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Susitna-Watana Hydroelectric Project Document
ARLIS Uniform Cover Page
Title:
Genetic baseline study for selected fish species, Study plan Section 9.14 :
Initial study report -- Part A: Sections 1-6, 8-10
SuWa 223
Author(s) – Personal:
Author(s) – Corporate:
Gene Conservation Laboratory, Commercial Fisheries Division, Alaska Department of Fish and
Game
AEA-identified category, if specified:
Initial study report
AEA-identified series, if specified:
Series (ARLIS-assigned report number):
Susitna-Watana Hydroelectric Project document number 223
Existing numbers on document:
Published by:
[Anchorage : Alaska Energy Authority, 2014]
Date published:
June 2014
Published for:
Alaska Energy Authority
Date or date range of report:
Volume and/or Part numbers:
Final or Draft status, as indicated:
Document type:
Pagination:
iv, 40, 2 p.
Related work(s):
The following parts of Section 9.14 appear in separate files:
Part A ; Part B ; Part C.
Pages added/changed by ARLIS:
Notes:
Contents: Part A. Sections 1-6, 8-10 -- Appendix A. Template for collection trip reports.
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
Initial Study Report
Part A: Sections 1-6, 8-10
Prepared for
Alaska Energy Authority
Prepared by
Gene Conservation Laboratory
Commercial Fisheries Division
Alaska Department of Fish and Game
June 2014
INITIAL STUDY REPORT GENETIC BASELINE STUDY FOR SELECTED FISH SPECIES (9.14)
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FERC Project No. 14241 Part A - Page i June 2014
TABLE OF CONTENTS
1. Introduction ....................................................................................................................... 1
2. Study Objectives................................................................................................................ 2
3. Study Area ......................................................................................................................... 2
4. Methods and Variances in 2013 ....................................................................................... 2
4.1. Sample Collection ................................................................................................... 3
4.1.1. Adult Chinook salmon collections .................................................. 3
4.1.2. Other adult salmon collections........................................................ 5
4.1.3. Juvenile Chinook salmon collections.............................................. 5
4.1.4. Other species collections................................................................. 6
4.1.5. Sampling coordination with other studies....................................... 7
4.1.6. Collection trip documentation......................................................... 7
4.2. Tissue Storage ......................................................................................................... 7
4.3. Laboratory Analysis ................................................................................................ 8
4.4. Data Retrieval and Quality Control ........................................................................ 8
4.5. Variances from Study Plan ..................................................................................... 8
5. Results ................................................................................................................................ 8
5.1. Sample Collection ................................................................................................... 8
5.1.1. Adult Chinook salmon collections .................................................. 8
5.1.2. Other adult salmon collections........................................................ 9
5.1.3. Juvenile Chinook salmon collections.............................................. 9
5.1.4. Other species collections................................................................. 9
5.1.5. Pacific salmon sampling coordination with other studies............... 9
5.1.6. Collection trip documentation....................................................... 10
5.2. Tissue Storage ....................................................................................................... 10
5.3. Laboratory Analysis .............................................................................................. 10
5.4. Data Retrieval and Quality Control ...................................................................... 10
6. Discussion......................................................................................................................... 10
6.1. Chinook Salmon Adults and Juveniles Above Devils Canyon ............................. 10
6.2. Chinook Salmon Adults in the Middle River Below Devils Canyon ................... 11
6.3. Chinook Salmon Adults Elsewhere ...................................................................... 11
6.4. Chinook Salmon Juveniles – Lower River ........................................................... 11
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6.5. Other Salmon Adults............................................................................................. 12
6.6. Other Fish Species ................................................................................................ 12
6.7. Coordination with Other Studies .......................................................................... 12
7. Completing the Study ..................................................................................................... 13
8. Literature Cited .............................................................................................................. 13
9. Tables ............................................................................................................................... 14
10. Figures .............................................................................................................................. 34
LIST OF TABLES
Table 4-1. Area, location, and sublocation of baseline samples of adult and juvenile
Chinook salmon spawning aggregates for genetic analysis. ..................................................15
Table 4-2. Location and sublocation of baseline samples of adult sockeye salmon
spawning aggregates for genetic analysis. .............................................................................20
Table 4-3. Location and sublocation of baseline samples of adult chum salmon spawning
aggregates for genetic analysis. .............................................................................................22
Table 4-4. Location and sublocation of baseline samples of adult coho salmon spawning
aggregates for genetic analysis. .............................................................................................24
Table 4-5. Location and sublocation of baseline samples of adult pink salmon spawning
aggregates for genetic analysis. .............................................................................................26
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. .....................................28
Table 4-7. Summary of survey flights conducted during 2013. ....................................................30
Table 4-8. Genetic sampling effort through time by river area for adult salmon species in
2013. .......................................................................................................................................31
Table 4-9. Juvenile Chinook salmon tissue collections across five habitat types in the
Lower Susitna River, through September 15, 2013. ..............................................................32
Table 4-10. Metadata and location of Chinook salmon samples collected above Devils
Canyon. ..................................................................................................................................33
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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. .................................................................................34
Figure 3-1. Collection strata for samples collected for genetic archive and/or analysis. ..............35
Figure 4-1. Baseline sampling locations for adult sockeye salmon. .............................................36
Figure 4-2. Baseline sampling locations for adult chum salmon. .................................................37
Figure 4-3. Baseline sampling locations for adult coho salmon. ..................................................38
Figure 4-4. Baseline sampling locations for adult pink salmon. ...................................................39
Figure 4-5. Baseline sampling locations for adult and juvenile (inset) Chinook salmon. ............40
APPENDICES
Appendix A. Template for collection trip reports.
