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Susitna‐Watana Hydroelectric Project Document
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Title:
Study of fish distribution and abundance in the middle and lower Susitna
River, Study plan Section 9.6, 2014-2015 Study Implementation Report SuWa 289
Author(s) – Personal:
Author(s) – Corporate:
R2 Resource Consultants Inc.
LGL Alaska Research Associates, Inc.
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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
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[Anchorage : Alaska Energy Authority, 2015]
Date published:
November 2015
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Alaska Energy Authority
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Study plan Section 9.6
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93 pages in various pagings
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Notes:
Contents:
[Main report]
Appendix A. 2014 sampling site maps
Appendix B. Juvenile chinook and coho salmon identification accuracy.
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)
Study of Fish Distribution and Abundance in the
Middle and Lower Susitna River
Study Plan Section 9.6
2014-2015 Study Implementation Report
Prepared for
Alaska Energy Authority
Prepared by
R2 Resource Consultants Inc.
LGL Alaska Research Associates, Inc.
November 2015
STUDY IMPLEMENTATION REPORT STUDY OF FISH DISTRIBUTION AND ABUNDANCE IN THE
MIDDLE AND LOWER SUSITNA RIVER (STUDY 9.6)
Susitna-Watana Hydroelectric Project Alaska Energy Authority
FERC Project No. 14241 Page i November 2015
TABLE OF CONTENTS
1. Introduction ............................................................................................................................ 1
2. Study Objectives .................................................................................................................... 2
3. Study Area .............................................................................................................................. 2
4. Methods .................................................................................................................................. 3
4.1. Study Site Selection ....................................................................................................... 3
4.1.1. Early Life History Sites .......................................................................................... 3
4.1.2. Fish Distribution and Abundance Sites ................................................................... 3
4.1.3. Radio Telemetry Sites and Surveys ........................................................................ 4
4.1.4. Winter Study Sites .................................................................................................. 4
4.1.5. Variances from Study Plan ..................................................................................... 5
4.2. Sampling Frequency....................................................................................................... 6
4.2.1. Variances from Study Plan ..................................................................................... 7
4.3. Objective 1: Fish Distribution, Relative Abundance, and Habitat Associations .......... 7
4.3.1. Tasks A and B: Fish Distribution and Relative Abundance Surveys ..................... 8
4.3.2. Task C: Fish Habitat Associations .......................................................................... 8
4.3.3. Variances from Study Plan ..................................................................................... 8
4.4. Objective 2: Seasonal Movements ................................................................................. 9
4.4.1. Task A: Describe seasonal movements using biotelemetry. ................................... 9
4.4.2. Variances from Study Plan ................................................................................... 10
4.5. Objective 3: Early Life History .................................................................................... 11
4.5.1. Task A: Describe emergence timing of salmonids. .............................................. 11
4.5.2. Task B: Determine movement patterns and timing of juvenile salmonids from
spawning to rearing habitats. ................................................................................ 11
4.5.3. Task C: Determine juvenile salmonid diurnal behavior over season. .................. 11
4.5.4. Task D: Collect baseline data to support the Fish Stranding and Trapping Study.
11
4.5.5. Variances from Study Plan ................................................................................... 12
4.6. Objective 4: Document Winter Movements and Timing and Location of Spawning for
Burbot, Humpback Whitefish, and Round Whitefish .................................................. 12
4.7. Objective 5: Document the Seasonal Size/Life stage Structure, Growth, and Condition
of Juvenile Anadromous and Resident Fish by Habitat Type ...................................... 12
4.7.1. Variances from Study Plan ................................................................................... 13
STUDY IMPLEMENTATION REPORT STUDY OF FISH DISTRIBUTION AND ABUNDANCE IN THE
MIDDLE AND LOWER SUSITNA RIVER (STUDY 9.6)
Susitna-Watana Hydroelectric Project Alaska Energy Authority
FERC Project No. 14241 Page ii November 2015
4.8. Objective 6: Document the Seasonal Distribution, Relative Abundance, and Habitat
Associations of Invasive Species (Northern Pike) ....................................................... 13
4.8.1. Variances from Study Plan ................................................................................... 13
4.9. Objective 7: Collect Tissue Samples from Juvenile Salmon and Resident and Non-
Salmon Anadromous Fish ............................................................................................ 13
4.9.1. Variances from Study Plan ................................................................................... 14
4.10. Winter Sampling Approach ......................................................................................... 14
4.10.1. Variances from Study Plan ................................................................................... 15
4.11. Fish Sampling Techniques ........................................................................................... 15
4.11.1. Fish Handling ........................................................................................................ 15
4.11.2. Winter Sampling Techniques ................................................................................ 16
5. Results ................................................................................................................................... 16
5.1. Objective 1: Fish Distribution, Relative Abundance, and Habitat Associations ......... 16
5.1.1. Task A: Fish Distribution...................................................................................... 16
5.1.2. Task B: Relative Abundance ................................................................................ 17
5.2. Objective 3: Early Life History ................................................................................... 17
5.3. Objective 4: Document winter movements and timing and location of spawning for
Burbot, Humpback Whitefish, and Round Whitefish. ................................................. 18
5.4. Objective 6: Document the seasonal distribution, relative abundance, and habitat
associations of invasive species (Northern Pike). ........................................................ 18
5.5. Objective 7: Collect tissue samples from juvenile salmon and all resident and non-
salmon anadromous fish. .............................................................................................. 18
6. Discussion ............................................................................................................................. 18
7. Conclusion ............................................................................................................................ 19
7.1. Modifications to Study Plan ......................................................................................... 19
8. Literature Cited ................................................................................................................... 20
9. Tables .................................................................................................................................... 23
10. Figures .................................................................................................................................. 50
STUDY IMPLEMENTATION REPORT STUDY OF FISH DISTRIBUTION AND ABUNDANCE IN THE
MIDDLE AND LOWER SUSITNA RIVER (STUDY 9.6)
Susitna-Watana Hydroelectric Project Alaska Energy Authority
FERC Project No. 14241 Page iii November 2015
LIST OF TABLES
Table 2-1. Methods by objective, task, species, and life stage, 2014. ......................................... 23
Table 4.1-1 Salmon early life history sampling effort, 2014. (Maps of sampling locations in
Appendix A).................................................................................................................................. 26
Table 4.1-2. Direct tributary sampling effort for fish distribution in the Middle River above
Devils Canyon by geomorphic reach, 2013 and 2014. (Maps of sampling locations in Appendix
A). The lower portions of Tsusena Creek and Chinook Creek could not be accessed in 2013 and
were repeat sampled in 2014. ........................................................................................................ 27
Table 4.1-3. Habitat types and number of sites sampled for distribution and relative abundance
sampling in the Middle River, 2013 and 2014. ............................................................................. 28
Table 4.1-4. Sites sampled for fish distribution and abundance in the Middle Susitna River by
season, 2014 (Maps of sampling locations in Appendix A). ........................................................ 29
Table 4.1-5. Antenna orientation for fixed telemetry receiver stations in the Middle and Upper
Susitna River, 2014. ...................................................................................................................... 30
Table 4.1-6. Habitat types sampled during 2013/14 winter study by gear type and month. ........ 31
Table 4.2-1. Monitoring efficiency (percent operational) of fixed radio telemetry receiver
stations in the Susitna River drainage in 2014, by week. ............................................................. 34
Table 4.2-2. Summary of aerial surveys of radio-tagged fish in the Lower and Middle Susitna
River, 2014-2015 .......................................................................................................................... 35
Table 4.4-1. Summary of PIT tagging implants and in-hand recaptures in the Middle and Lower
River Study Area, 2014................................................................................................................. 38
Table 4.4-2. Radio tag allocation by season and location, Middle and Lower Susitna River, 2014.
....................................................................................................................................................... 39
Table 4.4-3. Resident fish relocated by study month (2014-2015) with active radio tags that were
tagged and released in Middle and Lower Susitna River. ............................................................ 40
Table 4.7-1. Summary of size-at-life stage index used to classify Susitna River species, 2014. . 41
Table 4.7-2. Summary of fish with length and weight measurements collected in the Middle and
Lower Susitna River by hydrologic segment and study component, 2014. .................................. 42
Table 4.9-1. Summary of Fish Distribution and Abundance tissue collection for genetic baseline
development and field species calls, 2014. ................................................................................... 43
Table 4.9-2 Summary of fish collection for River Productivity (Study 9.8) scale, tissue and/or
stomach content sampling, 2014. .................................................................................................. 44
STUDY IMPLEMENTATION REPORT STUDY OF FISH DISTRIBUTION AND ABUNDANCE IN THE
MIDDLE AND LOWER SUSITNA RIVER (STUDY 9.6)
Susitna-Watana Hydroelectric Project Alaska Energy Authority
FERC Project No. 14241 Page iv November 2015
Table 5.1-1. An updated summary of fish distribution by Geomorphic Reach the in Middle and
Lower Susitna River, where ◊ indicates new locations from 2014. .............................................. 45
Table 5.1-2. 2014 Middle Susitna River fish observations by life stage and site. Includes the
seasonal sampling events from the following data sources: habitat stratified randomized
sampling (GRTS), direct tributary sampling, and opportunistic sampling ................................... 46
Table 5.2-1. Observations of juvenile anadromous and resident fish during three Early Life
History sampling events in the Middle Susitna River .................................................................. 48
LIST OF FIGURES
Figure 3-1. Susitna River fish distribution and abundance study area. ........................................ 51
APPENDICES
Appendix A: 2014 Sampling Site Maps
Appendix B: Juvenile Chinook and Coho Salmon Identification Accuracy
STUDY IMPLEMENTATION REPORT STUDY OF FISH DISTRIBUTION AND ABUNDANCE IN THE
MIDDLE AND LOWER SUSITNA RIVER (STUDY 9.6)
Susitna-Watana Hydroelectric Project Alaska Energy Authority
FERC Project No. 14241 Page v November 2015
LIST OF ACRONYMS, ABBREVIATIONS, AND DEFINITIONS
Abbreviation Definition
ADF&G Alaska Department of Fish and Game
AEA Alaska Energy Authority
AWC Anadromous Waters Catalog
BW backwater
CIRWG Cook Inlet Regional Working Group
CPUE catch-per-unit-effort
CWP clearwater plume
DIR direct sample tributary
ELH early life history
FA Focus Area
FDA fish distribution and abundance
FERC Federal Energy Regulatory Commission
GRTS generalized random tessellation stratified samples
FL fork length
ILP Integrated Licensing Process
In inches
IP Implementation Plan
ISR Initial Study Report
LR Lower River
MC main channel
Mm millimeters
MR Middle River
PIT passive integrated transponder
PRM Project River Mile
Project Susitna-Watana Hydroelectric Project
RP river productivity
RSP Revised Study Plan
SC side channel
SPD study plan determination
SS side slough
TM tributary mouth
Trib tributary
TWG technical workgroup
US upland slough
USR Updated Study Report
STUDY IMPLEMENTATION REPORT STUDY OF FISH DISTRIBUTION AND ABUNDANCE IN THE
MIDDLE AND LOWER SUSITNA RIVER (STUDY 9.6)
Susitna-Watana Hydroelectric Project Alaska Energy Authority
FERC Project No. 14241 Page 1 November 2015
1. INTRODUCTION
This Study of Fish Distribution and Abundance in the Middle and Lower Susitna River, Section
9.6 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
describing the current fish assemblage including spatial and temporal distribution, and relative
abundance by species and life stage in the Susitna River downstream of the proposed Watana
Dam (AEA 2012).
A summary of the development of this study, together with the Alaska Energy Authority’s
(AEA) implementation of it through the 2013 study season, appears in Part A, Section 1 of the
Initial Study Report (ISR) filed with FERC in June 2014 (AEA 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)).
On October 15, 2014, AEA held an ISR meeting for the Study of Fish Distribution and
Abundance in the Middle and Lower Susitna River. Since filing the ISR in June 2014, AEA has
continued to implement the FERC-approved plan for the Study of Fish Distribution and
Abundance in the Middle and Lower Susitna River. Study efforts applied to the Study of Fish
Distribution and Abundance in the Middle and Lower Susitna River subsequent to the ISR
include the filing of the following documents:
2013-2014 Winter Fish Study Technical Memorandum filed September 17, 2014 (R2
Resource Consultants, Inc. and LGL Alaska Research Associates, Inc. 2014);
Appendix 3. Protocol for Site-Specific Gear Type Selection; Version 5 filed November
14, 2014 (R2 Resource Consultants 2014a);
Draft Chinook and Coho Salmon Identification Protocol filed November 14, 2014 (R2
Resource Consultants 2014b).
The 2014 sampling efforts in the Middle and Lower River focused on:
Completion of the first full study year of Winter Fish Studies;
Completion of the second study year of Salmon Early Life History (ELH) sampling;
Continuation of resident fish radio tagging and tracking;
Fish distribution and abundance sampling at sites that were not sampled or partially
sampled in 2013 due to land access restrictions to fulfill and complete the first study year
of data collection.
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 Study of Fish Distribution and Abundance
in the Middle and Lower Susitna River since that reported in June 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 of the ISR for the Study of Fish Distribution and Abundance in the Middle
STUDY IMPLEMENTATION REPORT STUDY OF FISH DISTRIBUTION AND ABUNDANCE IN THE
MIDDLE AND LOWER SUSITNA RIVER (STUDY 9.6)
Susitna-Watana Hydroelectric Project Alaska Energy Authority
FERC Project No. 14241 Page 2 November 2015
and Lower Susitna River. It describes the methods and results implemented, and includes a
discussion of the results achieved.
2. STUDY OBJECTIVES
As established in RSP Section 9.6.1 (Table 2-1), there are seven study objectives. The following
components of those objectives were addressed by activities carried out in 2014:
1) Describe the seasonal distribution, relative abundance (as determined by CPUE, fish
density, and counts) and fish habitat associations of juvenile anadromous salmonids, non-
salmonid anadromous fishes and resident fishes.
2) Describe seasonal movements of juvenile salmonids and selected fish species such as
Rainbow Trout, Dolly Varden, Humpback Whitefish, Round Whitefish, Northern Pike,
Arctic Lamprey, Arctic Grayling, and Burbot, with emphasis on identifying foraging,
spawning and overwintering habitats within the mainstem of the Susitna River.
b. Describe seasonal movements using biotelemetry (passive integrated transponder
[PIT] and radio-tags).
3) Describe early life history, timing, and movements of anadromous salmonids.
a. Describe emergence timing of salmonids.
b. Determine movement patterns and timing of juvenile salmonids from spawning to
rearing habitats.
c. Determine juvenile salmonid diurnal behavior by season.
d. Collect baseline data to support the Stranding and Trapping Study.
4) Document winter movements and timing and location of spawning for Burbot,
Humpback Whitefish, and Round Whitefish.
5) Document the seasonal age class structure, growth, and condition of juvenile anadromous
and resident fish by habitat type.
6) Document the seasonal distribution, relative abundance, and habitat associations of
invasive species (Northern Pike).
7) Collect tissue samples from juvenile salmon and opportunistically from all resident and
non-salmon anadromous fish to support the Fish Genetic Baseline Study (Study 9.14).
3. STUDY AREA
The RSP established the Middle and Lower River study area as the Susitna River from RM 61
upstream to the proposed Watana Dam site (RM 184, RSP Figure 9.6-1). The downstream
boundary of the study area was subsequently adjusted in the Final Fish Distribution and
Abundance Implementation Plan (IP; AEA 2013) to PRM 32.3 (HRM 28.3) immediately
upstream of the confluence with the Yentna River upstream to the Watana Dam Site (PRM
187.1[RM 184], Figure 3-1).
In 2014, study efforts occurred in the Middle and Lower Susitna River from Montana Creek
(PRM 80.8) upstream to the proposed Watana Dam site (PRM 187.1). Excluding PIT antenna
array operation during the Winter Fish Studies (R2 Resource Consultants and LGL Alaska
STUDY IMPLEMENTATION REPORT STUDY OF FISH DISTRIBUTION AND ABUNDANCE IN THE
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Susitna-Watana Hydroelectric Project Alaska Energy Authority
FERC Project No. 14241 Page 3 November 2015
Research Associates 2014) at Montana Creek (PRM 80.8) and aerial tracking of radio tags
(Table 4.2-2), 2014 study efforts were concentrated in the Middle River Segment.
4. METHODS
This study employed a variety of field methods to build on the existing information related to the
distribution and abundance of fish species in the Middle and Lower Susitna River consistent with
the Study Plan except for specific variances as described below. The following sections provide
brief descriptions of study site selection, sampling frequency, the approach, and suite of methods
that were used to accomplish each objective of this study.
Fish Distribution and Abundance Implementation Plan
A final sampling scheme was developed as part of the detailed Fish Distribution and Abundance
Implementation Plan (IP, AEA 2013) for Studies 9.5 and 9.6 which was approved by FERC,
with modifications, on April 1, 2013. Implementation in 2014 included updating the Protocol for
Site-Specific Gear Type Selection (filed with FERC November 2014; R2 Resource Consultants
2014a). The gear selection protocol is a working document provided to field crews summarizing
the sampling approach using multiple gear types. Sampling methods by objective are presented
below and in Table 2-1. Brief descriptions of each sampling technique are provided in Section
4.12.
4.1. Study Site Selection
AEA implemented site selection as described in the IP as well as the Study Plan modifications
presented in ISR, Part C, Section 7.1.2 (AEA 2014). Field sampling sites in 2014 occurred for: the
study of salmon early life history, the study of fish distribution and abundance, radio-telemetry
tagging and tracking, and winter study sites. AEA implemented the site-selection methods as
described in the Study Plan with the exception of the variances explained below in Section 4.1.5.
4.1.1. Early Life History Sites
Salmon early life history (ELH) sampling took place every two weeks between ice break-up
(May 3, 2014) and July 1 in six Middle River Focus Areas downstream of Devils Canyon (Table
4.1-1; Figures A1-A6). During ELH sampling events, study locations in selected Focus Areas
included three 40-meter (131-feet) long sampling units immediately downstream of a
documented Chinook, Chum, or Coho Salmon spawning area (tributary mouths or side sloughs)
and three 40-meter (131-feet) sampling units that provided rearing habitat.
4.1.2. Fish Distribution and Abundance Sites
4.1.2.1. Middle River Tributaries above Devils Canyon
Tributaries selected for fish distribution and abundance sampling between the downstream end of
Devils Canyon (PRM 153.9) and the proposed Watana Dam Site (PRM 187.1) included all
known Chinook Salmon-bearing tributaries and other tributaries that were not listed in
ADF&G’s Anadromous Waters Catalog (AWC; ADF&G 2012). Initially seven tributary
STUDY IMPLEMENTATION REPORT STUDY OF FISH DISTRIBUTION AND ABUNDANCE IN THE
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Susitna-Watana Hydroelectric Project Alaska Energy Authority
FERC Project No. 14241 Page 4 November 2015
streams were selected for sampling based on: AWC catalog listings, drainage basin, historical
and 2012 sampling efforts, and the potential for impact from the proposed Project (Table 4.1-2).
As described in the IP, a direct sampling methodology was implemented on these seven tributary
streams. An average effort of two 100 m (328 ft) sites were sampled over a two day period.
Because of land access constraints, only two streams were fully sampled in 2013, Fog Creek and
Fog Creek Tributary; Tsusena and Chinook Creeks received partial sampling. In 2014, Tsusena
and Chinook Creeks were re-sampled; Unnamed Tributary 184, Devil Creek, and Cheechako
Creek were also sampled (Tables 4.1-2 and 4.1-4). The goal of sampling was to distribute two
days of sampling effort over the accessible study area in several locations that represented
multiple habitat types. Efforts were focused in the lower reaches, immediately upstream of the
tributary mouth, and below documented anadromous fish passage barriers (Figures A-10, A-11,
A-13).
4.1.2.2. Mainstem Middle River
Mainstem sampling followed GRTS site selection that occurred in 2013 (AEA 2014). In 2013, a
total of 162 sites were sampled from the 177 targeted sites in the Middle River including 76 sites
within Focus Areas and 86 sites outside of Focus Areas. In 2014, AEA sampled sites that were
inaccessible or partially sampled in 2013 because of land access constraints. This included 12
locations within Focus Areas and 15 outside of Focus Areas (Tables 4.1-3 and 4.1-4).
Combining efforts from 2013 and 2014, a total of 182 sites were sampled from a target of 177;
the sampled number exceeds the target because additional backwater and clearwater plume
habitats were sampled when encountered. Sampling locations for 2014 are depicted in Figures
A7-A13.
