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Susitna‐Watana Hydroelectric Project Document
ARLIS Uniform Cover Page
TK
1425
.S8
S92
no.306
Title:
SuWa 306
Letter from Wayne Dyok to James W. Balsiger, October 7, 2014, in
response to National Marine Fisheries Service's comments on Initial Study
Report on Susitna-Watana Hydroelectric Project
[Title devised by cataloger.]
Author(s) – Personal:
Wayne Dyok (writer of cover letter)
Author(s) – Corporate:
Alaska Energy Authority
AEA‐identified category, if specified:
AEA‐identified series, if specified:
Series (ARLIS‐assigned report number): Existing numbers on document:
Susitna-Watana Hydroelectric Project document number 306 20141008-5071 (FERC posting)
Published by: Date published:
Alaska Energy Authority October 7, 2014
Published for: Date or date range of report:
James W. Balsiger ; National Marine Fisheries Service,
Alaska Regional Office
Volume and/or Part numbers: Final or Draft status, as indicated:
Document type: Pagination:
Letter with attachments 3, 28, 17 pages
Related work(s): Pages added/changed by ARLIS:
Response to: Letter from James W. Balsiger to Wayne Dyok,
September 22, 2014, providing National Marine Fisheries
Service's comments on the Initial Study Report for the
Susitna-Watana Hydroelectric Project. (SuWa 305)
SuWa 305 is a comment to: Initial Study Report. (SuWa 223)
Notes:
Distributed also as a posting of FERC eSubscription to Docket 14241.
The enclosures contain detailed information that supplements the comments in the letter.
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/susitnadocfinder/
October 7 , 2014
James W. Balsiger
Administrator, Alaska Region
National Marine Fisheries Service
P.O. Box 21668
Juneau , Alaska 99802-1668
Re: Susitna-Watana Hydroelectric Project, FERC Project No. 14241-000
Dear Mr. Balsiger:
The Alaska Energy Authority (AEA) is in receipt of a letter from the National
Marine Fisheries Service (NMFS) dated September 22, 2014,1 in which you provide
comments on portions of the Initial Study Report (June 3, 2014) (ISR) for the proposed
Susitna-Watana Hydroelectric Project, Federal Energy Regulatory Commission (FERC)
Project No. 14241 (Project). Your letter raises a number of what it refers to as "issues
with the data ," including alleged questionable data collection methods , absence of
quantitative analysis, and inappropriate scale of data collection, among others. You
opine that these supposed anomalies mean that "it is not plausible that the data for
predictive modeling be used to describe baseline conditions or to predict potential
impacts ," and that "these issues must be resolved prior to conducting additional field
studies." In other words , you believe we are at a standstill.
Frankly , for NMFS to take the position that the massive amount of scientific data
AEA has collected and summarized in the ISR is unreliable is untenable, bordering on the
absurd. As documented in the ISR, AEA was largely successful in implementing the
PERC-approved study plan in 2013. This effort included , among many other studies , a
large-scale field effort for fishery studies with a suite of 10 studies covering more than
200 sampling sites across more than 200 miles of river , with sampling occurring during
not only the open water period but also during winter and spring periods. Your letter,
however, focuses on the limited exceptions in which AEA 's data collection varied from
PERC-approved study plan methods during the 2013 field season. These variances, as
we all know , occurred mostly due to private land access issues , and conditions in the field
such as the late ice breakup in the spring of 2013. The ISR includes a detailed
description of proposed modifications to the study plan to account for these variances.
Letter from James W . Balsiger, N ational Marine Fisheries Service , to Wayne Dyok, Alaska Energy Authority ,
Project No . 14241-000 (filed with Federal Energy Regulatory Commission on September 23 , 2014).
Noticeably absent from your letter is any critique or analysis of AEA 's proposed
modifications , or any alternative method that would help achieve study plan objectives in
light of the variances.
AEA also takes exception to any suggestion that it has not implemented the
PERC-approved study plan in a professional manner. The fisheries field work was led by
nationally renowned experts in their respective fields , representing five independent
contractors , all with significant hydropower licensing and Alaska experience. The field
technicians employed by these contractors are highly qualified , and many have advanced
degrees from the University of Alaska-Fairbanks and University of Alaska-Anchorage.
In contrast, NMFS ' s generalized comments either ignore the data and analysis presented
in the ISR, or reflect a fundamental lack of understanding of the methodologies being
relied upon by the PERC-approved study plan, which NMFS helped develop.
For example, NMFS asserts that AEA has misidentified or was unable to identify
juvenile fish species in its field sampling efforts. As you should know , all field
identifications of juvenile salmon are subject to error due to the inherent variations in
each species ' distinguishing characteristics at those life stages. Your letter claims we
have an unacceptable level of error because the juveniles we identified as Chinook
salmon in our samples were too large , and too many were found in sloughs or with
beaver ponds. We instructed our crews to make field calls based on the physical
characteristics used for distinguishing coho and Chinook salmon, not on their size or
where they were found. There are several possible explanations for why larger juveniles
might be found in the sloughs, including displacement during the 2012 fall flood, or
during 2013 spring flooding at breakup , or as a result of ice processes. Simply to dismiss
the possibility that these fish were Chinook because of where they were found would
have been unscientific. You also cite an unusually large number of unidentified juveniles
in our sampling. Our field crews followed instructions per AEA 's Quality
Assurance/Quality Control (QA/QC) measures that , when unable to make a call in the
few seconds that is safe to hold a juvenile fish out of water, they should subsample in a
location by photographing juveniles and collecting genetic samples and voucher
specimens. The senior scientists from our study team and Alaska Department of Fish and
Game staff review these photographs , genetic samples , and vouchers to verify field
identification. Some unidentified salmon calls remain at some sites , but these are not
material to the objectives of relevant studies (Studies 9.5 and 9 .6).
Under the PERC-approved study plan (Studies 8.5 , 9.5 , and 9.6), the purpose of
this particular data collection effort is to determine the distribution of fish species within
different aquatic habitats. This information will be used as inputs to habitat models.
Whether a specific juvenile salmon is correctly identified as coho versus Chinook salmon
will have no bearing whatsoever on the outcome of the habitat modeling because these
models will consider all life stages of all five of the Pacific salmon species present in the
Susitna basin. With respect to coho and Chinook salmon, the habitat suitability criteria
2
for the rearing life stages of these species substantially overlap , ensuring that the model
will adequately characterize the most protective habitat for both species.
Your letter also contains a number of outright errors and instances in which you
ignore available information. Among these , your letter states that there was an "absence
of pink salmon in any samples." However, pink salmon counts are reported in se v eral
tables in the ISR. Your letter also states that AEA did not include estimates of relative
abundance , yet relative abundance is presented in the ISR in text and detailed tables of
"catch per unit effort." Your letter states that fish passage criteria have not been
developed-they have been developed , and reviewed with licensing participants
including NMFS at the March 19, 2014 fish barriers technical meeting.
Attached to this letter is a comment-response table that addresses in detail each of
the comments in your September 22 letter. I think you will agree , on careful review of
our responses , that the 2013 study program provides a solid foundation of data upon
which we can continue to build.
AEA remains committed to implementing the comprehensive suite of studies
proposed in the PERC-approved study plan and encourages NMFS to work with us in
good faith in studying the feasibility of and potential effects associated with an
undertaking that is critically important to Alaskans. If you have questions or comments
concerning this matter, please feel free to contact me directly at (907) 771-3955.
Attachment
Cc: Distribution List
Samuel D. Rauch III
Jeff Wright
Ann Miles
Vince Yearick
Dr. Jennifer Hill
Nick Jayjack
Sincerely ,
V~???P7d
Wayne Dyok
Project Manager
Alaska Energy Authority
3
AEA’S RESPONSE TO NMFS SEPTEMBER 22, 2014 ISR COMMENT LETTER
Susitna-Watana Hydroelectric Project Alaska Energy Authority
FERC Project No. 14241 Page 1 October 2014
AEA’S RESPONSE TO NMFS SEPTEMBER 22, 2014 ISR COMMENT LETTER
OCTOBER 7, 2014
Comment
Page
Para
Comment
Number Comment Response
Page 4 1
Para 5
1 1) Habitat classification has not been
completed;
This comment ignores the data and analysis presented in the ISR. Remote habitat classification was
completed in 2013, as presented in Study 9.9 ISR Sections 5.1 and 5.2, and Study 6.5 ISR Section 5.4
and Part 2 of 3 Figures. Land access restrictions resulted in a delay to complete the field surveys to
ground-truth remote classification. The variance regarding delay in the ground-truthing study
component was addressed in Study 9.9 ISR Section 4.2.4.
The schedule for completion of the ground-truthing surveys was presented in 9.9 ISR Section 7.2.
All field work was completed in 2014 as described in the 2013 and 2014 Aquatic Habitat Mapping
Field Season Completion Progress Technical Memorandum that was filed with FERC on September
17, 2014.
Page 4
Para 6
2 2) Fish passage criteria have not been
developed;
AEA disagrees. With respect to Study 9.12 Fish Passage Barriers, AEA proposed leaping, depth, and
velocity criteria. AEA reviewed this criterion with the Licensing Participants during Interdisciplinary
Fish Barriers Technical Meeting on March 19, 2014.
Page 4
Para 7
3 3) Fish sampling study plans were not
followed; sampling units were
inappropriately subsampled;
This comment ignores the data and analysis presented in the ISR. The Fish Distribution and
Abundance Study Plan Determination and Final Implementation Plan (filed April 1, 2013) were
implemented by AEA field crew. However, as noted and explained in Study 9.5 ISR Section 4.4.4,
there were variances to the plan methods that occurred during implementation, including sub-
sampling GRTS panels and transects sites in the Upper River, as a result of conditions in the field.
NMFS does not acknowledge the reason for the variances or AEA’s proposed modifications to
account for them, nor does it explain why subsampling was inappropriate in the circumstances. AEA
conducted additional analysis of the data collected in the Upper River and proposed modifications in
Study 9.5 ISR Section 7.1.2 to ensure that the data will meet all Study 9.5 objectives. This
information also was presented in a Fish Technical Meeting on March 20, 2014 and input from
stakeholders including NMFS was solicited. The modifications, as proposed in Study 9.5 ISR
Section 7.2, were implemented in 2014 to collect data supplemental to the 2013 field effort. The
results of the 2014 surveys were summarized in the Proposed 2015 Modifications to Fish Distribution
and Abundance Study Plan Implementation Technical Memorandum filed with FERC on September
1 Page and Paragraph Numbering:
• Partial sentences at the top of a page are considered Sentence 1.
• Partial paragraphs at the top of a page are considered Paragraph 1.
• Paragraphs are numbered by their position on a page, not within a Section.
• Paragraphs are blocks of text separated by hard returns; each heading, bullet, and item in a numbered list is considered one paragraph.
20141008-5071 FERC PDF (Unofficial) 10/8/2014 10:58:27 AM
AEA’S RESPONSE TO NMFS SEPTEMBER 22, 2014 ISR COMMENT LETTER
Susitna-Watana Hydroelectric Project Alaska Energy Authority
FERC Project No. 14241 Page 2 October 2014
Comment
Page
Para
Comment
Number Comment Response
17, 2014.
Page 4
Para 8
4 4) Fish sampling locations did not
incorporate FERC recommendations;
This comment ignores the data and analysis presented in the ISR. Fish sampling locations followed
the FERC recommendations where feasible. As explained in Studies 9.5 and 9.6, there were some
variances due to field conditions and land access limitations. These variances did not affect the
quality or the integrity of the data collected, or the ability to meet study plan objectives.
Page 4
Para 9
5 5) Because the fish sampling did not follow
the sampling plan, this resulted in an
inability to estimate relative fish abundance;
AEA disagrees that variances from the sampling plan identified in Comments 3 and 4 resulted in an
inability to obtain accurate estimates. See answers to Comments 3 and 4. Estimates of relative
abundance are reported in Study 9.5 ISR Sections 5.1.2, 9.5, and Appendix E (Upper River Fish
Observations and Relative Abundance 2013) as well as Study 9.6 ISR Section 5.1.2 and Appendix E
(Relative Abundance Tables).
Page 4
Para 10
6 6) Fish seem to have been identified
incorrectly;
Please see below for responses to specific comments concerning fish identification.
Page 4
Para 11
7 7) Data were collected and reported at
inappropriate mesohabitat scales;
This comment ignores the data and analysis presented in the ISR. Fish Distribution and Abundance
(FDA) data were collected and reported at meso- and macro-habitat scales consistent with the study
plan (Study 9.5 ISR Section 4.4.2 and Study 9.6 ISR Section 4.4.2). Based on USFWS comments,
Comment 7 appears to be specific to the Barrier Study (Study 9.12) and the HSI/HSC component of
the IFS Study (Study 8.5). The Fish Barriers and IFS studies are collaborating, regarding target
species, passage criteria, and sampling locations. This will ensure that the model outputs from IFS
are useful for analysis of passage barriers.
Page 4
Para 12
8 8) Sampling sites among studies were not
co-located;
This is incorrect; the sampling sites were co-located. This comment ignores the data and analysis
presented in the ISR. AEA’s selection of sampling sites was consistent with the River Productivity
Implementation Plan. As presented in the River Productivity Implementation Plan Section 2.1: “All
stations established within the Middle River Segment will be located at Focus Areas established by
the Instream Flow Study (AEA 2012, Section 8.5.4.2.1.2), in an attempt to correlate
macroinvertebrate data with additional environmental data (flow, substrates, temperature, water
quality, riparian habitat, etc.) collected by other studies (e.g., AEA 2012, Section 5.5, Baseline Water
Quality), for uses in statistical analyses, and HSC/HSI development. Furthermore sites for Fish
Distribution and Abundance, Habitat Suitability Criteria, and River Productivity were all co-located
within Middle River Focus Areas. In 2013, private land access restrictions prevented fish sampling
in some desired locations, yet River Productivity sampling was able to be conducted because the sites
for that study were located in mainstem and within ordinary high water. Maps depicting the co-
locations of sampling sites among these three studies will be presented in the October 15, 2014 ISR
meeting.