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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 analyses
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
On December 14, 2012, Alaska Energy Authority (AEA) filed its Revised Study Plan (RSP) with
the Federal Energy Regulatory Commission (FERC or Commission) for the Susitna-Watana
Hydroelectric Project (FERC Project No. 14241) which included 58 individual study plans (AEA
2012). Included within the RSP was the Genetic Baseline Study for Selected Fish Species,
Section 9.14. RSP Section 9.14 focuses on understanding the genetic structure of selected species
within the Susitna River.
On February 1, 2013, FERC staff issued its study determination (February 1 SPD) for 44 of the
58 studies, approving 31 studies as filed and 13 with modifications. RSP Section 9.14 was one
of the 13 approved with modifications. In its February 1 SPD, FERC recommended the
following:
AEA consult with the FWS and NMFS prior to preparing the project operational plans;
distribute draft project operational plans to the agencies by March 31 of each year of
study implementation; allow 15 days for the agencies to provide comments on the draft
plans; file the final plans with the Commission by April 30 of each year of study
implementation; and include with the final plans, documentation of agency consultation,
a description of how agency comments are incorporated into the final plans, and an
explanation for why any agency comments are not incorporated into the final plans.
To the extent feasible, we recommend that AEA collect tissue samples over a
representative proportion of the entire adult Chinook salmon run.
We recommend that AEA include in the 2013 project operational plan, a schedule for
when the 2012 genetics studies would be available, and include provisions for filing those
results with the Commission through either the initial study report, or a supplemental
report in 2013. We also recommend that the report on the 2012 preliminary genetics
studies clearly describe the criteria, using current scientific literature, to determine
whether there is sufficient genetic uniqueness to estimate the percentage of Chinook
originating from Upper and Middle River habitats in areas sampled downstream.
Finally, we recommend that the report on the 2012 preliminary genetics studies clearly
describe whether the study results indicate that sufficient genetic uniqueness is found to
characterize the presence and relative proportion of fish originating from the Upper and
Middle River in selected Lower River habitats as described in section 9.14.4.7 of the
study plan.
In accordance with the February 1 SPD, AEA provided a draft 2013 Implementation Plan for the
Genetic Baseline Study for Selected Fish Species in the Susitna River, Alaska (Genetics
Implementation Plan [IP]) for review on March 31, 2013 and filed a final 2013 Genetics IP on
April 30, 2013. The 2013 Genetics IP supersedes portions of the Revised Study Plan.
In accordance with the February 1 SPD, AEA has adopted the FERC requested modifications.
Following the first study season, FERC’s regulations for the Integrated Licensing Process (ILP)
require AEA to “prepare and file with the Commission an initial study report describing its
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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)) This Initial
Study Report (ISR) on Genetic Baseline Study has been prepared in accordance with FERC’s
ILP regulations and details AEA’s status in implementing the study, as set forth in the FERC-
approved RSP and as modified by FERC’s February 1 SPD and the 2013 Implementation Plan
(collectively referred to herein as the “Study Plan”).
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).
3. STUDY AREA
As established in the 2013 Genetics IP Section 2.2, the study area encompasses the Susitna River
and its tributaries from Cook Inlet upstream to the Oshetna River confluence (RM 233.4 [PRM
261.3]; Figure 2). 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 (RM 98 – 184 [PRM 102.4 – 187.1]) and Upper Susitna River
(RM 184 – 233.4 [PRM 187.1 – 261.3]), tissue from juvenile Chinook salmon was collected in
the Lower River (< RM 98 [PRM 102.4]).
4. Methods and Variances in 2013
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 from 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 collection targets as described in the 2013 Genetics
IP Section 4.2, with no variances. 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 through 4-6). 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. 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.
Weekly survey flights were conducted from June 11 to September 15 in 2013 to determine the
timing and locations for sampling all five species of salmon (Table 4-7) with the most intensive
sampling of adult Chinook salmon occurring between July 15 and August 16 in 2013). Sampling
crews were dispatched when and where Chinook salmon were observed in spawning habitats.
Because Chinook salmon are generally spread out in streams and in lower abundance compared
to other salmon species, multi-day sampling trips were required to get an adequate sample from
each location (Table 4-1; Figure 4-5). During this time period, each of the three sampling crews
attempted to collect samples from at least two locations per week with an average of 2.5 days per
trip. The two extra days each week allowed crews to be relocated and resupplied with sampling
gear, food, and other camping supplies, and acquire information from GCL staff for their next
sampling location(s).