4.1.3. Radio Telemetry Sites and Surveys
Fixed radio telemetry stations were installed at seven locations in the Middle Susitna River in
2014 (Table 4.1-5). The primary objective of six stations was to track the movements of radio-
tagged fish in the mainstem of the Susitna River (Lane Creek [PRM 117; near the mouth of Lane
Creek], Gateway [PRM 130; upstream of Curry], Cheechako Creek [PRM 157.4], Chinook
Creek [PRM 160.5], Devils Island [PRM 167; upstream of Devil Creek], and near the Watana
Dam Site [PRM 186.8]). The seventh station, Indian River station, provided coverage of the
mainstem of the Susitna as well as Indian River (PRM 142.1). Tagging efforts in 2014 focused
on the Upper River, however limited tagging of Arctic Grayling (7) and Burbot (5) did take place
in the Middle River above Devils Canyon (Table 4.4-2). Aerial tracking of fishes radio tagged in
2014 and 2015 in the Middle and Lower River extended from the Lower Susitna River near the
mouth to the Watana Dam site (Table 4.2-2).
4.1.4. Winter Study Sites
Given the limited number of daylight hours and potential for extreme weather, sampling efforts
for the Winter Fish Study were limited to the reach of the Middle and Lower Susitna River easily
accessible from Talkeetna by snow machine, snowshoe, or railroad. The study area included the
lower reaches of Montana Creek (PRM 80.8) and the Susitna River between PRM 104.4 and
PRM 142.4. Three Focus Areas, FA-104 (Whiskers Slough), FA-128 (Slough 8A), and FA-138
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(Gold Creek), served as activity centers for intensive sampling (R2 Resource Consultants and
LGL Alaska Research Associates 2014). Supplemental sampling took place at five additional
locations including: the Cut (an upland slough between the Susitna and Chulitna Rivers), Slough
14, Gold Creek, Indian River, and Slough 17 (R2 Resource Consultants and LGL Alaska
Research Associates 2014). A site list by location, habitat, and sampling event is provided in
Table 4.1-6. PIT tag antenna arrays were operated at Montana Creek (PRM 80.8), Whiskers
Slough (FA-104) and Slough 8A (FA-128) during the 2013-2014 Winter Fish Study (R2
Resource Consultants and LGL Alaska Research Associates 2014).
4.1.5. Variances from Study Plan
Several 2013 variances related to study sites that were described in ISR Part A, Section 4
continued in 2014. In addition, implementation of the Study Plan in 2014 resulted in two new
variances related to radio telemetry fixed receiver and winter study sites. Unlike 2013, the 2014
Study Plan implementation includedaccess to Cook Inlet Regional Working Group (CIRWG)
and Alaska Railroad Corporation lands and the addition of Winter Study sites.
4.1.5.1. Early Life History Study Sites
The following variances from the Study Plan for site selection in 2014 were also implemented in
2013 (Study 9.6 ISR, Part A, Section 4.1.7) and were also proposed as Study Plan modifications
(Study 9.6 ISR, Part C, Section 7.1.2).
The Study Plan specified ELH sampling at six sites in each of five Middle River Focus
Areas (IP Section 5.5). However, with the addition of FA-113 (Oxbow I) following IP
development, sampling took place at six sites in each of six Focus Areas (Study 9.6 ISR
Part A, Section 4.1.7.1; Table 4.1-1). Expansion of ELH sampling is anticipated to
enhance AEA’s ability to meet the study objectives.
FERC’s SPD recommended that AEA sample mainstem habitats using separate strata for
main channel, split main channel and multi-split main channels. However, based on
licensing participants’ recommendations during the study plan development and ongoing
discussions in the Fish and Aquatic TWG meetings regarding the potential to extend an
unbalanced effort in these habitats, these three channel forms were sampled as a single
strata designated as main channel. During sampling, field crews noted macrohabitat type
(e.g., main channel, split channel, or multi-split main channel). This variance resulted in
30 fewer mainstem sites being sampled (Study 9.6 ISR Part A, Section 4.1.7.2, Table 4.1-
3). This may have decreased the ability to evaluate the distribution, abundance and
habitat associations for rare species in mainstem habitats; but is consistent with NMFS
and FWS concerns that there were too many level 3 and level 4 mainstem habitat
classifications. NMFS and FWS also stated that AEA’s proposed level 4, split main
channel and braided channel habitat types are a geomorphic classification and do not
provide habitat characteristics or values that should be distinguished at the macrohabitat
level (FERC SPD April 1 , 2013). This variance is not anticipated to impact AEA’s
ability to meet the seasonal distribution component of Objective 1; however, the degree
to which fish relative abundance and habitat associations vary among main channel
habitat types will be further analyzed.
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FERC Project No. 14241 Page 6 November 2015
4.1.5.2. Fish Distribution and Abundance Sites
Land ownership and accessibility influenced fish sampling in discrete areas of the Middle River
in 2013. In 2014, access was permitted on CIRWG and Alaska Railroad Corporation ARRC
lands resulting in sampling of 27 GRTS target locations and five direct sample tributaries that
were either not sampled or partially sampled in 2013. AEA completed a first year of sampling as
proposed in the study plan, but over two study years. While some interannual variability is
expected across all study sites, it is anticipated that the 2013 and 2014 datasets can be combined
for comparative analysis and study objectives relative to fish distribution and abundance can be
met.
Sampling in 2014 took place at 27 Middle River GRTS sites, bringing the total number sampled
to 182 sites and exceeded the target of 177 sites (Table 4.1-3). Additionally, between 2013 and
2014, 42 locations were sampled in 7 direct sample tributaries in and above Devils Canyon
(Table 4.1-2) bringing the total number of Middle River fish distribution and abundance sites to
224. This variance is expected to improve AEA’s ability to determine fish distribution,
abundance, and habitat associations in the Middle River.
4.1.5.3. Radio Telemetry Fixed Receiver Sites
In 2014, 10 total fixed receiver sites were used to monitor resident fish tags (Table 4.1-5). This
includes seven sites in the Middle River (Lane, Gateway, Indian River, Cheechako, Chinook,
Devils, and Watana Dam site) and three new stations that were added to the Lower River:
Montana Creek weir, Susitna at Sunshine, and Talkeetna River. Stations proposed (Section
5.8.2.1 of the IP ) but not monitored in 2014 included: 4th of July Creek, Indian River weir,
Slough 21, Montana Creek confluence, Whiskers Creek confluence, Portage Creek confluence,
and Fog Creek confluence. This reduction of fixed of fixed stations resulted in a similar number
of arrays to that used in 2013 and, as in 2013, was accompanied by an increase in the frequency
of mobile surveys from one survey per month during the non-salmon season as indicated in the
Study Plan, to one survey every 20 days. Surveys during the salmon season increased from one
survey per week to a minimum of two surveys per week. A preliminary analysis of the 2013
detection data showed that this study design allowed for more detail on the timing and location
of tagged fish than would have been collected with more fixed stations and fewer mobile
surveys. The increased frequency of mobile surveys more than compensated for operating fewer
fixed telemetry sites as it added more observations on seasonal timing and distribution. Thus,
this variance enhanced AEA’s ability to meet study objectives for radio-telemetry.
4.2. Sampling Frequency
AEA implemented the sampling frequency methods as described in the Study Plan with the
exception of the variances explained below in Section 4.2.1. Sampling frequency varied among
sites based on study objectives. Winter fish sampling occurred monthly from February through
April 2014 and was coordinated with the intergravel temperature monitoring, and the underwater
fish observation using sonar (R2 Resource Consultants and LGL Alaska Research Associates
2014). Following the 2014 Winter Fish study, sampling occurred seasonally during the ice-free
period. Biweekly ELH sampling began following break-up (May 3, 2014) and continued into
late June in an attempt to capture critical juvenile salmon out-migration from natal tributaries to
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rearing habitats (Table 4.1-1). Fish distribution and abundance sampling in 2014 was completed
during three sessions: early summer (June 30 to August 11), late summer (August 12 to
September 9) and fall (September 15 to October 8). Stationary radio receivers were operated
between May 2 and July 8 (Table 4.1-5) and were monitored for operational efficiency on a
weekly basis (Table 4.2-1). Aerial radio telemetry surveys were conducted approximately every
20 days from January 5 until June 12, 2014 two to five times per week from mid- June through
October 17, 2014 and approximately monthly from mid-October, 2014 to July 6, 2015 (Table
4.2-2).
4.2.1. Variances from Study Plan
Land ownership and site/weather conditions influenced the frequency of fish sampling in discrete
areas of the Middle River in 2013. In 2014, access was permitted on CIRWG and ARRC lands;
however the timing of final permit approval resulted in 10 of 27 GRTS sites and 3 of 5 direct
sample tributaries not being sampled during the early summer sampling period (Table 4.1-4).
Because data were successfully collected during subsequent sampling events, this variance is not
anticipated to affect AEA’s ability to meet the study objectives.
In 2013, aerial surveys occurred approximately weekly from July through October. At other
times of the year, the frequency and location of aerial surveys was at least monthly. In 2014,
AEA increased the frequency of the mobile surveys from weekly during the salmon monitoring
period and monthly during the non-salmon period (ISR Part A Section 5.8.2.2) to a minimum of
two times per week and every 20 days, respectively. An analysis of the 2013 telemetry data
indicated that the mobile data provided more detail on fish timing and distribution than would
have been provided by a lower frequency of mobile tracking and higher number of fixed
telemetry stations as proposed in the Study Implementation Plan, such that the variance did not
effect accomplishing the study objectives.
4.3. Objective 1: Fish Distribution, Relative Abundance, and Habitat
Associations
AEA implemented the methods as described in the IP including updates made to the Protocol for
Site-Specific Gear Type Selection (R2 Resource Consultants 2014a) with the exception of
variances explained below (Section 4.3.3). The general sampling approach was to gather data on
relative abundance as determined by catch per unit effort and density; complementary data on
fish size, life stage, and condition factor were also collected. For all sampling, main channel,
off-channel, and tributary habitats were further characterized in the field to the mesohabitat level
(pool, riffle, glide, etc.) for sampling purposes and for study of fish-habitat associations. The
sampling locations and fish capture methods (e.g., number of passes, amount of soak time, use of
block nets when feasible) were standardized such that they were repeatable on subsequent
sampling occasions.
In 2013 field crews reported difficulty with differentiating juvenile Chinook and Coho salmon in
the Middle and Lower River below Devils Canyon. In particular, larger juveniles undergoing
smoltification in upland sloughs were reportedly challenging and difficult to distinguish. This
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issue was also raised by certain licensing participants during their review and comments on the
ISR (NMFS 2014; FWS 2014). In 2014, identification challenges continued but were
substantially reduced (Appendix B) as crews received: (1) additional training at locations where
both species co-occurred and were difficult to distinguish, (2) the results of 2013 genetic
collections, (3) review and feedback on photos of field specimens, and (4) established a voucher
reference library to gage field calls with meristic characteristics. In 2014, crews continued to
collect genetics samples from Chinook and Coho salmon (Table 4.9-1; R2 Resource Consultants
2015 Table 4.7-1) as well as photos for senior review and AEA was able to implement
components of the proposed QAQC protocol for field determinations of these species (Appendix
B). Moving forward, AEA has proposed to implement the full suite of actions in the
identification protocol as described in the Draft Chinook and Coho Salmon Identification
Protocol (R2 Resource Consultants 2014b), filed with FERC November 14, 2014. These actions
will improve field identification in future study years and will provide a means of continued
evaluation the accuracy of field calls for juvenile Chinook and Coho salmon.
4.3.1. Tasks A and B: Fish Distribution and Relative Abundance Surveys
Fish distribution and abundance surveys included three seasonal sampling events during the ice-
free seasons with year-round sampling in select Focus Areas. Various methods were chosen
based on target species, life stage, and water conditions. Snorkeling and electrofishing were
preferred methods for juvenile fishes in clearwater areas where velocities were safe. Minnow
traps, beach seines, and fyke nets were employed as alternatives in deeper waters and in habitats
with limited access, low visibility, or high velocities. For larger fishes, gillnets, seines, hoop
traps, and angling were used. Whereas snorkeling, minnow trapping, backpack electrofishing,
and beach seines were applicable to sloughs and other slow-moving waters, gillnetting, boat
electrofishing, hoop traps, and trot lines were more applicable to the main channel. Two or more
survey methods were selected for each site based on target species and life stages (R2 Resource
Consultants 2014a). The decisions about what methods to apply were made by field crews after
initial site selection following guidance outlined in the gear selection protocol (R2 Resource
Consultants 2014a) and in accordance with state and federal fish sampling permit requirements.
Basic site and habitat information was collected for each mesohabitat sampled and detailed
records were kept on the level of sampling effort including soak times, sampling duration,
number of units, and specifications of gear used. Lastly, methods varied seasonally with the
extent of ice cover. Methods for winter sampling were based on winter 2012–2013 pilot studies
and included sonar imaging, underwater video, minnow traps, electrofishing, fyke nets, and trot
lines (R2 Resource Consultants and LGL Alaska Research Associates 2014).
4.3.2. Task C: Fish Habitat Associations
In conjunction with Tasks A and B, data were collected for fish distribution and abundance by
mesohabitat type nested within macrohabitats.
4.3.3. Variances from Study Plan
The following variances from the Study Plan related to sampling methods for fish distribution,
relative abundance and habitat association samplint that occurred in 2013 and were presented in
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9.6 ISR Section 4.4.4. These variances, which were also proposed as Study Plan modifications in
9.6 ISR, Part C, Section 7.1.2, were continued in 2014:
200 meter (565 ft) sampling length for all methods in main channel and side channel
habitats except for boat electrofishing and drift gill netting which consisted of 500 meter
(0.3 mi) sample lengths;
Single pass sampling for electrofishing, snorkeling, and minnow trapping
The use of block nets was limited to habitats where feasible;
Overnight soak duration for fyke nets and hoop traps;
Use of one gear type to survey some mesohabitats (approximately 5 percent) where
additional gears were not appropriate due to habitat conditions.
Soak time for drift gill nets set was up to 15 minutes due to currenets transporting the net
out of the sampling area.
Implementation of the Study Plan in 2014 did not result in any new variances for fish
distribution, relative abundance, and habitat association sampling methods. As described in the
Study 9.6 ISR, Part C (Section 7.1.2.6) these variances are not anticipated to detract from
AEA’s ability to meet the study objectives. An analysis of sampling sufficiency presented
therein describes the effectiveness of 2013 sampling methods with respect to capturing 92-100
percent of species present in each geomorphic reach and the adequacy of characterizating
baseline distribution, relative abundane, and habitat associations in the Middle and Lower River.
4.4. Objective 2: Seasonal Movements
AEA implemented the methods for Objective 2 as described in the Study Plan with the exception of
the variances explained in Section 4.4.2.
4.4.1. Task A: Describe seasonal movements using biotelemetry.
4.4.1.1. Field Methods
Biotelemetry techniques included radio telemetry and Passive Integrated Transponder (PIT)
technology. Half duplex PIT tags (12 and 23 mm) were surgically implanted in fish greater than
60 mm (2.4 in) to monitor movement and growth. Fish for PIT tagging were captured
opportunistically during fish distribution and abundance sampling.
PIT tagging in the Middle River took place from February through mid-September, 2014 and
focused on fish in proximity to intensive winter fish study locations and Focus Areas.
Recaptured fish provided information on the time and distance travelled and growth since the
fish was last handled. PIT tag antenna arrays with automated data logging were installed and
operated at Montana Creek, FA-104 (Whiskers Slough) and FA-128 (Slough 8A) during the
winter study period and were removed prior to ice breakup in 2014 (R2 Resource Consultants
and LGL Alaska Research Associates 2014). During the 2014 field season (November 2013-
October 2014), a total of 2,004 PIT tags were implanted in nine different fish species in the
Middle River (Table 4.4-1). Coho Salmon were the most frequently tagged species (n=1,193),
followed by juvenile Chinook Salmon (n=349). A total of 236 in-hand recaptures of PIT tagged
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fish occurred in the Middle River in 2014 providing information on movements and growth
(Table 4.4-1).
Radio telemetry efforts for resident fish were focused on the Upper River in 2014, limited
tagging of Arctic Grayling (16) and Burbot (5) in the Middle River above Devils Canyon took
place in 2014 (Table 4.4-2). Many of the tags deployed in 2013 remained active during all or a
portion of 2014; depending on radio tag model and specifications, tag life ranged from 80 to over
900 days (IP Table 5.8-2). Using minimum tag life estimates, 135 of 158 tags released in the
Middle and Lower River in 2013 were anticipated to continue transmitting during a portion or all
of 2014. Aerial surveys were partitioned into mainstem Susitna and tributary zones (Study 9.6
ISR Part A, Appendix B, Figures B20 and B21). A target of 30 Arctic Grayling, Burbot, Dolly
Varden, Longnose Sucker, Northern Pike, Lake Trout, Rainbow Trout, Humpback Whitefish,
and Round Whitefish was set for radio-tagging during non-spawning periods. During 2013-
2014, target numbers for radio tagging in the Middle/Lower River study area were met for Arctic
Grayling (51) and Rainbow Trout (44) and nearly met for Longnose Sucker (28) and Round
Whitefish (21) (Table 4.4-2). Targets have not been reached for less abundant species, including
Lake Trout that have not been captured during any sampling in the Middle or Lower River.
Summary information for tags at large (Table 4.4-3) indicate how many fish were actively
tracked by month in the Middle/Lower River from January 2014 through June 2015.
4.4.2. Variances from Study Plan
The following variances from the Study Plan related to biotelemetry occurred in 2013 (ISR, Part
A, Section 4.5.3). These variances, which were also proposed as Study Plan modifications in
ISR, Part C, Section 7.1.2, were continued in 2014.
Because of channel size and configuration and power supply requirements, antennas
could not be arranged in a longitudinal series; instead, a single antenna system wasused at
most locations (Study 9.6 ISR Part A, Section 4.5.3.1).
AEA measured the read range antennas with 12 and 23 mm tags to determine the
detection efficiency of PIT tag interrogation systems (Study ISR, Part A, Section 4.5.3.1).
The timing of implantation of radio tags as recommended by FERC was not adopted
(SPD B-135). The timing of fish tagging was based on minimizing impact to individual
fish and in particular to pre-spawning fish (Study 9.6 ISR, Part A, 4.5.3.2).
The number of fixed telemetry stations and frequency of mobile surveys were adjusted as
reported in Study 9.6 ISR Part A, Section 4.1.7.4 and described previously in Sections 4.1.5.3
and 4.2.1 of this SIR. The increased frequency of mobile surveys more than compensated
for operating fewer fixed telemetry sites as it added more observations on seasonal timing
and distribution. These variances combined to enhance AEA’s ability to meet study
objectives for radio-telemetry.
For resident fish, manual tracking, directed searching, or identification of habitat type was
not conducted during the period when adult salmon were being tracked (Study 9.6 ISR Part
A, Section 4.5.3.3), but these activites were conducted during the period when adult salmon
tags were not present. This variance in aerial telemetry survey method did not effect meeting
the stated objectives of the radio-telemetry component of the study because the number and
accuracy of the geographic positions of the tags were sufficient to characterize the seasonal
distribution and timing of resident fish. Range testing of the mobile telemetry antenna
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array demonstrated that all sections of river would be scanned during a survey for each
frequency. Further, the increased occurrence of surveys during both periods of when
salmon were present and not present (relative to that proposed in the IP), provided a
higher likelihood to detect tags.
4.5. Objective 3: Early Life History
In 2014, the second complete year of salmon ELH sampling, AEA implemented the second complete
year of salmon ELH sampling methods for Objective 3 as described in the Study Plan with the
exception of the variances explained below in Section 4.5.5.
4.5.1. Task A: Describe emergence timing of salmonids.
In conjunction with the Intergravel Monitoring component of the Fish and Aquatics Instream
Flow Study (Study 8.5), salmon redds in selected side channels and sloughs were monitored on a
monthly basis throughout the winter in Focus Areas: FA-104 (Whiskers Slough), FA-128
(Slough 8A), FA-138 (Gold Creek), and FA-144 (Slough 21). Studies included monitoring of
surface and intergravel water temperatures and spawning substrate composition. This task was
conducted as part of the Fish and Aquatics Instream Flow Study (Study 8.5) with methods
presented in Study 8.5 ISR, Part A, Section 4.5.1.2.1.
4.5.2. Task B: Determine movement patterns and timing of juvenile salmonids
from spawning to rearing habitats.
Bi-weekly sampling to document the distribution of newly emerged salmon in select Focus
Areas occurred from breakup (May 3, 2014) through July 1. Six Focus Areas, FA-104 (Whiskers
Slough), FA- 113 (Oxbow 1), FA-128 (Slough 8A), FA-138 (Gold Creek), FA-141 (Indian
River), and FA-144 (Slough 21), met the criteria of having both spawning and rearing habitat
and were selected for sampling (Table 4.1-1). Electrofishing, seining, and Fyke nets, were the
methods for collecting Salmon during the early life stage sampling. Visual observations of
salmon fry were noted by field crews. Three sampling events took place mid-May through late
June as described above in Section 4.2.
4.5.3. Task C: Determine juvenile salmonid diurnal behavior over season.
In the Study Plan (RSP Section 9.6.4.3.3) AEA proposed that sampling schedules would
encompass daylight, twilight, and evening periods. In 2014, this was accomplished during the
winter by passive sampling techniques (underwater video, sonar imaging, minnow traps, fyke
nets, and PIT interrogation sites) during the night and crepuscular periods. During ELH, this was
accomplished by the use of active sampling techniques during the day and fyke netting
overnight.