Page 4
Para 13
9 9) Tagging goals were not met; This comment ignores the data and analysis presented in the ISR. Tagging goals were generally, but
not precisely, met for every location and species in the Escapement Study in 2013 (9.7 Section 4.1.4).
These few discrepancies do not affect the quality or the integrity of the data collected. In the Lower
River, the targets were 700 Chinook salmon, 600 coho salmon, and 200 pink salmon. Actual tagging
20141008-5071 FERC PDF (Unofficial) 10/8/2014 10:58:27 AM
AEA’S RESPONSE TO NMFS SEPTEMBER 22, 2014 ISR COMMENT LETTER
Susitna-Watana Hydroelectric Project Alaska Energy Authority
FERC Project No. 14241 Page 3 October 2014
Comment
Page
Para
Comment
Number Comment Response
numbers were 698 Chinook salmon, 596 coho salmon, and 197 pink salmon. At the Yentna, 690
Chinook salmon were tagged as compared to the 700 fish target. In the Middle River, tagging targets
were met for all salmon species except sockeye; 139 sockeye were tagged out of the 200 fish target.
For resident species tagging target in Studies 9.5 and 9.6, the study plan indicated that “the goal is to
implant 30 radio transmitters per target species” and the winter movement objective specified “up to
30” fish as the target for burbot, humpback whitefish and round whitefish. In 2013, progress was
made toward these goals as indicated in Study 9.6 ISR Section 4.5.2 and Study 9.6 ISR Section 4.5.2.
Further progress toward the tagging goals was made in 2014 and will be presented at the ISR meeting
on October 15, 2014.
Page 4
Para 14
10 10) Fish targets for HSC sampling were not
met;
This comment ignores the data and analysis presented in the ISR and reflects a fundamental lack of
understanding of the methodologies being relied upon by the FERC-approved study plan. The
targets pertain to the total number of HSC data points collected over the entire licensing study period,
not one field season. Absolute target numbers were not established for HSC data collection (see RSP
8.5.4.5.1.1.5) for the first year of study, or the licensing study period in general. The FERC-approved
Study Plan noted that: “If possible, a minimum of 100 habitat use observations will be collected for
each target species life stage. However, the actual number of measurements will be based on a
statistical analysis that considers variability and uncertainty. While information will be collected on
all species and life stages encountered, the locations, timing, and methods of sampling efforts may
target key species and life stages identified in consultation with the TWG.” This was discussed
during several TWG meetings where it was emphasized that the approach AEA is taking in
developing HSC curves will include several components, including collection of new site specific
data, which is AEA’s and agencies preferred approach, as well as other approaches for species or life
stages infrequently encountered. AEA listed those in RSP 8.5.4.5.1.1 and included use of existing
site specific data collected during the 1980s studies, use of site specific data from other similar
Alaska systems, as well as professional opinion.
A summary of HSC collection efforts to date is provided below. As noted, there are a number of
species for which the numbers of observations have exceeded 100, including those for Chinook
salmon juvenile, Chum fry and spawning, Coho fry, Sockeye fry and spawning, Arctic Grayling fry,
and whitefish fry. These species and life stage mixes reflect the majority of the target species and life
stages that are central to the habitat-flow modeling for evaluating Project effects.
Species Lifestage 2013 2014
Through July
Project
Total
1980s
Total
Chinook Fry 54 164 218
20141008-5071 FERC PDF (Unofficial) 10/8/2014 10:58:27 AM
AEA’S RESPONSE TO NMFS SEPTEMBER 22, 2014 ISR COMMENT LETTER
Susitna-Watana Hydroelectric Project Alaska Energy Authority
FERC Project No. 14241 Page 4 October 2014
Comment
Page
Para
Comment
Number Comment Response
Juvenile 38 25 63
Chum Fry 14 258 272
Spawning 348 348 333
Coho Fry 99 181 280
Juvenile 56 28 84
Pink Fry 0 39 39
Spawning 59 0 59 NR
Sockeye Fry 79 299 378
Spawning 181 181 81
Arctic Grayling Fry 113 7 120
Juvenile 43 9 52
Adult 4 4 8 140
Burbot Juvenile 2 4 6
Adult 17 3 20 18
Dolly Varden Fry 20 20
Adult 1 1 2 2
Longnose Sucker Fry 41 46 87
Juvenile 52 27 79
Adult 70 3 73 157
Rainbow Trout Juvenile 5 2 7
Adult 6 1 7 143
Whitefish Fry 39 73 112
Juvenile 39 15 54
Adult 29 4 33 384
Additional HSC/HSI sampling is planned for the next year of study and it is anticipated that most
20141008-5071 FERC PDF (Unofficial) 10/8/2014 10:58:27 AM
AEA’S RESPONSE TO NMFS SEPTEMBER 22, 2014 ISR COMMENT LETTER
Susitna-Watana Hydroelectric Project Alaska Energy Authority
FERC Project No. 14241 Page 5 October 2014
Comment
Page
Para
Comment
Number Comment Response
HSC relationships will be updated. However, for species and life stages that are rarely observed,
final HSC curves may be based on additional data, including utilization data from 2012 and the 1980s
studies on the Susitna River. Even then, there may still be some species where few or no empirical
HSC/HSI data were able to be collected. In those cases, AEA will consider other methods for
developing curves. This may include the use of literature based curves, developing envelope curves
(see, for example, Jowett et al. 1991, and GSA BBEST 2011), guilding (e.g., creating a combined
HSC/HSI curve representing multiple species and/or life stages; see, for example, Vadas, Jr. and
Orth 2001, GSA BBEST 2011), developing curves based on expert opinion/round table discussions)
and the use of Bayesian statistical methods for updating data distributions (see, for example,
Hightower 2012).
Page 4
Para 15
11 11) The mainstem upper river migrant fish
trap was not installed;
This comment ignores the data and analysis presented in the ISR. This variance was identified in
Study 9.5 ISR Section 4.1.6.2 due to lack of access to areas above the ordinary high water mark.
AEA completed this task in 2014 as described in Study 9.5 ISR Section.7 and TM for Study 9.05.
Page 4
Para 16
12 12) A fish wheel was not installed, and fish
were not tagged near the entrance to Devils
Canyon;
This comment ignores the data and analysis presented in the ISR. This variance was described in
Study 9.7 ISR Section 4.1.8.1. This change in tagging location was compensated for by increased
fishwheel effort and an increase in tagging targets at the Curry fishwheels.
Page 4
Para 17
13 13) Additional problems associated with
late installation and operation of migrant
traps were likely influenced by
environmental conditions associated with
late breakup; and
Downstream migrant traps were installed and operated as indicated in the Study 9.5 ISR Section
9.5.4.4.10 and Study 9.6 ISR Section 9.6.4.4.10: “flow conditions permitting, traps will be fished on
a cycle of 48 hours on, 72 hours off throughout the ice-free period.” As soon as break-up and flow
conditions allowed in mid-June 2013 traps were fished immediately upon installation in June through
mid-October 2013. In 2014 breakup occurred earlier and migrant traps installation occurred in mid-
May with traps operated immediately after installation (the Proposed 2015 Modifications to Fish
Distribution and Abundance Study Plan Implementation Technical Memorandum filed with FERC on
September 17, 2014).
Page 4
Para 18
14 14) Juvenile salmon distribution and
abundance in 2013 were likely affected by
the record fall floods in 2012.
AEA agrees that floods can affect juvenile salmonid abundance. While the fall 2012 floods did not
approach the magnitude of the flood of record, they potentially distributed juvenile salmonids into
lateral habitats that may not otherwise be occupied during a low water year. AEA believes that the
range of hydrologic events that occur over the multi-year study period provide opportunities to better
understand the response of aquatic resources to flow fluctuations.
Page 4
Para 20 –
Page 5
Para 1
15 The actual implementation of the abundance
sampling program did not follow the
statistical models used to select sampling
units. In particular, subareas (mesohabitats)
within selected areas were ‘randomly’
selected for subsampling, and sampling was
not consistent between sampling events
AEA disagrees. This comment reflects a fundamental lack of understanding of the methodologies
being relied upon by the FERC-approved study plan. The random selection of meso-habitat units
within GRTS selected panel sites and at transects was implemented as proposed in the Fish
Distribution and Abundance Implementation Plan filed with FERC on March 1, 2013.
The use of different gears consistent with habitat characteristics was implemented as proposed in the
Fish Distribution and Abundance Implementation Plan filed with FERC on March 1, 2013 with
20141008-5071 FERC PDF (Unofficial) 10/8/2014 10:58:27 AM
AEA’S RESPONSE TO NMFS SEPTEMBER 22, 2014 ISR COMMENT LETTER
Susitna-Watana Hydroelectric Project Alaska Energy Authority
FERC Project No. 14241 Page 6 October 2014
Comment
Page
Para
Comment
Number Comment Response
(different gears, different effort, different
order of gears, different total area sampled,
etc.). Sampling error in the fish distribution
and relative abundance studies needs to be
accounted for in order for these studies to
accurately estimate fish distribution and
abundance. Estimates of numbers of
Chinook salmon that migrate above Devils
Canyon need to include the assumptions,
standard error, and resulting statistical
confidence intervals associated with that
estimate. Better descriptions of (and
statistical accounting for) both sampling and
non-sampling errors need to be provided.
The data used to describe fish-habitat
association preferences and the standard
errors associated with those species and
life-stage habitat correlations need to be
validated, as this analysis proposes to
describe macrohabitat relationships for fish.
These relationships will be used to evaluate
project effects, to validate instream flow
habitat model predictions, and to
extrapolate results from focus areas to
geomorphic reaches and river segments.
Ultimately these data will be used to
develop protection and mitigation measures
and to serve as a basis for post-project
monitoring.
modification described in Study 9.5 ISR Section 4.4.4 and Study 9.6 ISR Section 4.4.4.
AEA disagrees that sampling error will impact AEA’s ability to meet objectives of fish distribution
and abundance sampling for Studies 9.5 and 9.6. The fish distribution and relative abundance
methods were implemented consistent with Studies 9.5 and 9.6 RSPs, the Fish Distribution and
Abundance Implementation Plan, and FERC’s SPD.
As described in RSP Section 9.7.4.1.5 (Objective 1) and Section 9.7.4.6 (Objective 6), AEA planned
to examine fish on selected spawning grounds (e.g., Indian River) in part to establish mark rates
(proportion of fish tagged) so that inferences could be made about the representativeness of tagging
across stocks. In addition, AEA stated that mark rates from these areas can be used to estimate the
abundance passing the tagging sites (but not the abundance at the recovery site). If sufficient
sampling can be obtained and some assumptions met, some inference can be made about relative
abundance among recovery locations using the estimates of mark rates and the number of radio-
tagged fish present. However, it was not an objective of this study to produce a mark-recapture
estimate of the number of Chinook salmon migrating above Devils Canyon (or above the proposed
dam site).
In the FERC SPD (page B-13), NMFS and the USFWS requested that AEA add the additional goal
of estimating the numbers of fish above Devils Canyon (and the proposed dam site) to the study.
FERC did not recommend this additional goal be included in the study. Instead, FERC
recommended the study be modified to require AEA to include in the 2013 ISR an evaluation of the
feasibility of putting in a weir or sonar counting station at or near the dam site during the 2014 study
season to count anadromous fish.
In ISR Section 5.6.4, AEA used two different approaches to estimate of the number of Chinook
salmon that migrated above Devils Canyon in 2013. The first approach involved expanding the peak
aerial spawner count in tributaries above Devils Canyon (29 fish) by the estimated observer
efficiency (46.3 percent, as observed in the Indian River; 26/0.463 = 63 fish). This expanded count
should be considered a minimum number since only fish counted on the July 25-27 survey were
included. Chinook salmon were also observed in tributaries above Devils Canyon on four other
surveys, so it is possible that some of these fish were not present during the July 25-27 survey. Also,
this approach assumed that the observer efficiency in tributaries above Devils Canyon was similar to
that in the Indian River (which was ‘ground-truthed’ with weir counts in 2013).
The second approach involved expanding the number of radio-tagged Chinook salmon detected
above Devils Canyon (3 fish) by the marked fraction of Chinook salmon in the Middle River (6.3
20141008-5071 FERC PDF (Unofficial) 10/8/2014 10:58:27 AM
AEA’S RESPONSE TO NMFS SEPTEMBER 22, 2014 ISR COMMENT LETTER
Susitna-Watana Hydroelectric Project Alaska Energy Authority
FERC Project No. 14241 Page 7 October 2014
Comment
Page
Para
Comment
Number Comment Response
percent; 3/0.063 = 48 fish). It was highly unlikely that more than three fish migrated above Devils
Canyon. This approach assumed that the mark rate of fish above Devils Canyon was the same as the
mark rate of fish sampled in the Indian River. Sensitivity analyses were included in ISR Sections
5.6.4 and 6.6 to illustrate how extreme, but unlikely, parameter values affected the expanded counts
derived from both approaches.
In summary, too few tagged and untagged fish were observed above Devils Canyon to derive a
statistically valid estimate of the number of Chinook salmon that passed Impediment 3 (or the
proposed dam site). Regardless, the study was not designed to produce such estimates. As proposed
in the RSP, AEA used available data to make inferences about the abundance of Chinook salmon
above Devils Canyon. Although lacking statistical rigor, these estimates provided insight into the
order of magnitude of Chinook salmon abundance above Devils Canyon (e.g., 50-65 fish above
Devils Canyon in 2013 was likely, but 100 or more was unlikely). These estimates also illustrate
how difficult it would be to achieve sufficient samples sizes to derive a reasonably accurate and
precise mark-recapture estimate for Chinook salmon above Devils Canyon.
Summary of passage events for large Chinook salmon (MEF ≥ 50 cm) released in the Middle
River, 2012-2014. Small Chinook salmon, and large Chinook salmon released in the Lower
River, were not included in this table.