During the intensive Chinook salmon sampling period, two crews were dedicated to sampling in
the Susitna River. One crew was dedicated for sampling the Yentna River and northwestern
Cook Inlet during the weeks of July 17 and 24 in 2013. Additional field staff collected Chinook
salmon samples from locations along the road system in the Susitna River and Knik Arm from
June 24 to July 19, 2013. Crews in the Susitna River had a helicopter (Robinson R-44 II;
operated by Alpine Air Alaska, Inc.) on call for transport to and from sampling locations because
of the large area to be sampled and short window of opportunity each year to collect Chinook
salmon samples. The base of operations for the Alpine Air helicopter was Talkeetna. The
Yentna River crew chartered helicopter (Enstrom F28F) flights, as needed, through Talaheim
Lodge, based on the Talachulitna River.
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. For
the two 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, 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. 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.
Chinook salmon collections also occurred outside the three-week intensive sampling period as
early as the second week of June and as late as the second week of August in 2013 (Table 4-8).
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Collection trips during less intensive sampling periods were performed by two crews, but trip
lengths were longer (approximately 4 days – one trip per crew per week) due to the lower
availability of helicopter charters. Helicopter flights were chartered as needed, through Talaheim
Lodge and Alpine Air, to access sites above Devils Canyon and sites not efficiently accessed by
jet boat. Jet boats were used to access sites accessible from the road system in the Middle 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). Collections from adult pink,
sockeye, chum, and coho salmon began on July 29 and continued through August 23, 2013
(Table 4-8). During the intensive Chinook salmon collection period, samples from these other
salmon species were collected opportunistically by the two Susitna River crews. During the
week of August 19, each of the two sampling crews was assigned to one of the following
drainages to collect samples from at least three locations for each species: 1) the Talkeetna River,
and 2) the Chulitna River. Collection locations and method of transport to sampling locations
were determined after weekly survey flights. Odd-year pink salmon were present in the Middle
Susitna River and Talkeetna River, but not in the Chulitna River. From the weeks of August 26
to September 9, poor weather limited the number of these survey flights (Table 4-7) and high
water levels and turbid conditions precluded sampling (Table 4-8). 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).
• 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
4.1.3. Juvenile Chinook salmon collections
4.1.3.1. Above Devils Canyon
To address Objectives 3 and 4, tissue samples were to be collected from a target of 200 juvenile
Chinook salmon during the study period at the Oshetna River and in each of Kosina, Fog, and
Cheechako creeks. When possible in 2013, collections occurred at the same time as adult salmon
collection trips. Collections in 2013 included 71 samples in Kosina Creek and three samples in
the Oshetna River (Table 4-1); Cheechako and Fog creeks were not sampled.
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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.
Caudal fin tissue was collected from each juvenile Chinook salmon captured and placed in an
individual 2 ml (0.07 oz) vial. Pelvic fins were too small to handle in the field, so caudal fins
were sampled instead. Total length (snout-to-fork) was recorded for each sampled juvenile
Chinook.
4.1.3.2. Lower River collections
To address Objective 5, tissue samples were to be collected from 100 juvenile Chinook salmon
during the study period from 16 sites across five mainstem habitat types in the Lower Susitna
River (1,600 fish total).
Samples of juvenile Chinook salmon collected in the Lower River were classified by habitat type
to examine the potential for stock-specific variation in habitat type use. Habitat was classified
according to mapping units and categories used in Characterization and Mapping of Aquatic
Habitats Study (Study 9.9): main channel, side channel, side slough, backwater, tributary, and
tributary mouth. Over the 2-year study, AEA will attempt to collect samples from up to three
locations for each habitat type.
Juvenile Chinook salmon in the Lower River were captured using the same methods as described
for the juvenile Chinook collections above Devils Canyon. Minnow traps were checked at least
once per day. Few new fish were captured between checks and the sampling objective (100
samples per location) was not met in 2013. Multiple locations were selected because the
sampling objective could not be met at any of the locations initially selected. Tissue samples
were collected using the same methods as described for the juvenile Chinook collections above
Devils Canyon.
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). The eight juvenile putative Chinook salmon collected below Devils Canyon will be
analyzed with DNA markers to verify correct field species identification. All Pacific salmon
captured above Devils Canyon were sampled and identified in the field as Chinook salmon.
Species identification will be confirmed post-season using DNA.
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,
from which of the following areas the samples were collected: 1) Chulitna River, 2) Talkeetna
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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.
4.1.5. Sampling coordination with other studies
Tissue samples were also collected by four other studies in 2013: 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).
Sampling kits and collection protocols were distributed to study leads in advance of the field
season.
During the 2013 field season, a series of 15 weekly field progress updates (June 28th through
October 7th) were distributed to help coordinate sampling. These updates included upcoming
sampling activities for each contractor, progress made towards sampling targets for each
combination of species and study stratum, and a summary of sample deliveries to the GCL. In
season, there was also frequent direct communication among ADF&G, the contractor liaison,
and study leads designated for each interrelated study.
Collection progress was updated using a database accessible to leads for studies 9.5, 9.6, 9.7, and
9.16. Once samples were delivered to the GCL, they were entered into ADFG’s LOKI database.
Most of these samples were resident fish (Table 4-6) or juvenile Chinook salmon from above
Devils Canyon (Table 4-1). As part of the Salmon Escapement Study (Study 9.7), AEA also
collected samples from salmon at the Indian River weir, 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 of the Lower River, and RM 6 of the Yentna River). Sampling methods for
all fish tissue samples provided from the interrelated studies are described in the respective ISRs.