4.5.4. Task D: Collect baseline data to support the Fish Stranding and
Trapping Study.
The focus of this task was to provide baseline distribution and abundance data to support the
stranding and trapping component of the Fish and Aquatics Instream Flow Study (Study 8.5).
Fish distribution sampling occurred at six Focus Areas FA-104 (Whiskers Slough), FA- 113
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(Oxbow 1), FA-128 (Slough 8A), FA-138 (Gold Creek), FA-141 (Indian River), and FA-144
(Slough 21), and at representative habitat units to identify seasonal timing, size, and distribution
among habitat types for fish (particularly less than 50 mm [2 in]). Electrofishing, seining, and
fyke nets, were the methods for collecting salmon fry.
4.5.5. Variances from Study Plan
During ELH sampling, large pulses of newly emerged salmon fry were frequently collected
during sampling in particular with fyke nets. In 2014, in order to manage large volumes of fish
(Table 5.2.1) while minimizing impacts and returning them to the stream in a safe and timely
manner, chum and sockeye fry were grouped together. To differentiate between the emergent fry
and early parr of these two species in the field when they co-occurred would have required
holding these fragile life stages in buckets for extended periods while handling every fish and it
is unnecessary to document habitats protective of early life history stages of salmon. This
variance will not affect AEA’s ability to meet objective 3.
4.6. Objective 4: Document Winter Movements and Timing and
Location of Spawning for Burbot, Humpback Whitefish, and
Round Whitefish
AEA implemented the methods for Objective 4 as described in the Study Plan. Radio tags were
surgically implanted in nine Burbot, seven Humpback Whitefish, and twenty-one Round
Whitefish in 2013. These individuals were tracked during the 2013-2014 winter period (Table
4.4-3). During the 2014 open water season, an additional five Burbot were tagged in the Middle
River above Devils Canyon and tracked during the 2014-2015 winter (Table 4.4-3).
4.7. Objective 5: Document the Seasonal Size/Life stage Structure,
Growth, and Condition of Juvenile Anadromous and Resident
Fish by Habitat Type
AEA implemented the methods for Objective 5 as described in the Study Plan with the exception
of the variances explained in Section 4.7.1. In conjunction with Objectives 1 and 3, captured fish
were identified to species and classified to life stage or smolt index when possible. A summary
of fish length-at-maturation for the region was used as a basis for assigning life stages (Table
4.7-1). Each time a gear was used for sampling, a random sample of 25 individuals per species,
life stage, and site were measured for fork length (FL) in mm and measured in grams. For
species without a forked tail (e.g., sculpin and Burbot), total length was measured laterally along
the mid-line from the anterior edge of the snout to the posterior edge of the tail. Total sample
sizes of fish measured for length and weight by Study Component are presented in Table 4.7-2.
Species were classified by life stage (Table 4.7-1) and when sample sizes were sufficient, natural
breaks in length-frequency were used to further refine size bins with an emphasis on anadromous
salmon less than 50 mm (2 in). Recaptured PIT-tagged fish (Objective 2 Task B) provided
growth information. The number of fish PIT-tagged and recaptured is presented in Table 4.4-1.
Parameters recorded in each habitat unit included the number of fish by species and life stage;
fork length; weight; global positioning system (GPS) location of sampling unit; time of
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sampling; weather conditions; water temperature; water transparency; behavior; and the location
and distribution of observations.
4.7.1. Variances from Study Plan
The following variances from the Study Plan occurred in 2013 (ISR, Part A, Section 4.8.1) and
are summarized below. These variances, which were also proposed as Study Plan modifications
in ISR, Part C, Section 7.1.2, were continued in 2014.
Each time sampling gear was checked, 25 individuals of each species and life stage
were randomly selected to be measured for length and weighed. The sample size of 25
measurements per species per life stage per site was consistent with collecting the data
necessary to evaluate length frequency distributions and condition factor for sampled fish
and will not affect AEA’s ability to meet objective 5 (Study 9.6 ISR Part C, Section
7.1.2.6.3).
Ages were not assigned based on fish length. The objective of documenting the
seasonal age-class structure of juvenile anadromous and resident fish by habitat type
(RSP Section 9.6.4.3.5) was replaced with documenting seasonal size-structure by
habitat type (ISR, Part A, Section 4.8.1). Evaluating habitat associations by size instead
of age will continue to meet the objective of documenting the seasonal life stage use,
growth, and condition of species by habitat type and will not affect AEA’s ability to meet
objective 5.
4.8. Objective 6: Document the Seasonal Distribution, Relative
Abundance, and Habitat Associations of Invasive Species
(Northern Pike)
Tracking of Northern Pike that had been radio tagged in 2013 continued in 2014; however, no
sampling for, or additional tagging occurred in the Lower River within the known distribution of the
species. Five Northern Pike were radio-tagged and tracked in the Lower River in 2013 and 2014
(Table 4.4-3).
4.8.1. Variances from Study Plan
Tagging and tracking target numbers (30) for Northern Pike were not met during the first study
year in the Middle/Lower River (Study 9.6 ISR Part A, Section 4.9). This study has completed
one of two years, based on their abundance, AEA anticipates tagging goals for Northern Pike
will be met in the next year of study. This 2014 variance is not anticipated to affect AEA’s
ability to document fish movements under Objective 4.
4.9. Objective 7: Collect Tissue Samples from Juvenile Salmon and
Resident and Non-Salmon Anadromous Fish
AEA implemented the methods for Objective 7 as described in the Study Plan. In support of the
Genetic Baseline Study for Selected Fish Species (Study 9.14), fish tissues were collected
opportunistically in conjunction with all fish capture events. The target species and number of
total samples were reported in the Study Implementation Report for Study 9.14. Tissue samples
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included an axillary process from all adult salmon, caudal fin clips and swab samples from fish
greater than 60 mm (2.4 in), and whole fish less than 60 mm (2.4 in). In 2014, genetic samples
from juvenile and adult Chinook salmon were collected opportunistically from locations between
Devils Canyon Impediment 1 and the proposed Watana Dam location. A summary of tissues
collected in 2014 for genetic baseline development and for species identification purposes as part
of this study is presented in Table 4.9-1.
In support of the River Productivity (Study 9.10) trophic modeling, scales, tissue samples, and
stomach contents of target species were collected opportunistically in conjunction with fish
capture events at select Focus Areas: FA-104 (Whiskers Slough), FA-141 (Indian River), FA-
173 (Stephan Lake Complex), and FA-184 (Watana Dam). A summary of fish collected for
stomach content sampling in 2014 is presented in Table 4.9-2.
4.9.1. Variances from Study Plan
In addition to tissue samples collected in support of the Genetic Baseline Study for Selected Fish
Species (Study 9.14) genetics samples of Coho Salmon and Chinook Salmon were collected in
the Middle River consistent with the species identification protocol filed with FERC in
November 2014 (R2 Resource Consultants 2014b) and to inform the accuracy and improvement
of species identification in the field (Table 4.9-1; Appendix B).
4.10. Winter Sampling Approach
Prior to developing recommendations for the winter 2013/2014 study efforts in the ISR (AEA
2014) and consistent with the Study Plan, AEA discussed a proposed approach and gathered
input from licensing participants at the Fish and Aquatic Resources Technical Work Group
Meetings on September 23 and December 4, 2013 (R2 Resource Consultants 2013a and 2013b)
and the Fisheries Technical Meeting March 20, 2014 (R2 Resource Consultants 2014c). Based
on licensing participant feedback, a review of existing information, and pilot study efforts, AEA
developed the following specific winter fish sampling objectives with the goal to increase
knowledge of the winter ecology of fish species in the Middle Susitna River (Study 9.6 ISR Part
A, Appendix C):
1) Describe overwintering habitat associations of juvenile anadromous salmonids,
non-salmonid anadromous fishes and resident fishes.
2) Describe winter movements of juvenile salmonids and selected fish species such
as Arctic grayling, burbot, Dolly Varden, lamprey, northern pike, rainbow trout,
humpback whitefish, and round whitefish within select Focus Areas.
a. Describe seasonal movements using biotelemetry
3) Describe early life history, timing, and movements of anadromous salmonids.
a. Determine juvenile salmonid diurnal behavior by season.
4) Document the seasonal age class structure, growth, and condition of juvenile
anadromous and resident fish by habitat type.
5) Collect tissue samples from juvenile salmon and opportunistically from all
resident and non-salmon anadromous fish to support the Fish Genetic Baseline
Study (Study 9.14).
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To the extent practical based on ice conditions, sampling took place at the same stratified
macrohabitat locations randomly selected using the GRTS method for the fish distribution and
abundance sampling conducted July through October 2013. Each sampling event included
sampling in three replicate sites of each off-channel macrohabitat type within each of the three
Focus Areas: FA-104 (Whiskers Slough), FA-128 (Slough 8A), and FA-138 (Gold Creek) (R2
Resource Consultants and LGL Alaska Research Associates 2014). Each 200 m (656 ft) GRTS
panel was evaluated, beginning at the downstream end, to determine if a 40 m (131 ft) segment
had conditions suitable for sampling. Other satellite locations outside of GRTS panels at FA-141
(Indian River) were sampled opportunistically (R2 Resource Consultants and LGL Alaska
Research Associates 2014).
4.10.1. Variances from Study Plan
In the technical memorandum describing the winter fish study (Study 9.6 ISR Part A, Appendix
C), AEA indicated that sampling would not occur during the window of ice formation and
extremely short photoperiod between November and January. Extremely low flows and very
cold temperatures in November 2013 allowed for a limited duration sampling effort during early
winter. This additional sampling will increase knowledge regarding winter habitat use by fish in
the Middle River and will enhance AEA’s ability to meet winter fish studies objectives.
4.11. Fish Sampling Techniques
A combination of gillnet, electrofishing, angling, trot lines, minnow trapping, hoop trapping,
snorkeling, fishwheels, beach seining, and fyke netting techniques were used to sample or
observe fish in the Middle River, and those fish moving in and out of selected sloughs and
tributaries flowing into the Susitna River. Techniques used at a sampling site varied based on
habitat characteristics, season, and target species/life stage. All fish sampling and handling
techniques described within this study were selected in consultation with state and federal
regulatory agencies and sampling has been conducted under state collection permits. Limitations
on the use of some methods during particular time periods or locations (e.g., no electrofishing
when adult salmon are present) played a role in the selection of sampling techniques. Study
efforts in 2014 followed the gear specifications and descriptions of field application outlined in
the IP (AEA 2013) and supplemented by an updated version of IP Appendix 3, additional
guidance for gear selection (R2 Resource Consultants 2014a).
4.11.1. Fish Handling
Fish handling was done as described in the IP (AEA 2013). All captured or observed fish were
identified to species and life stage when possible. During ELH sampling it was not uncommon
to catch hundreds of newly emerged fry at a site. To quickly process and return fish to the water,
small Sockeye Salmon and Chum Salmon, very similar in appearance, were grouped together for
rapid count estimates. Following the 2014 field season, a Chinook and Coho Salmon
identification protocol was developed to address the wide range of phenotypic variation
encountered by field crews (R2 2014b).
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4.11.2. Winter Sampling Techniques
Multiple fish sampling techniques were utilized to sample multiple fish species, life stages,
habitat types, and various ice conditions. Sampling methods included minnow traps, backpack
electrofishing, fyke nets, trotlines/setlines, sonar and underwater video (R2 Resource Consultants
and LGL Alaska Research Associates 2014). Two techniques were typically used at each site to
sample a diversity of species and life stages. Because sampling efforts occurred in both open-
water leads and ice-covered sites, methods varied depending on conditions (ice coverage, ice
thickness, depth, velocity, and conductivity). In ice-covered sites, sampling methods included
setlines, trotlines, minnow traps, and underwater video. In open-water sites, methods included
baited minnow traps, trotlines, electrofishing, and fyke nets. To characterize diel behavior, in
addition to overnight minnow trapping and fyke netting, a select subset of sites sampled during
the day (three to four per Focus Area) were revisited during the night and sampled by
electrofishing. Night sampling sites were selected based on safe ice conditions and proximity to
winter spike camps.
5. RESULTS
Analysis of data collected in 2014 is not a component of this Study Implementation Report.
Some very general results in terms of counts and observations are presented in this section. Data
developed in support of the 2014 SIR is available for download at: http://gis.suhydro.org/SIR/09-
Fish_and_Aquatics/9.6-Fish_Dist_and_Abund_Mid_Lower_Susitna/.
5.1. Objective 1: Fish Distribution, Relative Abundance, and Habitat
Associations
5.1.1. Task A: Fish Distribution
In 2014, seventeen fish species were documented in the Middle Susitna River (Table 5.1-1).
Consistent with 2013, Northern Pike were not observed in Middle River collections (Tables 5.1-
1 and 5.1-2). Eighteen fish species were documented in the Middle and Lower Susitna River
study area over both the 2013 and 2014 study seasons (Table 5.1-1). These species include all
five of the North American Pacific Salmon species (i.e., Chinook, Chum, Coho, Pink, and
Sockeye Salmon), six other salmonid species (i.e., Arctic Grayling, Dolly Varden, Rainbow
Trout, Bering Cisco, and Humpback and Round Whitefish), and seven non-salmonid species
(i.e., Burbot, lamprey, Longnose Sucker, Northern Pike, sculpin, and Ninespine and Threespine
Stickleback). Sculpin and lamprey were not always identified to the species level during field
surveys; therefore, they are reported herein as sculpin and lamprey spp. Furthermore, when
sculpin and lamprey were identified to species, identifications were limited to Slimy Sculpin and
Arctic Lamprey, respectively.
The accuracy of field identification of Chinook and Coho salmon in 2014 was improved to
approximately 95% with photo QC (Appendix B). However, given the uncertainty associate with
Coho Salmon identifications in some Middle River habitats, AEA will combine data collected on
Chinook and Coho salmon from 2013 and 2014 collections to characterize the distribution,
relative abundance and habitat associations of these two juvenile salmon species. Where
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appropriate, AEA also will make use of the verified species identifications to look for species-
specific patterns in growth and movements. Futher discussion of the 2013 Coho Salmon
identification issue and management implications is presented in Appendix B.
Within the Middle River study area, Devils Canyon (i.e., Geomorphic Reaches MR-3 and MR-
4), and more specifically Impediment 1 (PRM 155.1) appeared to limit the distribution of several
resident and juvenile anadromous fish species (Table 5.1-1). While 18 species have been
documented within the Middle and Lower River study area downstream of Devils Canyon, only
eight species (i.e., Chinook Salmon, Arctic Grayling, Burbot, Dolly Varden, Longnose Sucker,
Rainbow Trout, sculpin, and Round Whitefish) have been documented upstream of Impediment
1 (PRM 155.1) within Devils Canyon. Although Humpback Whitefish were not observed in
MR-1 or MR-2, they were documented in the Upper River study area (ISR Study 9.5 Section
5.1.1). Four fish species, Chum, Chinook, Coho, and Sockeye salmon, have been documented in
MR-5 immediately downstream of Devils Canyon (PRM 155.1) and are widespread in the
Middle River below the Devils Canyon and the Lower River (Table 5.1-1). The most notable
Middle Susitna River fish distribution findings in 2014 were:
(1) The presence of a single Ninespine Stickleback in Whiskers Creek (MR-8) expanding the
range of the species upstream and into the Middle River;
(2) The presence of Bering Cisco at PRM 122.6 (MR-7) during gill net sampling under the
Salmon Escapement Study (9.7), expanding the range of this anadromous species
upstream and into the Middle River;
(3) The documentation of juvenile Chinook Salmon at new locations in the Middle River
above Devils Canyon including lower Unnamed Tributary 184 and Geomorphic Reach
MR-1 immediately below the proposed Watana Dam site.
(4) The observation of a single Rainbow Trout in Devil Creek (FDA-MR4-DEV-DIR2). The
individual had presumably dispersed from High Lake which drains into Devil Creek at
RM 2.2 near where the observation took place (Appendix A). High Lake is reported by
locals as containing a good fishery for rainbow trout (http://www.highlakelodge.com).
Rainbow Trout were not previously known to be present in the Susitna River basin
within or above Devils Canyon. Devil Creek joins the Susitna River in Devils Canyon
just upstream of anadromous salmon Impediment 3 (PRM 164.7).
5.1.2. Task B: Relative Abundance
Fish observations from three seasonal fish distribution and abundance sampling events in the
Middle River totaled 7,898 fish (Table 5.1-2). These data will be used for future estimates of
relative abundance and species-habitat associations.
5.2. Objective 3: Early Life History
A combination of juvenile anadromous and resident fish species were captured during three ELH
sampling events between May and June, 2014 (Table 5.2-1). Juvenile Pacific salmon were
abundant in Focus Area sites, especially newly emerged Coho, Chinook, and Chum/Sockeye
salmon fry (Table 5.2-1). Salmon fry were most numerous in the following locations: 1) FA –
104 (Whiskers Creek), site ELH-104-Spawning 2; 2) FA-128 (Slough 8A), site ELH-128-
Rearing 2; 3) Slough 11, site ELH-138-Spawning 1; 4) FA-141 (Indian River), site ELH-141-
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Spawning 1; and 5) Slough 20, site ELH-144-Rearing 1 (Appendix A). Catch of resident fishes
primarily consisted of Longnose Sucker, sculpin, and Threespine Stickleback (Table 5.2-1).
Other species present in lower numbers included Arctic Grayling, Arctic Lamprey, Burbot, Dolly
Varden, Rainbow Trout, Ninespine Stickleback, Humpback Whitefish, and Round Whitefish
(Table 5.2-1).
Although AEA was not able to document precise emergence timing, evidence about emergence
timing was collected for all five Pacific salmon species. While, a few Chum/Sockeye salmon
alevin were documented in mid-March during the Winter Fish Study (R2 Resource Consultants
and LGL Alaska Research Associates 2014), Coho, Pink and Chum/Sockeye Salmon alevin were
also collected during the first ELH sampling event in mid-May (Table 5.2-1).
5.3. Objective 4: Document winter movements and timing and
location of spawning for Burbot, Humpback Whitefish, and
Round Whitefish.
Documentation of winter movements and spawning locations for Burbot, Humpback Whitefish,
and Round Whitefish occurred during the 2013-2014 winter; three Burbot, and eleven Round
Whitefish had active tags and were alive in the Middle and Lower River study area in November
2013 (Table 4.4-3). Additionally, five Burbot and fifteen Round Whitefish tagged in the Upper
River study area were alive with active tags in November 2013. Ongoing efforts, including
analysis of aerial survey data will be used to address this objective.
5.4. Objective 6: Document the seasonal distribution, relative
abundance, and habitat associations of invasive species
(Northern Pike).
No Northern Pike were collected in 2014. Northern Pike radio tagged in 2013 were tracked in
2014 and 2015 (Table 4.4-3).
5.5. Objective 7: Collect tissue samples from juvenile salmon and
all resident and non-salmon anadromous fish.
Fish tissues were collected opportunistically in conjunction with all fish capture events in
support of the Fish Genetic Baseline Study (Study 9.14). Tissue samples consisted of an axillary
process of the pelvic fin from all adult salmon, caudal fin clips from fish greater than 60 mm (2.4
in), and whole fish less than 60 mm (2.4 in). A summary of fish collected for genetic baseline
development and for identification purposes (R2 2014b) as part of this study is presented in
Table 4.9-1.
6. DISCUSSION
The current status of the Study of Fish Distribution and Abundance in the Mi ddle and Lower
Susitna River is ongoing. As indicated in Section 4, tasks associated with each of the seven
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study objectives were initiated in 2013. The 2014 study year was focused on the following study
components:
(1) Completion of the first full year of Winter Fish Studies (R2 Resource Consultants and
LGL Alaska Research Associates 2014);
(2) Completion of a second year of study under Salmon Early Life History (Objective 3);
(3) Continuation of radio telemetry tracking of resident fish tagged in 2013, with limited
tagging effort taking place in the Middle River above Devils Canyon (Objective 2b);
(4) Fish Distribution and Abundance sampling at sites that were not sampled, or only
partially sampled, in 2013 due to land access restrictions. Sampling in 2014 was intended
to complete the first year of data collection under Objective 1;
(5) Development of a standardized identification protocol for Chinook and Coho salmon and
field guide specific to the Susitna River (R2 2014b).
Data from 2013 and 2014 will be combined with a second year of study for a comprehensive
baseline description in the Updated Study Report and impact analysis.
7. CONCLUSION
In 2014, AEA continued to conduct baseline documentation studies of fish distribution and
abundance in the Middle and Lower Susitna River. The field work, data collection, data
analysis, and reporting for the Study of Fish Distribution and Abundance in the Middle and
Lower Susitna River has provided data pertinent to addressing all study objectives in the FERC-
approved Study Plan. With this 2014 report, AEA has now completed at least the first year of
data collection for all study objectives for the Study of Fish Distribution and Abundance in the
Middle and Lower Susitna River. The Salmon Early Life History Sampling under Objective 3
and radio telemetry under Objective 2b are exceptions to the previous statement. ELH has
completed two full years of sampling while and radio telemetry has completed one year of
tagging and two years of data collection on tracking. AEA expects that with the continued
execution of the Study Plan with variances noted, will result in fully meeting all study objectives
and provide data needed for impact assessment.
