be exceeded (see results section;
Table 4-6).
The approved study methods include only opportunistic collection of resident fish species.
Targets of 50 fish per species may not be met for those species that were not present during
sampling, or were not susceptible to the sampling gear. No laboratory or statistical analyses are
planned for genetic samples from resident species in this study. The objective for taking these
samples was to develop a repository of genetic samples for target resident fish species captured
within the Lower, Middle, and Upper Susitna River drainage. This was always planned as an
opportunistic activity to occur while sampling for other Susitna-Watana Hydro Project licensing
studies or other non-related projects.
7. CONCLUSION
During the last two years, progress was made toward all but one objective. In 2014, progress
was made in collecting juvenile and adult Chinook Salmon from above Devils Canyon,
collecting adult Chinook Salmon from upper Cook Inlet tributaries, opportunistically collecting
other salmon and non-salmon species from the Susitna River and genotyping Chinook Salmon
for SNPs and µSATs. Progress on sample collection to date exceeds expectations for Objectives
1, 2, and 3 but has not met all study goals.
We anticipated that assessing temporal stability in allele frequencies for Chinook Salmon
captured above Devils Canyon was going to be challenging even with samples taken over three
or four years (2014 IP; ISR Part B Attachment 1, section 2.1.1). With accessibility issues to
CIRWG lands in 2013 and only one full year of sampling (2014), challenges in testing of
temporal stability within locations both within and above Devils Canyon are anticipated. This
testing is a key to elucidate population structure (Objective 3) and determine the MSA potential
for identifying Chinook Salmon originating from tributaries within and above Devils Canyon
captured below Devils Canyon (Objective 4). However, these samples may be adequate to detect
high temporal variation in allele frequencies among years. Samples from additional years will be
required to examine temporal stability in allele frequencies among years within specific locations
in tributaries within and above Devils Canyon and to provide more precise estimates of variation
in allele frequencies among years.
Laboratory analysis has begun and data have been collected to start examining Objectives 3 and
4. The panel of 48 SNP markers has been successfully screened from at least 50 fish from 38
locations and from at least 100 fish from 24 locations within the Susitna River drainage; from at
least 100 fish from three locations and at least 50 fish in four locations within West Side of Cook
Inlet; and from at least 100 fish from three locations and at least 50 fish from 5 collections within
Knik Arm (Table 4-13). These data should be adequate to characterize the genetic population
structure of Chinook Salmon from Upper Cook Inlet (Objective 3).
Low DNA yields for some collections from within and above Devils Canyon may reduce the
number of markers available for statistical analysis (Objectives 3 and 4). However,
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microsatellites have been successfully screened for most of the collections (Table 4-13) and this
marker type is likely to yield the most informative tests given the high heterozygosity and large
numbers of alleles present.
Standard population structure statistical analyses will be completed on Chinook Salmon from
throughout Upper Cook Inlet to understand how genetic variation is partitioned. Statistical
analysis to test among hypotheses for Chinook Salmon captured within and above Devils
Canyon will be determined through consultations with USFWS and NOAA.
8. LITERATURE CITED
Alaska Energy Authority (AEA). 2012. Revised Study Plan: Susitna-Watana Hydroelectric
Project FERC Project No. 14241. December 2012. Prepared for the Federal Energy
Regulatory Commission by the Alaska Energy Authority, Anchorage, Alaska.
http://www.susitna-watanahydro.org/study-plan.
Banks, M. A., M. S. Blouin, B. A. Baldwin, V. K. Rashbrook, H. A. Fitzgerald, S. M.
Blankenship, and D. Hedgecock. 1999. Isolation and inheritance of novel microsatellites
in Chinook Salmon (Oncorhynchus tshawytscha). Journal of Heredity 90:281-288; errata
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Cairney, M., J. B. Taggart, and B. Hoyheim. 2000. Characterization of microsatellite and
minisatellite loci in Atlantic salmon (Salmo salar L.) and cross-species amplification in
other salmonids. Molecular Ecology 9:2175-2178.
Campbell, N. R., and S. R. Narum. 2008. Identification of novel single-nucleotide
polymorphisms in Chinook salmon and variation among life history types. Transactions
of the American Fisheries Society, 137(1), 96-106.
Campbell, N. R., and S. R. Narum. 2009. Identification and characterization of heat shock
response–related single-nucleotide polymorphisms in O. mykiss and O. tshawytscha.
Molecular Ecology Resources, 9(6), 1460-1466.
Clemento, A. J., A. Abadía‐Cardoso, H. A. Starks and J. C. Garza. 2011. Discovery and
characterization of single nucleotide polymorphisms in Chinook Salmon, Oncorhynchus
tshawytscha. Molecular ecology resources, 11(s1), 50-66.Grieg, C. A., and M. A. Banks.
1999. Five multiplexed microsatellite loci for rapid response run identification of
California’s endangered winter Chinook Salmon. Animal Genetics 30(4):318-320.
Grieg, C., D. P. Jacobson, and M. A. Banks. 2003. New tetranucleotide microsatellites for fine-
scale discrimination among endangered Chinook Salmon (Oncorhynchus tshawytscha).
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Larson, W. A., J. E. Seeb, C. E. Pascal, W. D. Templin and L. W. Seeb. 2014. Single-nucleotide
polymorphisms (SNPs) identified through genotyping-by-sequencing improve genetic
stock identification of Chinook Salmon (Oncorhynchus tshawytscha) from western
Alaska. Canadian Journal of Fisheries and Aquatic Sciences, 71(5), 698-708.Miller et al.
2008
Olsen, J. B., P. Bentzen, and J. S. Seeb. 1998. Characterization of seven microsatellite loci
derived from Pink Salmon. Molecular Ecology. 7:1087-1089.
Pollard, W. R., G. F., Hartman, C. Groot and P. Edgell. 1997. Field identification of coastal
juvenile salmonids. Harbor Publishing.
Rexroad, C. E., III, R. L. Coleman, A. M., Martin, W. K. Hershberger, and J. Killefer. 2001.
Thirty-five polymorphic microsatellite markers for rainbow trout (Oncorhynchus mykiss).
Animal Genetics 32:317-319.
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M., DeCovich, N., Garza, J. C., Guthrie, C., Lundrigan, T., Moran, P., Narum, S.,
Stephenson, J., Supernault, J., Teel, D., Templin, W. D., Wenburg, J. K., Young, S., and
Smith, C. T. 2007. Development of a standardized DNA database for Chinook Salmon.