4.1.6. Collection trip documentation
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 (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 as described in Section 4.3 of the 2013
Genetics IP, 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) placed into
plastic plates and freeze-dried; 2) once dry, moisture-indicating desiccant beads were added and
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the plate sealed completely with aluminum foil heat-activated tape; and 3) tissue samples stored
at room temperature.
4.3. Laboratory Analysis
Laboratory analysis began during the fourth quarter of 2013 (Figure 7.1), and methods were
described in detail in the 2013 Genetics IP Section 4.4.
4.4. Data Retrieval and Quality Control
Data retrieval and quality control will be accomplished as part of different ongoing activities, the
first of which began in the fourth quarter of 2013. The 2013 Genetics IP Section 4.5 contains
detailed descriptions of data retrieval and quality control methods.
4.5. Variances from Study Plan
In 2013, there were no variances from the collection, storage and analysis methods described in
the Genetic Baseline Study Plan; 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 Devils 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. AEA will attempt to meet sampling targets for
the locations on CIRWG lands in the next year of study if permission is granted to access these
sites. 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.
5. RESULTS
5.1. Sample Collection
Sample collection results include all collections delivered to the GCL by September 15, 2013.
5.1.1. Adult Chinook salmon collections
Survey flights to determine distribution and availability of Chinook salmon for sampling
occurred from the week of June 8 to August 19 (Table 4-8). Fifty sites were surveyed from the
air. AEA attempted to sample at 30 sites and successfully sampled at 27 sites (Table 4-1).
Samples from 1,131 adult Chinook salmon were collected. Most of these samples were taken
from the Susitna River drainage (1,073). Two of these samples were from above Devils Canyon.
The remaining samples came from other drainages within upper Cook Inlet.
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5.1.2. Other adult salmon collections
Survey flights to determine distribution and availability of other adult salmon species for
sampling occurred from the week of July 29 to August 19 (Table 4-8). Of the 85 sites visited, 25
sites were surveyed from the air but sampling was not attempted (no fish or too few fish
observed to justify sampling), 34 sites were sampled but no fish were captured, and 26 sites were
successfully sampled for at least one adult salmon. Samples from 295 sockeye salmon were
collected from 13 streams (Table 4-2). Samples from 641 chum salmon were collected from 14
streams (Table 4-3). Samples from 68 coho salmon were collected from 5 streams (Table 4-4).
Samples from 1,041 pink salmon were collected from 12 streams (Table 4-5).
5.1.3. Juvenile Chinook salmon collections
5.1.3.1. Above Devils Canyon
Sampling trips to collect juvenile Chinook salmon above Devils Canyon were conducted seven
times in 2013. A total of 138 samples from juvenile Chinook salmon collected above Devils
Canyon are available for analysis. Samples from 103 juvenile Chinook salmon were collected in
2013 from two tributaries above Devils Canyon (Oshetna River, n=32; Kosina Creek, n=71;
Table 4-1). Of the 32 samples collected in the Oshetna River, 29 were acquired by ISR Study
9.5 (Study of Fish Distribution and Abundance in the Upper Susitna River). No samples were
collected in Fog or Cheechako creeks in 2013. Archived tissues collected in 2012 are also
available from Fog Creek (n=35).
5.1.3.2. Lower River collections
Sampling trips to collect juvenile Chinook salmon in the Lower River were conducted four times
in 2013. Samples from eight juvenile Chinook salmon were collected from the Lower River
(Table 4-1). These samples were all collected from slough habitat on July 5, 2013 (Table 4-9).
5.1.4. Other species collections
In 2013, opportunistic sampling for other (resident) species was conducted during all sampling
trips and by the four interrelated AEA studies. In total, samples were collected from 1,255 fish,
with sampling sites further broken into one of six potential strata (Table 4-6). The target sample
size of 50 total fish per species 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 eight species (Alaska blackfish, Pacific lamprey,
coastrange sculpin, Pacific staghorn sculpin, prickly sculpin, lake trout, Bering cisco, and lake
whitefish).
5.1.5. Pacific salmon sampling coordination with other studies
As part of the Salmon Escapement Study (Study 9.7), Pacific salmon were collected by AEA at
the Indian River weir and from salmon radio-tagged at Curry. The 9 Chinook, 2 pink, 1 sockeye,
and 13 chum salmon samples collected at the Indian River weir will be added to the baseline if
needed. The 609 Chinook (including jacks), 232 coho, 201 chum, 199 pink, and 139 sockeye
salmon samples taken from salmon radio-tagged at Curry will be used if the final spawning
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locations can be determined from telemetry and sampling targets have not been met. Because of
uncertainty about whether these samples will be added to the baseline, these collections are not
reported in Tables 4-1 and 4-5.
In addition, samples of Pacific salmon were collected at fishwheel sites as part of AEA-funded
projects administered by the ADF&G Division of Sport Fish, but those samples were not
delivered to GCL by September 15, 2013.