7.1. Modifications to Study Plan
AEA plans to implement the modifications identified in the Study 9.6 ISR, Part C, Section 7.1.2.
In addition, AEA proposes the following two modifications to the Study Plan.
1) AEA plans to collect additional tissue samples for genetic analysis and to implement the
Chinook and Coho salmon identification protocol as presented in R2 Resource Consultants
(2014b).
2) AEA plans to minimize handling impacts to newly emerged fry and small parr during future
winter or early spring sampling. When large numbers of individual fish are collected in samples
a sub-sample of 100 individuals from the collection will be identified to species, while the
remaining fish will be grouped by guild for example Sockeye/Chum or Coho/Chinook.
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8. LITERATURE CITED
Adams, F.J. 1999. Status of rainbow trout in tributaries of the upper King Salmon River, Becharof
National Wildlife Refuge, Alaska, 1990-92. U.S. Fish and Wildlife Service, Alaska Fisheries
Technical Report Number 53, King Salmon, Alaska.
Alaska Department of Fish and Game (ADF&G). 1981. APA Report 318, Subtask 7.10. Phase 1,
Final draft report. Resident fish investigation on the lower Susitna River. Anchorage, AK.
99503.
ADF&G. 1982. Aquatic Studies Procedures Manual: Phase I. Prepared by Alaska Department of Fish
and Game, Su-Hydro Aquatic Studies Program. Prepared for Alaska Power Authority,
Anchorage, Alaska. pp 111.
ADF&G. 2012. Anadromous Waters Catalog. http://www.sf.adfg.state.ak.us/SARR/AWC/index.cfm.
Accessed December 2012.
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.
Alaska Energy Authority (AEA). 2013. Final Susitna River Fish Distribution and Abundance
Implementation Plan: Susitna-Watana Hydroelectric Project FERC Project No. 14241. March
2013. Prepared for the Federal Energy Regulatory Commission by the Alaska Energy
Authority, Anchorage, Alaska. http://www.susitna-watanahydro.org/wp-
content/uploads/2013/03/Attachment-A.pdf.
Alaska Energy Authority. 2014. Initial Study Report, Study of Fish Distribution and Abundance in
the Middle and Lower Susitna River, Study Plan Section 9.6. Susitna-Watana Hydroelectric
Project, FERC Project No. 14241. June 2014. Anchorage, Alaska. http://www.susitna-
watanahydro.org/type/documents.
Burr, 1993. Maturity of lake trout from eleven lakes in Alaska. Northwest Science, Vol 67, No. 2,
1993. Connolly, P.J., I.G. Jezorek, K.D. Martens, and E.F. Prentice. 2008. Measuring the
Performance of Two Stationary Interrogation Systems for Detecting Downstream and
Upstream Movement of PIT-Tagged Salmonids. North American Journal of Fisheries
Management 28:402-417.
Delaney, K., D. Crawford, L. Dugan, S. Hale, K Kuntz, B. Marshall, J. Mauney, J. Quinn, K.
Roth, P Suchanek, R. Sundet, and M. Stratton. 1981. Resident Fish Investigation on the
Lower Susitna River. Prepared by Alaska Department of Fish and Game, Susitna Hydro
Aquatic Studies. Prepared for Alaska Power Authority, Anchorage, AK. 311 pp.
STUDY IMPLEMENTATION REPORT STUDY OF FISH DISTRIBUTION AND ABUNDANCE IN THE
MIDDLE AND LOWER SUSITNA RIVER (STUDY 9.6)
Susitna-Watana Hydroelectric Project Alaska Energy Authority
FERC Project No. 14241 Page 21 November 2015
Docker, M. F. 2009. A review of the evolution of nonparasitism in lampreys and an update of the
paired species concept. Pages 71-114 in L. R. Brown, S. D. Chase, M. G. Mesa, R. J.
Beamish, and P. B. Moyle, editors. Biology, management, and conservation of lampreys in
North America, American Fisheries Society Symposium 72. American Fisheries Society,
Bethesda, MD.Dolloff, C.A., D.G. Hankin, and G.H Reeves. 1993. Basinwide Estimation of
Habitat and Fish Populations in Streams. USDA Forest Service General Technical Report
SE-GTR-83. pp 25.
HDR, Inc and LGL. 2014. Eulachon Run Timing, Distribution, and Spawning in the Susitna
River. Initial Study Report. Prepared for Alaska Energy Authority. Susitna-Watana
Hydroelectric Project (FERC No. p-14241).
Heard, W. R. 1966. Observations on lampreys in the Naknek River System of Southwest
Alaska.Copeia 1966(2):332-339.
National Marine Fisheries Service (NMFS). 2014. National Marine Fisheries Service Comments
on the Initial Study Report for the Susitna-Watana Hydroelectric Project, FERC Project
No. 14241. Filed with the FERC September 22, 2014.
R2 Resource Consultants, Inc. 2013a. Fish Distribution and Abundance in the Middle and Lower
Susitna River: Winter Studies. PowerPoint Presentation, Technical Workgroup meeting
on September 23, 2013. Prepared for Alaska Energy Authority, Anchorage, Alaska.
Susitna-Watana Hydroelectric Project, FERC no. P-14241. http://www.susitna-
watanahydro.org/wp
content/uploads/2013/09/RSP9.6_FDA_Winter_2013_09_23_TWG.pdf
R2 Resource Consultants, Inc. 2013b. Fish and Aquatic Resources. PowerPoint Presentation,
Technical Workgroup meeting on December 4, 2013. Prepared for Alaska Energy
Authority, Anchorage, Alaska. Susitna-Watana Hydroelectric Project, FERC no. P-
14241. http://www.susitna-watanahydro.org/wp-content/uploads/2013/11/
FishandAquaticsDecTWG.pdf
R2 Resource Consultants, Inc. 2014a. Susitna River Fish Distribution and Abundance
Implementation Plan: Appendix 3. Protocol for Site-Specific Gear Type Selection;
Version 5. Susitna-Watana Hydroelectric Project. November 2014.
R2 Resource Consultants, Inc. 2014b Fish Distribution and Abundance in the Upper and
Middle/Lower Susitna River (Studies 9.5 and 9.6): Draft Chinook and Coho Salmon
Identification Protocol. Susitna-Watana Hydroelectric Project. November 2014.
R2 Resource Consultants, Inc. 2014c. Fish and Aquatic Resources. Winter Studies PowerPoint
Presentation, Technical Workgroup meeting on March 20, 2014. Prepared for Alaska
Energy Authority, Anchorage, Alaska. Susitna-Watana Hydroelectric Project, FERC no.
P-14241. http://www.susitna-watanahydro.org/wp-content/uploads/2014/03/2014-03-
20TT_FDA_ML_WinterPresentation.pdf
STUDY IMPLEMENTATION REPORT STUDY OF FISH DISTRIBUTION AND ABUNDANCE IN THE
MIDDLE AND LOWER SUSITNA RIVER (STUDY 9.6)
Susitna-Watana Hydroelectric Project Alaska Energy Authority
FERC Project No. 14241 Page 22 November 2015
R2 Resource Consultants Inc. & LGL Alaska Research Associates, Inc. 2014. 2013-2014 Winter
Fish Study Technical Memorandum. Susitna-Watana Hydroelectric Project. September
2014.
R2 Resource Consultants Inc. 2015. 2014 Year-End Completion Report for Study of Fish
Distribution and Abundance in the Upper Susitna River. Technical Memorandum for
Alaska Energy Authority. Susitna-Watana Hydroelectric Project. November 2015.
Russell, R. 1977. Rainbow trout life history studies, in the lower Talarik Creek-Kvichak Drainage.
Alaska Department of Fish and Game, Completion Report, D-J Study G-II-E, Juneau, AK.
U.S. Fish and Wildlife Service (USFWS). 2014. Comments on the Initial Study Report for the
Susitna-Watana Hydroelectric Project, FERC Project No. 14241. Filed with the FERC
September 22, 2014.
Vladykov, V. D., and E. Kott. 1978. A new nonparasitic species of the holarctic lamprey genus
Lethenteron Creaser and Hubbs, 1922 (Petromyzontidae) from northwestern North America
with notes on other species of the same genus. University of Alaska, Fairbanks, AK.
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9. TABLES
Table 2-1. Methods by objective, task, species, and life stage, 2014.
Obj Task
Species/
Life Stage Study Sites Methods Used by Season
1A Distribution and Relative
Abundance
Juvenile Salmon,
non-salmon
anadromous,
resident
Focus Areas +
representative
habitat types
Ice Free Season:
Single pass sampling
Selection of methods will be site-specific, species-specific, and life-stage-specific.
For juvenile and small fish sampling, electrofishing, snorkeling, seining, Fyke nets,
and angling where feasible and appropriate.
For adults, directed efforts with seines, gillnets, trot lines, and angling.
To the extent possible, the selected transects will be standardized and the methods
will be repeated during each sampling period at a specific site to evaluate temporal
changes in fish distribution.
Additional info from radio telemetry studies (Objective #2).
Select Focus
Areas
(accessible)
Winter:
Based on winter 2012-2013 pilot studies
Sonar Imaging, underwater video, minnow traps, e-fishing, fyke netting, and trot
lines.
1B Fish habitat associations Juvenile Salmon,
non-salmon
anadromous,
resident
Focus Area study
sites+
representative
habitat types
Analysis of data collected under Objective 1: Distribution. Combination of fish
presence, distribution, and density by mesohabitat type by season.
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Obj Task
Species/
Life Stage Study Sites Methods Used by Season
2 Describe seasonal
movements using
biotelemetry (PIT and radio
tags)
All species Ice-Free Season:
PIT tags: tags opportunistically implanted in target species from a variety of capture
methods in Focus Areas.
Radio tags surgically implanted in up to 30 individuals of sufficient body size of each
target species distributed temporally and longitudinally. .
Winter:
Based on winter 2012-2013 pilot studies.
DIDSON, video camera, minnow traps, electrofishing, seines and trot lines.
PIT arrays at Montana Creek, FA-104, and FA-128
Aerial tracking of radio tags (adults).
3A Describe emergence timing
of salmonids
Juvenile salmonids Select Focus
Areas
Bi-weekly sampling using fyke nets, seines, electrofishing and minnow traps in
Salmon spawning and rearing areas within Focus Areas.
3B Determine movement
patterns and timing of
juvenile salmonids from
spawning to rearing habitats
Juvenile salmonids Focus Areas Focus on timing of emergence and movement of newly emergent fish from spawning
to rearing areas or movement of juvenile fish <50 mm in winter (i.e., the post-
emergent life stages most vulnerable to load-following operations)
DIDSON or underwater video to monitor movement into or out of specific habitats
3C Determine juvenile salmonid
diurnal behavior by season
Juvenile salmonids Focus Areas Stratified time of day sampling to determine whether fish are more active day/night
DIDSON and/or video camera methods to observe fish activity
Potentially electrofishing and seining
3D Collect baseline data to
support the Stranding and
Trapping Study
Focus Areas +
supplement with
additional
representative
habitat types as
necessary.
Opportunistic support to ID seasonal timing, size and distribution among habitat
types for fish <50 mm in length.
Estimate presence/absence, relative abundance, and density using similar methods
as Objectives 1A, 1B, 1C, and 2 for fish <50 mm
Focus on slough and other mainstem lateral habitats
DIDSON, video camera, electrofishing, seines, out-migrant traps and fyke nets.
Monthly measurements of fish size/ growth
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Obj Task
Species/
Life Stage Study Sites Methods Used by Season
4 Winter movements, timing,
and location of spawning
Burbot, Humpback
Whitefish, and
Round Whitefish
Mainstem
habitats
Radio tags surgically implanted in up to 30 fish of sufficient body size of each
species distributed temporally & longitudinally.
To capture Burbot for radio-tagging, use hoop traps late Aug-early Oct following
methods by Evenson (1993).
To capture whitefish for radio-tagging, use fish wheels opportunistically and directed
efforts including angling, seines & gillnets.
Use aerial tracking of radio tags to pinpoint winter aggregations of fish; sample these
areas with trot lines (similar to 1980s).
Collect, examine, and preserve gonads to determine spawning status.
5 Document growth, and
condition by season
juvenile
anadromous and
resident fish
Focus Area study
sites+
representative
habitat types
Stock biology measurements- length from captured fish up to 100 individuals per
season per species per life stage and up to 30 fish per month per species per habitat
type in Focus Areas.
Emphasis placed on juvenile salmonids <50mm.
Opportunistically support Stranding and Trapping Study
6 Seasonal presence/absence
and habitat associations of
invasive species
Northern Pike All study sites Same methods as #1 and #2 above.
The presence/absence of Northern Pike and other invasive fish species will be
documented in all samples
Additional direct efforts with angling as necessary
7 Collect tissue samples to
support the Genetic
Baseline Study
All All study sites in
which fish are
handled
Opportunistic collections in conjunction with all capture methods listed above.
Tissue samples include axillary process from all adult Salmon, caudal fin clips from
fish >60 mm, and whole fish <60 mm.
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Table 4.1-1 Salmon early life history sampling effort, 2014. (Maps of sampling locations in Appendix A)
Location
ELH Event 1 ELH Event 2 ELH Event 3
Start Date End Date Start Date End Date Start Date End Date
5/19/2014 5/26/2014 6/2/2014 6/9/2014 6/18/2014 6/25/2014
Number of Sites Number of Sites Number of Sites
Middle River
Devils Canyon (PRM 153.9-169.6)
FA-144 (Slough 21) 6 6 6
FA-141(Indian River) 6 6 6
FA-138 (Gold Creek) 6 6 6
FA-128 (Slough 8A) 6 6 6
FA-113 (Oxbow I) 6 6 6
FA-104 (Whiskers Slough) 6 6 6
Grand Total 36 36 36
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Table 4.1-2. Direct tributary sampling effort for fish distribution in the Middle River above Devils Canyon by geomorphic reach, 2013 and 2014. (Maps of sampling
locations in Appendix A). The lower portions of Tsusena Creek and Chinook Creek could not be accessed in 2013 and were repeat sampled in 2014.
Target Tributary Geomorphic
Reach PRM
Listed
in
AWC
Average
Wetted
Width
(m)
Drainage
Basin
Area
(km2)
Sample
Type
Number
of Sites
2013
Meters
Sampled
2013
Number
of Sites
2014
Meters
Sampled
2014
Watana Dam (PRM 187.1)
Tsusena Creek MR-2 184.6 No 30.7 374.3 Direct 2 200 8 709
Unnamed Tributary MR-2 184 No 15.1 NA Direct - 4 287
Fog Creek MR-2 179.3 Yes 9 381.2 Direct 5 231 - -
Fog Trib MR-2 N/A Yes NA NA Direct 6 417 - -
Devils Creek MR-4 164.8 No 21.2 190.6 Direct - 6 554
Impediment 3 Devils Canyon (PRM 164.7)
Chinook Creek MR-4 160.5 Yes 12.3 58.3 Direct 2 200 5 426
Cheechako Creek MR-4 155.9 Yes 15.9 94.3 Direct - 4 221
Impediment 1 Devils Canyon (PRM 155.1)
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Table 4.1-3. Habitat types and number of sites sampled for distribution and relative abundance sampling in the Middle River, 2013 and 2014.
Focus
Stratum Habitat Stratum
Geomorphic Reach Total MR-1 MR-2 MR-5 MR-6 MR-7d MR-8
Targeted Sampled Targeted Sampled Targeted Sampled Targeted Sampled Targeted Sampled Targeted Sampled Targeted Sampled
Focus Areas
Main Channel 3 2 3 3 2e 2 (1g) 3 1 3 1 3 3
17 17 Split Main Channelf 1 1 1
Multi-Split Main Channelf 1 1
Side Channel 2e 2 3 3 3 3 3 3 3 3 14 14
Side Slough 3 3 3b 1b 3 3
12 12 Side Slough Beaver
Complex 3 5c
Upland Slough 3 0a (3) 3 3 3b 1b 3b
18 18 Upland Slough Beaver
Complex 3 3 3d 5c 3c
Backwater 1 1 1 2 2 (1g) 3 4
Tributary 1 0a (1) 1 0a (1) 2 2 (1g) 3d 3 (2g) 1 1 8 8
Tributary Mouth 1 1 1 0a (1) 2 2 1d 1 5 5
Clearwater Plume 1 1 1 (1g) 1 1 1 2 4
Subtotal Focus Areas 5 5 14 16 5 5 24 24 18 19 13 13 79 82
Non Focus
Areas
Main Channel 3 3 3 1 (1) 3 2 3 3 3 1 3 2
18 18 Split Main Channelf 1 1 2 1
Multi-Split Main Channelf
Side Channel 1e 1 3 3 3 3 3 3 3 3 13 13
Side Slough 3 3 3 3 3 3 3 3 3 3
18 18 Side Slough Beaver
Complex 3 3
Upland Slough 3 0a (3) 3 2a (1) 3 1b 3 3
18 18 Upland Slough Beaver
Complex 3 3 3 5c
Backwater 1 1 3 3 1 1 1 1 6 6
Tributary 3 0a (3) 3 2a (1) 3 3 (1g) 9 9
Tributary Mouth 3 2 (1) 1 0a(1) 3 3 2d 2 9 9
Clearwater Plume 3 3 (1) (1) 3 2 (1) 1 1 7 9
Subtotal Non-Focus
Areas 4 4 22 23 7 8 27 27 25 25 13 13 98 100
Total number of sampling sites 9 9 36 39 12 13 51 51 43 44 26 26 177 182
Notes:
a site not accessible in 2013 to sample CIRI Lands or Alaska Railroad Corporation.
b Sloughs w/o Beaver Complexes were found upon visitation to support beaver activity and were reclassified.
c Sloughs with Beaver Complexes were added due to observed beaver activity in classified Upland Sloughs or Side Sloughs w/o Beaver Complexes.
d number of target sites per strata modified from IP table 5.3-1 with inclusion of FA-113 in MR-7, May 2013.
e number of target sites modified from IP Table 5.3-1 due to sample unit length increases.
f This strata combined into Main Channel for sites selection purposes.
g Site re-sampled in 2014 due to partial sample in 2013 (land access).
() sites in parenthesis were sampled in 2014.
STUDY IMPLEMENTATION REPORT STUDY OF FISH DISTRIBUTION AND ABUNDANCE IN THE
MIDDLE AND LOWER SUSITNA RIVER (STUDY 9.6)
Susitna-Watana Hydroelectric Project Alaska Energy Authority
FERC Project No. 14241 Page 29 November 2015
Table 4.1-4. Sites sampled for fish distribution and abundance in the Middle Susitna River by season, 2014 (Maps of
sampling locations in Appendix A).
Sample Type SITE ID Early Summer Late Summer Fall Total Samples
GRTS Sample Selection
Watana Dam Site (PRM 187.1)
FDA-MR2-184-NF3-Trib* X X X 3
FDA-MR2-184-P12-MC X X X 3
FDA-MR2-182-P112-CWP X X X 3
FDA-MR2-182-P112-TM X X X 3
FDA-MR2-181-NF6-TRIB X X X 3
FDA-MR2-178-P20-US X X F 2
FDA-MR2-176-P21-US X D F 1
FDA-MR2-176-P22-US X X F 2
FDA-MR2-175-NF4-TRIB X X X 3
FDA-MR2-173-P19-TRIB X X X 3
FDA-MR2-173-P21-US X X X 3
FDA-MR2-173-P22-US X X F 2
FDA-MR2-173-P23-US X X F 2
Impediment 1 (PRM 155.1) - Impediment 3 (PRM 164.7) Devils Canyon
FDA-MR5-153-P55-CWP NS X X 2
FDA-MR5-153-P55-TM X X X 3
FDA-MR5-151-P25-MC NS X X 2
FDA-MR5-151-P46-CWP X X X 3
FDA-MR5-151-P49-TRIB X X X 3
FDA-MR5-151-P50-TM X X X 3
FDA-MR6-148-NF2-Trib NS X X 2
FDA-MR6-143-PO62-US NS X X 2
FDA-MR6-130-P086-CWP NS X X 2
FDA-MR6-128-P73-TRIB NS X X 2
FDA-MR7-115-P176-TRIB NS X X 2
FDA-MR7-115-P2-BW NS X X 2
FDA-MR7-113-P143-TRIB NS X X 2
FDA-MR7-110-NFOS1-TRIB NS X X 2
Direct Sample Tributary
Watana Dam Site (PRM 187.1)
FDA-MR2-TSU-DIR1 X X X 3
FDA-MR2-TSU-DIR2 X X X 3
FDA-MR2-TSU-DIR3 X X X 3
FDA-MR2-TSU-DIR4 X X X 3
FDA-MR2-184-DIR1* X X X 3
FDA-MR2-184-DIR2 X X X 3
FDA-MR2-184-DIR3 X X X 3
FDA-MR2-184-DIR4 X X X 3
FDA-MR4-DEV-DIR1 NS X X 2
FDA-MR4-DEV-DIR2 NS X I 1
FDA-MR4-DEV-DIR3 NS X X 2
Impediment 3 Devils Canyon (PRM 164.7
FDA-MR4-CHI-DIR1 NS X X 2
FDA-MR4-CHI-DIR2 NS X X 2
FDA-MR4-CHI-DIR3 NS X X 2
FDA-MR4-CHI-DIR4 NS X X 2
FDA-MR4-CHE-DIR1 NS X X 2
FDA-MR4-CHE-DIR2 NS X I 1
FDA-MR4-CHE-DIR3 NS X I 1
Impediment 1 Devils Canyon (PRM 155.1)
Total Sites Sampled 24 43 36 103
Notes:
NS: not sampled, D: dry site, F: frozen site, I: inaccessible site
* Designates the same site that applies to both GRTS and Direct Sample Tributary
STUDY IMPLEMENTATION REPORT STUDY OF FISH DISTRIBUTION AND ABUNDANCE IN THE
MIDDLE AND LOWER SUSITNA RIVER (STUDY 9.6)
Susitna-Watana Hydroelectric Project Alaska Energy Authority
FERC Project No. 14241 Page 30 November 2015
Table 4.1-5. Antenna orientation for fixed telemetry receiver stations in the Middle and Upper Susitna River, 2014.