Fisheries 32(11):540–552.
Smith, C. T., C. M. Elfstrom, L. W. Seeb and J. E. Seeb. 2005a. Use of sequence data from
rainbow trout and Atlantic salmon for SNP detection in Pacific salmon. Molecular
Ecology, 14(13), 4193-4203.
Smith, C. T., J. E. Seeb, P. Schwenke, and L. W. Seeb. 2005b. Use of the 5′-nuclease reaction
for single nucleotide polymorphism genotyping in Chinook Salmon. Transactions of the
American Fisheries Society, 134(1), 207-217.
Smith, C. T., A. Antonovich, W. D. Templin, C. M. Elfstrom, S. R. Narum, and L. W. Seeb.
2007. Impacts of marker class bias relative to locus-specific variability on population
inferences in Chinook Salmon: a comparison of single-nucleotide polymorphisms with
short tandem repeats and allozymes. Transactions of the American Fisheries Society,
136(6), 1674-1687.
Thompson, F. M., S. N. Wick, and B. L. Stratton. 1986. Alaska Department of Fish and Game
Susitna River Aquatics Studies Program. Report # 13, Volume 1: Adult Salmon
Investigations May – October 1985. Alaska Power Authority, Anchorage, Alaska.
Waples, R. S. and O. Gaggiotti. 2006. INVITED REVIEW: What is a population? An
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and their degree of connectivity. Molecular ecology, 15(6): 1419-1439.
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Williamson, K. S., J. F. Cordes, and B. May. 2002. Characterization of microsatellite loci in
Chinook Salmon (Oncorhynchus tshawytscha) and cross-species amplification in other
salmonids. Molecular Ecology Notes. 2:17-19.Magnus, D. L., D. Brandenberg, K. F.
Crabtree, K. A. Pahlke, and S. A. McPherson. 2006. Juvenile salmon capture and coded
wire tagging manual. Alaska Department of Fish and Game, Special Publications No.
06-31, Anchorage.
9. TABLES
STUDY IMPLEMENTATION REPORT GENETIC BASELINE STUDY FOR SELECTED FISH SPECIES (STUDY 9.14)
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Table 4-1. Area, location, and sublocation of baseline samples of adult and juvenile Chinook Salmon spawning aggregates for genetic analysis.
Area Location Sublocation
Map
No.
Year(s) Collected
(# archived)
Sample sizes
This project
Ideal Expected
(all years) 2013 2014 Total
Adult Chinook Salmon
West Side Chuitna River 1 2008, 2009 (142) 200 58 - - 142
Cook Inlet Beluga River Coal Creek 2 2009, 2010, 2011 (120) 200 80 - - 120
Theodore River 3 2010, 2011, 2012 (189) 200 11 47 - 236
Lewis River 4 2011, 2012 (86) 200 86 0 - 86
Yentna
Drainage
Clearwater Creek 5 2012 (25) 200 50 - - 25
Drainage Nakochna River 6 n/a - - 22 22
Red Creek 7 2012 (29) 200 58 82 - 111
Happy River 8 2012 (19) 200 38 S - 19
Red Salmon Creek 9 2012 (12) 200 24 S 15 27
Hayes River 10 2012 (5) 200 10 45 24 74
Canyon Creek 11 2012 (32) 200 64 61 - 93
Talachulitna River 12 1995, 2008, 2010 (180) 200 20 - - 180
Lake Creek Sunflower Creek 13 2009, 2011 (127) 200 71 S - 127
Kahiltna River Peters Creek 14 2009, 2010, 2011, 2012 (110) 200 55 - - 110
Susitna
Drainage
Chulitna River Middle Fork 15 2009, 2010 (182) 200 18 61 243
Drainage East Fork 16 200
200
64 33
715
West Fork 17 200 S -
Honolulu Creek 18 200 31 75
Pass Creek 19 n/a 33 71
Spink Creek 20 200 56 18
Byers Creek 21 200 55 54
Troublesome Creek 22 200 71 48
Tokositna River (Bunco Creek) 23 200 103 -
Tokosina River (Bunco Lake inlet stream) 24 n/a 3 -
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Area Location Sublocation
Map
No.
Year(s) Collected
(# archived)
Sample sizes
This project
Ideal Expected
(all years) 2013 2014 Total
Susitna
Drainage
Upper Susitna River Oshetna River 25 200
50
0 -
107
Drainage Kosina Creek 26 2012 (10) 200 3 -
Kosina Creek (radio tag) 26 2012 (2) n/a - 1
Watana Creek 27 200 S -
Middle Susitna River
above Devils Canyon Tsusena Creek 28 200 S -
Tsusena Creek (radio tag) 28 n/a 1 -
Fog Creek 30 200 0 12
Susitna River mainstem n/a n/a 1 -
Middle Susitna River
within Devils Canyon Devil Creek 31
200 S 1
Devil Creek (radio tag) 31 n/a 1 -
Chinook Creek 32 200 S 7
Chinook Creek (radio tag) 32 n/a 1 -
Cheechako Creek 33 n/a - 57
Cheechako Creek (radio tag) 33 n/a 6 4
Middle Susitna River
below Devils Canyon Portage Creek 34 2009, 2010, 2011 (141) 200 59 25 - 166
Indian River 35 2012 (1) 200
75
81 20
127
Gold Creek 36
200 S -
4th of July Creek 37
n/a - 25
Lane Creek 38 200 S -
Chase Creek 39 200 S -
STUDY IMPLEMENTATION REPORT GENETIC BASELINE STUDY FOR SELECTED FISH SPECIES (STUDY 9.14)
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Area Location Sublocation
Map
No.