20141008-5071 FERC PDF (Unofficial) 10/8/2014 10:58:27 AM
AEA’S RESPONSE TO NMFS SEPTEMBER 22, 2014 ISR COMMENT LETTER
Susitna-Watana Hydroelectric Project Alaska Energy Authority
FERC Project No. 14241 Page 8 October 2014
Comment
Page
Para
Comment
Number Comment Response
As stated in Study 9.5 ISR Section 5.1.3 and Study 9.6 ISR Section 5.1.3 data presented on habitat
associations was preliminary and based only on counts and therefore have no standard error
associated with these data. Once QAQC has been completed on the fish data, the analysis of fish-
habitat associations will be completed with additional inputs including relative abundance, species
2012 2013 2014 Total
Tags Released at Curry 352 536 590 1,478
Number of Tags Detected Above:
Gateway 313 445 491 1,249
Impediment 1 23 17 11 51
Impediment 2 20 13 8 41
Impediment 3 10 3 2 15
Proposed Dam Site 6 2 1 9
Percent of Tags Released Detected Above:
Gateway 88.9 83.0 83.2 84.5
Impediment 1 6.5 3.2 1.9 3.5
Impediment 2 5.7 2.4 1.4 2.8
Impediment 3 2.8 0.6 0.3 1.0
Proposed Dam Site 1.7 0.4 0.2 0.6
Percent of Tags Past Gateway Detected Above:
Impediment 1 7.3 3.8 2.2 4.1
Impediment 2 6.4 2.9 1.6 3.3
Impediment 3 3.2 0.7 0.4 1.2
Proposed Dam Site 1.9 0.4 0.2 0.7
Number of Tags That Approached Impediment 1 (within 1 km)34 60 32 126
Percent of Tags Released That Approached Impediment 1 9.7 11.2 5.4 8.5
Percent of Tags Past Gateway That Approached Impediment 1 10.9 13.5 6.5 10.1
20141008-5071 FERC PDF (Unofficial) 10/8/2014 10:58:27 AM
AEA’S RESPONSE TO NMFS SEPTEMBER 22, 2014 ISR COMMENT LETTER
Susitna-Watana Hydroelectric Project Alaska Energy Authority
FERC Project No. 14241 Page 9 October 2014
Comment
Page
Para
Comment
Number Comment Response
richness, and life stages supported. As stated in the RSP Section 9.6.4.3.1, Study 9.5 ISR Section
5.1.3, and Study 9.6 ISR Section 5.1.3 fish-habitat associations will be evaluated at the meso-habitat
level. These data will not be used to validate the instream flow model but to further characterize at
macrohabitat that are subject to flow effects at the meso-habitat level.
Page 5
Para 3
16 Data collection methods need improvement.
For example, detection and recovery of PIT
(passive Integrated Transponder) tags need
to be improved to yield useful data to meet
study goals and objectives. Location of the
detection arrays did not cover the entire
channel and was biased toward fish
migrating down channel. Also, because too
few tags were recovered, efficiency
estimates could not be made.
This comment reflects a fundamental lack of understanding of the methodologies being relied upon
by the FERC-approved study plan. As stated in RSP Sections 9.5.4.4.1.2 and 9.6.4.4.1.2, remote
telemetry techniques were “intended to provide detailed information on relatively few individual
fish.” PIT tags were used to “document relatively localized movements of fish as well as growth
information from tagged individuals.” Due to the size of the study rivers, the necessity for installing
arrays across split channels, side-channels and/or as partial coverage arrays across a portion of the
main channel is described in the Fish Distribution and Abundance Implementation Plan Section
5.6.5. Furthermore, both FA-104 and FA-128, the PIT tag arrays spanned the entire channels.
Data from PIT tag arrays provided limited but valuable information on fish movements. As indicated
in Study 9.5 ISR Section 5.2.2.2 and Study 9.6 ISR Section 5.2.2.2, antenna arrays recorded 29,047
detections of 33 fish in the Upper River and 126,351 detections of 664 fish at Middle River arrays.
These resightings provided information on local and inter-stream movements of individual for six
species in the Upper River and 11 species in the Middle River as well as site-specific growth rates for
individuals of several species (Study 9.6 ISR Section 5.5.1).
Page 5
Para 4
17 Misidentification of juvenile fish by species
induces significant error, and application of
this erroneous data would result in
inaccurate conclusions. Our review of the
Initial Study Report finds that a very high
percentage of the juvenile salmonids were
misidentified. We also question the
accuracy of all juvenile fish sampling data
because of the following details:
AEA disagrees. This comment reflects a fundamental lack of understanding of the methodologies
being relied upon by the FERC-approved study plan. NMFS concern appears to be centered on the
potential mis-identification of coho versus Chinook salmon in certain habitats that were part of fish
distribution studies. Whether those identifications are correct or not has no bearing on the outcome
of the habitat-modeling studies that will consider all of the Pacific salmon species. AEA has focused
a substantial effort into the development of resource specific models that will link with habitat-flow
based models for evaluating the effects of flow regulation below the dam on various fish species and
processes both spatially and temporally. The biological inputs to the habitat models will be provided
primarily via the HSC analysis that includes a suite of flow sensitive parameters associated with
different species and life stages. The HSC data are being collected in accordance with the study plan
and will result in a series of species specific HSC curves that will be brought into the fish-habitat
modeling. At this time the plan is to run the habitat-flow models for all of the target salmonid species
and life stages including sockeye and chum salmon adults/spawning, which are the species most
often associated with the lateral habitats that are likely to be most influenced by Project operations, as
well as coho, Chinook, and pink salmon.
Page 5
Para 5
18 large numbers of unidentified salmonid
juveniles (some of which were PIT tagged);
AEA disagrees that numbers of unidentified juvenile salmonids are significant.
20141008-5071 FERC PDF (Unofficial) 10/8/2014 10:58:27 AM
AEA’S RESPONSE TO NMFS SEPTEMBER 22, 2014 ISR COMMENT LETTER
Susitna-Watana Hydroelectric Project Alaska Energy Authority
FERC Project No. 14241 Page 10 October 2014
Comment
Page
Para
Comment
Number Comment Response
In Study 9.6 ISR Table 5.1-2: 865 undifferentiated Pacific salmon Juveniles in MR, five percent of
all juvenile salmon, ~ half from Slough 6A. 436 fish identified after photo review and classified to
species. Resulting in a total of 429 undifferentiated Pacific salmon remaining in database, 2.5
percent of total.
In Study 9.46 ISR Table 5.1-3: 78 undifferentiated Pacific salmon juveniles in LR, two percent of
total.
AEA is in the process of reviewing photos from the Lower River, which should reduce the number of
unidentified juvenile salmonids.
In 2013, 11 undifferentiated pacific salmon were PIT-tagged (67 reported in ISR but photo review
resulted in identification of 56 of the 67); four of these 11 tagged unidentified pacific salmon met
length criteria to be two-year-olds. Ten of these 11 fish have photos that are under review. In total
1,872 Chinook salmon and 2,793 Coho salmon were PIT-tagged in 2013 and Winter 2014.
Page 5
Para 6
19 anomalous length distributions and habitat
associations (e.g., juvenile Chinook 150
mm fork-length;
Summary of large juvenile Chinook and coho salmon. Based on growth modeling, juvenile Chinook
and coho >100mm in May and June were presumed to be two-year-old fish and >120mm from July-
April were presumed to be two-years of age. These data are not consistent with data from the 1980s
and are undergoing additional analysis.
Location PRM Habitat Chinook
salmon
Coho
salmon
Pacific
salmon,
undifferenti
ated
Total
DMT-Talkeetna
Station 106.9 MS Susitna River 72 8 3 83
Indian River
DMT 142.1 Tributary 70 4 74
FA-141-Slough
17 142.3
Upland Slough
Beaver Complex 70 16 1 87
Montana Creek
DMT 80.8 Tributary 37 4 41
FA-104-Slough
3A 105.7
Upland Slough
Beaver Complex 15 25 1 41
FA-104-SS 105 Side Slough 14 2 16
20141008-5071 FERC PDF (Unofficial) 10/8/2014 10:58:27 AM
AEA’S RESPONSE TO NMFS SEPTEMBER 22, 2014 ISR COMMENT LETTER
Susitna-Watana Hydroelectric Project Alaska Energy Authority
FERC Project No. 14241 Page 11 October 2014
Comment
Page
Para
Comment
Number Comment Response
PRM-63.5-US 62.5
Upland Slough
Beaver Complex 9 11 20
FA-115-Slough
6A 116.2
Upland Slough
Beaver Complex 6 31 37
Genetics samples were collected from 37 of these large Chinook and four large coho salmon, 2013.
An additional 29 samples were collected from Chinook salmon >100 mm collected July 2013-April
2014. Analysis of these samples is currently underway. A total of approximately 600 Chinook
salmon tissue samples have been delivered to ADF&G for analysis and can be used to determine
overall Chinook salmon identification error rate if needed.
Approximately 24 voucher specimens have been collected for Chinook (10) and coho salmon (14).
These fish will be used for meristic counts to determine species ID. Our ADF&G permit limited us
to 10 per species but was recently modified to up to 20 Chinook and coho salmon.
31 photos of these large Chinook salmon are also available for review. Review is complete for R2
photos but need to review photos from HDR and Golder. Results of photo review will be used in
combination with genetics and meristic data to evaluate accuracy of field identification.
Page 5
Para 7
20 the large abundance of juvenile Chinook
in beaver ponds;
Habitats where Chinook salmon were collected in 2013 and winter 2014. Larger Chinook salmon are
defined in Comment Number 19. 681 juvenile Chinook salmon were collected from upland slough
beaver complexes compared to 3,414 coho salmon. Approximately 14 percent of Chinook salmon
were associated with upland slough beaver complexes. The highest habitat supporting collection was
tributaries, over 21 percent of total collections. Of larger Chinook salmon, roughly a third, 100 out of
313, were associated with upland slough beaver complexes.
Macro Habitat
Chinook salmon Coho salmon
Pacific salmon,
undifferentiated Total
All
Sizes
Larger
fish
All
Sizes
Larger
fish All Sizes
Larger
fish
Additional Open
Water
1 32 1 33
Backwater 31 1 107 3 141
Clear Water Plume 69 2 144 14 227
Main Channel 1,038 74 1,210 23 79 3 2,327
20141008-5071 FERC PDF (Unofficial) 10/8/2014 10:58:27 AM
AEA’S RESPONSE TO NMFS SEPTEMBER 22, 2014 ISR COMMENT LETTER
Susitna-Watana Hydroelectric Project Alaska Energy Authority
FERC Project No. 14241 Page 12 October 2014
Comment
Page
Para
Comment
Number Comment Response
Side Channel 176 12 291 1 42 509
Para Side Channel
Complex
11 1 3 14
Side Slough 177 3 554 147 878
Side Slough Beaver
Complex 76 1 221 11 25 322
Tributary 1,875 43 1,411 6 53 3,339
Tributary Mouth 615 70 2,123 7 28 2,766
Upland Slough 108 6 378 19 1 487
Upland Slough
Beaver Complex
681 100 3,414 65 131 1 4,226
Grand Total 4,858 313 9,885 133 526 4 15,269
Page 5
Para 8
21 the absence of pink: salmon in any
samples; and
This is incorrect. Pink salmon were caught during winter sampling and ELH. Winter data are
provided in Study 9.6 ISR Appendix C Tables C2.2-5 and c2.2-5 and Figure C A1-17. ELH data are
provided in Study 9.6 ISR Tables 5.3-1, 5.3-2, and 5.3-3.
Page 5
Para 9
22 the disappearance of sockeye salmon
from Indian River between the February
draft Initial Study Report and the June draft
Initial Study Report).
This is incorrect. AEA reviewed ISRs for Studies 9.5, 9.6, 9.7, and 8.5 and the numbers of reported
sockeye salmon did not differ between the Draft and Final ISR.
Page 5
Para 10
23 Considering the length distributions and
habitat associations reported, we have
reservations also about the identification of
these juvenile fish and conclude that many
juvenile salmonids identified as Chinook
salmon were coho salmon.
AEA disagrees. See Comment Response Number 20. Consistent with QAQC protocol’s AEA is
verifying fish identifications. In addition, 681 out of the 757 total Chinook salmon in habitats with
beaver influence came from three sloughs: Slough 6A, Slough 17, and Slough 3B (Whiskers). The
photo review, meristic, and genetic sampling are ongoing for these sites and will provide an estimate
of error associated with field identifications. Based on the recent photo review for Slough 6A we are
confident that Chinook and coho salmon do co-occur at this site; however, we also anticipate
additional corrections to field identifications due to the phenotypic variations evident in juvenile
salmon at this location. We have over 500 photos of Chinook and coho salmon that can be used for
photo-based QAQC in addition to more than 550 genetic samples of Chinook and coho salmon for
verification of field identification.
Page 5
Para 11 –
Page 6
24 There is an absence of quantitative analysis
of habitat sampling, fish distribution and
relative abundance, and early life history
AEA disagrees with these assertions. This comment reflects a fundamental lack of understanding of
the methodologies being relied upon by the FERC-approved study plan. As shown in the ISR
sufficient data has been collected to indicate that progress has been made towards meeting study
20141008-5071 FERC PDF (Unofficial) 10/8/2014 10:58:27 AM
AEA’S RESPONSE TO NMFS SEPTEMBER 22, 2014 ISR COMMENT LETTER
Susitna-Watana Hydroelectric Project Alaska Energy Authority
FERC Project No. 14241 Page 13 October 2014
Comment
Page
Para
Comment
Number Comment Response
Para 1 data collected to date. Deviations from the
Revised Study Plan (RSP) and FERC staff
recommendations make developing
estimates from these data difficult or even
impossible. These data are the basis of the
fish and habitat sampling design and must
be collected appropriately for the study to
yield useful information. Without better
integration of historical data into assessment
of current results (e.g., the data from studies
collected in 2012, which used different
methodology and locations), these data
should not be used to assess habitat
associations for salmon by species and life
stage. Much of the data on species
distribution, relative abundance, and habitat
associations appears anomalous in
comparison to available science on these
species and their life stages as known
through data previously collected and past
studies conducted in the Susitna River and
environs.
objectives in spite of variances. Furthermore, AEA has proposed modification where needed to
improve data collection efforts based on a quantitative analysis of the data in the ISR. In all cases the
study modifications implemented in 2014 have been shown to be successful at improving rigor of the
data set as presented in Fish Distribution and Abundance Technical Memorandum filed with FERC
on September 17, 2014.