Station PRM Install
Date
Removal
Date
Antenna Orientation
Rationale Antenna 1 Antenna
2 Antenna 3
Lower River
Montana
Creek weir NA - -
Down
Montana
Creek
Up
Montana
Creek
Salmon spawning stream
Susitna River
at Sunshine 83 - - Down
Susitna
Up
Susitna Monitor fish in the Lower River
Talkeetna
River NA - -
Down
Talkeetna
River
Up
Talkeetna
River
Salmon spawning stream
Middle River
Lane Creek 116.8 May
10 Oct 3 Down
Susitna
Up
Susitna
Across
Susitna
Monitor for Curry tagged fish
moving downstream; Monitor
for Lower River tagged fish
moving into Middle River
Gateway 130.1 Jun
14 Sep 23 Down
Susitna
Up
Susitna Monitor for Curry tagged fish
moving upstream
Indian River 142.1 May 2 Oct 28 Down
Susitna
Up
Susitna
Up Indian
River Salmon spawning stream
Impediment 1 Devils Canyon (PRM 155.1)
Cheechako
Creek 157.4 Jun
13 Oct 9 Down
Susitna
Up
Susitna Monitor site for fish passing
above Impediment 1
Chinook
Creek 160.5 Jun
13 Oct 2 Down
Susitna
Up
Susitna Monitor site for fish passing
above Impediment 2
Impediment 3 Devils Canyon (PRM 164.7)
Devils Island 166.9 Jun
13 Dec 3 Down
Susitna
Up
Susitna Monitor site for fish passing
above Impediment 3
Near Watana
Dam Site 186.8 Jul 8 Nov 5 Down
Susitna
Up
Susitna Monitor fish moving past
proposed dam site
Proposed Watana Dam Site (PRM 187.1) Upper River Boundary
Watana
Creek 196.9 Jun
14 Oct 10 Down
Susitna
Up
Susitna
Up Watana
Creek
Large accessible tributary
within impoundment zone
Kosina
Creek 209.1 Apr
30 Nov 4 Down
Susitna
Up
Susitna
Up Kosina
Creek Salmon spawning stream
Watana Reservoir Low Pool 222.5
Watana Reservoir Full Pool 232.5
Oshetna
River 235.1 May
20 Oct 9 Down
Susitna
Up
Susitna
Up Oshetna
River
Monitor site for fish in
mainstem Susitna River and
entering Oshetna River
STUDY IMPLEMENTATION REPORT STUDY OF FISH DISTRIBUTION AND ABUNDANCE IN THE
MIDDLE AND LOWER SUSITNA RIVER (STUDY 9.6)
Susitna-Watana Hydroelectric Project Alaska Energy Authority
FERC Project No. 14241 Page 31 November 2015
Table 4.1-6. Habitat types sampled during 2013/14 winter study by gear type and month.
Site ID Focus Area Macro Habitat Gear Type Nov Feb Mar Apr
WFS-104.5-OP1 NFA Upland Slough Minnow Trap X X X
WFS-104-154 FA-104a Side Channel
Electrofish X X X X
Minnow Trap X X X
Video X X X
WFS-104-156 FA-104 Side Slough Fyke Net X X
Minnow Trap X X X X
WFS-104-157 FA-104 Side Slough
Minnow Trap X X X X
Video X X X
Sonar X X X
WFS-104-159T2 FA-104 Tributary
Electrofish X
Fyke Net X X X
Minnow Trap X X
WFS-104-159T3 FA-104 Tributary Minnow Trap X
WFS-104-159T4 FA-104 Tributary Electrofish X X
WFS-104-159 FA-104 Tributary
Fyke Net X X X X
Minnow Trap X X X X
Video X X X
Sonar X X X
WFS-104-160 FA-104 Upland Slough Minnow Trap X X X X
Video X X X
WFS-104-161 FA-104 Upland Slough
Minnow Trap X X X
Video X X X
Sonar X X X
WFS-104-162 FA-104 Upland Slough Minnow Trap X X X X
Video X X X X
WFS-104-OP1 FA-104 Upland Slough Electrofish X X
WFS-104-OP2 FA-104 Side Channel Electrofish X X X
WFS-104-OP3 FA-104 Side Slough Minnow Trap X X
Video X
WFS-128-115 FA-128b Side Channel Minnow Trap X
Video X
WFS-128-156 FA-128 Upland Slough Minnow Trap X X X
Video X X X
WFS-128-157 FA-128 Upland Slough
Electrofish X X X
Minnow Trap X X X
Video X
WFS-128-158 FA-128 Upland Slough Minnow Trap X X X
Video X
WFS-128-63OP2 FA-128 Side Channel Minnow Trap X
WFS-128-63 FA-128 Side Channel Minnow Trap X
WFS-128-64 FA-128 Side Channel
Electrofish X
Fyke Net X
Minnow Trap X X X
WFS-128-69 FA-128 Side Slough Electrofish X X
Minnow Trap X X X
WFS-128-71 FA-128 Side Slough
Electrofish X
Fyke Net X X
Minnow Trap X X X X
Video X X X
WFS-128-73 FA-128 Tributary Mouth Video X
WFS-128-O70 FA-128 Side Slough Electrofish X X
Minnow Trap X X X
STUDY IMPLEMENTATION REPORT STUDY OF FISH DISTRIBUTION AND ABUNDANCE IN THE
MIDDLE AND LOWER SUSITNA RIVER (STUDY 9.6)
Susitna-Watana Hydroelectric Project Alaska Energy Authority
FERC Project No. 14241 Page 32 November 2015
Site ID Focus Area Macro Habitat Gear Type Nov Feb Mar Apr
WFS-128-OP1 FA-128 Main Channel Backwater
Fyke Net X X X
Trotline X X
Video X X
WFS-128-OP2 FA-128 Side Slough Electrofish X X
WFS-128-OP3 FA-128 Upland Slough Electrofish X X X
Video X
WFS-128-WO109 FA-128 Side Slough Electrofish X X
Video X
WFS-128-WO112 FA-128 Side Channel Trotline X
WFS-128-WO118 FA-128 Side Channel Trotline X X
Video X
WFS-128-WO119 FA-128 Side Channel Electrofish X
WFS-128-WO120 FA-128 Side Channel Electrofish X
Fyke Net X
WFS-128-WO121 FA-128 Side Channel Minnow Trap X
Video X
WFS-128-WO150 FA-128 Side Slough Fyke Net X
Minnow Trap X X
WFS-138-102 FA-138c Side Channel Minnow Trap X X X
Trotline X
WFS-138-108 FA-138 Side Channel
Electrofish X X
Minnow Trap X X X X
Video X X X
WFS-138-11 FA-138 Side Channel
Electrofish X
Trotline X
Video X X X
Sonar X X X
WFS-138-134 FA-138 Side Slough
Electrofish X X
Fyke Net X
Minnow Trap X X X X
WFS-138-134UP FA-138 Side Slough Electrofish X X X
WFS-138-161 FA-138 Upland Slough Minnow Trap X X X
Video X
WFS-138-65 FA-138 Side Channel Electrofish
Minnow Trap X X X
WFS-138-66 FA-138 Side Slough Minnow Trap X X X X
Video X X
WFS-138-67 FA-138 Side Slough Minnow Trap X X X X
Video X X X X
WFS-138-76 FA-138 Upland Slough Minnow Trap X X X
WFS-138-O77 FA-138 Upland Slough Minnow Trap X
Video X
WFS-138-OP1 FA-138 Side Slough Video X X X
Sonar X X X
WFS-138-OP2 FA-138 Side Channel Electrofish X
Minnow Trap X
WFS-138-OP3 FA-138 Side Slough
Minnow Trap X
Video X X X
Sonar X X X
WFS-138-OP4 FA-138 Main Channel, Single Trotline X
WFS-138-OP5 FA-138 Upland Slough Minnow Trap X X
Video X X
STUDY IMPLEMENTATION REPORT STUDY OF FISH DISTRIBUTION AND ABUNDANCE IN THE
MIDDLE AND LOWER SUSITNA RIVER (STUDY 9.6)
Susitna-Watana Hydroelectric Project Alaska Energy Authority
FERC Project No. 14241 Page 33 November 2015
Site ID Focus Area Macro Habitat Gear Type Nov Feb Mar Apr
WFS-138-OP6 FA-138 Main Channel, Multi Split Electrofish X
Minnow Trap X
WFS-138-WO127 FA-138 Side Channel
Electrofish X X
Fyke Net X
Minnow Trap X X
WFS-140-OP1 NFA Main Channel, Clearwater Plume
Fyke Net X
Minnow Trap X X X
Trotline X X
Video X
WFS-141-58 FA-141d Main Channel, Backwater
Fyke Net X
Minnow Trap X X
Video X
WFS-141-75 FA-141 Tributary Mouth
Fyke Net X
Minnow Trap X X X
Trotline X X
Video X X X
WFS-141-81 FA-141 Upland Slough Minnow Trap X X
Video X X
WFS-141-OP1 FA-141 Main Channel Electrofish X
Video X
WFS-141-OP2 FA-141 Tributary Electrofish X
Notes:
a FA-104 (Whiskers Creek)
b FA 128 (Slough 8A)
c FA-138 (Gold Creek)
d FA-141 (Indian River)
STUDY IMPLEMENTATION REPORT STUDY OF FISH DISTRIBUTION AND ABUNDANCE IN THE
MIDDLE AND LOWER SUSITNA RIVER (STUDY 9.6)
Susitna-Watana Hydroelectric Project Alaska Energy Authority
FERC Project No. 14241 Page 34 November 2015
Table 4.2-1. Monitoring efficiency (percent operational) of fixed radio telemetry receiver stations in the Susitna River drainage in 2014, by week.
Week 2014
Montana
Weir
Sunshine
Mouth
(PRM 83.8)
Talkeetna
Station
Lane
Station
(PRM 116.8)
Gateway
(PRM
130.1)
Indian
River
(PRM
142.1) Impediment 1 Devils Canyon (PRM 155.1) Cheechako (PRM
157.4)
Chinook
(PRM 160.5) Impediment 3 Devils Canyon (PRM 164.7) Devils Station
(PRM 166.9)
Watana Dam
Site
(PRM 186.8)
4/28 - 5/4 nd nd nd nd nd 100 nd nd nd nd
5/5 - 5/11 nd nd nd nd nd 100 nd nd nd nd
5/12 - 5/18 nd nd nd nd nd 100 nd nd nd nd
5/19 - 5/25 nd 100 nd 100 nd 100 nd nd nd nd
5/26 - 6/1 nd 100 100 100 nd 100 nd nd nd nd
6/2 - 6/8 100 100 100 100 nd 100 nd nd nd nd
6/9 - 6/15 100 100 100 100 100 100 100 100 32b nd
6/16 - 6/22 100 100 100 100 100 100 100 100 93b nd
6/23 - 6/29 100 100 100 9a 100 100 100 100 100 nd
6/30 - 7/6 100 100 100 94a 58a 100 100 100 100 nd
7/7 - 7/13 100 100 100 100 100 100 100 100 100 100
7/14 - 7/20 100 100 100 100 100 100 100 100 100 100
7/21 - 7/27 100 100 100 100 100 100 100 100 100 100
7/28 - 8/3 100 100 100 100 100 100 100 100 74b 100
8/4 - 8/10 100 100 100 100 100 100 100 100 100 100
8/11 - 8/17 100 100 100 100 100 100 100 100 100 100
8/18 - 8/24 100 100 100 100 100 100 100 100 100 100
8/25 - 8/31 100 100 100 100 100 100 100 100 100 100
9/1 - 9/7 100 100 100 100 100 100 100 100 100 30a
9/8 - 9/14 100 100 100 100 100 100 100 100 100 94a
9/15 - 9/21 100 100 100 100 100 100 100 100 100 100
9/22 - 9/28 100 100 100 100 100 100 100 100 100 100
9/29 - 10/5 nd nd nd 100 nd 100 100 100 100 100
10/6 - 10/12 nd nd nd nd nd 100 100 nd 100 100
10/13 - 10/19 nd nd nd nd nd 100 nd nd 100 100
10/20 - 10/26 nd nd nd nd nd 100 nd nd 100 100
10/27 - 11/2 nd nd nd nd nd 100 nd nd 100 39b
11/3 - 11/9 nd nd nd nd nd nd nd nd 88b 0b
11/10 - 11/16 nd nd nd nd nd nd nd nd 65b nd
11/17 - 11/23 nd nd nd nd nd nd nd nd 95b nd
11/24 - 11/30 nd nd nd nd nd nd nd nd 8b nd
12/1 - 12/7 nd nd nd nd nd nd nd nd 0b nd
12/8 - 12/14 nd nd nd nd nd nd nd nd nd nd
Notes:
Percentages were calculated as the number of hours of recorded receiver activity divided by the number of hours in the week; "-" = 'not deployed'. Receivers
were considered active in a given hour if at least one fish detection, beacon hit, or noise event was recorded during the hour.
a receiver not scanning
b low power/dead battery
STUDY IMPLEMENTATION REPORT STUDY OF FISH DISTRIBUTION AND ABUNDANCE IN THE
MIDDLE AND LOWER SUSITNA RIVER (STUDY 9.6)
Susitna-Watana Hydroelectric Project Alaska Energy Authority
FERC Project No. 14241 Page 35 November 2015
Table 4.2-2. Summary of aerial surveys of radio-tagged fish in the Lower and Middle Susitna River, 2014-2015 (1 of 3).
Zone From PRMTo PRMZone NumberJan 6,7Jan 28,29,30Feb 17,18,19Mar 18,19,20Apr 8,9Apr 30, May 1May 20,21Jun 1011-JunJun 16,17,18Jun 21,22Jun 24,25,26Jun 28,29Jul 1,2Jul 4,5Jul 6Jul 10,11Jul 12Jul 13,14Jul 16,17Jul 19,20Jul 22,23Jul 25,26Jul 28,29Jul 31, Aug 1Aug 3,4Aug 6,7Aug 9,10Aug 12,13Aug 15,16,17Aug 18,19Aug 21,22Aug 24,25Aug 27,28Aug 29,30,31Sep 2,3Sep 5,6Sep 8,9Sep 10Sep 14,15Sep 17,18Sep 20,21Sep 24,25Sep 30, Oct 1Oct 1Oct 7,8Oct 9Oct 14,15,16Oct 17Oct 28,29,30Nov 4Dec 3Dec 16,17Jan 6Feb 2Feb 4Feb 19Mar 3Mar 25Apr 14Apr 23May 20Jun 3,4Jun 23Jul 6Beyond Confluence --4 H H H H H H H H H
Confluence - Yentna 3.5 32.4 5 H H H H H H H H H H H H H H H H H H H H H H H H H H H H H H
Yentna River 32.4 -22 H H H H H H H H H H H H H H H H H H H H H H H H H H H H H H H H H H H
Yentna - Deshka 32.4 45 35 H H H H H H H H H H H H H H H H H H H H H H H H H H H H H H H H H H H H H
Deshka River 44.9 -42 H H H H H H H H H H H H H H H H H H H H H H H H H H H H H H H H H H H
Willow and L. Willow Cr 52.2 55.6 53 H H H H H H H H H H H H H H H H H H H H H H H H H H H H H H H H
Kashwitna River 64.7 -54 H H H H H H H H H H H H H H H H H H H H H H H H H H H H H H H H H H
Deshka - Kashwitna 45 64.7 55 H H H H H H H H H H H H H H H H H H H H H H H H H H H H H H H H H H H H H
Caswell Creek 67.4 -62 H H H H H H H H H H H H H H H H H H H H H H H
Sheep Creek 70.1 -63 H H H H H H H H H H H H H H H H H H H H H H H H H H H H H H
Goose Creek 76.9 -64 H H H H H H H H H H H H H H H H H H H H H H H H H H H H
Kashwitna - Montana 64.7 80.7 65 H H H H H H H H H H H H H H H H H H H H H H H H H H H H H H H H H H H H H H H H H H H
Montana Creek 80.9 -71 H H H H H H H H H H H H H H H H H H H H H H H H H H H H H H H H H H H H H H H H H
Montana - Sunshine 80.7 88.5 75 H H H H H H H H H H H H H H H H H H H H H H H H H H H H H H H H H H H H H H H H H H H H H
Sunshine Creek 88.1 -76 H H H H H H H H H H H H H H H H H H H H H H H H H H H H H H H H H H H H
Rabideux Creek 87.4 -77 H H H H H H H H H H H H H H H H H H H H H H H H H H H H H H H H H H H H H H H H
Birch Creek 93.5 -79 H H H H H H H H H H H H H H H H H H H H H H H H H H H
Talkeetna River 101 -81 H H H H H H H H H H H H H H H H H H H H H H H H H H H H H H H H H H H H H H H H H H H H
Chulitna River 101.7 -83 H H H H H H H H H H H H H H H H H H H H H H H H H H H H H H H H H H H H H H H H H H H H
Sunshine - Talkeetna 88.5 102.3 85 H H H H H H H H H H H H H H H H H H H H H H H H H H H H H H H H H H H H H H H H H H H H H H
Lower River
STUDY IMPLEMENTATION REPORT STUDY OF FISH DISTRIBUTION AND ABUNDANCE IN THE
MIDDLE AND LOWER SUSITNA RIVER (STUDY 9.6)
Susitna-Watana Hydroelectric Project Alaska Energy Authority
FERC Project No. 14241 Page 36 November 2015
Table 4.2-2. Summary of aerial surveys of radio-tagged fish in the Lower and Middle Susitna River, 2014-2015 (2 of 3).
STUDY IMPLEMENTATION REPORT STUDY OF FISH DISTRIBUTION AND ABUNDANCE IN THE
MIDDLE AND LOWER SUSITNA RIVER (STUDY 9.6)
Susitna-Watana Hydroelectric Project Alaska Energy Authority
FERC Project No. 14241 Page 37 November 2015
Table 4.2-2. Summary of aerial surveys of radio-tagged fish in the Lower and Middle Susitna River, 2014-2015 (3 of 3).
STUDY IMPLEMENTATION REPORT STUDY OF FISH DISTRIBUTION AND ABUNDANCE IN THE
MIDDLE AND LOWER SUSITNA RIVER (STUDY 9.6)
Susitna-Watana Hydroelectric Project Alaska Energy Authority
FERC Project No. 14241 Page 38 November 2015
Table 4.4-1. Summary of PIT tagging implants and in-hand recaptures in the Middle and Lower River Study Area, 2014.
Study Component Chinook Salmon Chum Salmon Coho Salmon Sockeye Salmon Arctic Grayling Burbot Dolly Varden Humpback Whitefish Lake Trout Pacific Salmon, Unspecified Rainbow Trout Round Whitefish Whitefish, Unspecified Implant Total Recapture Total* Implant Recapture Implant Implant Recapture Implant Recapture Implant Recapture Implant Recapture Implant Recapture Implant Recapture Implant Implant Implant Recapture Implant Recapture Implant 2014 FDA, ML Early Life History 28 24
384 71 13
2
12 1
1
11
24 3 1 476 99
2014 FDA, ML Seasonal Sampling 202 5
169 21 24
45 3 46 5 64
5 35 4 37 3
627 41
2014 FDA, ML River Productivity 42
34
44 2 3
14
19
1 157 2
2014 FDA ML, Winter Studies 77 13
606 78 36 3 1
15
1
4 2
2
744 94
2014 Middle/Lower River Total 349 42
1,193 170 73 3 92 5 76 6 65
1
9 62 4 82 6 2 2,004 236
2013 Middle/Lower River Total 1,696 223 13 2,092 352 81 8 378 42 223 32 70 10 86 1
309 74 300 23
5,248 765*
Middle/Lower River Total 2,045 265 13 3,285 522 154 11 470 47 299 38 135 10 87 1
9 371 78 382 29 2 7,252 1,001
Notes:
* Recapture total includes individual fish detected on PIT antennas in 2013.