Year(s) Collected
(# archived)
Sample sizes
This project
Ideal Expected
(all years) 2013 2014 Total
Susitna Talkeetna River Prairie Creek 40 1995, 2008 (169) 200 31 32 - 201
Drainage no name creek #2 41 n/a
100
25 28
373
no name creek #1 42 n/a 71 13
upper mainstem 43 200 S -
Iron Creek 44 200 57 46
Disappointment Creek 45 200 64 69
Sheep River 46 200 S -
Larson Creek 47 200 S -
Chunilna Creek (Clear Creek) 48 2009, 2012 (130) 200 65 5 - 135
Lower Susitna River,
upstream of Deshka
River
Montana Creek 49 2008, 2009, 2010 (218) 200 0 213 227 658
Birch Creek 50 200
50
S -
226 Sheep Creek 51 200 24 36
North Fork Kashwitna River 52 200 12 50
Little Willow Creek 53 200 55 49
Willow Creek 54 1991,1997, 2005, 2009 (309) 200 0 - - 309
Deshka River Moose Creek 55 1995, 2012 (103) 200 52 - - 103
Deshka River weir 56 2005 (200) 200 0 - - 200
Alexander Creek Sucker Creek 57 2011, 2012 (143) 200 57 - - 143
Knik Arm Matanuska River Kings River 58 200 25 4 S 52 Granite Creek 59 200 12 36
Moose Creek 60 1995, 2008, 2009, 2012 (155) 200 45 - - 155
Eagle River South Fork 61 2009, 2011, 2012 (73) 200 24 - 4 77
Meadow Creek 62 2009 (6) 200 12 - - 6
Ship Creek 63 2009 (311) 200 0 - - 311
Little Susitna River 64 2009, 2010 (125) 200 75 - - 125
STUDY IMPLEMENTATION REPORT GENETIC BASELINE STUDY FOR SELECTED FISH SPECIES (STUDY 9.14)
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Area Location Sublocation
Map
No.
Year(s) Collected
(# archived)
Sample sizes
This project
Ideal Expected
(all years) 2013 2014 Total
Juvenile Chinook Salmon
Susitna Upper Susitna River Oshetna River 25 200
70
59a 3
398
Drainage Kosina Creek 26 200 130 3
Upper Susitna River mainstem n/a n/a - 30
Middle Susitna River
within and above Devils
Canyon
Tsusena Creek 28 n/a - 1
Unnamed Tributary 184 29 n/a - 1
Fog Creek 30 200 - -
Devil Creek 31 n/a - 14
Chinook Creek 32 n/a - 62a
Cheechako Creek 33 2012 (35) 200 - 58a
Middle Susitna River above n/a n/a - 2
Lower Susitna River 5 habitat types n/a 1,600 1,600 8 - 8
(100 fish/habitat type times 3 or 4 collections)
a Chain-of-custody forms indicate one more fish that we received for each of these collections (duplicate entries).
Note: Sample sizes show number of samples and sample years for collections already in the Gene Conservation Laboratory archives (Ar chived), number of
samples to obtain the ideal archived sample size (Ideal), the anticipated number to be collected over the original three years of this project based on past
sampling effort and success and information from the Anadromous Waters Catalog and local biologists (Expected), progress made toward sampling targets
in 2013 and 2014, and the resulting total sample size after combining the amount archived with the new samples (Total). Bold and underlined values in the
Total column indicate sample sizes in 2013 and 2014 met or exceeded expected numbers. An “S” in the 2013 and 2014 columns indicates that a survey was
performed but sampling was not attempted, a “-“ indicates that no survey was performed. Some of the expected numbers are for groups of locations.
Sampling locations originally not included in the implementation plan have been included, and are indicated by an “n/a” ideal and expected value. New
locations that are now included in grouped locations are sharing the expected value for their group. Map numbers (Map No.) correspond to location numbers
on Figure 4-5.
STUDY IMPLEMENTATION REPORT GENETIC BASELINE STUDY FOR SELECTED FISH SPECIES (STUDY 9.14)
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FERC Project No. 14241 Page 23 October 2015
Table 4-2. Location and sublocation of baseline samples of adult Sockeye Salmon spawning aggregates for genetic analysis.
Sample sizes
This project
Area Location Sublocation Map No. Year(s) Collected
(# archived) Ideal Expected
(all years) 2013 2014 Total
Susitna River
above three
rivers
confluence
Chulitna River Middle Fork 2 100 100 - - 0
East Fork 1 100 - -
Pass Creek 5 n/a n/a 2 - 2
Spink Creek 4 2007, 2008 (126) 100 0 0 19 145
Byers Lake 3 1993, 2006, 2007 (243) 100 0 23 - 266
(Tokositna River) Sloughs 7 100 100 S - 0
(Tokositna River) Swan Lake 8 2006, 2007, 2009 (109) 100 0 0 - 109
no-name creek 6 n/a n/a 6 - 6
Middle Susitna
River below Devils
Canyon
Portage Creek 9 n/a
100
8 -
10 5th of July Creek 10 n/a 2 -
McKenzie Creek 11 100 0 -
Chase Creek 12 100 0 -
Mainstem sloughs
above Three Rivers
Confluence
sloughs 8A,11, and 21 13 1995, 1996, 1997 (156) 100 0 119 275
slough 9 14 n/a n/a 66 66
Susitna River
above three
rivers
confluence
Talkeetna River unnamed creek 15 n/a 0 1 - 1
Stephan Lake 16 1993, 1994, 2007 (346) 100 0 - - 346
Prairie Creek 17 n/a 0 2 - 2
Iron Creek 18 100 50 0 - 0
Disappointment Creek 19 n/a 0 11 - 11
STUDY IMPLEMENTATION REPORT GENETIC BASELINE STUDY FOR SELECTED FISH SPECIES (STUDY 9.14)
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Sample sizes
This project
Area Location Sublocation Map No. Year(s) Collected
(# archived) Ideal Expected
(all years) 2013 2014 Total
Susitna River above
three rivers
confluence
Talkeetna River Sloughs 20 1997 (79) 100 21 0 - 79
Sheep River 21 2008 (190) 100 0 S - 190
Larson Lake - Eastern shore 23 2011 (90) 100 10 S - 90
Larson Creek 22 1992, 1993 (200) 100 0 S - 200
Larson Lake - outlet stream 24 2011 (126) 100 0 S 21 147
Chunilna Creek 25 100 100 18 - 18
Mama and Papa Bear Lakes 26 1997, 2007 (106) 100 0 75 - 181
Fish Creek 27 n/a 0 3 - 3
Note: Sample sizes show number of samples and sample years for collections alread y in the Gene Conservation Laboratory archives (Archived), number of
samples to obtain the ideal archived sample size (Ideal), the anticipated number to be collected over the original three years of this project based on past
sampling effort and success and information from the Anadromous Waters Catalog and local biologists (Expected), progress made toward sampling targets
in 2013 and 2014, and the resulting total sample size after combining the amount archived with the new samples (Total). Bold and underlined values in the
Total column indicate sample sizes in 2013 and 2014 met or exceeded expected numbers. An “S” in the 2013 column indicates that a survey was performed
but sampling was not attempted, a “-“ indicates that no survey was performed. Some of the expected numbers are for groups of locations. Sampling
locations originally not included in the implementation plan have been included, and are indicated by an “n/a” ide al and expected value. New locations that
are now included in grouped locations are sharing the expected value for their group. Map numbers (Map No.) correspond to location numbers on Figure 4-
1.