Page 6
Para 2
25 One of the main objectives of radio-tagging
was locating spawning locations. The
proposed activity of circling over a tag that
remained in the same location for a period
of time was not done (mainly for salmon).
For non-salmon species, it was proposed to
tag some species after their spawning
season and monitor the tag in the following
year to locate spawning locations. It
remains to be seen if this actually worked.
If not, the objective of locating spawning
locations was not met.
This comment reflects a fundamental lack of understanding of the methodologies being relied upon
by the FERC-approved study plan. AEA met the study plan objective within Study 9.7. Aerial
telemetry survey methods are stated in RSP 9.7 Section 9.7.4.2.2:
“When tagged fish are within 2 km of their last seen location, the helicopter will circle at a lower
altitude to pinpoint the fish location to mainstem, side channel, or slough habitats. As well, when
aggregations of two or more tagged fish are found stationary (i.e., within 2 km on one or more
surveys) and/or when visual observations of spawning fish are made from the helicopter, ground and
boat-based surveys will pinpoint spawning locations to within 5-10 meters,” and Study 9.7 ISR
Section 4.2.2.
“When aggregations of two or more tagged fish were found stationary (i.e., within 2 km on one or
more surveys), spawning locations were more intensively tracked to achieve relatively high
resolution geographic positions.”
20141008-5071 FERC PDF (Unofficial) 10/8/2014 10:58:27 AM
AEA’S RESPONSE TO NMFS SEPTEMBER 22, 2014 ISR COMMENT LETTER
Susitna-Watana Hydroelectric Project Alaska Energy Authority
FERC Project No. 14241 Page 14 October 2014
Comment
Page
Para
Comment
Number Comment Response
Aerial survey protocol with respect to identifying the position of a radio-tag adapted to the local
physical environment, weather conditions, timing relative to the migration, helicopter pilots, and
abundance of radio-tags, but always maintained the stated goal of achieving each position to within
300 meters. Obtaining an accurate fix on a tag did not necessarily require circling or changing
altitude although those maneuvers were used; sometimes it involved hovering, changing orientation
of the antenna, or simply making an additional pass at a particular location. Therefore, the adaptive
protocol provided higher accuracy of positions than the original protocol.
The aerial protocol was adapted to conditions during the salmon season with respect to monitoring
non-salmon frequencies (RSP 9.6, Section 4.5.3.3). More specifically, “Resident tag frequencies
were programmed into a receiver and scanned automatically. No manual tracking, directed
searching, or identification of habitat type was conducted during the period when adult salmon were
being tracked.” (ISR 9.6, Section 4.5.3.3). This was done to accommodate the high number of
frequencies that needed to be scanned for salmon and resident fish (i.e., it was impossible for two
crew to actively monitor six to eight receivers), and “may make habitat use inferences less accurate if
habitat delineations were much smaller than the resolution of the tag positions.” The adapted
approach was not necessary during surveys above Devils Canyon nor during the period when only
resident tags were being tracked.
The 2013 data on spawning and holding locations for radio tagged salmon were reported in Study 9.7
ISR Section 5.5.3.
AEA notes that as part of the radio tagging surveys in the Middle River, there was cross-
communication between the radio tagging teams and HSC study teams. In instances where stationary
adult fish were observed, ground or boat based surveys were conducted and measurements of depth
and velocity made at a number of locations to define the areas as potential spawning locations.
Furthermore, telemetry tagging targets are stated in IP 9.5/9.6 Section 5.8.1 and Study 9.6 ISR
Section 4.5.2.1.
“Tags will be surgically implanted (see Appendix 5) in 60 fish of sufficient body size (i.e., ≥200
grams) of each target species. For each species, 30 tags will be allocated to the Upper River, and 30
tags will be allocated to the combined Middle/Lower River. To the extent possible given the
constraints of field sampling conditions, …”
FERC recommended (SPD at B-135) tagging 10 of a 30 tag species allocation prior to and during
20141008-5071 FERC PDF (Unofficial) 10/8/2014 10:58:27 AM
AEA’S RESPONSE TO NMFS SEPTEMBER 22, 2014 ISR COMMENT LETTER
Susitna-Watana Hydroelectric Project Alaska Energy Authority
FERC Project No. 14241 Page 15 October 2014
Comment
Page
Para
Comment
Number Comment Response
spawning periods for Arctic grayling, burbot, Dolly Varden, humpback whitefish, rainbow trout, and
round whitefish. As Study 9.6 ISR Section 4.5.3.2, AEA’s implementation varied from this
recommendation. However, tagging the identified species during the specified periods was
conducted based on the surgeon’s discretion. For 2013 and 2014, tagging resulted in the FERC
recommendation being achieved for Arctic grayling and rainbow trout in the Middle-Lower River,
and Arctic grayling and burbot in the Upper River (Table 1). Further, the available tags-at-large in
spawning periods subsequent to tagging also achieved the FERC recommendation for burbot and
round whitefish in the Middle-Lower River (Table 2). The species yet to achieve the
recommendation are Dolly Varden and humpback whitefish in the Middle-Lower River, and round
whitefish in the Upper River. Note that the FERC recommendation will not be met for Dolly Varden,
humpback whitefish, and rainbow trout in the Upper River because there have been none of sufficient
size caught (i.e., too low abundance). Activities in 2015 will target achievement of feasible targets
by applying tags in June. Therefore, the approach being used is achieving the tagging targets
designed to allow locating spawning locations.
Page 6
Para 4
26 We do not believe that data has been
collected among individual related studies
at an appropriate scale to allow fish/habitat
associations to be made and extrapolated.
A related concern is that fish and habitat
data have not been collected at a
biologically relevant scale.
This comment reflects a fundamental lack of understanding of the methodologies being relied upon
by the FERC-approved study plan. The scale at which fish data were to be collected was described in
the RSP Sections 8.5.4.5.1.1.3, 9.5.4.4.3, 9.5.4.4.2, 9.6.4.4.3, and 9.6.4.4.2 and in the results of data
collected at these scales are presented in Studies 8.5 ISR Section 4.5.1.3, 9.5 ISR Sections 4.4.3 and
4.4.2, and 9.6 ISR Section 4.4.3 and 4.4.2. These studies followed the Study Plan for scale at which
data were to be collected and no variance was implemented with respect to scale for data on
fish/habitat associations. Furthermore, as fish distribution and abundance data collected at the
mesohabitat level were nested within macrohabitats (Study 9.6 ISR 4.4.3) and again within
Geomorphic Reaches which will facilitate use of the data by other studies.
As a point of clarification, AEA is not developing fish/habitat associations so they can be
extrapolated. Rather, AEA is developing HSC curve sets that will be used in the habitat-flow models
for defining how Project operations may influence fish habitats (target species and life stages) within
different habitat types. AEA has identified several approaches for extrapolating the results of this
type of analysis to other areas of the Middle River but has not selected a specific approach pending
further stakeholder review.
Page 6
Para 5
27 To assess project-caused impacts to
fisheries resources (for example), the
sampling effort must be at a scale relevant
to Susitna River fish species and life stages
and must adequately quantify baseline
conditions for accurate extrapolation. In
some instances, the spatial scale of data
See AEA’s response to Comment 26 regarding scale.
Fish sampling followed the sampling plan. In RSP Section 9.6.4.1 it stated that “winter sites will be
selected based on information gathered during 2012-2013 pilot studies . . . attempts will be made to
sample all Focus Areas.” The winter pilot study was conducted in Winter 2013 at two Focus Areas
as described in the Study 9.6 RSP Section 9.6.4.5. AEA made recommendations based upon the
winter pilot study for sampling sites, as stated in Study 9.6 ISR Appendix C Section 6.1.1, and the
20141008-5071 FERC PDF (Unofficial) 10/8/2014 10:58:27 AM
AEA’S RESPONSE TO NMFS SEPTEMBER 22, 2014 ISR COMMENT LETTER
Susitna-Watana Hydroelectric Project Alaska Energy Authority
FERC Project No. 14241 Page 16 October 2014
Comment
Page
Para
Comment
Number Comment Response
collection implemented varies
inappropriately within and among studies,
resulting in a mismatch between the data
collected and the purpose of its collection.
Additionally, the temporal scale of data
collection needs improvement. The Initial
Study Report indicates that winter fish
sampling did not occur in all focus areas as
proposed. Early spring sampling occurred
only in three focus areas due to record late
breakup. Initial sampling following
breakup and installation of migrant traps did
not occur until the middle of June (after
juvenile outmigration had begun), and
spring sampling for fish distribution and
abundance was not conducted.
Improvements need to be made to capture
the full seasonality of fish life history
strategies which vary considerably within a
single season. (Fish move around, and the
extent of that movement must be captured
through sampling. A single-day of
sampling is insufficient to understand the
habitat associations of many different and
mobile species and life-stages of fish.)
2014 Winter Study was expanded to three Focus Areas and opportunistic sampling at accessible sites
outside of the Focus Areas. Results of the first year of the winter study for fish are presented in the
Study 9.5 Winter Study Technical Memorandum filed with FERC on September 17, 2014.
In 2013 Early Life History sampling began two weeks after winter sampling was stopped and
continued bi-weekly through June with the exception that no sampling was conducted for two weeks
during the dynamic break up in mid-May 2013 (Study 9.6 ISR Section 4.6). As stated in Study 9.6
ISR Section 4.6.2 ELH sampling included six Focus Areas identified to have both spawning and
rearing habitat as well as additional sites in the Upper (Study 9.5 ISR 4.6.2), Middle, and Lower
River (Study 9.6 ISR 4.6.5). Sample sites for these various fish study components were visited
multiple times during the Winter Study (1-3 times), Early Life History Study (3 times), and Fish
Distribution and Abundance Study (3 times). Some sites were visited during all three seasonal study
components and ended up being sampled more than eight times in 2013.
Downstream migrant traps were installed and operated as indicated in the Study 9.5 ISR Section
9.5.4.4.10 and Study 9.6 ISRs Section 9.6.4.4.10: “flow conditions permitting, traps will be fished on
a cycle of 48 hours on, 72 hours off throughout the ice-free period.” As soon as break-up and flow
conditions allowed in mid-June 2013 traps were installed fished immediately upon installation in
June through mid-October 2013. In 2014 breakup occurred earlier and migrant traps installation
occurred in mid-May with traps operated immediately after installation (the Proposed 2015
Modifications to Fish Distribution and Abundance Study Plan Implementation Technical
Memorandum filed with FERC on September 17, 2014).
ELH sampling was conducted in 2013 during May and June in the Upper (Study 9.5 ISR Section
4.6.2, Middle and Lower (Study 9.6 ISR Section 4.62) River segments.
For clarification, the spring break-up of 2013 did not reach the magnitude or the late timing of the
breakup of record. AEA believes that the range of hydrologic events that occur over the multi-year
study period provide opportunities to better understand the response of aquatic resources to spring
break up and flow fluctuations associated with Project operations. While the harsh and dangerous
field conditions associated with the spring breakup of 2013 inhibited AEA’s ability to install migrant
traps, data collected in spring 2013 will be combined with other data collected to evaluate the
response of juvenile fish to Project operations over a range of environmental conditions.
Furthermore, data on fish movement were documented with downstream migrant traps and
biotelemetry as indicated in Study 9.5 ISR Sections 4.5.1 and 4.5.2, and Study 9.6 ISR Sections 4.5.1
and 4.5.2. Results for biotelemetry included a total of more than 150,000 repeat detections of tags for
20141008-5071 FERC PDF (Unofficial) 10/8/2014 10:58:27 AM
AEA’S RESPONSE TO NMFS SEPTEMBER 22, 2014 ISR COMMENT LETTER
Susitna-Watana Hydroelectric Project Alaska Energy Authority
FERC Project No. 14241 Page 17 October 2014
Comment
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Para
Comment
Number Comment Response
more than 1,000 tagged fish (Study 9.5 ISR Sections 5.2.1 and 5.2.2, and Study 9.6 ISR Sections
5.2.1 and 5.2.2).
Page 6
Para 6
28 The error inherent in the inappropriate scale
of data collection would be compounded by
the proposal to extrapolate study results
throughout the river; this would perpetuate
and increase sampling errors across the
entire length and width of the river and its
habitats. Resource agencies are particularly
concerned about this proposal to “scale up,”
and requested rationale for its
implementation (Riverine Modeling
Integration Meeting, November 2013). The
ability to “scale up” is only valid when the
initial sampling has been conducted
accurately and at a scale relevant to
resource concerns, which is not the case
with studies conducted thus far.
See above Response to Comment 26 on extrapolation. Additionally, AEA provided several options
for scaling up/extrapolating results of the habitat-flow models being developed during the April 15-
17, 2014 Riverine Modelers Meeting (see http://www.susitna-watanahydro.org/wp-
content/uploads/2014/04/2014_04_17TT_Riverine_SpatialExtrapolation.pdf ). AEA intends to seek
the input of the Licensing Participants prior to selecting the specific option for scaling.
Page 6
Para 8 –
Page 7
Para 1
29 Review of the Initial Study Report reveals
that sampling sites for the various study
disciplines have not been consistently and
thoroughly co-located, as laid out in the
RSP as modified by FERC staff
recommendations, to provide an assessment
of baseline conditions of habitats relative to
fish use and preference. For example,
invertebrate sampling locations (River
Productivity 9.8) were not co-located with
fish sampling locations. Rather than
addressing this issue, or NMFS’s previous
concerns about the number of middle river
sampling locations, AEA is proposing a
study modification to sample in tributaries
above the dam inundation zone. At some
locations, sampling of variables such as
depth and velocity was appropriately co-
located, but other variables that should also
AEA disagrees with the assertion that it did not follow the FERC-approved study plan with respect to
co-location of sampling sites.