5.1.6. Collection trip documentation
A total of 11 entries were made into the GCL Oracle database to document survey trips and 61
entries were made to document collection trips.
5.2. Tissue Storage
For most of the collections (75 percent), samples were placed into bottles (multiple fish per
container). In the remaining collections, samples were placed into vials (one fish per container).
5.3. Laboratory Analysis
Laboratory and statistical analyses are ongoing and no results are available for inclusion in this
Initial Study Report. Preliminary analyses will be used to inform consultations with USFWS and
NMFS. Final analysis methods will be informed by these consultations.
5.4. Data Retrieval and Quality Control
Data retrieval and quality control are ongoing and no results are available for inclusion in this
Initial Study 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
through September 15, 2013 were sufficient to maintain progress toward study objectives
(“Expected” columns in Tables 4-1 to 4-5). AEA will attempt to meet sampling targets for the
locations on CIRWG lands in the next year of study if permission is granted to access these sites.
However, even if sampling targets are met, limited access to these sites in 2013 may have
reduced the power to test for stability in allele frequencies across years for Chinook salmon
(testing between hypotheses 1a, 1b; Figure 2-1). Analysis of collections from 2013 and
subsequent years will provide insight into whether there is a loss in power and, if there is, the
magnitude of this loss in power.
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
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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. Coho salmon adults were not sampled in Prairie and Portage creeks, and sampling
effort for adult sockeye salmon was reduced.
6.2. Chinook Salmon Adults in the Middle River Below Devils
Canyon
Major strides were made toward collecting Chinook salmon in the Susitna drainage below Devils
Canyon in 2013. Overall, 1,071 fish were collected from 23 sites. These numbers are close to
what was anticipated for 2013 and 2014 combined (1,032 fish from 20 to 29 sites), although the
geographic distribution of the collections differs. In the Yentna River, 202 fish were collected
from three sites (project expected 390 fish from 9 sites over two years). In the Chulitna River,
444 fish were collected from 9 sites; (project expected 218 fish from 2 to 8 sites over two years).
In the Middle River, below Devils Canyon, 95 fish were collected from 2 sites (project expected
134 fish from 2 to 6 sites over two years). In Talkeetna River, 246 fish were collected from 6
sites (project expected 131 fish from 2 to 6 sites over two years). Finally, from the Lower River,
84 fish were collected from 3 sites (project expected 159 fish from 5 to 9 sites over two years).
6.3. Chinook Salmon Adults Elsewhere
Progress was made toward collecting Chinook salmon in the other drainages from Upper Cook
Inlet in 2013. In the western side of Cook Inlet, 42 fish were collected from one site (study
expected 235 fish from 4 sites over two years). In the Knik Arm, 16 fish were collected from
two sites (study expected 181 fish from 5 to 7 sites over two years). Additional samples
collected in 2013 are expected to arrive at the GCL from ADF&G Division of Sport Fish from
weirs at three of these sites.
6.4. Chinook Salmon Juveniles – Lower River
Despite four trips to collect juvenile Chinook salmon in the Lower River, only eight fish were
sampled; all were from slough habitat on one sampling day (Table 4-9). Therefore, additional
ADF&G staff, with vast experience annually capturing thousands of juvenile Chinook salmon
from Southeast Alaska rivers, were invited to conduct a four-day training course on the Lower
River during the week of September 23, 2013. This course was intended to train field crews on
how to cure bait and bait traps and how to identify appropriate locations for setting traps and
pulling seines following the methods outlined in Magnus et al. (2006). These techniques were
applied late in the season in 2013 and will be applied during the next year of study. Results from
these sampling efforts will be used to guide future sampling for juvenile Chinook salmon in the
Lower River.
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6.5. Other Salmon Adults
Fish were sometimes not found in sublocations where ADF&G expected to find them, but the
study teams were able to capture fish in other sublocations within the targeted location. This was
especially the case for pink and chum salmon, where less was known about the spawning
distribution at the beginning of this study (Tables 4-3 and 4-5).
For odd-year pink salmon, AEA sampled fewer than the targeted 300 fish within the Chulitna
River (one fish), but met target sample numbers in the Middle Susitna River and Talkeetna
River. These odd-year pink salmon do not appear to utilize spawning habitats in the Chulitna
River. Odd-year pink salmon will not be available in 2014, so AEA’s ability to meet the target
sample sizes for odd-year pink salmon in the Chulitna River will depend on the schedule of
future sampling.
Section 4.2.2 of the 2013 Genetics IP described a schedule of weekly survey flights between
June 8 and September 23, and Section 4.2.3 described the plan for three sampling crews between
late July and late September for adult salmon species other than Chinook salmon. Poor weather
between August 19 and September 15, 2013 resulted in four fewer survey flights (Table 4-7)
than planned. These cancelled survey flights represent 18 percent (4/22) of the survey flights
planned for the season. This poor weather period also kept crews out of the field for three of the
eight weeks (Table 4-8) called for in the 2013 Implementation Plan. This reduced survey effort
came during the expected run timing of chum, sockeye, and coho salmon to their spawning
grounds. For these three species, less progress was made towards achieving the sampling targets
than expected in 2013, but it is anticipated that the sample targets can be achieved during the
next year of study to meet study objectives (Table 4-5).