STUDY IMPLEMENTATION REPORT GENETIC BASELINE STUDY FOR SELECTED FISH SPECIES (STUDY 9.14)
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FERC Project No. 14241 Page 25 October 2015
Table 4-3. Location and sublocation of baseline samples of adult Chum Salmon spawning aggregates for genetic analysis.
Sample sizes
This project
Area Location Sublocation Map No. Year(s) Collected
(# archived) Ideal Expected
(all years) 2013 2014 Total
Susitna River above
Three Rivers
Confluence
Chulitna River Middle Fork 1 100
200
0 -
46 West Fork 2 100 S -
Byers Creek 3 100 18 -
Troublesome Creek 4 100 28 -
Spink Creek 5 2007, 2008 (45) 100 55 2 - 47
Tokositna River mainstem 6 100 50 S - 0
Middle Susitna River
below Devils Canyon
Portage Creek 7 100 100 147 - 147
Indian River 8 100 100 136 - 136
Gold Creek 9 n/a n/a 5 - 5
sloughs above Three Rivers Confluence 10 1996 (103) 0 0 72 - 175
5th of July Creek 11 n/a n/a 34 - 34
4th of July Creek 12 n/a n/a 56 - 56
Lane Creek 13 n/a n/a 1 - 1
Whiskers Creek 14 n/a n/a 3 - 3
STUDY IMPLEMENTATION REPORT GENETIC BASELINE STUDY FOR SELECTED FISH SPECIES (STUDY 9.14)
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Sample sizes
This project
Area Location Sublocation Map No. Year(s) Collected
(# archived) Ideal Expected
(all years) 2013 2014 Total
Susitna River above
Three Rivers
Confluence
Talkeetna River upper mainstem 16 100
200
S -
1 Disappointment Creek 17 100 S -
Sheep River 18 100 S -
Larson Creek 20 100 S -
Fish Creek 19 100 1 -
Sloughs 15 1995 (50) 100 50 20 - 70
Chunilna Creek 21 1993 (87) 100 13 136 - 223
Note: Sample sizes show number of samples and sample years for collections already in the Gene Conservation Laboratory archives (Archived), number of
samples to obtain the ideal archived sample size (Ideal), the anticipated number to be collected over the original three years of this project based on past
sampling effort and success and information from the Anadromous Waters Catalog and local biologists (Expected), progress made toward sampling targets
in 2013 and 2014, and the resulting total sample size after combining the amount archived with the new samples (Total). Bold and underlined values in the
Total column indicate sample sizes in 2013 and 2014 met or exceeded expected numbers. An “S” in the 2013 column indicates that a survey was performed
but sampling was not attempted.. Some of the expected numbers are for groups of locations. Sampling locations originally not included in the
implementation plan have been included, and are indicated by an “n/a” ideal and expected value . New locations that are now included in grouped locations
are sharing the expected value for their group. Map numbers (Map No.) correspond to location numbers on Figure 4-2.
STUDY IMPLEMENTATION REPORT GENETIC BASELINE STUDY FOR SELECTED FISH SPECIES (STUDY 9.14)
Susitna-Watana Hydroelectric Project Alaska Energy Authority
FERC Project No. 14241 Page 27 October 2015
Table 4-4. Location and sublocation of baseline samples of adult Coho Salmon spawning aggregates for genetic analysis.
Sample sizes
This project
Area Location Sublocation Map No. Year(s) Collected
(# archived) Ideal Expected
(all years) 2013 2014 Totala
Susitna
River
above
three
rivers
confluence
Chulitna River Middle Fork 2 100
200
0 0
167 East Fork 1 100 0 0
Honolulu Creek 3 100 4 0
Byers Creek 4 2014a (56) 100 0 0
Troublesome Creek 5 2014a (15) 100 92 0
Spink Creek 6 2008 (38); 2014a (62) 100 62 0 0 100
Tokositna River mainstem 7 100 100 S 0 65
Tokositna River (Bunco Creek) 8 2014a (56) 100 9 0
Tokositna River (Swan Lake) 9 2009 (20) 100 80 0 0 20
Middle Susitna River Portage Creek 10 2014a (61) 100
200
0 0
218
below Devils Canyon Indian River 11 2014a (52) 100 105 0
Gold Creek 12 100 S 0
McKenzie Creek 13 100 S 0
Lane Creek 14 100 S 0
Sloughs 15 100 75 42 0 42
Chase Creek 16 100 75 S 0 0
Whiskers Creek 17 2014a (2) 100 75 79 0 81
STUDY IMPLEMENTATION REPORT GENETIC BASELINE STUDY FOR SELECTED FISH SPECIES (STUDY 9.14)
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Sample sizes
This project
Area Location Sublocation Map No. Year(s) Collected
(# archived) Ideal Expected
(all years) 2013 2014a Total
Susitna
River
above
three rivers
confluence
Talkeetna River upper mainstem 18 100 25 S 0 0
Prairie Creek 19 2014a (53) 100 75 S 0 53
Iron Creek 20 2014a (21) n/a n/a 28 0 49
Sheep River 21 100 50 115 0 115
Larson Lake - outlet 22 2011 (84); 2014a (48) 100 16 S 0 132
Chunilna Creek 23 2014a (69) 100 75 66 0 135
Fish Creek 24 2014a (65) n/a n/a 1 0 66
a Includes samples collected under an unrelated general fund project in 2014.
Note: Sample sizes show number of samples and sample years for collections already in the Gene Conservation Laboratory archives (Archived), number of
samples to obtain the ideal archived sample size (Ideal), the anticipated number to be collected over the original three years of this project based on past
sampling effort and success and information from the Anadromous Waters Catalog and local biologists (Expected), progress made toward sampling targets
in 2013 and 2014, and the resulting total sample size after combining the amount archived with the new samples (Total). Bold and underlined values in the
Total column indicate sample sizes in 2013 and 2014 met or exceeded expected numbers. An “S” in the 2013 column indicates that a survey was pe rformed
but sampling was not attempted. Some of the expected numbers are for groups of locations. Sampling locations originally n ot included in the
implementation plan have been included, and are indicated by an “n/a” ideal and expected value. New locations that are now in cluded in grouped locations
are sharing the expected value for their group. Map numbers (Map No.) correspond to location numbers on Figure 4-3.