Regarding Sentence 1: As an initial matter, the RSPs never specified the co-location of sample sites
across study disciplines. It did specify the location of 10 specific Focus Areas that would be
evaluated relative to the different resource disciplines (RSP 8.5.4.2.1.2).
AEA disagrees with NMFS comments regarding the locations of the groundwater measurements. The
Focus Areas represent areas of intensive study across resource disciplines (see approved Study Plan,
Section 8.5.4.2.1.2). Detailed two-dimensional hydraulic models are being developed for each of the
Focus Areas and will support analysis by other resource disciplines being conducted within those
areas. The Focus Areas represent a variety of habitat types with varying complexity that factored
directly into determining the types and level of detail of resource specific studies. Thus, where
groundwater influence was important relative to habitat features that included riparian communities,
then detailed groundwater studies and riparian investigations occurred. For those where groundwater
exchange was not as important, e.g., those associated with tributaries (Focus Area 141 – Indian River,
Focus Area 151 – Portage Creek) than groundwater studies were scaled back or not included as part
of the overall study of that Focus Area.
20141008-5071 FERC PDF (Unofficial) 10/8/2014 10:58:27 AM
AEA’S RESPONSE TO NMFS SEPTEMBER 22, 2014 ISR COMMENT LETTER
Susitna-Watana Hydroelectric Project Alaska Energy Authority
FERC Project No. 14241 Page 18 October 2014
Comment
Page
Para
Comment
Number Comment Response
be co-located such as groundwater
exchange were not. NMFS recommends
that at Focus Areas data collection for the
full suite of interdependent variables should
be co-located.
Page 7
Para 2
30 The cumulative effects of deficiently
implemented sampling methods, failure to
co-locate sampling sites, lack of integrative
links, and discrepancies in data collection
scales are magnified because these data are
proposed for inputs to models. Model
calibration, validation and decision making
processes will then be used to assess
potential impacts to resources.
AEA disagrees. This comment reflects a fundamental lack of understanding of the methodologies
being relied upon by the FERC-approved study plan. As describe in the ISR, AEA anticipates that
the data generated will provide the necessary inputs for the models within the FERC-approved study
plan.
Page 7
Para 3
31 NMFS recommends that the data issues be
resolved as soon as possible. Accurate data
is required to calibrate and validate
proposed models; and quality data from
individual studies is necessary to integrate
models without amplifying errors
unknowingly. Given these concerns about
the data, it is not plausible to use the data
for the predictive modeling that is proposed
to describe baseline conditions or to predict
potential project impacts.
AEA disagrees with NMFS assertion that the models cannot be used to predict potential project
impacts. Those models were fundamentally designed to be able to evaluate Project effects related to
flow regulation and the data that have been and will continue to be collected to support their
development have been rigorously collected and checked in accordance with a stringent set of
QA/QC protocols.
Page 7
Para 4
32 These issues of data integrity and data
collection are based in part on studies being
conducted with significant differences from
the FERC-modified RSP. These issues
must be resolved prior to conducting
additional field studies. NMFS cannot
develop appropriate recommendations for
study modifications or make new study
requests for the second year of study given
the current issues with the studies and the
data.
AEA disagrees that there are significant differences in how the studies have been implemented versus
the FERC-approved study plans. AEA acknowledges that there have been some slight variances in
the plans but has specified those in the ISR and noted that none of the variances will substantively
affect the completion of the respective studies.
Page 7 33 During the Riverine Modeling Integration AEA disagrees. The time frames of 0, 25, and 50 years were selected because they represent time
20141008-5071 FERC PDF (Unofficial) 10/8/2014 10:58:27 AM
AEA’S RESPONSE TO NMFS SEPTEMBER 22, 2014 ISR COMMENT LETTER
Susitna-Watana Hydroelectric Project Alaska Energy Authority
FERC Project No. 14241 Page 19 October 2014
Comment
Page
Para
Comment
Number Comment Response
Para 7 Meeting (November 2013), 25- and 50-year
scenarios for predicting project impacts to
the physical river channel and habitats were
proposed. While those timelines are
consistent with the study plan and may
present a manageable timeframe for the
modeling work (B. Fullerton, POC meeting,
November 2013), they may not answer
questions related to assessing impacts on
important biological resources in a
biologically meaningful timeframe. Models
need to be sensitive enough to detect
changes that are biologically meaningful to
the species and habitats likely to be affected
by project operations. As currently
planned, this is not the case.
intervals that span the potential length of the FERC license, and as well are reasonable increments
from which to gauge and compare changes in channel morphology (RSP 6.6, Section 6.6.4.2.2.1) that
may translate into changes in fish habitat. Having time intervals at shorter increments of
geomorphological modeling would be less likely to elicit substantive changes in channel
morphologies and would therefore be less likely to elicit changes in the results of the habitat-flow
modeling.
However, the greatest potential effects of Project operations on fish and fish habitats are on the actual
regulation of flows that would occur over much shorter time intervals (annual, seasonal, weekly,
daily, hourly) and for which the habitat-flow models are being developed to evaluate. As described
in RSP 8.5, Section 8.5.7.4.1.1, the “[t]emporal analysis will involve the integration of hydrology,
Project operations, the Mainstem Open-water Flow Routing Model, and the various habitat-flow
response models to project spatially explicit habitat changes over time. Several analytical tools will
be utilized for evaluating Project effects on a temporal basis. This will include development and
completion of habitat-time series that represent habitat amounts resulting from flow conditions
occurring over different time steps (e.g., daily, weekly, monthly), as well as separate analysis that
address effects of rapidly changing flows (e.g., hourly) on habitat availability and suitability. The
Mainstem Open-water Flow Routing Model and habitat models will be used to process output from
the Project operations model. This will be done for different operating scenarios, hydrologic time
periods (e.g., ice free periods: spring, summer, fall; ice-covered period: winter [will rely on Ice
Processes Model – Section 7.6]), Water Year types (wet, dry, normal), and biologically sensitive
periods (e.g., migration, spawning, incubation, rearing) and will allow for the quantification of
Project operation effects on the following:
• Habitat areas (for each habitat type – main channel, side channel, slough, etc.) by
species and life stage; this will also allow for an evaluation of the effects of breaching
flows on these respective habitat areas and biologically sensitive periods (e.g.,
breaching flows in side channels during egg incubation period resulting in temperature
change).
• Varial zone area (i.e., the area that may become periodically dewatered due to Project
operations, subjecting fish to potential stranding and trapping and resulting in reduced
potential invertebrate production).
• Effective spawning areas for fish species of interest (i.e., spawning sites that remain
wetted through egg incubation and hatching).
• Other riverine processes”
These shorter time intervals (hourly, daily, weekly, monthly) represent those that are the most
biologically meaningful in the sense that they would have the most direct and immediate effect on
20141008-5071 FERC PDF (Unofficial) 10/8/2014 10:58:27 AM
AEA’S RESPONSE TO NMFS SEPTEMBER 22, 2014 ISR COMMENT LETTER
Susitna-Watana Hydroelectric Project Alaska Energy Authority
FERC Project No. 14241 Page 20 October 2014
Comment
Page
Para
Comment
Number Comment Response
fish and fish habitats. If warranted, it will also be possible to evaluate effects over longer time steps
that encompass Project operations over several different water years.
Page 7
Para 8 –
Page 8
Para 1
34 NMFS has identified a need to develop and
incorporate biological input and output
parameters and evaluate these under an
appropriate range of operational scenarios
(e.g., base load, ecological flows, load-
following, run-of-river). The temporal
scales (i.e., 25-and 50-year scales) that are
needed must have biological relevance. For
example, 5-, 10-, and 15-year operational
scenarios should be considered to
demonstrate the model’s ability to detect
generational impacts to fish populations and
habitat persistence (e.g., Susitna River
Chinook salmon, 5-7 years; or 2-4 years for
eulachon). NMFS is concerned that the
present model cannot answer the biological
questions it proposes to answer.
See AEA’s response to Comment 33.
Page 8
Para 2
35 Some study plan data collection efforts do
not provide the information needed for the
integrated modeling efforts. For example,
during the November 2013 Riverine
Modelling Integration meeting, it was
revealed that the Water Quality Modeling
study would require data on the spatial
distribution of groundwater discharge to
surface water bodies. Analytical or
numerical groundwater flow simulation
would be one way to satisfy this input
requirement. However, the Groundwater
Study in the Initial Study Report does not
explicitly state that analytical or numerical
groundwater flow simulations would be
undertaken in support of the other physical
process models.
AEA disagrees. This comment reflects a fundamental lack of understanding of the methodologies
being relied upon by the FERC-approved study plan. The data collection effort will provide the
information needed for integrated modeling efforts.
AEA notes that there have been two, three day Riverine Modelers meetings designed to provide
Licensing Participants with updates on model development and integration and to solicit feedback
and suggestions on model refinements. The first of these was held from November 13-15, 2013, the
second April 15-17, 2014. During both meetings, each of the resource modelers explained first the
specific models they were working on and the model dependencies on other models or data sources,
as well as the model outputs to other models. Review of the November meeting notes
(http://www.susitna-watanahydro.org/wp-content/uploads/2014/02/2013.11.13Modelers_Notes.pdf)
indicates questions did occur related to the Water Quality model that pertained to the integration of
groundwater. These comments were addressed by noting that data from targeted grab samples as
well as data from groundwater wells would be used, as well as data from other locations. Additional
information was provided on the groundwater study during the April Proof of Concept meetings
(http://www.susitna-watanahydro.org/wp-
content/uploads/2014/04/2014_04_15TT_Riverine_Presentation-Groundwater.pdf), and more
20141008-5071 FERC PDF (Unofficial) 10/8/2014 10:58:27 AM
AEA’S RESPONSE TO NMFS SEPTEMBER 22, 2014 ISR COMMENT LETTER
Susitna-Watana Hydroelectric Project Alaska Energy Authority
FERC Project No. 14241 Page 21 October 2014
Comment
Page
Para
Comment
Number Comment Response
recently in two Technical Memoranda (GWS and R2 2014a, http://www.susitna-
watanahydro.org/wp-
content/uploads/2014/09/07.5_GW_GWS_T6_TM_Aquatic_Hydro_Final_Draft_20140925.pdf;
GWS and R2 2014b, http://www.susitna-watanahydro.org/wp-
content/uploads/2014/09/07.5_GW_GWS_T5_TM_Riparian_Final_Draft_20140926.pdf ) which
describe some of the analysis leading to development of preliminary groundwater/surface water
relationships in selected Focus Areas.
Page 8
Para 3
36 Model integration is at this point largely an
ad hoc exercise. A stand-alone model
integration study is required to allow
stakeholders to develop confidence in the
models, understand inputs and outputs, and
have the conceptual linkages demonstrated
via an interactive riverine working model.
Many questions remain about the predictive
capabilities of the models, particularly
under integration and model assumptions.
Sensitivity and uncertainty analyses need to
be conducted to contribute to understanding
of model limitations. The full extent of
mismatch of purported integration of
models is currently unknown, even to the
project proponent, much less to
stakeholders reviewing study results.
AEA disagrees. This comment reflects a fundamental lack of understanding of the methodologies
being relied upon by the FERC-approved study plan. The model integration is not an ad-hoc
exercise. The two Riverine Modelers Meetings held in November 2013 and April 2014 respectively
were specifically held in response to stakeholder concerns about model integration. Review of the
presentations from both of these meetings which are available on AEA’s website
(http://www.susitna-watanahydro.org/meetings/past-meetings/) clearly demonstrate the linkages
between the models and how individual model outputs will be used in evaluating Project effects for
each resource discipline, with an emphasis on effects on fish habitats. The meeting notes for the two
meetings provide a clear record of the major topics discussed and stakeholder questions pertaining to
model integration. Indeed, one of the comments provided at the end of the April meeting by a USGS
representative suggested that the modeling and model integration efforts were moving in the right
direction – “…. thought it was a great meeting and that the studies are making good progress. Feels
that there has been tremendous amount of focus on where the problem areas are and are a lot further
along than in November 2013.” Since then, the resource modelers have continued working in a
collaborative fashion on each of the respective models.
Page 8
Para 5
37 Decision Support Systems (DSS) are critical
for evaluating potential impacts of the
project. We believe that their development
should be expedited to the extent possible
without excluding input from stakeholders.
AEA agrees that DSS are important for evaluating Project effects and presented several options for
this during the November modelers meetings (http://www.susitna-watanahydro.org/wp-
content/uploads/2013/11/SuWa-DSS-presentation-20131115_DRAFT.pdf). As was noted in the
Study Plan (RSP Section 8.5.4.8.1), the development of the DSS including selection of indicator
variables will be done in a collaborative process with stakeholder input.
Page 8
Para 6 –
Page 9
Para 1
38 The RSP (Instream Flow Study 8.5 RSP)
includes the use of conceptual ecological
models as the DSS to assess the project’s
impacts on a free flowing river and its
resources. Also, the Fish Passage study
includes use of a DSS to assess the
feasibility and effectiveness of different fish
passage options. It is our understanding
AEA does not consider the DSS to be a conceptual ecological model but rather a platform to reduce
the complexity of information and focus attention on tradeoffs involved with decisions regarding
project operations. Likewise, AEA notes that the Fish Passage Study does not include a DSS type
evaluation, but rather utilization of an analytical tool to weigh various passage options. The
development of both of these will be done in a collaborative framework. As to the schedule of the
DSS, the major elements of this are scheduled for 2015, and will require stakeholder inputs at various
intervals.