6.6. Other Fish Species
Sample collections through September 15, 2013 were sufficient to attain or make progress
towards study objectives for some resident species (Objective 1). Although the target sample
size 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 collection to one of six location “strata” in the drainage. ADF&G asked each
field crew to collect up to 50 specimens from their strata to ensure the minimum for the drainage
was met. 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 (e.g., rainbow trout; 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.
6.7. Coordination with Other Studies
Tissue samples from salmon radio-tagged by interrelated Study 9.7 provided a relatively high
number of backup salmon samples in 2013. These samples will continue to be archived at the
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GCL in the winter of 2013/2014; those fish whose final destinations can be determined will then
be used to help fill any incomplete baselines at the end of this study. For resident fish species,
the coordination with studies 9.5, 9.6, 9.7, and 9.16 allowed considerable success in 2013 (full or
partial collection of samples for 12 of 20 species identified in the 2013 Study Plan). Species
with no collections were likely either not in the study areas or were not vulnerable to the capture
gear, making it unlikely that their collection targets can be reached with opportunistic sampling.
7. COMPLETING THE STUDY
[Section 7 appears in the Part C section of this ISR.]
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.
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.
Pollard, W. R., G. F., Hartman, C. Groot and P. Edgell. 1997. Field identification of coastal
juvenile salmonids. Harbor Publishing.
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
empirical evaluation of some genetic methods for identifying the number of gene pools
and their degree of connectivity. Molecular ecology, 15(6): 1419-1439.
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9. TABLES
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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. 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 two 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 this year (2013), and the resulting total
sample size after combining the amount archived with the 2013 samples (Total). 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” 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.
Sample sizes
This project
Area Location Sublocation
Map
No. Year(s) Collected (# archived) Ideal Expected
(all years) 2013 Total
Adult Chinook salmon
West Side Cook
Inlet
Chuitna River 1 2008, 2009 (142) 200 58 - 142
Beluga River Coal Creek 2 2009, 2010, 2011 (120) 200 80 - 120
Theodore River 3 2010, 2011, 2012 (189) 200 11 42 231
Lewis River 4 2011, 2012 (86) 200 86 0 86
Yentna Drainage Clearwater Creek 5 2012 (25) 200 50 - 25
Red Creek 6 2012 (29) 200 58 82 111
Happy River 7 2012 (19) 200 38 S 19
Red Salmon Creek 8 2012 (12) 200 24 S 12
Hayes River 9 2012 (5) 200 10 45 50
Canyon Creek 10 2012 (32) 200 64 75 107
Talachulitna River 11 1995, 2008, 2010 (180) 200 20 - 180
Lake Creek Sunflower Creek 12 2009, 2011 (127) 200 71 S 127
Kahiltna River Peters Creek 13 2009, 2010, 2011, 2012 (110) 200 55 - 110
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Sample sizes
This project
Area Location Sublocation
Map
No. Year(s) Collected (# archived) Ideal Expected
(all years) 2013 Total
Susitna Drainage Chulitna River Middle Fork 14 2009, 2010, 2011 (182) 200 18 29 211
East Fork 15 200
200
63
415
West Fork 16 200 S
Honolulu Creek 17 200 31
Pass Creek 18 n/a 33
Spink Creek 21 200 56
Byers Creek 19 200 54
Troublesome Creek 20 200 71
Tokositna River (Bunco Creek) 22 200 104
Tokosina River (Bunco Lake inlet
stream)
23 n/a
3
Upper Susitna River Oshetna River 24 200
50
0
12
Kosina Creek 25 2012 (10) 200 2
Watana Creek 26 200 S
Middle Susitna River
above Devils
Canyon
Tsusena Creek 27 200
S
Fog Creek 28 200 0
Devil Creek 30 200 S
Chinook Creek 32 200 S
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Sample sizes
This project
Area Location Sublocation
Map
No. Year(s) Collected (# archived) Ideal Expected
(all years) 2013 Total
Middle Susitna River
below Devils
Canyon
Portage Creek 31 2009, 2010, 2011 (141) 200 59 25 166
Indian River 33 2012 (1) 200
75
70
71 Gold Creek 34
200 S
Lane Creek 35 200 S
Chase Creek 36 200 S
Talkeetna River Prairie Creek 37 1995, 2008 (169) 200 31 33 202
no name creek #2 40 n/a
100
25
207
no name creek #1 39 n/a 71
upper mainstem 38 200 S
Iron Creek 41 200 47
Disappointment Creek 42 200 64
Sheep River 43 200 S
Larson Creek 44 200 S
Chunilna Creek (Clear Creek) 45 2009, 2012 (130) 200 65 6 136
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Sample sizes
This project
Area Location Sublocation
Map
No.