STUDY IMPLEMENTATION REPORT STUDY OF FISH DISTRIBUTION AND ABUNDANCE IN THE
MIDDLE AND LOWER SUSITNA RIVER (STUDY 9.6)
Susitna-Watana Hydroelectric Project Alaska Energy Authority
FERC Project No. 14241 Page 39 November 2015
Table 4.4-2. Radio tag allocation by season and location, Middle and Lower Susitna River, 2014.
Tags Applied Total Applied by Location
Species May/June July August Sept Total Middle River Above
Devils Canyon Devils Canyon (PRM 153.9 - 169.6) Middle River Below
Devils Canyon Lower River
Arctic grayling 16 (11) 0 (17) 0 (1) 0 (6) 16 (35) 27 15 0
Burbot 0 (2) 0 (0) 0 (5) 5 (2) 5 (9) 5 3 6
Dolly Varden 0 (1) 0 (6) 0 (2) 0 (0) 0 (9) 0 3 6
Humpback whitefish 0 (3) 0 (4) 0 (0) 0 (0) 0 (7) 0 7 0
Lake trout 0 (0) 0 (0) 0 (0) 0 (0) 0 (0) 0 0 0
Longnose sucker 0 (13) 0 (8) 0 (6) 0 (1) 0 (28) 0 25 3
Northern pike 0 (0) 0 (0) 0 (5) 0 (0) 0 (5) 0 0 5
Rainbow trout 0 (11) 0 (17) 0 (3) 0 (13) 0 (44) 0 23 21
Round whitefish 0 (11) 0 (3) 0 (0) 0 (7) 0 (21) 0 20 1
Format: tags applied in 2014 (tags applied in 2013). No tags applied in 2015. Tagging during spawning periods conducted at the discretion of the
surgeon as based on fish condition.
STUDY IMPLEMENTATION REPORT STUDY OF FISH DISTRIBUTION AND ABUNDANCE IN THE
MIDDLE AND LOWER SUSITNA RIVER (STUDY 9.6)
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FERC Project No. 14241 Page 40 November 2015
Table 4.4-3. Resident fish relocated by study month (2014-2015) with active radio tags that were tagged and released in Middle and Lower Susitna River.
Species Jan '14 Feb '14 Mar '14 Apr '14 May '14 Jun '14 Jul '14 Aug'14 Sep'14 Oct '14 Nov '14 Dec '14 Jan '15 Feb '15 Mar '15 Apr '15 May '15 Jun '15 Arctic Grayling 9 9 9 9 8 14 10 9 9 8 8 7 7 7 7 7 7 6
Burbot 2 2 2 1 1 1 1 1 6 6 6 5 4 4 4 4 4 3
Dolly Varden 2 2 2 2 2 2 1 0 0 0 0 0 0 0 0 0 0 0
Longnose Sucker 4 3 3 3 2 1 1 0 0 0 0 0 0 0 0 0 0 0
Rainbow Trout 21 21 21 21 18 17 16 13 11 10 10 10 10 10 10 9 9 7
Humpback Whitefish 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
Round Whitefish 9 9 8 7 5 3 3 1 1 1 1 1 1 1 1 1 1 0
Lake Trout 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
Northern Pike 4 4 4 3 3 3 3 3 2 2 2 2 2 2 2 2 1 0
STUDY IMPLEMENTATION REPORT STUDY OF FISH DISTRIBUTION AND ABUNDANCE IN THE
MIDDLE AND LOWER SUSITNA RIVER (STUDY 9.6)
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FERC Project No. 14241 Page 41 November 2015
Table 4.7-1. Summary of size-at-life stage index used to classify Susitna River species, 2014.
Species Life stage Source Juvenile Juvenile-or-adult Adult
Chinook Salmon alevin, fry, parr, smolt index
Chum Salmon alevin, fry, parr, smolt index
Coho Salmon alevin, fry, parr, smolt index
Pink Salmon alevin, fry, parr, smolt index
Sockeye Salmon alevin, fry, parr, smolt index
Alaska Blackfish <42 42–113 >113 Kirsch et al. (2014)
Arctic Grayling <190 190–328 >328 Kirsch et al. (2014)
Arctic Lamprey <125 125-219 >219 Heard 1966; Docker 2009;
Vladykov and Kott 1978
Burbot <280 280–498 >498 Kirsch et al. (2014)
Dolly Varden <83 >83 - Kirsch et al. (2014)
Eulachon <165 >165 HDR and LGL (2014)
Longnose Sucker <188 188–348 >348 Kirsch et al. (2014)
Northern Pike <330 330–448 >448 Kirsch et al. (2014)
Sculpin (slimy) <51 51–68 >68 Kirsch et al. (2014)
Threespine Stickleback <40 40-70 >70 ADFG 1981
Lake Trout <300 300-430 430 Burr 1993
Rainbow Trout <200 200-325 >325 Russell 1977, Adams 1999
Bering Cisco Not Applicable
Whitefish, Humpback <280 280–363 >363 Kirsch et al. (2014)
Whitefish, Round <199 199–318 >318 Kirsch et al. (2014)
Whitefish, Unspecified <199 199-363 >363
Adams, F.J. 1999. Status of rainbow trout in tributaries of the upper King Salmon River, Becharof National Wildlife Refuge,
Alaska, 1990-92. U.S. Fish and Wildlife Service, Alaska Fisheries Technical Report Number 53, King Salmon, Alaska.
ADFG. 1981. APA Report 318, Subtask 7.10. Phase 1, Final draft report. Resident fish investigation on the lower Susitna River.
Anchorage, AK. 99503.
Burr, 1993. Maturity of lake trout from eleven lakes in Alaska. Northwest Science, Vol 67, No. 2, 1993.
Delaney, K., D. Crawford, L. Dugan, S. Hale, K Kuntz, B. Marshall, J. Mauney, J. Quinn, K. Roth, P Suchanek, R. Sundet, and
M. Stratton. 1981. Resident Fish Investigation on the Lower Susitna River. Prepared by Alaska Department of Fish and Game,
Susitna Hydro Aquatic Studies. Prepared for Alaska Power Authority, Anchorage, AK. 311 pp.
Docker, M. F. 2009. A review of the evolution of nonparasitism in lampreys and an update of the paired species concept. Pages
71-114 in L. R. Brown, S. D. Chase, M. G. Mesa, R. J. Beamish, and P. B. Moyle, editors. Biology, management, and
conservation of lampreys in North America, American Fisheries Society Symp 72. American Fisheries Society, Bethesda, MD.
HDR, Inc and LGL. 2014. Eulachon Run Timing, Distribution, and Spawning in the Susitna River. Initial Study Report. Prepared
for Alaska Energy Authority. Susitna-Watana Hydroelectric Project (FERC No. p-14241).
Heard, W. R. 1966. Observations on lampreys in the Naknek River System of Southwest Alaska.Copeia 1966(2):332-339.
Kirsch, J.M., J.D. Buckwalter, and D.J. Reed. 2014. Fish Inventory and Anadromous Cataloging in the Susitna River,
Matanuska River, and Knik River Basins, 2003 and 2011. ADF&G: Fishery Data Series No 14-04.
Russell, R. 1977. Rainbow trout life history studies, in the lower Talarik Creek-Kvichak Drainage. Alaska Department of Fish
and Game, Completion Report, D-J Study G-II-E, Juneau, AK.
Vladykov, V. D., and E. Kott. 1978. A new nonparasitic species of the holarctic lamprey genus Lethenteron Creaser and Hubbs,
1922 (Petromyzontidae) from northwestern North America with notes on other species of the same genus. University of Alaska,
Fairbanks, AK.
STUDY IMPLEMENTATION REPORT STUDY OF FISH DISTRIBUTION AND ABUNDANCE IN THE
MIDDLE AND LOWER SUSITNA RIVER (STUDY 9.6)
Susitna-Watana Hydroelectric Project Alaska Energy Authority
FERC Project No. 14241 Page 42 November 2015
Table 4.7-2. Summary of fish with length and weight measurements collected in the Middle and Lower Susitna River by hydrologic segment and study component, 2014.
Study Component Chinook Salmon Chum Salmon Coho Salmon Pink Salmon Sockeye Salmon Chum Salmon / Sockeye Salmon Pacific Salmon, Unspecified Arctic Grayling Arctic Lamprey Burbot Dolly Varden Humpback Whitefish Lamprey, Unspecified Longnose Sucker Ninespine Stickleback Rainbow Trout Round Whitefish Salmonid, Unspecified Sculpin, Unspecified Threespine Stickleback Whitefish, Unspecified Grand Total FDA, ML Early Life History 562 28 1,259 165 185 1,949 21 3 3 21 1 2 17 321 1 27 32 1 517 171 17 5,303
FDA, ML Seasonal Sampling 721 1 968 132 77 7 82 27 129 134 1 12 114
139 153 2 585 92 10 3,386
FDA, ML River Productivity 216
170 116
3 1
18 32
1 557
FDA ML, Winter Studies 160 85 1,025 180 18 1 2 15 1
55 8
6 4 3 622 17
2,202
2014 Middle/Lower River Total 1,659 114 3,422 165 497 2,026 46 202 32 168 137 3 84 443 1 190 221 6 1,724 280 28 11,448
STUDY IMPLEMENTATION REPORT STUDY OF FISH DISTRIBUTION AND ABUNDANCE IN THE
MIDDLE AND LOWER SUSITNA RIVER (STUDY 9.6)
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FERC Project No. 14241 Page 43 November 2015
Table 4.9-1. Summary of Fish Distribution and Abundance tissue collection for genetic baseline development and field
species calls, 2014.
Study Component Location
Chinook
Salmon
Coho
Salmon
Pacific
Salmon,
Unspecified Total
FDA, ML Seasonal Sampling Unnamed Tributary 184 1
1
FDA, ML Seasonal Sampling Susitna River PRM 173-184 2 2
FDA, ML River Productivity Susitna River PRM 173-184 4 4
FDA, ML Seasonal Sampling Devil Creek 14 14
Impediment 3 Devils Canyon PRM 164.7
FDA, ML Seasonal Sampling Chinook Creek 55 55
ADF&G Genetics (Study 9.14) Chinook Creek 6 6
FDA, ML Seasonal Sampling Cheechako Creek 44 44
ADF&G Genetics (Study 9.14) Cheechako Creek 11 11
Impediment 1 Devils Canyon PRM 155.1
FDA, ML Early Life History Middle River below Devils Canyon 61 22 83
FDA, ML Seasonal Sampling Middle River below Devils Canyon 16 4 2 22
FDA, ML River Productivity Middle River below Devils Canyon 117 76 193
FDA ML, Winter Studies Middle River below Devils Canyon 19 19
Lower River PRM 102.4
FDA, ML River Productivity Lower River 46 43 1 90
ADF&G Genetics (Study 9.14) Lower River Tributaries 11 11
2014 Middle/Lower River Total 407 145 3 555
STUDY IMPLEMENTATION REPORT STUDY OF FISH DISTRIBUTION AND ABUNDANCE IN THE
MIDDLE AND LOWER SUSITNA RIVER (STUDY 9.6)
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FERC Project No. 14241 Page 44 November 2015
Table 4.9-2 Summary of fish collection for River Productivity (Study 9.8) scale, tissue and/or stomach content sampling,
2014.
Station Sampling Site Habitat Type
Chinook
Salmon
Coho
Salmon
Arctic
Grayling
Rainbow
Trout
Grand
Total
Watana Dam PRM 187.1
FA-184 (Watana
Dam)
RP-184-1 Tributary Mouth
16
16
RP-184-2 Side Channel 3
13
16
RP-184-3 Main Channel
9
9
FA-173 (Stephan
Lake Complex)
RP-173-1 Tributary Mouth
18
18
RP-173-2 Main Channel 1
15
16
RP-173-3 Side Channel
4
4
RP-173-4 Side Slough
9
9
RP-173-5 Upland Slough
0
Devils Canyon Impediments 1-3 (PRM 155.1-164.7)
FA-141 (Indian River)
RP-141-1 Tributary Mouth 16 7 1 11 35
RP-141-2 Side Channel 20 1
21
RP-141-3 Main Channel 24
6
30
RP-141-4 Upland Slough 9
3 12
FA-104 (Whiskers
Slough)
RP-104-1 Tributary Mouth 17 23 1 3 44
RP-104-2 Side Slough 3 21
24
RP-104-3 Main Channel 16
13
29
RP-104-4 Upland Slough 7 24
31
RP-104-5 Side Channel 16 12 5
33
Lower River
Montana Creek
Mouth
RP-81-1 Upland Slough 5 29
1 35
RP-81-2 Tributary Mouth 7 15 1 1 24
RP-81-3 Main Channel 17 7
24
RP-81-4 Side Channel 15 1 3
19
Grand Total 176 140 114 19 449
STUDY IMPLEMENTATION REPORT STUDY OF FISH DISTRIBUTION AND ABUNDANCE IN THE
MIDDLE AND LOWER SUSITNA RIVER (STUDY 9.6)
Susitna-Watana Hydroelectric Project Alaska Energy Authority
FERC Project No. 14241 Page 45 November 2015
Table 5.1-1. An updated summary of fish distribution by Geomorphic Reach the in Middle and Lower Susitna River, where ◊ indicates new locations from 2014.
Locationa PRM Chinook Salmon Chum Salmon Coho Salmon Pink Salmon Sockeye Salmon Salmon, Unspecified Arctic Grayling Burbot Dolly Varden Lake Trout Lamprey Longnose Sucker Northern Pike Rainbow Trout Sculpin, Unspecified Stickleback, Ninespine Stickleback, Threespine Whitefish, Bering Cisco Whitefish, Humpback Whitefish, Round Whitefish, Unspecified Upper River Study Area 187.1-234.5 X X X X X X X X X X
Watana Dam PRM 187.1
MR-1 184.6-187.1 ◊ X X X X X X X
Tsusena Creek 184.6 X X X ◊ X X
MR-2 169.6-184.6 X X X X X X X X
Unnamed Tributary 184 ◊ ◊ ◊ ◊ ◊
Fog Creek 173.9 ○ X X
MR-3b 166.1-169.6 -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- --
Devil Creek 164.8 ◊ ◊ ◊ ◊
Impediment 3 Devils Canyon (PRM 164.7)
Chinook Creek 160.5 ◊ X X
Cheechako Creek 155.9 ◊ ◊ ◊ ◊
MR-4b 153.9-166.1 -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- -- --
Impediment 1 Devils Canyon (PRM 155.1)
MR-5a 148.4-153.9 X X X X X X X X X X X X X X X
MR-6a 122.7-148.4 X X X X X X X X X X X X X X X X
MR-7a 107.8-122.7 X X X X X X X X X X X X X X ◊ X X X
MR-8a 102.4-107.8 X X X X X X X X X X X X X ◊ X X X X
Middle / Lower River (PRM 102.4)
LR-1a 87.9-102.4 X X X X X X X X X X X X X X X ○ ○ X X
LR-2a 65.6-87.9 X X X X X X X X X X X X X X X X ○ X X
LR-3a 44.6-65.6 X X X X X X X X X X X X X X X ○ ○ X X
LR-4a 32.3-44.6 X X X X X X X X ○ X X X X X X X X X X X
Notes:
Includes the following data sources: 2013 & 2014 early-life history sampling, 2013 & 2014 habitat stratified randomized sampling (GRTS), 2013 & 2014 direct tributary sampling,
2013 rotary screw trap catch, 2013 resident fish catch at Curry fishwheel (PRM 124), 2013 & 2014 opportunistic sampling , 2013 & 2014 targeted sampling for radio tagging, 2013
& 2014 river productivity sampling, 2013 & 2014 habitat suitability criteria sampling, and 2014 resident fish catch during gill net sampling for escapement (9.7).
X Species observed during FDA 2013 surveys, ◊ species observed in 2014 suveys but not 2013.
A Geomorphic reaches MR-1, MR-5, MR-6, MR-7, MR-8, LR-1, LR-2, LR-3, and LR-4 include sites located in the mainstem Susitna River and its associated off-channel
and tributary habitats within the Zone of Hydrologic Influence (ZHI). Directed sampling efforts outside of the ZHI did not occur in these reaches.
B The mainstem Sustina River in geomorphic reaches MR-3 and MR-4 were not sampled during on-the-ground surveys in 2013 or 2014.
○ Species present during 1980s licensing efforts (Delaney et al 1981) or ADF&G Inventory 2003-2012 (Kirsch et al. 2014).
STUDY IMPLEMENTATION REPORT STUDY OF FISH DISTRIBUTION AND ABUNDANCE IN THE
MIDDLE AND LOWER SUSITNA RIVER (STUDY 9.6)
Susitna-Watana Hydroelectric Project Alaska Energy Authority
FERC Project No. 14241 Page 46 November 2015
Table 5.1-2. 2014 Middle Susitna River fish observations by life stage and site. Includes the seasonal sampling events from the following data sources: habitat stratified randomized sampling (GRTS), direct tributary sampling, and opportunistic sampling (1 of 2).
Site ID Chinook Salmon Chum Salmon Coho Salmon Pink Salmon Sockeye Salmon Chum Salmon / Sockeye Salmon Pacific Salmon, Unspecified Fry Parr Smolt Juvenile Jack Adult Carcass Not Recorded Juvenile Adult Fry Parr Smolt Juvenile Adult Carcass Not Recorded Adult Parr Smolt Fry Parr Smolt Juvenile Carcass Not Recorded FDA-MR1-184-P2-MC
1
FDA-MR2-TSU-DIR
1
FDA-MR2-184-P12-MC
FDA-MR2-184-NF3-TRIB
1
FDA-MR2-184-DIR
FDA-MR2-182-P112-TM
FDA-MR2-182-P112-CWP
1
FDA-MR2-181-NF6-TRIB
FDA-MR2-178-P020-US
FDA-MR2-178-OP1-US
FDA-MR2-176-P021-US
FDA-MR2-175-NF4-TRIB
FDA-MR2-173-P23-US
FDA-MR2-173-P22-US
FDA-MR2-173-P21-US
FDA-MR2-173-P20-TM
1
2
FDA-MR2-173-P19-TRIB
FDA-MR2-173-P012-US
FDA-MR4-DEV-DIR
94
1 1
Impediment 3 Devils Canyon PRM 164.7
FDA-MR4-CHI-DIR
244
FDA-MR4-CHE-DIR
146
5
3
Impediment 1 Devils Canyon PRM 155.1
FDA-MR5-153-P55-TM
FDA-MR5-153-P55-CWP
FDA-MR5-151-P50-TM 117 559
1 165 213 227
1
33 1
92
FDA-MR5-151-P49-TRIB 22 25
1 3
22 25
5
14 6
2
FDA-MR5-151-P46-CWP 4 33
448 8 6
2
1
FDA-MR5-151-P25-MC
4 1
1
FDA-MR6-148-NF2-TRIB
40
1
1 33
31
2
FDA-MR6-144-P68-SS
35
2
39 1
1
FDA-MR6-143-PO62-US
102 3 1
1
160 72 1
106 24
90 72 5 1
FDA-MR6-141-P81-US
5
51 10
1
FDA-MR6-130-P086-CWP
2
FDA-MR6-128-P73-TRIB
55 4
2 66
2
1
FDA-MR7-115-P2-BW
1
32 128
2
265
140
1
FDA-MR7-115-P176-TRIB
4
1 217
1 1
1
2
FDA-MR7-115-P121-US
213
FDA-MR7-113-P143-TRIB
10
108
1
13
FDA-MR7-110-NFOS1-TRIB
7
30 111 5 245 47
1
Grand Total 143 1,365 14 5 1 10 2 3 1 636 312 1,359 88 277 52 1 1 8 372 26 188 98 72 20 1 98
STUDY IMPLEMENTATION REPORT STUDY OF FISH DISTRIBUTION AND ABUNDANCE IN THE
MIDDLE AND LOWER SUSITNA RIVER (STUDY 9.6)
Susitna-Watana Hydroelectric Project Alaska Energy Authority
FERC Project No. 14241 Page 47 November 2015
Table 5.1-2. Middle Susitna fish distribution and abundance sampling observations, 2014 by site. Includes the seasonal sampling events from the following data sources: habitat stratified randomized sampling (GRTS), direct tributary sampling, and opportunistic sampling (2 of
2).