20141008-5071 FERC PDF (Unofficial) 10/8/2014 10:58:27 AM
AEA’S RESPONSE TO NMFS SEPTEMBER 22, 2014 ISR COMMENT LETTER
Susitna-Watana Hydroelectric Project Alaska Energy Authority
FERC Project No. 14241 Page 22 October 2014
Comment
Page
Para
Comment
Number Comment Response
that AEA intends to develop the conceptual
ecological model DSS using manual
matrices by early 2015 (FERC 2013) and to
use a modified existing DSS for fish
passage (currently past due). Considering
the potential of these DSSs to support
critical assessments of impacts from the
project, development of the DSS should be
a collaborative process with mutual
development of, and agreement about
fundamental objectives, assumptions,
critical inputs, weighting methods, and
other parts of the models. Formulation of
the fundamental objectives for the DSS may
reveal important, time-sensitive data gaps
that require modifications to existing studies
or perhaps development of new studies. An
example for the fish passage DSS is
reservoir ice studies: we expect to be used
to design tributary collectors for
outmigrating juvenile fish but don’t know if
the model will provide that information. An
example for the conceptual ecological
model is the groundwater studies which we
expect will allow estimation of project
impacts to areas of upwelling, but project
effects to upwelling are not one of the goals
of that study. Therefore, we request that the
schedule for DSS development be
accelerated so potential data needs not
currently covered in the existing study plans
can be identified and added to the study
plan.
Page 10
Para 1
39 Enclosure 2: NMFS Comments on the
2014 Fish Genetics Implementation Plan
These comments were reviewed and incorporated in the Final 2014 Genetics Implementation Plan
filed with the Study 9.14 ISR on June 3, 2014. A comment-response table was filed with the Study
9.14 ISR Part B Section 8. These comments are not addressed here again.
Page 14 40 Enclosure 3: NMFS Initial Comments to AEA filed the 2015 Implementation Technical Memorandum on September 10, 2014. AEA expects
20141008-5071 FERC PDF (Unofficial) 10/8/2014 10:58:27 AM
AEA’S RESPONSE TO NMFS SEPTEMBER 22, 2014 ISR COMMENT LETTER
Susitna-Watana Hydroelectric Project Alaska Energy Authority
FERC Project No. 14241 Page 23 October 2014
Comment
Page
Para
Comment
Number Comment Response
Para 3 –
Page 17,
Para 1
AEA regarding the 2014 Pilot Study for
Cook Inlet Beluga Whales and Eulachon:
Beginning in early May 2014, NMFS staff
were contacted and asked to meet with AEA
and their contractors (hereinafter referred to
collectively as AEA) to discuss AEA’s
plans to modify the [RSP as modified by
FERC’s determination] for the Cook Inlet
Beluga Whale Study (Study 9.17). AEA
informed NMFS staff of their intent to
conduct a boat-based pilot study involving
both a Cook Inlet beluga whale research
effort and a eulachon research effort.
Despite the very short notice from the
intended start date of the research activities,
NMFS agreed to provide some initial
comments and preliminary
recommendations to AEA. These initial
comments were primarily provided to help
reduce the high harassment and harm
potential this pilot project could have on the
endangered Cook Inlet beluga whales, and
to help AEA avoid violating both the
Marine Mammal Protection Act and the
Endangered Species Act. These comments
were not an endorsement of the pilot study,
nor an acknowledgement that the pilot study
would constitute the second year of the
required FERC-approved study plans.
These comments were sent to AEA by
email on May 14, 2014, and are reproduced
in Enclosure 3. As a result of these NMFS
comments, AEA did make modifications to
the pilot study in an effort to reduce the
harassment potential to Cook Inlet beluga
whales. NMFS has had multiple meetings
that through implementation of this plan along with the continued implementation of the Eulachon
Study (Study 9.16), AEA will meet all Study Plan objectives.
From May through August, AEA held a series of four meetings (May 7, May 22, August 7, and
August 26, 2014) with NMFS personnel to discuss alternative methods for collecting data on Cook
Inlet beluga whales (CIBW) and their prey. The intent of these meetings was to openly discuss and
collaborate on the development of alternative study methods that could be used by AEA to better
understand potential impacts of the project on CIBWs while minimizing any potential impacts of
conducting the research itself. During the first meeting in May 2014, AEA described preliminary
plans to test the feasibility of using boat-based surveys to document relationships between beluga
whales and their prey in Cook Inlet at the mouth of the Susitna River. Upon review of a written
description of the proposed methods, NMFS provided, via email, the comments also contained in this
letter from NMFS to FERC. Although AEA felt there was very little risk of harassment and no
chance of harm to CIBW’s from the proposed boat-based survey methods, NMFS concerns were
incorporated into revised pilot-study methods (discussed with NMFS during the May 22, 2014
meeting) that focused solely on beluga whale prey and included provisions to specifically avoid
beluga whales. Nine surveys were conducted in June and July, 2014 as described in the 2014 Cook
Inlet Beluga Whale Prey Study Implementation Technical Memorandum filed with FERC on
September 26, 2014 (LGL 2014a). The surveys in 2014 were successful in detecting fish and marine
mammals; however, it was decided that the boat-based surveys should not be carried out in 2015
because of concerns regarding the potential disturbance of CIBW. Documenting habitats where
CIBW and their prey are closely associated may require approaching beluga whales at closer
distances than deemed appropriate as well as limitations to the survey method caused by weather (see
further details in the 2014 Cook Inlet Beluga Whale Prey Study Implementation Technical
Memorandum filed with FERC on September 26, 2014 (LGL 2014a), and the Cook Inlet Beluga
Whale Study 2015 Implementation Plan Technical Memorandum filed with FERC on September 30,
2014).
AEA has provided NMFS with several documents throughout the process of discussing CIBW study
methods. A description of AEA’s plans to conduct limited field work in 2014 and, based on the
results, submit a Cook Inlet Beluga Whale Study 2015 Implementation Plan in September 2014 was
included in Study 9.17 ISR Section 7.1 and Attachment 1 (LGL and R2 2014). The two meetings
with NMFS in August were primarily intended to discuss the methods that would be included in the
Cook Inlet Beluga Whale Study 2015 Implementation Plan. Prior to the August 7, 2014 meeting,
AEA shared with NMFS an outline and rationale for proposed methods to be included in the Cook
Inlet Beluga Whale Study 2015 Implementation Plan. Preliminary results from the 2014 field work
were discussed with NMFS at the beginning of that meeting and that occupied a majority of the time
20141008-5071 FERC PDF (Unofficial) 10/8/2014 10:58:27 AM
AEA’S RESPONSE TO NMFS SEPTEMBER 22, 2014 ISR COMMENT LETTER
Susitna-Watana Hydroelectric Project Alaska Energy Authority
FERC Project No. 14241 Page 24 October 2014
Comment
Page
Para
Comment
Number Comment Response
with AEA to discuss the progress and status
of the 2014 pilot study since early May.
During several meetings, AEA has provided
inconsistent information regarding their
plans for 2015 Cook Inlet beluga studies.
At this time, it is unclear which aspects of
the FERC-approved study plans for Cook
Inlet beluga whales AEA intends to
implement in 2015, if any. Additionally,
AEA has a pattern of providing information
to NMFS immediately prior to a meeting
(e.g., one hour in advance) or after the
meeting, but has an expectation that NMFS
will provide official comments during the
meeting. This process has substantially
limited the ability of NMFS to provide
meaningful comments to AEA. Finally,
while the focus of Study 9.17 is on Cook
Inlet beluga whales, NMFS reiterates that
the Marine Mammal Protection Act pertains
to all marine mammals, regardless of any
additional protections under the Endangered
Species Act. Thus, harassment of any
marine mammal resulting from AEA’s
activities is prohibited.
allotted for the meeting. AEA used the remaining meeting time to describe to NMFS the intent and
content of the 2015 study outline. Because there was insufficient time to fully discuss the outline and
content of the Cook Inlet Beluga Whale Study 2015 Implementation Plan, a follow-up meeting with
NMFS was scheduled for August 26, 2014. Prior to the August 26, 2014 meeting, AEA provided the
identical meeting materials and outline to NMFS as was provided ahead of the August 7, 2014
meeting. The rationale and content of the outline and methods to be included in the Cook Inlet
Beluga Whale Study 2015 Implementation Plan were more fully discussed during the meeting on
August 26, 2014 and the results of that discussion were incorporated into the Cook Inlet Beluga
Whale Study 2015 Implementation Plan Technical Memorandum filed with FERC on September 30,
2014 (LGL 2014b).
REFERENCES
AEA (Alaska Energy Authority). 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.
20141008-5071 FERC PDF (Unofficial) 10/8/2014 10:58:27 AM
AEA’S RESPONSE TO NMFS SEPTEMBER 22, 2014 ISR COMMENT LETTER
Susitna-Watana Hydroelectric Project Alaska Energy Authority
FERC Project No. 14241 Page 25 October 2014
Geo-Watersheds Scientific and R2 Resource Consultants, Inc. 2014a. Preliminary Groundwater and Surface-Water Relationships in
Lateral Aquatic Habitats within Focus Areas FA-128 (Slough 8A) and FA-138 (Gold Creek) in the Middle Susitna River,
Technical Memorandum, Study 7.5. Susitna-Watana Hydroelectric Project, FERC No. P-14241. Prepared for Alaska Energy
Authority, Anchorage, Alaska. September 2014. 136 pp. http://www.susitna-watanahydro.org/wp-
content/uploads/2014/09/07.5_GW_GWS_T6_TM_Aquatic_Hydro_Final_Draft_20140925.pdf.
Geo-Watersheds Scientific and R2 Resource Consultants, Inc. 2014b. Groundwater and Surface-Water Relationships in Support of
Riparian Vegetation Modeling, Technical Memorandum, Study 7.5. Susitna-Watana Hydroelectric Project, FERC No. P-
14241. Prepared for Alaska Energy Authority, Anchorage, Alaska. September 2014. 58 pp. http://www.susitna-
watanahydro.org/wp-content/uploads/2014/09/07.5_GW_GWS_T5_TM_Riparian_Final_Draft_20140926.pdf.
GSA BBEST (Guadalupe, San Antonio, Mission, and Aransas Rivers and Mission, Copano, Aransas, and San Antonio Bays Basin and
Bay Expert Science Team). 2011. Environmental flows recommendations report. Final submission to the Guadalupe, San
Antonio, Mission, and Aransas Rivers and Mission, Copano, Aransas, and San Antonio Bays Basin and Bay Area Stakeholder
Committee, Environmental Flows Advisory Group, and Texas Commission on Environmental Quality. March 1, 2011.
Unpublished report available online http://www.tceq.texas.gov/permitting/water_rights/eflows/guadalupe-sanantonio-bbsc.
Hightower, J.E., J.E. Harris, J.K. Raabe, P. Brownell, and C.A. Drew. 2012. A Bayesian Spawning Habitat Suitability Model for
American Shad in Southeastern United States Rivers. Journal of Fish and Wildlife Management, 2(3): 184-198.
http://scholarworks.umass.edu/fishpassage_journal_articles/2046.
Jowett, I.G., J. Richardson, B.J.F. Biggs, C.W. Hickey and J.M. Quinn. 1991. Microhabitat preferences of benthic invertebrates and
the development of generalised Deleatidium spp. habitat suitability curves, applied to four New Zealand rivers. New Zealand
Journal of Marine and Freshwater Research 25(2):187-199.
LGL (LGL Alaska Research Associates, Inc.). 2014a. 2014 Cook Inlet Beluga Whale Prey Study Implementation Technical
Memorandum, Study 9.17. Susitna-Watana Hydroelectric Project, FERC No. P14241. Prepared for Alaska Energy Authority,
Anchorage, Alaska. September 2014. 23 pp. http://www.susitna-watanahydro.org/wp-
content/uploads/2014/09/9.17_CIBW_DRAFT_TM_20140909.pdf
LGL (LGL Alaska Research Associates, Inc.). 2014b. Cook Inlet Beluga Whale Study 2015 Implementation Plan Technical
Memorandum, Study 9.17. Susitna-Watana Hydroelectric Project, FERC No. P14241. Prepared for Alaska Energy Authority,
Anchorage, Alaska. September 2014. 17 pp. http://www.susitna-watanahydro.org/wp-
content/uploads/2014/09/9.17_CIBW_DRAFT_2015_IP_20140911-1.pdf
20141008-5071 FERC PDF (Unofficial) 10/8/2014 10:58:27 AM
AEA’S RESPONSE TO NMFS SEPTEMBER 22, 2014 ISR COMMENT LETTER
Susitna-Watana Hydroelectric Project Alaska Energy Authority
FERC Project No. 14241 Page 26 October 2014
LGL and R2 (LGL Alaska Research Associates, Inc. and R2 Resource Consultants, Inc.). 2014. Initial Study Report, Part C:
Executive Summary and Section 7, Study 9.17. Susitna-Watana Hydroelectric Project, FERC No. P-14241. Prepared for
Alaska Energy Authority, Anchorage, Alaska. June 2014. 39 pp. http://www.susitna-watanahydro.org/wp-
content/uploads/2014/06/09.17_CIBW_ISR_PartC.pdf
Vadas, Jr., R.L., and D.J. Orth. 2001. Formulation of habitat suitability models for stream fish guilds: Do the standard methods
work? Transactions of the American Fisheries Society 130:217-235.
20141008-5071 FERC PDF (Unofficial) 10/8/2014 10:58:27 AM
AEA’S RESPONSE TO NMFS SEPTEMBER 22, 2014 ISR COMMENT LETTER
Susitna-Watana Hydroelectric Project Alaska Energy Authority
FERC Project No. 14241 Page 27 October 2014
Table 1. Radio-tags released in resident fish, 2013-2014.