Year(s) Collected (#
archived) Ideal Expected
(all years) 2013 Total
Lower Susitna
River, upstream of
Deshka River
Montana Creek 46 2008, 2009, 2010 (218) 200 0 - 218
Birch Creek 47 200
50
S
84 Sheep Creek 48 200 22
North Fork Kashwitna River 49 200 12
Little Willow Creek 50 200 50
Willow Creek 51 1991,1997, 2005, 2009 (309) 200 0 - 309
Deshka River Moose Creek 52 1995, 2012 (103) 200 52 - 103
Deshka River weir 53 2005 (200) 200 0 - 200
Alexander Creek Sucker Creek 54 2011, 2012 (143) 200 57 - 143
Knik Arm Matanuska River Kings River 55 200 25 4 16
Granite Creek 56 200 12
Moose Creek 57 1995, 2008, 2009, 2012 (155) 200 45 - 155
Eagle River South Fork 58 2009, 2011, 2012 (73) 200 24 - 73
Meadow Creek 59 2009 (6) 200 12 - 6
Ship Creek 60 2009 (311) 200 0 - 311
Little Susitna River 61 2009, 2010 (125) 200 75 - 125
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Sample size
This project
Area Location Sublocation Map
No. Year(s) Collected (for
Archive) Ideal Expected
(all years) 2013 Total
Juvenile Chinook salmon
Susitna Drainage Above Devils
Canyon
Oshetna River 24
2012 (35)
200
70
32*
138
Kosina Creek 25 200 71
Fog Creek 28 200 0
Cheechako Creek 29 200 -
Susitna Drainage Lower River 5 habitat types n/a 1,600 1,600 8 8
(100 fish/habitat type times 3 or 4 collections)
*29 juvenile Chinook salmon samples acquired by ISR Study 9.5 Fish Distribution and Abundance in the Upper Susitna River
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Table 4-2. Location and sublocation of baseline samples of adult sockeye salmon spawning aggregates for genetic analysis. 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 two 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 this year (2013), and the resulting total sample size after
combining the amount archived with the new samples (Total). 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” 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 4-1.
Sample sizes
This project
Area Location Sublocation
Map
No. Year(s) Collected (# archived) Ideal
Expected
(all years) 2013 Total
Susitna River
above three
rivers
confluence
Chulitna River Middle Fork 2 100 100 0 0
East Fork 1 100 0
Pass Creek 5 n/a n/a 2 2
Spink Creek 4 2007, 2008 (126) 100 0 0 126
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 80 236
slough 9 14 n/a 64 64
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Sample sizes
This project
Area Location Sublocation
Map
No. Year(s) Collected (# archived) Ideal
Expected
(all years) 2013 Total
Susitna River
above three
rivers confluence
Talkeetna River no-name 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
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 126
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
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Table 4-3. Location and sublocation of baseline samples of adult chum salmon spawning aggregates for genetic analysis. 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 two 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 this year (2013), and the resulting total sample size after
combining the amount archived with the new samples (Total). 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” 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.
Sample sizes
This project
Area Location Sublocation
Map
No.
Year(s) Collected (# archived) Ideal
Expected
(all years) 2013 Total
Susitna River
above Three
Rivers
Confluence
Chulitna River Middle Fork 1 100
200
0
43 West Fork 2 100 S
Byers Creek 3 100 18
Troublesome Creek 4 100 25
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 8 100 100 123 123
Gold Creek 9 n/a n/a 5 5
sloughs above Three Rivers
Confluence 10 1996 (103) 0 0 70 173
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
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Sample sizes
This project
Area Location Sublocation
Map
No.
Year(s) Collected (# archived) Ideal
Expected
(all years) 2013 Total
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
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Table 4-4. Location and sublocation of baseline samples of adult coho salmon spawning aggregates for genetic analysis. 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 two 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 this year (2013), and the resulting total sample size after
combining the amount archived with the new samples (Total). 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” 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 4-3.
Sample sizes
This project
Area Location Sublocation
Map
No.
Year(s) Collected (# archived) Ideal
Expected
(all years) 2013 Total
Susitna River
above three
rivers confluence
Chulitna River Middle Fork 2 100
200
0
0 East Fork 1 100 0
Honolulu Creek 3 100 0
Byers Creek 4 100 0
Troublesome Creek 5 100 0
Spink Creek 6 2008 (38) 100 62 0 38
Tokositna River mainstem 7 100 100 S 0
Tokositna River (Bunco Creek) 8 100 0
Tokositna River (Swan Lake) 9 2009 (20) 100 80 0 20
Middle Susitna River Portage Creek 10 100
200
0
1
below Devils
Canyon Indian River 11 100 1
Gold Creek 12 100 S
McKenzie Creek 13 100 S
Lane Creek 14 100 S
Sloughs 15 100 75 2 2
Chase Creek 16 100 75 S 0
Whiskers Creek 17 100 75 62 62
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Sample sizes
This project
Area Location Sublocation
Map
No. Year(s) Collected (# archived) Ideal
Expected
(all years) 2013 Total
Susitna River
above three
rivers confluence
Talkeetna River upper mainstem 18 100 25 S 0
Prairie Creek 19 100 75 S 0
Sheep River 20 100 50 S 0
Larson Lake - outlet 21 2011 (84) 100 16 S 84
Chunilna Creek 22 100 75 2 2
Fish Creek 23 n/a n/a 1 1
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Table 4-5. Location and sublocation of baseline samples of adult pink salmon spawning aggregates for genetic analysis. 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 two 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 this year (2013), and the resulting total sample size after
combining the amount archived with the new samples (Total). 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” 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 4-4.