STUDY IMPLEMENTATION REPORT GENETIC BASELINE STUDY FOR SELECTED FISH SPECIES (STUDY 9.14)
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FERC Project No. 14241 Page 29 October 2015
Table 4-5. Location and sublocation of baseline samples of adult Pink Salmon spawning aggregates for genetic analysis.
Sample sizes
This project
Area Location Sublocation Map No.
Year(s)
Collected
(for Archive)
Ideal Expected (all years) 2013 2014 Total
Susitna River
above three
rivers
confluence
Chulitna River Middle Fork 1 100
100
0 0
117 Spink Creek 3 100 0 116
Troublesome Creek 2 100 0 0
no name creek 4 n/a 1 0
Middle Susitna
River below
Devils Canyon
Portage Creek 5 100 50 136 0 136
Indian River 6 100 100 116 0 116
Gold Creek 7 100
50
106 0
467
5th of July Creek 8 n/a 2 0
4th of July Creek 9 n/a 107 0
slough 9 10 n/a 116 0
McKenzie Creek 11 100 0 0
Lane Creek 12 100 115 0
Chase Creek 13 100 0 0
Whiskers Creek 14 100 21 0
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Sample sizes
This project
Area Location Sublocation Map No.
Year(s)
Collected
(for Archive)
Ideal Expected
(all years) 2013 2014 Total
Talkeetna River upper mainstem 15 100 25 0 0 0
Disappointment Creek 16 n/a 0 127 0 127
Sheep River 17 100 25 0 0 0
Larson Creek 18 100 100 0 0 0
Chunilna Creek 19 100 100 101 0 101
Fish Creek 20 n/a 0 101 0 101
Note: Sample sizes show collections already in the Gene Conservation Laboratory archives (Archived), number of samples to obtain the ideal archived sample
size (Ideal), the anticipated number to be collected over the original three years of this project based on past sampling effort and success and information
from the Anadromous Waters Catalog and local biologists (Expected), progress made toward sampling targets in 2013 and 2014, and the resulting total
sample size after combining the amount archived with the new samples (Total). Bold and underlined values in the Total column indicate sample sizes in met
or exceeded expected numbers. Sampling locations originally not included in the implementation plan have been included, and are indicated by an “n/a”
ideal and expected value. New locations that are now included in grouped locations are sharing the expected value for their g roup. Map numbers (Map No.)
correspond to location numbers on Figure 4-4.
STUDY IMPLEMENTATION REPORT GENETIC BASELINE STUDY FOR SELECTED FISH SPECIES (STUDY 9.14)
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FERC Project No. 14241 Page 31 October 2015
Table 4-6. Resident and non-salmon anadromous fish species targeted for genetic tissue sampling in the Susitna River and samples sizes collected in
2013 and 2014. Sample collections are reported for the Gene Conservation Laboratory (GCL), interrelated studies (other), and the combined total (N).
Species
Target
sample
size
(total)
Collection Strata
Total
collected Upper Susitna River
Middle Susitna River
above Devils
Canyon
Middle Susitna River
below Devils Canyon Lower Susitna River Talkeetna River Chulitna River
GCL GCL
other
studies N GCL
other
studies N GCL
other
studies N GCL
other
studies N GCL
other
studies N GCL
other
studies N
Blackfish,
Alaska 50 0
Burbot 50 1 57 58 6 6 80 80 2 51 53 197
Dolly
Varden 50 183 183 3 2 5 23 23 4 4 8 35 35 254
Eulachon 50 283 283 283
Grayling,
Arctic 50 20 135 155 90 90 2 76 78 7 20 27 5 5 3 3 358
Lamprey,
Arctic* n/a 10 10 10
Lamprey,
Pacific 50 0
Pike,
Northern 50 19 19 19
Sculpin,
Coastrange 50 0
Sculpin,
Pacific
Staghorn
50
0
Sculpin,
Prickly 50 0
Sculpin,
Slimy 50 45 44 89 1 50 51 57 57 6 50 56 1 1 254
Stickleback,
Ninespine 50 17 17 17
Stickleback,
Threespine 50 50 63 113 113
STUDY IMPLEMENTATION REPORT GENETIC BASELINE STUDY FOR SELECTED FISH SPECIES (STUDY 9.14)
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Species
Target
sample
size
(total)
Collection Strata
Total
collected Upper Susitna River
Middle Susitna River
above Devils
Canyon
Middle Susitna River
below Devils Canyon Lower Susitna River Talkeetna River Chulitna River
GCL GCL
other
studies N GCL
other
studies N GCL
other
studies N GCL
other
studies N GCL
other
studies N GCL
other
studies N
Sucker,
Longnose 50 89 89 22 22 4 84 88 51 51 250
Trout, Lake 50 1 1 1
Trout,
Rainbow 50 24 68 92 44 10 54 14 14 38 38 198
Whitefish,
Bering
Cisco
50 2 2
2
Whitefish,
Humpback 50 4 4 35 35 10 10 49
Whitefish,
Lake 50 0
Whitefish,
Round 50 1 90 91 30 30 1 202 203 10 50 60 1 8 9 4 4 397
* Collected, but not on original list of target species
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Table 4-7. Summary of survey flights conducted during 2013 and 2014. Surveys were performed in order to determine potential sampling locations for five
salmon species (Chinook, sockeye, pink, chum, and Coho Salmon). X’s indicate the occurrence of a survey flight in a given collection strata (Figure 3-1) on a certain
date. Survey flight number 17 shows no X’s because the survey was cancelled due to poor survey conditions.
Collection strata
Survey # Date
Upper
Susitna
River
Middle
Susitna
above and
within
Devils
Canyon
Middle
Susitna
below
Devils
Canyon
Lower
Susitna
River
Talkeetna
River
Chulitna
River
West
Side
Cook
Inlet
Yentna Drainage Knik Arm
1 6/11/2013 X X X X X
2 7/8/2013 X X X 3 7/9/2013 X X X X 5 7/15/2013 X X X
6 7/16/2013 X X 7 7/17/2013 X 8 7/22/2013 X X X X 9 7/23/2013 X X 10 7/24/2013 X 11 7/29/2013 X X X X 12 7/30/2013 X X 13 8/5/2013 X X X 14 8/6/2013 X X X X X 15 8/12/2013 X 16 8/13/2013 X X X 17 8/19/2013 18 8/26/2013 X X
19 9/15/2013 X X
20 7/1/2014 X
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Table 4-8. Genetic sampling effort through time by river area for adult salmon species and juvenile Chinook Salmon in 2013 and 2014. Salmon species
sampled are reported by week and strata. X’s indicate where sampling occurred in each week of the Project field season for all salmon species, and for sampling
locations where Chinook Salmon were the only target species. Species sampled: Chinook (K), sockeye (S), pink (P), chum (Ch), and coho (Co) salmon. Sampling
occurred from 6/8/2013 through 9/15/2013 and from 6/16/14 through 8/4/14.