Site ID Arctic Grayling Arctic Lamprey Burbot Dolly Varden Fish, Species Unspecified Lamprey, Unspecified Longnose Sucker Rainbow Trout Salmonid, Unspecified Sculpin, Unspecified Stickleback, Threespine Whitefish, Humpback Whitefish, Round Whitefish, Unspecified Grand Total Juvenile Juvenile/Adult Adult Not Recorded Juvenile Juvenile/Adult Adult Juvenile Juvenile/Adult Not Recorded Juvenile Juvenile/Adult Carcass Not Recorded Not Recorded Juvenile Juvenile/Adult Juvenile Juvenile/Adult Adult Not Recorded Juvenile Juvenile Juvenile/Adult Not Recorded FDA-MR1-184-P2-MC 7 6 3 12
3 4
1 66
14
2 119
FDA-MR2-TSU-DIR 16 81 25 3
11
1
24
1
1
2 170
1
337
FDA-MR2-184-P12-MC 8 5 3
16
FDA-MR2-184-NF3-TRIB 2 2
2
1 51
1
60
FDA-MR2-184-DIR 7 18
4 29
2
1 34
95
FDA-MR2-182-P112-TM
20
20
FDA-MR2-182-P112-CWP 1
2
1
16
21
FDA-MR2-181-NF6-TRIB
1
10 5
3
19
FDA-MR2-178-P020-US
-
FDA-MR2-178-OP1-US
4
1
9
14
FDA-MR2-176-P021-US
-
FDA-MR2-175-NF4-TRIB
1
11
12
FDA-MR2-173-P23-US
3
21
14
38
FDA-MR2-173-P22-US
16
1
1
18
FDA-MR2-173-P21-US
1
1
FDA-MR2-173-P20-TM
1
8
12
FDA-MR2-173-P19-TRIB 2
2
5
1 5
15
FDA-MR2-173-P012-US
1
5
2
8
FDA-MR4-DEV-DIR
1 152 1 1 2
1
4
258
Impediment 3 Devils Canyon PRM 164.7
FDA-MR4-CHI-DIR
25 84
8
2 22
385
FDA-MR4-CHE-DIR
1
3 31
1
5
195
Impediment 1 Devils Canyon PRM 155.1
FDA-MR5-153-P55-TM
1
1
FDA-MR5-153-P55-CWP
2
2
FDA-MR5-151-P50-TM
8
3 1
9 1
1 25
1,457
FDA-MR5-151-P49-TRIB 1 11 10
6
1
5 2 4
75
4
244
FDA-MR5-151-P46-CWP
10 7
5
1
3
4
532
FDA-MR5-151-P25-MC 1
1
1 8
1
18
FDA-MR6-148-NF2-TRIB
14 1
2 1 19
145
FDA-MR6-144-P68-SS
13 2
20
29
2 144
FDA-MR6-143-PO62-US
27 1
24 1
13
73
777
FDA-MR6-141-P81-US
16 1
5 12
1 2
13 1
118
FDA-MR6-130-P086-CWP
6
8
FDA-MR6-128-P73-TRIB
1 1
1 43
176
FDA-MR7-115-P2-BW
7 3
7 2 3 1
23 9 1 28 4 26 8 768
FDA-MR7-115-P176-TRIB
1
38
59
325
FDA-MR7-115-P121-US
454
667
FDA-MR7-113-P143-TRIB
1
183
2 1
319
FDA-MR7-110-NFOS1-TRIB
16 9 2 14 2
3 12 3
8 9 1
28 1
554
Grand Total 45 134 56 15 16 9 2 121 10 3 46 342 1 14 8 12 101 16 262 16 8 2 14 741 543 1 159 10 26 12 7,898
STUDY IMPLEMENTATION REPORT STUDY OF FISH DISTRIBUTION AND ABUNDANCE IN THE
MIDDLE AND LOWER SUSITNA RIVER (STUDY 9.6)
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FERC Project No. 14241 Page 48 November 2015
Table 5.2-1. Observations of juvenile anadromous and resident fish during three Early Life History sampling events in the Middle Susitna River (1 of 2).
ELH Site Gemorphic Reach Chinook Salmon Chum Salmon Coho Salmon Pink Salmon Sockeye Salmon Chum Salmon/ Sockeye Salmon Pacific salmon, unspecified Fry Parr Smolt Juvenile Parr Smolt Juvenile Alevin Fry Parr Smolt Alevin Fry Parr Smolt Alevin Fry Fry Parr Juvenile ELH-104-Rearing 1 MR-8 18 15
223 27
7 13
30 86
ELH-104-Rearing 2 MR-8 15 2
73 84 11
3 44 1
372
ELH-104-Rearing 3 MR-8 20
34 4
60 66
ELH-104-Spawning 1 MR-8 2 1
4 2
9
1
29
ELH-104-Spawning 2 MR-8 3 39
1
299 82 293
21 4
14 200 30
ELH-104-Spawning 3 MR-8 17
1
83 2
1
321 296
ELH-113-Rearing 1 MR-7
27 1
5
ELH-113-Rearing 2 MR-7 35 6 3
3
4 139 17
8
38 2
ELH-113-Rearing 3 MR-7 17 2
7 3
2
21 30 15
ELH-113-Spawning 1 MR-7 12 11 1
1
4 22 14
8
46 2
ELH-113-Spawning 2 MR-7 4
71 4
1
87 85
4
ELH-113-Spawning 3 MR-7 5
78 8 35
7 42
ELH-128-Rearing 1 MR-6 1
1 1
3
39 43
ELH-128-Rearing 2 MR-6 1
3 110
3
3 723 1,157
ELH-128-Rearing 3 MR-6
71 12
340 72
ELH-128-Spawning 1 MR-6 3 1 1
2
5 5 1
2
316 1
ELH-128-Spawning 2 MR-6 4 2
12 4
1 2
554 320
ELH-128-Spawning 3 MR-6
7 6
6 1
7
254 355
ELH-138-Rearing 1 MR-6 8
4 3
4
1 9
ELH-138-Rearing 2 MR-6
26 13
1 5
ELH-138-Rearing 3 MR-6
92 17
1
ELH-138-Spawning 1 MR-6 2
1 1
2,000 1,250
ELH-138-Spawning 2 MR-6 26 1
1
179 53
ELH-138-Spawning 3 MR-6 1
2
112 2
ELH-141-Rearing 1 MR-6 13 1
1 10
1 32
60
ELH-141-Rearing 2 MR-6 70 3
5
4
589 1
ELH-141-Rearing 3 MR-6
72
10 71
1
ELH-141-Spawning 1 MR-6 118 1
1 2
168 1
782 901
ELH-141-Spawning 2 MR-6 98
2 9
19
22 489 85 1
ELH-141-Spawning 3 MR-6 9 2
1
1
172 213
ELH-144-Rearing 1 MR-6 6
2
2
1,425 1
ELH-144-Rearing 2 MR-6
1 1
12 28
12 2
2
ELH-144-Rearing 3 MR-6
7
4
5 56
53 23
2
ELH-144-Spawning 1 MR-6 11 1
9
1
6 118 101
2
ELH-144-Spawning 2 MR-6 10
2
1
152
ELH-144-Spawning 3 MR-6 8
3
474
Total 537 89 85 1 13 15 1 3 1,106 605 557 1 265 166 40 31 9,808 5,374 46 11
Grand Total 712 29A 2,271 266 206A 9,839A 5,431B
Notes:
A Newly emerged Chum Salmon and Sockeye Salmon were not differentiated to species
B 5,393 (99%) unspecified Pacific Salmon were estimated from visual observations.
STUDY IMPLEMENTATION REPORT STUDY OF FISH DISTRIBUTION AND ABUNDANCE IN THE
MIDDLE AND LOWER SUSITNA RIVER (STUDY 9.6)
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FERC Project No. 14241 Page 49 November 2015
Table 5.2-1. Observations of juvenile anadromous and resident fish during three Early Life History sampling events in the Middle Susitna River (2 of 2).
Site Id Geomorhpic Reach Arctic Grayling Arctic Lamprey Lamprey, Unspecified Burbot Dolly Varden Longnose Sucker Rainbow Trout Salmonid, Unspecified Sculpin, Unspecified Stickleback, Ninespine Stickleback,Threespine Whitefish, Humpback Whitefish, Round Whitefish, Unspecified Grand Total Juvenile Adult Juvenile Fry Juvenile Juvenile/Adult Adult ELH-104-Rearing 1 MR-8
1
1
1
5 1 4
414
ELH-104-Rearing 2 MR-8
14
21
625
ELH-104-Rearing 3 MR-8
2
2
82
44
294
ELH-104-Spawning 1 MR-8
4 1
2
62
2
40 157
ELH-104-Spawning 2 MR-8 2 4 15 1
1 1 7 5
9
7
3
1,038
ELH-104-Spawning 3 MR-8
3 1 2
1 10
7
728
ELH-113-Rearing 1 MR-7
3
28
64
ELH-113-Rearing 2 MR-7
7
40
2
5
9
283
ELH-113-Rearing 3 MR-7
1
7
88
ELH-113-Spawning 1 MR-7
55
2 1
7
4 1 1
180
ELH-113-Spawning 2 MR-7
20
272
ELH-113-Spawning 3 MR-7
1
171
ELH-128-Rearing 1 MR-6
11
98
ELH-128-Rearing 2 MR-6
1
81
2,081
ELH-128-Rearing 3 MR-6
3
17
515
ELH-128-Spawning 1 MR-6
3
1
28
366
ELH-128-Spawning 2 MR-6
2
2
1
1
901
ELH-128-Spawning 3 MR-6
80
716
ELH-138-Rearing 1 MR-6
1 52
74
ELH-138-Rearing 2 MR-6
7
52
ELH-138-Rearing 3 MR-6
26
124
260
ELH-138-Spawning 1 MR-6
33
3,285
ELH-138-Spawning 2 MR-6
13
247
ELH-138-Spawning 3 MR-6
1
2
119
ELH-141-Rearing 1 MR-6
4
109
ELH-141-Rearing 2 MR-6
1
1
2 606
ELH-141-Rearing 3 MR-6 1
3
10
17
185
ELH-141-Spawning 1 MR-6
5
1,861
ELH-141-Spawning 2 MR-6
2
1 49
679
ELH-141-Spawning 3 MR-6
1
19
1 1
1
1 413
ELH-144-Rearing 1 MR-6
1 1
1
1,433
ELH-144-Rearing 2 MR-6
149
2
2
211
ELH-144-Rearing 3 MR-6
52
2 204
ELH-144-Spawning 1 MR-6
1
2 1
53
295
ELH-144-Spawning 2 MR-6
1
13
169
ELH-144-Spawning 3 MR-6
2
1
8
488
Total 3 4 19 21 1 376 3 9 13 6 3 679 1 247 2 32 45 20,218 Grand Total 3 4 19 21 1 376 31 3 679 1 247 2 32 45
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10. FIGURES
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Figure 3-1. Susitna River fish distribution and abundance study area.
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APPENDIX A: 2014 SAMPLING SITE MAPS
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TABLE OF FIGURES
Figure A1. Salmon early life history sampling locations FA-104 (Whiskers Slough), 2014. ........ 1
Figure A2. Salmon early life history sampling locations FA-113 (Oxbow I), 2014 ...................... 2
Figure A3. Salmon early life history sampling locations FA-128 (Slough 8A), 2014. .................. 3
Figure A4. Salmon early life history sampling locations FA-138 (Gold Creek), 2014. ................. 4
Figure A5. Salmon early life history sampling locations FA-141 (Indian River), 2014. ............... 5
Figure A6. Salmon early life history sampling locations FA-144 (Slough 21), 2014. ................... 6
Figure A7. Seasonal GRTS and opportunistic fish distribution and abundance sampling locations
PRM 110-116, 2014. ....................................................................................................................... 7
Figure A8. Seasonal GRTS and opportunistic fish distribution and abundance sampling locations
PRM 128-131, 2014. ....................................................................................................................... 8
Figure A9. Seasonal GRTS and opportunistic fish distribution and abundance sampling locations
PRM 142-148, 2014. ....................................................................................................................... 9
Figure A10. Seasonal GRTS, and opportunistic fish distribution and abundance sampling
locations PRM 152-156, and direct tributary sampling at Cheechako Creek, 2014. .................... 10
Figure A11. Seasonal direct tributary fish distribution and abundance sampling locations,
Chinook Creek and Devil Creek, 2014. ........................................................................................ 11
Figure A12. Seasonal GRTS, and opportunistic fish distribution and abundance sampling
locations, PRM 173-180, 2014. .................................................................................................... 12
Figure A13. Seasonal GRTS and opportunistic fish distribution and abundance sampling
locations PRM 182-187 and tributary direct sampling locations for Unnamed Tributary 184.0
and Tsusena Creek, 2014. ............................................................................................................. 13
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Figure A1. Salmon early life history sampling locations FA-104 (Whiskers Slough), 2014.
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Figure A2. Salmon early life history sampling locations FA-113 (Oxbow I), 2014
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Figure A3. Salmon early life history sampling locations FA-128 (Slough 8A), 2014.
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Figure A4. Salmon early life history sampling locations FA-138 (Gold Creek), 2014.
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Figure A5. Salmon early life history sampling locations FA-141 (Indian River), 2014.
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Figure A6. Salmon early life history sampling locations FA-144 (Slough 21), 2014.
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Figure A7. Seasonal GRTS and opportunistic fish distribution and abundance sampling locations PRM 110-116, 2014.
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Figure A8. Seasonal GRTS and opportunistic fish distribution and abundance sampling locations PRM 128-131, 2014.
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Figure A9. Seasonal GRTS and opportunistic fish distribution and abundance sampling locations PRM 142-148, 2014.
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Figure A10. Seasonal GRTS, and opportunistic fish distribution and abundance sampling locations PRM 152-156, and direct tributary sampling at Cheechako Creek,
2014.
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Figure A11. Seasonal direct tributary fish distribution and abundance sampling locations, Chinook Creek and Devil Creek, 2014.
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Figure A12. Seasonal GRTS, and opportunistic fish distribution and abundance sampling locations, PRM 173-180, 2014.
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Figure A13. Seasonal GRTS and opportunistic fish distribution and abundance sampling locations PRM 182-187 and tributary direct sampling locations for Unnamed
Tributary 184.0 and Tsusena Creek, 2014.
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APPENDIX B: JUVENILE CHINOOK AND COHO SALMON
IDENTIFICATION ACCURACY
Susitna-Watana Hydroelectric Project
(FERC No. 14241)
Study of Fish Distribution and Abundance in the
Middle and Lower Susitna River
Study Plan Section 9.6
2014-2015 Study Implementation Report
Appendix B: Juvenile Chinook and Coho Salmon
Identification Accuracy
Prepared for
Alaska Energy Authority
Prepared by
R2 Resource Consultants Inc.
LGL Alaska Research Associates, Inc.
November 2015
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TABLE OF CONTENTS
1. Introduction ............................................................................................................................ 1
2. Accuracy of Chinook and Coho Salmon Species Identification ........................................ 2
3. Evaluation of AEA’s photographic QA/QC for Field Identifications of Juvenile
Salmonids ................................................................................................................................ 3
4. Management Implications ..................................................................................................... 4
5. Literature Cited ..................................................................................................................... 6
6. Tables ...................................................................................................................................... 7
7. Figures .................................................................................................................................. 13
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LIST OF TABLES
Table B-1. Accuracy of 2012-2014 QC3 species identification as determined by genetic analysis
of tissue. .......................................................................................................................................... 7
Table B-2. Accuracy of QC3 species identification by month and year. Accuracy was determined
by genetic analysis tissue samples from N fish. ............................................................................. 8
Table B-3. QC3 Species ID accuracy by geomorphic reach; percent accuracy was determined by
genetic analysis of tissue samples from N juvenile fish. ................................................................ 9
Table B-4. 2014 species ID photo review quality control as determined by comparing photo-
based species determination with genetic analysis of tissues from N fish. .................................. 10
Table B-5. Documented co-occurrence of verified juvenile Chinook and Coho salmon in 53 of
60 Middle and Lower River habitat features. ............................................................................... 11
LIST OF FIGURES
Figure B-1. Examples of morphological variability among juvenile Chinook Salmon (left) and
Coho Salmon (right) parr from the Susitna River and lower tributary reaches between PRM 80
and PRM 160.5. Species identification was verified through genetic analysis. ........................... 13
Figure B-2. Distributions of the Susitna River habitat suitability criteria data for the open-water
period (median, 25% and 75% interquartile, range) collected for juvenile Chinook and Coho
salmon: a) water depth criteria, b) velocity criteria, and c) temperature criteria. (source: 2013
and 2014 habitat suitability criteria microhabitat database http://gis.suhydro.org/SIR/08-
Instream_Flow/8.5-Fish_and_Aquatics_Instream_Flow/). .......................................................... 14
Figure B-3. Results of 2014 isotopic model showing contributions from freshwater, marine, and
terrestrial food sources to juvenile Chinook and Coho salmon by site and season (Source: R2 and
UAF 2015; Tables 5.4-4, 5.4-5, and 5.4-6). ................................................................................. 15
Figure B-4. Size distributions of genetically-verified juvenile Chinook and Coho salmon for the
Middle and Lower Susitna Rivers, 2013-2014. ............................................................................ 16
Figure B-5. Age at length of genetically-verified Chinook and Coho salmon based on scale
analysis (Source: R2 and UAF 2015; Figures 5.4-5 and 5.4-6). ................................................... 17
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1. INTRODUCTION
In 2014, certain licensing participants expressed concern about the amount of sampling error
apparent in AEA’s fish distribution and abundance studies. This appendix addresses that general
concern, and more specifically, the concern that level of error associated with Chinook and Coho
Salmon species identifications by AEA’s fish study teams was higher than acceptable within the
fisheries profession and therefore, compromises the use of the study results to support
management decisions. To do so within this appendix, available literature that addresses error in
ecological field sampling and fish identifications is summarized. Then, the accuracy of the fish
collections from Studies 9.5 and 9.6 Fish Distribution and Abundance in the Upper and Middle
and Lower Rivers, respectively, is reviewed, and the efficacy of the QAQC protocol that AEA
proposed to improve accuracy is evaluated. Finally and most importantly, the management
implications associated with having a known level of uncertainty around species identifications
of juvenile Chinook and Coho salmon is discussed.
Although it is not often estimated or even discussed, sampling error is ubiquitous in all
ecological sampling and observer bias is widespread in studies that rely upon humans to collect
data (Elphick 2008). While it is often assumed that the degree of error can be attributed to a lack
of training and experience of observers, studies have shown that training and experience can
reduce or change the type of sampling error that occurs (Fitzpatrick et al. 2009), but cannot
eliminate observer error (Elphick 2008, Kirsch et al. 2014). Understanding the bias/error
associated with ecological data sets allows researchers to take steps to potentially reduce that
error, but more importantly, to evaluate the influence of the uncertainty imposed by error might
have on the use of the data for management decisions. Since error is unavoidable, it is important
to know what implications, if any, the error would have for use of the data.
For fish surveys, field crews are often asked to identify fish to genus or species where possible.
Field identification of fishes relies on phenotypes (such as coloration, or fin shape) and meristics
(countable traits such as fin rays), and natural variations in these traits can make field
identification challenging (Moyle 2002). A literature search for studies that addressed
uncertainty in species identification based on phenotypes revealed only one study with
freshwater fishes.
A recent experimental study conducted by the USFWS estimated error associated with the
identification of fish species in California (Kirsch et al. 2014). This study demonstrated an
overall average accuracy of 84 percent for all observers. In addition, although accuracy
increased with observer experience (accuracy was approximately 60 percent for inexperienced
observers and 80 percent for observers with approximately 18 months of experience in the
region), it remained highly variable among observers ranging from 85 to 95 percent for even the
most experienced observers (15 years of experience) demonstrating that there is an individual
human component to bias that experience and training do not affect. It is important to note, that
during this experiment the identification of test specimen had to be agreed upon by four expert
California fish scientist and the specimen for which the experts could not agree were excluded
from the experiment. Thus, these results might be underestimates of identification error for
difficult determinations where considerable overlap in phenotypic variation occurs. This study
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by Kirsch et al. provides a basis of comparison for documented observer error during fish species
identification.
2. ACCURACY OF CHINOOK AND COHO SALMON SPECIES
IDENTIFICATION
During 2013 field sampling for Study 9.6, field crews identified that a proportion of the juvenile
salmon catch were challenging to identify to species due to high variability in color patterns and
meristics that overlapped across species. In particular for juvenile Chinook and Coho salmon,
large variation among individuals with respect to species defining characteristics: 1) the spacing
of parr marks, 2) the coloration of the leading edge of the fins, and 3) the shape of the anal fin,
resulted in a large amount of uncertainty in identifying some fish to species (Figure C-1). To
address this concern, in 2014 additional onsite training was provided to field crews, crews were
instructed to increase photo-documentation of challenging fish, and laboratory confirmation of
field identification through collection of tissue samples for DNA analysis was initiated to
provide feedback and evaluate field identification accuracy. Field identifications were reviewed
for quality control based on photo documentation and a final QC3 species determination was
made.