Sample sizes
This project
Area Location Sublocation
Map
No.
Year(s) Collected (for
Archive) Ideal
Expected
(all years) 2013 Total
Susitna River
above three rivers
confluence
Chulitna River Middle Fork 1 100
100
0
1 Spink Creek 3 100 0
Troublesome Creek 2 100 0
no name creek 4 n/a 1
Middle Susitna River
below Devils
Canyon
Portage Creek 5 100 50 136 136
Indian River 6 100 100 114 114
Gold Creek 7 100
50
106
446
5th of July Creek 8 n/a 2
4th of July Creek 9 n/a 107
slough 9 10 n/a 116
McKenzie Creek 11 100 0
Lane Creek 12 100 115
Chase Creek 13 100 0
Whiskers Creek 14 100 15
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Sample sizes
This project
Area Location Sublocation
Map
No.
Year(s) Collected (for
Archive) Ideal
Expected
(all years) 2013 Total
Talkeetna River upper mainstem 15 100 25 0 0
Disappointment Creek 16 n/a 0 127 127
Sheep River 17 100 25 0 0
Larson Creek 18 100 100 0 0
Chunilna Creek 19 100 100 101 101
Fish Creek 20 n/a 0 101 101
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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. 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
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 0 0 0 0 0 0
Burbot 50 0 0 4 4 2 102 104 0 0 108
Dolly
Varden 50 1 1 3 3 5 5 4 3 7 35 35 0 51
Eulachon 50 0 0 0 283 283 0 0 283
Grayling,
Arctic 50 17 17 21 21 45 14 59 7 4 11 5 5 3 3 116
Lamprey,
Arctic* n/a 9 9 9
Lamprey,
Pacific 50 0 0 0 0 0 0 0
Pike,
northern 50 0 0 0 16 16 0 0 16
Sculpin,
coastrange 50 0 0 0 0 0 0 0
Sculpin,
Pacific
staghorn
50 0 0 0 0 0 0 0
Sculpin,
prickly 50 0 0 0 0 0 0 0
Sculpin,
slimy 50 15 15 40 100 140 0 52 52 0 0 207
Stickleback,
ninespine 50 0 0 0 7 7 0 0 7
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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
other
studies N GCL
other
studies N GCL
other
studies N GCL
other
studies N GCL
other
studies N GCL
other
studies N Stickleback,
threespine 50 0 0 0 50 92 142 0 0 142
Sucker,
longnose 50 0 0 5 5 1 102 103 0 0 108
Trout, lake 50 0 0 0 0 0 0 0
Trout,
rainbow 50 0 1 1 40 40 40 7 47 19 19 23
2
3 130
Whitefish,
Bering cisco 50 0 0 0 0 0 0 0
Whitefish,
humpback 50 3 3 0 0 0 0 0 3
Whitefish,
lake 50 0 0 0 0 0 0 0
Whitefish,
round 50 2 2 0 57 9 66 0 1 1 6 6 75
* Collected, but not on original
list of target species
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Table 4-7. Summary of survey flights conducted during 2013. Surveys were performed throughout the summer of 2013 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 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
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Table 4-8. Genetic sampling effort through time by river area for adult salmon species in 2013. 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.
Collection Strata
Area sampled
(all salmon species)
Area sampled
(Chinook salmon only)
Week of Species sampled Talkeetna Chulitna
Middle
Susitna
below Devils
Canyon
Lower
Susitna
Middle
Susitna
above Devils
Canyon 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 x
7/15/2013 K x x x 7/22/2013 K 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 K, 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 *
* Sampling efforts disrupted by adverse weather conditions.
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Table 4-9. Juvenile Chinook salmon tissue collections across five habitat types in the Lower Susitna River, through September 15, 2013. Collection numbers of juvenile Chinook salmon tissues are reported for 16 collection sites over 5 different habitat types (main channel, backwater, braid, channel edge, and
slough) in the Lower Susitna River. Totals per stratum are reported (totals).
Habitat Type
Main channel Braid Channel edge Slough Backwater
collection site number collection site number collection site number collection site number collection site number
DATE 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16
7/5/2013
8
Totals:
8
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Table 4-10. 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
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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. 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. 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. 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. 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. 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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PART A - APPENDIX A: TEMPLATE FOR COLLECTION TRIP REPORTS
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LOKI Trip Report Form
Trip Start Date Trip End Date Trip Name
Charter Transportation
Lodging Report Date Report Author
Waypoint Name: Potential Access:
camp/survey/collection latitude longitude
waypoint comments
Waypoint Name: Potential Access:
camp/survey/collection latitude longitude
waypoint comments
Waypoint Name: Potential Access:
camp/survey/collection latitude longitude
waypoint comments
Waypoint Name: Potential Access:
camp/survey/collection latitude longitude
waypoint comments
Waypoint Name: Potential Access:
camp/survey/collection latitude longitude
waypoint comments
Waypoint Name: Potential Access:
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camp/survey/collection latitude longitude
waypoint comments
TRIP COMMENTS ON REVERSE SIDE
TRIP COMMENTS