Collection Strata
Area sampled
Area sampled
(all salmon species) (Chinook Salmon only)
Week of Species sampled Talkeetna Chulitna
Middle
Susitna
below Devils
Canyon
Lower
Susitna
Middle
Susitna within
and above
Devils
Canyon
Upper
Susitna Yentna Knik West
6/8-25/2013 K x
6/24/2013 K x x
7/1/2013 K x x x
7/8/2013 K x x
7/15/2013 K, S x x x 7/22/2013 K x x x x x 7/29/2013 K, S, Ch, P, Co, x x x x 8/5/2013 K,S, Ch, P,Co x x x x 8/12/2013 S, Ch, P, Co x x x x 8/19/2013 S, Ch, P x x 8/26/2013 * 9/2/2013 * 9/9/2013 * 9/16/2013 Co x
9/23/2013 Co x x
9/30/2013 Co x x
6/16/2014 K x x 6/30/2014 K x x x
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Collection Strata
Area sampled
Area sampled
(all salmon species) (Chinook Salmon only)
Week of Species sampled Talkeetna Chulitna
Middle
Susitna
below Devils
Canyon
Lower
Susitna
Middle
Susitna within
and above
Devils
Canyon
Upper
Susitna Yentna Knik West
7/7/2014 K x 7/14/2014 K x x x x x 7/21/2014 K x x x x 7/28/2014 K x x 8/4/2014 K, S, P x
* Sampling efforts disrupted by adverse weather conditions.
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Table 4-9. Marker name and source for the microsatellite (µSAT), 48 single nucleotide polymorphism (SNP),
and 188 SNP marker sets.
An “x” in the marker set column indicates whether a marker is included in a marker set.
Marker Set
Name µSAT 48 SNPs 188 SNPs Source1
Ogo2v1 x
A
Ogo4v1 x
A
Oki100v1 x
B
Omm1080v1 x
C
Ots201bv1 x
D
Ots208bv1 x
E
Ots211v1 x
E
Ots212v2 x
E
Ots213v1 x
E
Ots3Mv1 x
F
Ots9v1 x
F
OtsG474v1 x
G
Ssa408uosv1 x
H
Ots_GTH2B-550
x x I
Ots_100884-287
x J
Ots_101554-407
x J
Ots_104569-86
x J
Ots_105105-613
x J
Ots_105385-421
x J
Ots_105407-117
x J
Ots_107074-284
x J
Ots_108390-329
x J
Ots_108820-336
x J
Ots_109525-816
x J
Ots_109693-392
x J
Ots_110495-380
x J
Ots_110551-64
x J
Ots_111084b-619
x J
Ots_112301-43
x J
Ots_112419-131
x J
Ots_112820-284
x J
Ots_112876-371
x J
Ots_113242-216
x J
Ots_113457-40R
x J
Ots_115987-325
x J
Ots_117432-409
x J
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Marker Set
Name µSAT 48 SNPs 188 SNPs Source1
Ots_118205-61
x J
Ots_123921-111
x J
Ots_127236-62
x J
Ots_128693-461
x J
Ots_131460-584
x J
Ots_94857-232R
x J
Ots_94903-99R
x J
Ots_96222-525
x J
Ots_96500-180
x J
Ots_96899-357R
x J
Ots_AldB1-122
x J
Ots_arf-188
x x K
Ots_AsnRS-60
x x K
Ots_CD59-2
x L
Ots_cox1-241
x M
Ots_DESMIN19-SNP1
x J
Ots_E2-275
x x K
Ots_Est1363
x N
Ots_Est740
x N
Ots_ETIF1A
x x L
Ots_FARSLA-220
x x O
Ots_FGF6A
x x I
Ots_FGF6B
x x I
Ots_GH2
x x P
Ots_GnRH-271
x x K
Ots_GPDH-338
x x K
Ots_GPH-318
x x O
Ots_GST-207
x x O
Ots_HFABP-34
x Q
Ots_HGFA-446
x x K
Ots_hnRNPL-533
x x O
Ots_hsc71-5'-453
x R
Ots_Hsp90a
x J
Ots_HSP90B-100
x x O
Ots_HSP90B-385
x x O
Ots_IGF-I.1-76
x x K
Ots_Ikaros-250
x x K
Ots_il13Ra2B-37
x Q
Ots_il-1racp-166
x x K
Ots_ins-115
x x K
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Marker Set
Name µSAT 48 SNPs 188 SNPs Source1
Ots_IsoT
x N
Ots_LEI-292
x x O
Ots_LWSop-638
x x K
Ots_mapK-3'-309
x S
Ots_MetA
x x L
Ots_MHC1
x x P
Ots_MHC2
x x P
Ots_NAML12-SNP1
x J
Ots_nelfd-163
x T
Ots_nkef-192
x M
Ots_NOD1
x x I
Ots_ntl-255
x S
Ots_P450
x x P
Ots_P450-288
x x U
Ots_P53
x x P
Ots_parp3-286
x S
Ots_PGK-54
x x I
Ots_pop5-96
x S
Ots_ppie-245
x S
Ots_Prl2
x x P
Ots_PSMB1-197
x x O
Ots_RAD10099
x V
Ots_RAD10252
x V
Ots_RAD10400
x V
Ots_RAD10583
x V
Ots_RAD1072
x V
Ots_RAD10807
x V
Ots_RAD1104-38
x Q
Ots_RAD11425
x V
Ots_RAD11441
x V
Ots_RAD1149
x V
Ots_RAD11821
x V
Ots_RAD11839
x V
Ots_RAD1282
x V
Ots_RAD1372
x V
Ots_RAD14482
x V
Ots_RAD14528
x V
Ots_RAD14650
x V
Ots_RAD14852
x V
Ots_RAD1507
x V
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Marker Set
Name µSAT 48 SNPs 188 SNPs Source1
Ots_RAD1510
x V
Ots_RAD15440
x V
Ots_RAD1609
x V
Ots_RAD161
x V
Ots_RAD16976
x V
Ots_RAD17721
x V
Ots_RAD17873
x V
Ots_RAD1832-39
x Q
Ots_RAD21143
x V
Ots_RAD21978
x V
Ots_RAD22318
x V
Ots_RAD2234
x V
Ots_RAD2357
x V
Ots_RAD2442