There are two terms that we can use to characterize the uncertainty in species identifications that
were made during 2012-2013 fish surveys. The first term, sampling accuracy, characterizes the
correctness of the species determinations when the fish are taken from a mixed pool of unknown
species, and is calculated as the correct number of Chinook and Coho salmon determinations by
the study team divided by the known number of each species in the collection as determined by
DNA analysis. The second term is species-specific accuracy and describes the error around the
study team identifying a species as itself in the field, in other words, identifying a Chinook
Salmon a Chinook and, likewise, calling a Coho Salmon a Coho. Species-specific error is
determined by dividing the number of correct field identifications for each species by the
genetically verified number of that species. This term is important to evaluate because it helps
us to understand where the identification error is arising from, such as misidentification of one
species, the other, or both.
The results of the genetic analysis from 1,226 fish confirmed that fish crews had an overall
sampling accuracy when identifying Chinook and Coho salmon of 86 percent (Table C-1), with
84 percent and 90 percent sampling accuracy for Chinook and Coho salmon, respectively.
Genetic analysis also showed that species-specific accuracy was one-directional in 2013 (Table
C-2). In 2013, observers identified true Chinook Salmon with high species-specific accuracy of
96 percent (only 12 out of 320 verified Chinook Salmon were called Coho Salmon); but, they
erroneously identified 122 out of 290 verified juvenile Coho Salmon as Chinook resulting in a
species-specific accuracy rate of 57 percent. The species-specific error numbers indicated that it
was the incorrect assignment of Coho Salmon that caused the problem in 2013. Photographic
QAQC confirmed that it was the variation of distinguishing characteristics of Coho Salmon and
how they overlapped with those used to distinguish Chinook Salmon that caused the error in
2013.
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In 2014, species-specific accuracy remained stable for Chinook Salmon and improved
dramatically for Coho Salmon, such that no directional error was evident. The 2014 species-
specific accuracy rates were 95 percent for Chinook Salmon (22 errors out of 403 verified
Chinook) and 96 percent for Coho Salmon (7 errors out of 186 verified Coho). This
improvement likely is related to additional training and feedback provided to field crews about
specific characteristics of Coho Salmon in the Middle Susitna River as well as implementation of
photographic QAQC of field identification as is discussed below.
It is important to note that this problem was isolated to the Middle River below Devils Canyon
and in the Lower River. The juvenile salmon collected in the Middle River within Devils
Canyon (between Impediment 1 and 3) and above Impediment 3, as well as in the Upper River
were phenotypically distinct and were assigned as Chinook Salmon with 100 percent accuracy
(Table C-3) in all survey years 2012-2014. This high level of accuracy was likely related to the
facts that 1) there were no Coho Salmon collected in any of the samples within and above the
Canyon and there was no co-occurrence of juvenile Pacific Salmon upstream of Impediment 1 in
Devils Canyon, although this was not known with certainty prior to initiation of AEA’s recent
field surveys and genetic sampling.
Even within the Middle and Lower River Segments, the results of genetic analysis show that the
species identifications were similar to or greater than accuracy levels reported elsewhere
(USFWS 2014) except in two Middle River Segment reaches, MR-6 and MR-7 (Table C-3).
Importantly, the lowest accuracy of 33 percent, evident in MR-7, was based on a small sample
size of nine genetically verified Chinook Salmon that came from two habitats: the Oxbow side
channel and a side slough at PRM 117. This information points to localized areas where the
phenotypic variation among juvenile salmon is high and poses challenges for species
identification. Photographic review of juveniles collected in Oxbow side-channel showed the
fish to be in the process of smoltification and confirmed the difficultly in species identification
due to a lack of distinguishing characteristics. This was the only reach where photographic
review was less than 90 percent accurate when compared to genetically verified specimen (Table
C-4).
3. EVALUATION OF AEA’S PHOTOGRAPHIC QA/QC FOR FIELD
IDENTIFICATIONS OF JUVENILE SALMONIDS
In 2014, AEA developed and filed with FERC a proposed protocol entitled Fish Distribution and
Abundance in the Upper and Middle/Lower Susitna River (Studies 9.5 and 9.6): Draft Chinook
and Coho Identification Protocol (R2 2014) to improve the accuracy of species determinations
for juveniles of these two salmon species. The protocol consists of five components: 1) site-
specific training in areas where these species have co-occurred and identification has proven
challenging; 2) standardized genetic verification across habitats; 3) collection of up to 20
voucher specimen of each species for meristic analysis by field crews; 4) collection and senior
review of photographs for all undifferentiated Pacific salmon and all PIT-tagged Chinook and
Coho salmon and 5) development of a Susitna specific identification guide for use by field
crews. In 2013, an evaluation of the photographic QA/QC was implemented on 317 juvenile
salmon that had both photos and genetic tissue samples taken at the time of capture. A
comparison of the 2014 QC3 species determination (final study team determination after
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photographic quality control of field identifications) showed that species identification from
photo QA/QC was accurate for 96 percent of the Chinook Salmon identifications and 98 percent
for Coho Salmon (Table C-4). This high level of accuracy supports the use of photographic
review for verifying field identifications in AEA’s future studies downstream of Devils Canyon.
Further support for AEA’s proposed protocol comes from Moyle (2002) who recommended the
use of photographic review of recently caught field specimen and collection of voucher
specimens to improve fish identification accuracy and account for natural variation in
morphology and human perception.
Finally, the value of AEA’s field protocol extends beyond reducing any misidentification of
juvenile Coho or Chinook salmon. In some habitats, such as Slough 6A, 2013 field crews were
only able to identify large numbers of juvenile salmonids to genus, based on phenotypic
characteristics, and thus called them Undetermined Pacific Salmon (SAMs). This resulted in
SAMs in preliminary datasets. Use of photographic QA/QC has allowed AEA to re-classify the
majority of these SAMs. For example, in Slough 6A the number of SAMS was reduced from 335
to 14 after implementing the QA/QC verification protocol. Through application of AEA’s
QA/QC protocol, presence of both juvenile Coho and Chinook salmon has been positively
documented within many habitat features surveyed including upland sloughs with active beaver
dams (Table C-5). Finally, application of AEA’s QA/QC verification protocol confirmed results
documenting age 2 juvenile Chinook Salmon rearing in the Middle River Segment of the Susitna
River. Because this age class has not been evident in previous sampling, licensing participants
expressed concern during the October 2014 Initial Study Report meetings that the larger sized
juvenile Chinook Salmon collected by field crews in 2013 were misidentified Coho Salmon and
questioned the accuracy of the 2013 field data. AEA’s protocol allowed for confirmation of the
presence of larger sized, age 2 Chinook Salmon, documenting new information about the life
history diversity of this species in the Middle River Segment. Application of AEA’s species
identification protocol has proven valuable at reducing observer error, and substantiating
findings from 2012-2014 fish studies.
4. MANAGEMENT IMPLICATIONS
As discussed above, all ecological sampling has inherent error and studies that rely upon humans
to collect data will have observer bias. Understanding this error is important, but the
significance of the error is determined by considering how the error may affect use of the study
results. How might observer bias in calling a juvenile Coho Salmon a juvenile Chinook Salmon
affect an analysis of AEA’s potential impact and subsequent management decisions? To address
this, the ecology of juvenile Chinook and Coho salmon in the Susitna River basin needs to be
understood. The following description is based largely on analysis of photographically and
genetically-verified juvenile Chinook and Coho salmon from FDA 2013 and 2014 databases
(Study 9.6), and analysis of juvenile Chinook and Coho salmon identified in 2013 and 2014 and
recorded in the HSC database (Study 8.5).
Data from 2013 and 2014 field studies suggest that juvenile Chinook and Coho salmon in the
Middle and Lower Segments of the Susitna River show considerable overlap in ecological niches
during the open water period. Data from fish sampling indicate that these juveniles occupy
similar habitats within the Middle Susitna River and co-occurred in 87 percent of the habitat
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features where species identification were verified (Table B-5). In addition, site-specific habitat
suitability criteria data collected by Study 8.5 show that juvenile Chinook and Coho salmon are
keying in on similar habitat conditions such as shallow water depths, and water velocities less
than 0.5 feet per second and temperature (Figure B-2). Within these habitats, the isotopic data
collected under Study 9.8 indicates that these fish rely upon similar food resources both across
habitats and across seasons (Figure B-3). Finally, the size distributions of the genetically-
verified juvenile Chinook and Coho salmon show considerable overlap in size (Figure B-4) and
support AEA’s finding from scale analysis that both species exhibit life history diversity that
includes freshwater rearing for more than one year (Figure B-5). Based on these data from the
Middle River Segment, many juvenile Chinook and Coho salmon are rearing in the same habitats
during open-water periods, are exposed to similar microhabitat conditions, depend upon similar
food resources, grow to similar sizes, and are of similar ages while rearing in mainstem
freshwater habitats.
Given the ecological similarities between juvenile Chinook and Coho salmon in the Middle and
Lower Susitna River during the open-water period and the low accuracy with identifying Coho
Salmon in some areas in 2013, AEA will combine data collected on Chinook and Coho salmon
from 2013 and 2014 collections to characterize the distribution, relative abundance and habitat
associations of these two juvenile salmon species when evaluating Project impacts. Where
appropriate, AEA also will make use of the verified field identifications to look for species-
specific patterns in growth and movements. Evaluations of Project effects using a pooled
juvenile Chinook/Coho salmon data may overestimate the distribution, abundance and
movement timing for individual species. However, overestimating each species’ habitat use or
range of movement timing would support more protective measures than could be justified for
each species individually. Draft HSC are being developed that may show small differences
between juvenile Chinook and Coho salmon (Study 8.5), especially when considering both open-
water and ice periods. Final effects analyses may consider an approach where protection of
habitats occupied by both juvenile Chinook and Coho lifestages is based on the lifestage that is
most susceptible to effects of Project operations. AEA is confident in the integrity of study
results and their ability to support a rigorous evaluation of potential Project impacts and where
appropriate, development of Protection, Mitigation, and Enhancement measures for these
ecologically similar life stages.
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5. LITERATURE CITED
Elphick, C.S. 2008. How you count counts: the importance of methods research in applied
ecology. Journal of Applied Ecology, 2008, 45, 1313-1320.
Fitzpatrick, M.C., E.L. Preisser, A.M. Ellison, and J.S. Elkinton. 2009. Observer bias and the
detection of low-density populations. Ecological Applications, 19(7), 2009, pp. 1673-
1679.
Kirsch, J, M. Marshall, L. Smoth. 2014. Fish identification accuracy with implications to
monitoring within the San Francisco Estuary, CA. Interagency Ecological Program for
the San Fransisco Estuary, IEP Newsletter vo. 27. No. 2. 2014. Pgas 37-43.
Moyle, P. 2002. Inland Fishes of California. University of California Press, Berkeley and Los
Angeles, California. 502 pgs.
R2 Resource Consultants, Inc. 2014. Fish Distribution and Abundance in the Upper and
Middle/Lower Susitna River (Studies 9.5 and 9.6): Draft Chinook and Coho
Identification Protocol. Filed with the Federal Energy Regulatory Commission by Alaska
Energy Authority, November 17, 2014.
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6. TABLES
Table B-1. Accuracy of 2012-2014 QC3 species identification as determined by genetic analysis of tissue.
QC3 Species ID* N
Species-Genetic Determination
% Correct
Chum
Salmon
Chinook
Salmon
Coho
Salmon
Sockeye
Salmon
Chinook Salmon 854 3 721 126 4 84.4%
Coho Salmon 371
35 334 2 90%
Pacific Salmon, Unspecified 1
1
-
Total Samples 1,226 3 757 460 6 86.10%
*Includes species identification changes for 53 fish in 2014 data set after review of 317 photos.
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Table B-2. Accuracy of QC3 species identification by month and year. Accuracy was determined by genetic analysis tissue samples from N fish.
Year and Month of
QC3 ID*
Chinook Salmon Coho Salmon Both Species
N Number
of Coho
Number
of Chinook % correct N Number of
Chinook
Number
of Coho % correct N % correct
2012 Total 35 35 100%
35 100%
Aug-12 35 0 35 100% 0
35 100%
2013 Total 430 122 308 72% 170 12 158 93% 600 78%
Mar-13 6 2 4 67% 37 0 37 100% 43 95%
Apr-13 22 3 19 86% 2 0 2 100% 24 88%
Jun-13 124 51 73 59% 43 6 37 86% 167 66%
Jul-13 97 14 83 86% 8 0 8 100% 105 87%
Aug-13 116 36 80 69% 42 5 37 88% 158 74%
Sep-13 64 15 49 77% 26 0 26 100% 90 83%
Oct-13 1 1 0 0% 12 1 11 92% 13 85%
2014 Total 389 7 381 97% 201 22 179 89% 591 94%
Apr-14 19 2 17 89% 0
19 89%
May-14 33 0 33 100% 39 6 33 85% 72 92%
Jun-14 48 4 44 92% 75 9 66 88% 123 89%
Jul-14 33 `1 32 97% 0
33 97%
Aug-14 167 0 167 100% 37 2 35 95% 204 99%
Sep-14 49 0 49 100% 45 3 42 93% 94 97%
Oct-14 41 0 41 100% 5 2 3 60% 46 93%
Grand Total 855 689 84% 371 337 90% 1226 86%
*Includes species identification changes for 53 fish in 2014 data set after review of 317 photos.
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Table B-3. QC3 Species ID accuracy by geomorphic reach; percent accuracy was determined by genetic analysis of tissue
samples from N juvenile fish.
Geomorphic Reach
QC3 Species ID
Total Chinook Salmon Coho Salmon
N % Correct N % Correct N % Correct
UR-2 65 100%
65 100%
UR-4 141 100%
141 100%
UR-5 5 100%
5 100%
UR-6 17 100%
17 100%
MR-1 4 100%
4 100%
MR-2 3 100%
3 100%
Impediment 3 PRM 164.8
MR-4 14 100%
14 100%
Impediment 1 PRM 155.1
MR-4 151 100%
151 100%
MR-6 219 71% 83 77% 303 73%
MR-7 9 33% 36 89% 45 78%
MR-8 142 63% 176 97% 318 82%
LR-2 85 88% 73 95% 158 91%
LR-3 2 100%
2 100%
Total 857 84% 368 90% 1226 86%
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Table B-4. 2014 species ID photo review quality control as determined by comparing photo-based species determination
with genetic analysis of tissues from N fish.
Geomorphic
Reach
Chinook Salmon Coho Salmon Sockeye Salmon Total
N
%
Correct N
%
Correct N
%
Correct N
%
Correct
UR-2 2 100%
2 100%
UR-4 9 100%
9 100%
UR-5 1 100%
1 100%
UR-6 15 100%
15 100%
MR-1 4 100%
4 100%
MR-2 3 100%
3 100%
MR-4 105 100%
105 100%
MR-6 54 94% 17 88% 2 0% 73 90%
MR-7 3 0% 19 100%
22 86%
MR-8 24 88% 30 100%
54 94%
LR-2 14 100% 15 100%
29 100%
Grand Total 234 96% 81 98% 2 0% 317 96%
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Table B-5. Documented co-occurrence of verified juvenile Chinook and Coho salmon in 53 of 60 Middle and Lower River
habitat features.
Geomorphic
Reach Feature Name Macrohabitat Type Chinook Salmon
Present
Coho Salmon
Present
MR-5 FA-151 Portage Creek Plume Main Channel-CWP Yes Yes
MR-5 FA-151 Portage Creek Mouth Tributary Mouth Yes Yes
MR-5 FA-151 Portage Creek Tributary Yes Yes
MR-5 FA-151 MC Main Channel Yes Yes
MR-6 Slough 14 Upland Slough Yes Yes
MR-6 PRM 137 US Upland Slough No Yes
MR-6 PRM 134 US Upland Slough No Yes
MR-6 PRM 130 US Upland Slough Yes Yes
MR-6 Jack Long Creek Tributary Yes Yes
MR-6 FA-144 Slough 21 US Upland Slough Yes Yes
MR-6 FA-144 Slough 21 SS Side Slough Yes Yes
MR-6 FA-144 Slough 20 Upland Slough Yes Yes
MR-6 FA-144 Side Channel 21 Side Channel Yes Yes
MR-6 FA-141 Slough 19 Upland Slough Yes Yes
MR-6 FA-141 Slough 17 BW Upland Slough-Backwater Yes Yes
MR-6 FA-141 Slough 17 Upland Slough Yes Yes
MR-6 FA-141 SC Side Channel Yes Yes
MR-6 FA-141 MC Main Channel Yes Yes
MR-6 FA-141 Indian River Mouth Tributary Mouth Yes Yes
MR-6 FA-141 Indian River CWP Main Channel Yes Yes
MR-6 FA-141 Indian River Tributary Yes Yes
MR-6 FA-138 Upper Side Slough 11 Side Slough Yes Yes
MR-6 FA-138 Slough Slough 13 Upland Slough Yes Yes
MR-6 FA-138 Slough Slough 12 Upland Slough No Yes
MR-6 FA-138 Slough 11 Side Slough Yes Yes
MR-6 FA-128 US Upland Slough Yes Yes
MR-6 FA-128 Slough 8A Side Slough Yes Yes
MR-6 FA-128 Skull Creek Mouth Tributary Mouth Yes Yes
MR-6 FA-128 Skull Creek Tributary Yes Yes
MR-6 FA-128 Side Channel 8A Side Channel Yes Yes
MR-6 Curry DMT Main Channel Yes Yes
MR-7 PRM 117 SS Side Slough Yes Yes
MR-7 PRM 113 US Upland Slough No Yes
MR-7 FA-115 Unnamed Trib 115.4 Tributary Yes Yes
MR-7 FA-115 Slough 6A BW Upland Slough-Backwater Yes Yes
MR-7 FA-115 Slough 6A Upland Slough No Yes
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Geomorphic
Reach Feature Name Macrohabitat Type Chinook Salmon
Present
Coho Salmon
Present
MR-7 FA-113 Unnamed Trib 113.7 Tributary Yes Yes
MR-7 FA-113 Slash Creek Tributary Yes Yes
MR-7 FA-113 Oxbow I US Upland Slough No Yes
MR-7 FA-113 Oxbow I SS Side Slough Yes Yes
MR-7 FA-113 Oxbow I MC Main Channel No Yes
MR-7 FA-113 Gash Creek Tributary Yes Yes
MR-7 Chase Creek Main Channel Yes Yes
MR-8 PRM 106.9 TKA Station DMT Main Channel Yes Yes
MR-8 PRM 106 US Upland Slough Yes Yes
MR-8 FA-104 Whiskers Unnamed Side Slough Side Slough No Yes
MR-8 FA-104 Whiskers Slough Side Slough Yes Yes
MR-8 FA-104 Whiskers Creek Main Channel Yes Yes
MR-8 FA-104 Slough 3B Side Slough Yes Yes
MR-8 FA-104 Slough 3A Upland Slough Yes Yes
MR-8 FA-104 SC Side Channel Yes Yes
MR-8 FA-104 MC Main Channel Yes Yes
Lower River PRM 102.4
LR-1 Birch Creek Tributary Yes Yes
LR-2 Montana Creek Tributary Yes Yes
LR-2 Montana Creek Mouth Tributary Delta Yes Yes
LR-2 Sheep Creek Slough Upland Slough Yes Yes
LR-2 Slough near Montana Creek Upland Slough Yes Yes
LR-2 Susitna Main Channel near Montana Creek Main Channel Yes Yes
LR-2 Susitna Side Channel near Montana Creek Side Channel Complex Yes Yes
LR-3 Little Willow Creek Tributary Yes Yes
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7. FIGURES
Figure B-1. Examples of morphological variability among juvenile Chinook Salmon (left) and Coho Salmon (right) parr
from the Susitna River and lower tributary reaches between PRM 80 and PRM 160.5. Species identification was verified
through genetic analysis.
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a)
b)
c)
Figure B-2. Distributions of the Susitna River habitat suitability criteria data for the open-water period (median, 25% and
75% interquartile, range) collected for juvenile Chinook and Coho salmon: a) water depth criteria, b) velocity criteria,
and c) temperature criteria. (source: 2013 and 2014 habitat suitability criteria microhabitat database
http://gis.suhydro.org/SIR/08-Instream_Flow/8.5-Fish_and_Aquatics_Instream_Flow/).
0
1
2
3
4
5
Chinook Salmon Coho SalmonWater Depth (feet)0
0.5
1
1.5
2
2.5
Chinook Salmon Coho SalmonWater Velocity (feet/second)0
3
6
9
12
15
18
Chinook Salmon Coho SalmonTemperature (°C)
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Figure B-3. Results of 2014 isotopic model showing contributions from freshwater, marine, and terrestrial food sources to juvenile Chinook and Coho salmon by site
and season (Source: R2 and UAF 2015; Tables 5.4-4, 5.4-5, and 5.4-6).
RP-104-1 RP-81-3 RP-104-4 RP-104-5 RP-81-1 RP-81-2 RP-104-1 RP-104-5
Spring Summer Fall
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Figure B-4. Size distributions of genetically-verified juvenile Chinook and Coho salmon for the Middle and Lower Susitna Rivers, 2013-2014.
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Figure B-5. Age at length of genetically-verified Chinook and Coho salmon based on scale analysis (Source: R2 and
UAF 2015; Figures 5.4-5 and 5.4-6).