x V
Ots_RAD249
x V
Ots_RAD2687
x V
Ots_RAD3123
x V
Ots_RAD3391
x V
Ots_RAD3470
x V
Ots_RAD3513-49
x Q
Ots_RAD3635
x V
Ots_RAD3703
x V
Ots_RAD3737
x V
Ots_RAD3752
x V
Ots_RAD3766
x V
Ots_RAD3769
x V
Ots_RAD3858
x V
Ots_RAD3925
x V
Ots_RAD4043
x V
Ots_RAD4185
x V
Ots_RAD4438
x V
Ots_RAD4486
x V
Ots_RAD4778
x V
Ots_RAD4999
x V
Ots_RAD5189
x V
Ots_RAD5426-36
x V
Ots_RAD5429
x V
Ots_RAD6097
x V
Ots_RAD6121
x V
Ots_RAD6184
x V
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Marker Set
Name µSAT 48 SNPs 188 SNPs Source1
Ots_RAD6688
x V
Ots_RAD7145
x V
Ots_RAD7165
x V
Ots_RAD7695
x V
Ots_RAD7936-50
x Q
Ots_RAD8200-45
x Q
Ots_RAD8354
x V
Ots_RAD8442
x V
Ots_RAD856
x V
Ots_RAD8560
x V
Ots_RAD9039
x V
Ots_RAD9480-51
x Q
Ots_RAD9536
x V
Ots_RAD962-35
x V
Ots_RAD9704
x V
Ots_RAD995
x V
Ots_RAG3
x x I
Ots_redd1-187
x S
Ots_S7-1
x x I
Ots_SClkF2R2-135
x x K
Ots_SERPC1-209
x x O
Ots_SL
x x P
Ots_SWS1op-182
x x K
Ots_TAPBP
x x L
Ots_TF1-SNP1
x J
Ots_Tf-3545
x U
Ots_TGFB
x L
Ots_TLR3
x L
Ots_Tnsf
x x P
Ots_tpx2-125
x T
Ots_txnip-321
x S
Ots_u07-07.161
x W
Ots_u07-17.135
x W
Ots_u07-25.325
x W
Ots_u07-53.133
x W
Ots_u202-161
x x K
Ots_u211-85
x x K
Ots_U212-158
x x K
Ots_U2446-123
x Q
Ots_u4-92
x x K
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Marker Set
Name µSAT 48 SNPs 188 SNPs Source1
Ots_u6-75
x x K
Ots_unk526
x x I
Ots_vatf-251
x S
Ots_zn593-346
x T
Ots_Zp3b-215 x x K
1 A) Olsen et al. 1998, B) Department of Fisheries and Oceans Canada, unpublished, C) Rexroad and Coleman
2001, D) Oregon State University, unpublished, E) Greig et al. 2003, F) Banks et al. 1999, G) Williamson et al.
2002, H) Cairney et al. 2000, I) Northwest Fisheries Science Center, unpublished, J) Clemento et al. 2011, K) Smith
et al. 2005a, L) Washington State University, unpublished, M) Campbell and Narum 2008, N) Miller et al. 2008, O)
Smith et al. 2007, P) Smith et al. 2005b, Q) University of Washington, unpublished, R) Campbell and Narum 2009,
S) Columbia Rivier Inter-Tribal Fish Commission, unpublished, T) University of Washington and Washington
Department of Fish and Wildlife, unpublished, U) Alaska Department of Fish and Game, unpublished, V) Larson et
al. 2014, W) Washington Department of Fish and Wildlife, unpublished.
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Table 4-10. Species clustering in scatter plots for each of the seven standard markers used for discriminating
among Pacific and Atlantic salmon at the Gene Conservation Laboratory.
Locus Salmon/trout species in cluster Cluster #
OKESSA1-OKE Chinook 1
Chum, Atlantic 2
Sockeye 3
Pink, Coho, Rainbow 4
OKI1-OKI Chinook, Rainbow 1
Coho 2
Chum 3
Sockeye, Atlantic, Pink 4
ONEOGO1-ONE Pink 1
Sockeye 2
Coho, Rainbow, Chinook, Chum, Atlantic 3
OTSOKI1-OKI Sockeye, Rainbow 1
Coho, Chinook 2
Pink 3
Chum 4
Atlantic 5
OTSSSA1-OTS Chinook 1
Coho, Rainbow, Chum, Atlantic, Sockeye, Pink 2
SSA1-SSA Atlantic 1
Coho, Rainbow, Chinook, Chum, Sockeye, Pink 2
Atlantic 1
Rainbow 2
Sockeye 3
Coho, Chinook, Chum, Pink 4
SSA4-SSA Atlantic 1
Pink, Rainbow 2
Coho, Chinook, Chum, Sockeye 3
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Table 4-11. Metadata and location of Chinook Salmon samples collected above Devils Canyon. Length (in millimeters) and sex were determined for Chinook
Salmon sampled above Devils Canyon on August 6, 2013. Creek name, latitude, and longitude are also reported for these data.
Fish # Date Length Sex Creek Latitude/Longitude
1 8/6/2013 980 M Kosina 62.701/ -147.986
2 8/6/2013 575 F Kosina 62.633/ -148.031
3 8/13/2013 570 M Kosina 62.756/ -147.955
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Table 4-12. Area, sampling location, sublocation, and number of samples successfully analyzed at greater than or equal to 80% of markers for the 13
microsatellite (uSATs), 48 single nucleotide polymorphism (SNP), and 188 SNP marker sets.
Map numbers (Map No.) correspond to location numbers on Figure 4-5.
# Samples Successfully Analyzed Samples
collected Area Location Sublocation Map No. 13 uSATs 48 SNPs 188 SNPs
Adult Chinook Salmon
West Side Cook Inlet Chuitna River
1 0 138 95 142
Beluga River Coal Creek 2 0 118 41 120
Theodore River
3 0 191 84 236
Lewis River
4 0 87 0 86
Yentna Drainage Clearwater Creek 5 25 25 25 25
Nakochna River
6 0 0 0 22
Red Creek
7 0 111 82 111
Happy River
8 0 18 0 19
Red Salmon Creek
9 0 27 0 27
Hayes River
10 26 74 26 74
Canyon Creek
11 0 92 0 93
Talachulitna River
12 57 178 0 180
Lake Creek Sunflower Creek 13 0 126 74 127
Kahiltna River Peters Creek 14 0 107 0 110
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# Samples Successfully Analyzed Samples
collected Area Location Sublocation Map No. 13 uSATs 48 SNPs 188 SNPs
Susitna Drainage Chulitna River Middle Fork 15 0 229 95 243
East Fork 16 0 96 0 97
West Fork 17 0 0 0 0
Honolulu Creek 18 0 104 0 106
Pass Creek 19 0 102 0 104
Spink Creek 20 0 74 8 74
Byers Creek 21 0 101 0 109
Troublesome Creek 22 0 119 0 119
Tokositna River (Bunco Creek) 23 0 100 94 103
Tokosina River (Bunco Lake inlet stream) 24 0 0 0 3
Upper Susitna River Oshetna River 25 0 0 0 0
Kosina Creek 26 13 13 11 13
Kosina Creek (radio tag) 26 3
3
Watana Creek 27 0 0 0 0
Middle Susitna River above
Devils Canyon Tsusena Creek 28 0 0 0 0
Tsusena Creek (radio tag) 28 1 1 1 1
Fog Creek 29 12 12 12 12
Susitna River mainstem 1 1 1 1
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# Samples Successfully Analyzed Samples
collected Area Location Sublocation Map No. 13 uSATs 48 SNPs 188 SNPs
Susitna Drainage
Middle Susitna River wiithin
Devils Canyon Devil Creek 30 1 1 1 1
Devil Creek (radio tag) 30 1 1 1 1
Chinook Creek 31 7 7 7 7
Chinook Creek (radio tag) 31 1
1
Cheechako Creek 32 57 57 57 57
Cheechako Creek (radio tag) 32 10 10 10 10
Middle Susitna River below
Devils Canyon Portage Creek 33 93 161 97 166
Indian River 34 98 99 97 101
Gold Creek 35 0 0 0 0
4th of July Creek 36 0 0 0 25
Lane Creek 37 0 0 0 0
Chase Creek 38 0 0 0 0
Talkeetna River Prairie Creek 39 48 194 95 201
no name creek #2 40 0 53 0 53
no name creek #1 41 0 83 0 84
upper mainstem 42 0 0 0 0
Iron Creek 43 57 103 57 103
Disappointment Creek 44 0 131 0 133
Sheep River 45 0 0 0 0
Larson Creek 46 0 0 0 0
Chunilna Creek (Clear Creek) 47 0 130 52 135
# Samples Successfully Analyzed Samples
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Area Location Sublocation Map No. 13 uSATs 48 SNPs 188 SNPs collected
Susitna Drainage
Lower Susitna River,
upstream of Deshka River
Montana Creek 48 0 213 0 658
Birch Creek 49 0 0 0 0
Sheep Creek 50 0 59 0 60
North Fork Kashwitna River 51 12 61 12 62
Little Willow Creek 52 13 103 13 104
Willow Creek 53 69 212 49 309
Deshka River Moose Creek 54 0 52 35 103
Deshka River weir 55 200 200 0 200
Alexander Creek Sucker Creek 56 0 144 125 143
Knik Arm Matanuska River Kings River 57 0 0 0 4
Granite Creek 58 0 50 0 48
Moose Creek 59 0 128 59 155
Eagle River South Fork 60 0 71 0 77
Meadow Creek 61 0 6 0 6
Ship Creek 62 0 59 0 311
Little Susitna River 63 0 124 95 125
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# Samples Successfully Analyzed Samples
collected Area Location Sublocation Map No. 13 uSATs 48 SNPs 188 SNPs
Juvenile Chinook Salmon
Susitna Drainage Upper Susitna River Oshetna River 25 62 52 0 62
Kosina Creek 26 130 129 0 130
Upper Susitna River mainstem n/a 29 0 0 30
Middle Susitna River
within and above Devils
Canyon Tsusena Creek n/a 1 0 0 1
Fog Creek 29 0 0 0 0
Devil Creek 30 14 0 0 14
Chinook Creek 31 61 0 0 62
Cheechako Creek 32 92 35 35 93
Unnamed Tributary 184 n/a 1 0 0 1
Middle Susitna River above n/a 2 2 2 2
Susitna Drainage Lower Susitna River 5 habitat types n/a 0 0 0 8
(100 fish/habitat type times 3 or 4
collections)
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10. FIGURES
Figure 2-1. A generalized flow chart to distinguish among hypotheses of population structure for Chinook
Salmon collected over spawning habitat above Devils Canyon in the Middle and Upper Susitna River. Only a
self-sustaining population (Hypothesis 1a) will potentially result in genetic variation suitable for mixed-stock analysis
for estimating the proportion of juvenile Chinook Salmon mixtures collected in the Middle and Lower Susitna River that
originate from above Devils Canyon.
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Figure 3-1. Collection strata for samples collected for genetic archive and/or analysis.
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Figure 4-1. Baseline sampling locations for adult Sockeye Salmon sampled through 2014. Circles indicate the number of samples in the Gene Conservation
Laboratory archives. Numbers correspond to map numbers on Table 4-3.
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Figure 4-2. Baseline sampling locations for adult Chum Salmon sampled through 2014. Circles indicate the number of samples in the Gene Conservation
Laboratory archives. Numbers correspond to map numbers on Table 4-4.
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Figure 4-3. Baseline sampling locations for adult Coho Salmon sampled through 2014. Circles indicate the number of samples in the Gene Conservation
Laboratory archives. Numbers correspond to map numbers on Table 4-5.
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Figure 4-4. Baseline sampling locations for adult Pink Salmon sampled through 2014. Circles indicate the number of samples in the Gene Conservation
Laboratory archives. Numbers correspond to map numbers on Table 4-6.
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Figure 4-5. Baseline sampling locations for adult and juvenile (inset) Chinook Salmon sampled through 2014. Circles indicate the number of samples in
the Gene Conservation Laboratory archives. Numbers correspond to map numbers in Table 4-2. The Lower Susitna River (below project river mile (PRM) 102.4),
Middle River (RM 102.4-187.1) and Upper River (RM 187.1-235.1) segments are highlighted with the proposed dam at PRM 187.1.
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APPENDIX A: NON-LETHAL JUVENILE FINFISH OMNISWAB
SAMPLING FOR DNA ANALYSIS
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