River Section
2013 2014
Total
'13+'14
Total
FERC
period
Balance
of 30
target
Middle-Lower Ma/Ju July August Sept Total Ma/Ju July August Sept Total
Arctic grayling 11 17 1 5 34 8 0 0 0 8 42 19 -12
Burbot 2 0 5 2 9 0 0 0 5 5 14 7 16
Dolly Varden 1 6 2 0 9 0 0 0 0 0 9 2 21
Humpback whitefish 3 4 0 0 7 0 0 0 0 0 7 0 23
Lake trout 0 0 0 0 0 0 0 0 0 0 0 -30
Longnose sucker 13 8 6 1 28 0 0 0 0 0 28 -2
Northern pike 0 0 5 0 5 0 0 0 0 0 5 -25
Rainbow trout 11 17 3 13 44 0 0 0 0 0 44 11 -14
Round whitefish 11 3 0 7 21 0 0 0 0 0 21 0 9
2013 2014
Total
'13+'14
Total
FERC
period
Balance
of 30
target
Upper Ma/Ju July August Sept Total Ma/Ju July August Sept Total
Arctic grayling 0 31 1 26 58 53 0 0 0 53 111 53 -81
Burbot 0 0 0 7 7 14 0 0 19 33 40 26 -10
Dolly Varden 0 0 0 0 0 0 0 0 0 0 0 0 30
Humpback whitefish 0 0 0 0 0 0 0 0 0 0 0 0 30
Lake trout 0 0 0 0 0 0 0 0 12 12 12 -18
Longnose sucker 0 5 0 5 10 17 0 0 17 34 44 --14
Northern pike 0 0 0 0 0 0 0 0 0 0 0 -30
Rainbow trout 0 0 0 0 0 0 0 0 0 0 0 0 30
Round whitefish 0 0 0 18 18 7 0 0 16 23 41 0 -11
20141008-5071 FERC PDF (Unofficial) 10/8/2014 10:58:27 AM
AEA’S RESPONSE TO NMFS SEPTEMBER 22, 2014 ISR COMMENT LETTER
Susitna-Watana Hydroelectric Project Alaska Energy Authority
FERC Project No. 14241 Page 28 October 2014
Table 2. Radio-tags at large by month.
Mid-or-Lower-Susitna-released resident fish at large, by study month. Tags released in a given month become "at-large" in the following month.
Species Jun '13 Jul '13 Aug '13 Sep '13 Oct '13 Nov '13 Dec '13 Jan '14 Feb '14 Mar '14 Apr '14 May '14 Jun '14 July '14 Aug'14 Sep'14
Total
FERC
period
Arctic Grayling 0 11 24 17 18 13 12 8 8 8 8 8 6 13 10 10 14
Burbot 0 2 2 4 4 3 3 2 2 2 1 1 1 1 1 6 10
Dolly Varden 0 1 5 6 4 4 3 3 3 3 3 3 3 2 1 1 6
Humpback Whitefish 0 1 4 0 0 0 0 0 0 0 0 0 0 0 0 0 4
Lake Trout 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 -
Longnose Sucker 0 8 9 7 5 4 4 1 0 0 0 0 0 0 0 0 -
Northern Pike 0 0 0 3 3 3 3 3 3 3 3 3 2 2 2 2 -
Rainbow Trout 0 11 25 14 21 21 20 20 20 20 20 17 16 16 15 15 33
Round Whitefish 0 10 13 11 13 11 11 9 9 7 7 5 3 3 2 2 15
Shaded cells are FERC periods to tag a total of 10 of 30 tags.
Upper-Susitna-released resident fish at large, by study month
Species Jun '13 Jul '13 Aug '13 Sep '13 Oct '13 Nov '13 Dec '13 Jan '14 Feb '14 Mar '14 Apr '14 May '14 Jun '14 July '14 Aug'14 Sep'14
Total
FERC
period
Arctic Grayling 0 0 24 19 40 36 27 25 23 22 21 18 15 57 47 47 33
Burbot 0 0 0 0 6 5 5 4 4 4 4 3 2 15 12 31 31
Dolly Varden 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
Humpback Whitefish 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
Lake Trout 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 12 -
Longnose Sucker 0 0 3 1 5 5 2 2 1 1 1 1 1 17 15 32 -
Northern Pike 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 -
Rainbow Trout 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
Round Whitefish 0 0 0 0 18 15 12 9 6 5 5 4 3 10 9 25 9
20141008-5071 FERC PDF (Unofficial) 10/8/2014 10:58:27 AM
Wayne Dyok
Susitna Project Manager
Alaska .Energy Authority
813 W. Northern Light Boulevard
Anchorage, AK 99503
UNITED STATES DEPARTMENT OF COMMERCE
National Oceanic and Atmospheric Administration
National Marine Fisheries Service
P.O. Box 21668
Juneau, Alaska 99802-1668
September 22,2014
RE: FERC Project P-14241, Proposed Susitna-Watana Hydropower Project
Dear Mr. Dyok:
The Alaska Energy Authority (AEA) has requested that the National Marine Fisheries Service
(NMFS) comment on portions of the Initial Study Report for the proposed Susitna-Watana
Hydropower project (June 3, 2014). We also include here comments previously submitted on the
2014 Fish Genetics Implementation Plan and on the pilot 2014 Cook Inlet beluga whale and
eulachon studies (May 12 and May 14, 2014). We expect that the Alaska Energy Authority
(AEA) will address these issues at the upcoming meeting on the Initial Study Report in October
2014.
Briefly, our enclosed comments on the Initial Study Report's fish studies (9.5 Upper River Fish
Distribution and Abundance, 9.6 Lower and Middle River Fish Distribution and Abundance, and
9.7 Salmon Escapement) identify issues with the integrity of data, the ability to effectively
integrate modeled studies, and the progress and detail of the decision support systems. Model
integration is a key concern, especially for assessing baselines and project impacts on the Susitna
River.
NMFS recommends that the data issues be resolved as soon as possible. For NMFS to effectively
review this project, the studies must accurately identify fish species, develop accurate habitat
models, and use the best available science to understand anadromous fish distribution and habitat
associations. Moreover, the studies require accurate data to calibrate and validate proposed
models and to integrate these models without inadvertently amplifying errors. Given the current
issues with the data, it is not plausible that the data for predictive modeling be used to describe
baseline conditions or to predict potential impacts. Modifications, additions, and new study
requests for the second year of studies cannot be developed given the current issues with the
data; these issues must be resolved prior to conducting additional field studies.
In regards to the 2014 Studies and the Final Study Plan, NMFS requests that the AEA adhere to
the schedule the Federal Energy Regulatory Commission (FER C) established for the
ALASKA REGION • www.fakr.noa&.20V
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Licensing Process (ILP) for this project in their January 28, 2014 determination. In that
determination, FERC ordered the AEA to submit the final Initial Study Report on June 3, 2014
and to hold a meeting in October to present the results of the Initial Study Report and discuss any
proposed changes. Although the AEA has just released reports of the studies it conducted in
2014 and intends to discuss those studies at the October meeting, NMFS is not prepared to step
outside the FERC-ordered process and consider those studies at this time. The limited time
allocated would be more effectively spent addressing problems with the 2013 study
implementation and discussing study modifications or new studies.
Any studies that the AEA conducted in 2014 cannot be construed as "Year 2 ILP Studies,"
because the Initial Study Report was not yet complete at the time the studies were conducted.
Conducting the studies before completing the Initial Study Report precluded participants from
recommending any changes to the study or making new study requests based a review of a
completed Initial Study Report. As noted by FERC in an May 6, 2014 e-mail on the
Implementation Plan for the Genetic Baseline Study for Selected Fish Species in the Susitna
River, Alaska:
... to clarify, we just reviewed our Study Determination letter and confirmed that
the genetics operational plans are due by April30 of 'each year of study
implementation.' Because our January 2014letter grantedAEA's request, in part, for
second season studies to be conducted in 2015 rather than 2014 ... it follows that
the genetics operational plan for the second study season is due by April30, 2015, and
not by April30, 2014.
(Nicholas Jayjack, March 6, 2014 email to Susan Walker)
Although NMFS provided courtesy reviews and comments to the AEA on 2014 studies for fish
genetics (Enclosure 2) and the Cook Inlet beluga whales/eulachon pilot study (Enclosure 3) by
mid-May of 2014, NMFS does not consider any 2014 study to be the second year of study under
the ILP process.
We consider these concerns significant and in need of resolution for NMFS to fulfill its statutory
responsibilities. In the context of this project, we construe those responsibilities as follows:
1) to identify study data gaps;
2) to make recommendations for the second year of studies (and beyond);
3) to understand the project's ability to quantify baseline and proposed project
operational impacts to fish and wildlife resources;
4) to support recommendations for the protection, mitigation, and enhancement measures
associated with the project; and
2
5) to make informed decisions pursuant to our Section 18 Fishway Prescription authority
under Federal Power Act.
The II.P schedule for this project has been altered and now affords the ABA an opportunity to
make necessary changes to studies for this project prior to entering the second year of study.
This will allow for development and implementation of a more accurate, effective, and cost-
effective plan of study for this important project.
In our November 30, 2014, FERC filing we will provide detailed recommendations to address
specific concerns related to the individual Initial Study Reports of June 3, 2014. If you have
questions regarding this letter, please contact Susan Walker at (907) 586-7646 or
Susan. Walker@noaa.gov).
Enclosures (3)
cc:
e-filed under FERC docket P-14241 as distribution to all Susitna licensing participants
Sarah Goad, AIDEA
Betsy McGregor, AEA
Nicholas Jayjack, FERC
Joe Klein, ADFG
Soch Lor, USFWS
Mike Bethe, ADFG
3
U000Enctosure1:DetailsregardingDataIntegrity,ModelIntegration/Proof-of-ConceptandDecisionSupportSystems.oDATAISSUES:oDataCollection:QualityAssuranceandQualityControl,andMethodologiesQNMFSisconcernedwiththecurrentstatusandimplementationofaquaticstudiesandbelievesthat,unlesstheseissuesareaddressed,manystudyobjectiveswillnotbemet.Ourprimary0concernsareasfollows:0o11)Habitatclassificationhasnotbeencompleted;VO22)Fishpassagecriteriahavenotbeendeveloped;33)Fishsamplingstudyplanswerenotfollowed;samplingunitswereinappropriatelyosubsampled;o44)FishsamplinglocationsdidnotincorporateFERCrecommendations;o55)Becausethefishsamplingdidnotfollowthesamplingplan,thisresultedinaninabilitytooestimaterelativefishabundance;66)Fishseemtohavebeenidentifiedincorrectly;O77)Datawerecollectedandreportedatinappropriatemesohabitatscales;88)Samplingsitesamongstudieswerenotco-located;o99)Tagginggoalswerenotmet;o1010)FishtargetsforHSCsamplingwerenotmet;o1111)Themainstemupperrivermigrantfishtrapwasnotinstalled;1212)Afishwheelwasnotinstalled,andfishwerenottaggedneartheentrancetoDevilsCanyon;1313)AdditionalproblemsassociatedwithlateinstallationandoperationofmigranttrapswereOlikelyinfluencedbyenvironmentalconditionsassociatedwithlatebreakup;and1414)Juvenilesalmondistributionandabundancein2013werelikelyaffectedbytherecordfallofloodsin2012.Weareprovidingsomeadditionalclarificationonsomeoftheseconcerns.015TheactualimplementationoftheabundancesamplingprogramdidnotfollowtheQstatisticalmodelsusedtoselectsamplingunits.Inparticular,subareas(mesohabitats)withinselectedareaswere‘randomly’selectedforsubsampling,andsamplingwasnotconsistentbetweensamplingevents(differentgears,differenteffort,differentorderofgears,differenttotalC)areasampled,etc).Samplingerrorinthefishdistributionandrelativeabundancestudiesneedsotobeaccountedforinorderforthesestudiestoaccuratelyestimatefishdisthbulionand0abundance.EstimatesofnumbersofChinooksalmonthatmigrateaboveDevilsCanyonneedtoincludetheassumptions,standarderror,andresultingstatisticalconfidenceintervalsassociatedwiththatestimate.Betterdescriptionsof(andstatisticalaccountingfor)bothsamplingandnon-Usamplingerrorsneedtobeprovided.Thedatausedtodescribefish-habitatassociationUo40n
C7—Cpreferencesandthestandarderrorsassociatedwiththosespeciesandlife-stagehabitatcorrelationsneedtobevalidated,asthisanalysisproposestodescribemacrohabitatrelationshipsforfish.Theserelationshipswillbeusedtoevaluateprojecteffects,tovalidateinstreamflowhabitatmodelpredictions,andtoextrapolateresultsfromfocusareastogeomorphicreachesandCriversegments.UltimatelythesedatawillbeusedtodevelopprotectionandmitigationmeasuresCandtoserveasabasisforpost-projectmonitoring.CDatacollectionandanalysisCC16Datacollectionmethodsneedimprovement.Forexample,detectionandrecoveryofPIT(PassiveIntegratedTransponder)tagsneedtobeimprovedtoyieldusefuldatatomeetstudygoalsandobjectives.Locationofthedetectionarraysdidnotcovertheentirechannelandwasbiasedtowardfishmigratingdownchannel.Also,becausetoofewtagswererecovered,Cefficiencyestimatescouldnotbemade.C17Misidentificationofjuvenilefishbyspeciesinducessignificanterror,andapplicationofthiserroneousdatawouldresultininaccurateconclusions.OurreviewoftheInitialStudyReportfindsthataveryhighpercentageofthejuvenilesalmonidsweremisidentified.WealsoquestionCtheaccuracyofalljuvenilefishsamplingdatabecauseofthefollowingdetails:CC18•largenumbersofumdentifledsalmomdjuveniles(someofwhichwerePITtagged);19•anomalouslengthdisthbutionsandhabitatassociations(e.g.,juvenileChinook150mmfork-length;C20•thelargeabundanceofjuvenileChinookinbeaverponds;C21•theabsenceofpinksalmoninanysamples;andC22•thedisappearanceofsockeyesalmonfromIndianRiverbetweentheFebruaryCdraftInitialStudyReportandtheJunedraftInitialStudyReport).c23Consideringthelengthdistributionsandhabitatassociationsreported,wehavereservationsalsoCabouttheidentificationofthesejuvenilefishandconcludethatmanyjuvenilesalmonidsCidentifiedasChinooksalmonwerecohosalmon.c24Thereisanabsenceofquantitativeanalysisofhabitatsampling,fishdistributionandrelativeCabundance,andearlylifehistorydatacollectedtodate.DeviationsfromtheRevisedStudyPlanC(RSP)andFERCstaffrecommendationsmakedevelopingestimatesfromthesedatadifficultorCevenimpossible.Thesedataarethebasisofthefishandhabitatsamplingdesignandmustbe-ccollectedappropriatelyforthestudytoyieldusefulinformation.Withoutbetterintegrationofhistoricaldataintoassessmentofcurrentresults(e.g.,thedatafromstudiescollectedin2012,whichuseddifferentmethodologyandlocations),thesedatashouldnotbeusedtoassesshabitatCassociationsforsalmonbyspeciesandlifestage.Muchofthedataonspeciesdistribution,Crelativeabundance,andhabitatassociationsappearsanomalousincomparisontoavailableC.5
U0000.CscienceonthesespeciesandtheirhfestagesasknownthroughdatapreviouslycollectedandpaststudiesconductedintheSusithaRiverandenvirons.0o25Oneofthemainobjectivesofradio-taggingwaslocatingspawninglocations.Theoproposedactivityofcirclingoveratagthatremainedinthesamelocationforaperiodoftimewasnotdone(mainlyforsalmon).Fornon-salmonspecies,itwasproposedtotagsomespeciesaftertheirspawningseasonandmonitorthetaginthefollowingyeartolocatespawningolocations.Itremainstobeseenifthisactuallyworked.Ifnot,theobjectiveoflocating0spawninglocationswasnotmet0Scale026Wedonotbelievethatdatahasbeencollectedamongindividualrelatedstudiesatanappropriateoscaletoallowfish/habitatassociationstobemadeandextrapolated.Arelatedconcernisthatfishandhabitatdatahavenotbeencollectedatabiologicallyrelevantscale.Q27Toassessproject-causedimpactstofisheriesresources(forexample),thesamplingeffortmustobeatascalerelevanttoSusithaRiverfishspeciesandlifestagesandmustadequatelyquantifybaselineconditionsforaccurateextrapolation.Insomeinstances,thespatialscaleofdataOcollectionimplementedvariesinappropriatelywithinandamongstudies,resultinginamismatchbetweenthedatacollectedandthepurposeofitscollection.Additionally,thetemporalscaleofodatacollectionneedsimprovement.TheInitialStudyReportindicatesthatwinterfishsamplingodidnotoccurinallfocusareasasproposed.Earlyspringsamplingoccurredonlyinthreefocus0areasduetorecordlatebreakup.Initialsamplingfollowingbreakupandinstallationofmigrant0trapsdidnotoccuruntilthemiddleofJune(afterjuvenileoutmigrationhadbegun),andspringCsamplingforfishdistributionandabundancewasnotconducted.Improvementsneedtobemade0tocapturethefullseasonalityoffishlifehistorystrategieswhichvaryconsiderablywithinasingleseason.(Fishmovearound,andtheextentofthatmovementmustbecapturedthroughosampling.Asingle-dayofsamplingisinsufficienttounderstandthehabitatassociationsof0manydifferentandmobilespeciesandlife-stagesoffish.)28Theerrorinherentintheinappropriatescaleofdatacollectionwouldbecompoundedbytheproposaltoextrapolatestudyresultsthroughouttheriver;thiswouldperpetuateandincreaseUsamplingerrorsacrosstheentirelengthandwidthoftheriveranditshabitats.Resource0agenciesareparticularlyconcernedaboutthisproposalto“scaleup,”andrequestedrationaleforoitsimplementation(RiverineModelingIntegrationMeeting,November2013).Theabffityto“scaleup”isonlyvalidwhentheinitialsamplinghasbeenconductedaccuratelyandatascalerelevanttoresourceconcerns,whichisnotthecasewithstudiesconductedthusfar.Co-locationofsamplingsites29ReviewoftheInitialStudyReportrevealsthatsamplingsitesforthevariousstudydisciplineshavenotbeenconsistentlyandthoroughlyco-located,aslaidoutintheRSPasmodifiedby6
LFERCstaffrecommendations,toprovideanassessmentofbaselineconditionsofhabitatsrelativetofishuseandpreference.Forexample,invertebratesamplinglocations(RiverProductivity9.8)werenotco-locatedwithfish.samplinglocations.Ratherthanaddressingthisissue,orNMFS’spreviousconcernsaboutthenumberofmiddleriversamplinglocations,AEACisproposingastudymodificationtosampleintributariesabovethedaminundationzone.AtCsomelocations,samplingofvariablessuchasdepthandvelocitywasappropriatelyco-located,butothervariablesthatshouldalsobeco-locatedsuchasgroundwaterexchangewerenot.CNMFSrecommendsthatatFocusAreasdatacollectionforthefullsuiteofinterdependent.variablesshouldbeco-located.30Thecumulativeeffectsofdeficientlyimplementedsamplingmethods,failuretoco-locateCsamplingsites,lackofintegrativelinks,anddiscrepanciesindatacollectionscalesaremagnifiedcbecausethesedataareproposedforinputstomodels.Modelcalibration,validationanddecisioncmakingprocesseswillthenbeusedtoassesspotentialimpactstoresources.31NMFSrecommendsthatthedataissuesberesolvedassoonaspossible.AccuratedataisCrequiredtocalibrateandvalidateproposedmodels;andqualitydatafromindividualstudiesiscnecessarytointegratemodelswithoutamplifyingerrorsunknowingly.Giventheseconcernsaboutthedata,itisnotplausibletousethedataforthepredictivemodelingthatisproposedtodescribebaselineconditionsortopredictpotentialprojectimpacts.32TheseissuesofdataintegrityanddatacollectionarebasedinpartonstudiesbeingconductedwithsignificantdifferencesfromtheFERC-modifiedRSP.Theseissuesmustberesolvedpriortoconductingadditionalfieldstudies.NMFScannotdevelopappropriaterecommendationsforstudymodificationsormakenewstudyrequestsforthesecondyearofstudygiventhecurrentCissueswiththestudiesandthedata.C________________________CCCMODELINTEGRATION/PROOF-OF-CONCEPT:Biologicalrelevance33DuringtheRiverineModelingIntegrationMeeting(November2013),25-and50-yearscenariosforpredictingprojectimpactstothephysicalriverchannelandhabitatswereproposed.Whilethosetimelinesareconsistentwiththestudyplanandmaypresentamanageabletimeframeforthemodelingwork(B.Fullerton,POCmeeting,November2013),theymaynotanswerquestionsrelatedtoassessingimpactsonimportantbiologicalresourcesinabiologicallymeaningfultimeftame.Modelsneedtobesensitiveenoughtodetectchangesthatarebiologicallymeaningfultothespeciesandhabitatslikelytobeaffectedbyprojectoperations.Ascurrentlyplanned,thisisnotthecase.34lvtFShasidentifiedaneedtodevelopandincorporatebiologicalinputandoutputparametersandevaluatetheseunderanappropriaterangeofoperationalscenarios(e.g.,baseload,ecologicalflows,load-following,nm-of-river).Thetemporalscales(i.e.,25-and50-yearscales)7CCCCCCCCCCCC
U000Othatareneededmusthavebiologicalrelevance.Forexample,5-,10-and15-yearoperationalscenariosshouldbeconsideredtodemonstratethemodel’sabilitytodetectgenerationalimpactsotofishpopulationsandhabitatpersistence(e.g.,SusithaRiverChinooksalmon,5-7years;or240yearsforeulachon).NMFSisconcernedthatthepresentmodelcannotanswerthebiological0questionsitproposestoanswer.035Somestudyplandatacollectioneffortsdonotprovidetheinformationneededfortheintegratedomodelingefforts.Forexample,duringtheNovember2013RiverineModellingIntegrationomeeting,itwasrevealedthattheWaterQualityModelingstudywouldrequiredataonthespatial0distributionofgroundwaterdischargetosurfacewaterbodies.AnalyticalornumericalC)groundwaterflowsimulationwouldbeonewaytosatisfythisinputrequirement.However,theGroundwaterStudyintheInitialStudyReportdoesnotexplicitlystatethatanalyticalorOnumericalgroundwaterflowsimulationswouldbeundertakeninsupportoftheotherphysicalprocessmodels.0o36Modelintegrationisatthispointlargelyanadhocexercise.Astand-alonemodelintegrationostudyisrequiredtoallowstakeholderstodevelopconfidenceinthemodels,understandinputsOandoutputs,andhavetheconceptuallinkagesdemonstratedviaaninteractivetiverineworkingmodel.Manyquestionsremainaboutthepredictivecapabilitiesofthemodels,particularlyunderointegrationandmodelassumptions.Sensitivityanduncertaintyanalysesneedtobeconductedtoocontributetounderstandingofmodellimitations.ThefullextentofmismatchofpurportedQintegrationofmodelsiscurrentlyunknown,eventotheprojectproponent,muchlesstoostakeholdersreviewingstudyresults.DECISIONSUPPORTSYSTEMS:37DecisionSupportSystems(DSS)arecriticalforevaluatingpotentialimpactsoftheproject.Weobelievethattheirdevelopmentshouldbeexpeditedtotheextentpossiblewithoutexcludinginputofromo38TheRSP(InstreamFlowStudy8.5RSP)includestheuseofconceptualecologicalmodelsasthe0DSStoassesstheproject’simpactsonafreeflowingriveranditsresources.Also,theFishoPassagestudyincludesuseofaDSStoassessthefeasibilityandeffectivenessofdifferentfishopassageoptions.ItisourunderstandingthatAEAintendstodeveloptheconceptualecologicalomodelDSSusingmanualmatricesbyearly2015(FERC2013)andtouseamodifiedexistingDSSforfishpassage(currentlypastdue).ConsideringthepotentialoftheseDSSstosupportcriticalassessmentsofimpactsfromtheproject,developmentoftheDSSshouldbea-collaborativeprocesswithmutualdevelopmentof,andagreementaboutfundamentalobjectives,Uassumptions,criticalinputs,weightingmethods,andotherpartsofthemodels.FormulationofOthefundamentalobjectivesfortheDSSmayrevealimportant,time-sensitivedatagapsthatQrequiremodificationstoexistingstudiesorperhapsdevelopmentofnewstudies.AnexampleforothefishpassageDSSisreservoiricestudies:weexpecttobeusedtodesigntributarycollectorsforoutmigratingjuvenilefishbutdon’tknowifthemodelwillprovidethatinformation.An8
example for the conceptual ecological model is the groundwater studies which we expect will
allow estimation of project impacts to areas of upwelling, but project effects to upwelling are not
one of the goals of that study. Therefore, we request that the schedule for DSS development be
accelerated so potential data needs not currently covered in the existing study plans can be
identified and added to the study plan.
9
U00039Enclosure2:NMFSCommentsonthe2014FishGeneticsImplementationPlanSUMMARY:oNMFSFisheriesgeneticists;Dr.JeffGuyon,SupervisoryResearchGeneticistandtheoFisheriesGeneticsProgramManagerattheTedStevensMarineResearchLaboratoryofoNOAA’sAlaskaFisheriesScienceCenterandDr.RobinWaples,SeniorScientistatNOAA’soNorthwestFisheriesScienceCenter,reviewedthe“ImplementationPlanfortheGeneticBaselineoStudyforSelectedFishSpeciesintheSusithaRiver,Alaska.”NMFSappreciatesthatABAandtheAlaskaDepartmentofFish&Game(ADF&G)incorporatedmostofthecommentsandsuggestionsprovidedtoABAinourreview,andincludedthetopicsdiscussedwithADF&G,oU.S.FishandWildifeServiceandNMFSatthetechnicalmeetinginMarchinthefinal2014Oimplementationplan.COMMENTSPROVIDEDTOABA:oThisreportreflectsacarefullythought-outapproachtosamplingfromnaturalpopulationstooprovidebaselinedatapriortoaproposedhydroelectricproject.Asproposed,theprojectwouldonodoubtproduceagreatdealofveryusefulinformation.Commentsbelowareintendedtohelpimprovecertainaspectsoftheexperimentaldesignand/ordataanalysis.oHypothesesforChinooksalmon:oPage3:NMFSagreesthatdeparturesfromHWE[Hardy-WeinbergEquffibriumJcouldsupportohypothesislb(fishaboveDevilsCanyonarederivedfromspawnersaboveandbelow),butonlyoifthedeparturesareinthedirectionofadeficitofheterozygotes,asexpectedundertheWahiundoeffect(populationmixture).However,Hypothesis2wouldnotnecessarilyproduceanysuchdeparturesifallthefishabovethecanyonwerederivedfromasinglelowerpopulation.C)Page3:“Ontheotherhand,lowgeneticdivergencebetweenfishspawningaboveDevilsCanyonoandfishspawninginaggregatesbelowthecanyonwouldindicatethatalargeproportionoftheofishascendingDevilsCanyonarestraysorcolonizers,andhavenotestablishedaself-sustainingopopulation(supportforHypothesis2).”Thisconclusioncannotbesupportedsimplyfromfailingtofindadifference.Itwouldbenecessarytoconductapoweranalysistodeterminehowlargeadifference(e.g.,Fstvalue)couldexistandnotbedetectedasstatisticallyUsignificant.Then,itwouldbenecessarytotranslatethegeneticdataintoestimatesofgeneflow0toevaluatewhatlevelsofconnectivityareconsistentwiththeobserveddata.Samplingdesign:NMFSconcursthatthatsamplesfrommultipleyearsareessentialtobeabletomakesenseoftherelativemagnitudeofspatialandtemporaldifferences.Threeyearsofsamplesmaybeinadequateforthispurpose,especiallyconsideringthatChinookandperhapssomeoftheotherspecieshavegenerationlengthsmuchlongerthanthreeyears.10
The required sample sizes depend on the particular objective, as well as the {unknown)
differences among populations. In general the numbers proposed seem reasonable. However,
the logic for requiring larger samples for msat [microsatellite] analyses is inadequately
explained. This may be based on the idea that larger samples are required to provide precise .
estimates of all the low frequency alleles involved with msats. However, that is not the
objective; the objective is to use all the data to draw biological conclusions about the species of
interest. From this perspective, each msat locus is worth several SNP [single nucleotide
polymorphism] loci in terms of information content, as a large number of empirical studies have
demonstrated.
Analyses:
Page 12-13: NMFS strongly recommends that the Pis [primary investigators] not remove
putative siblings as proposed. Siblings, in fact, contribute part of the signal in genetic analyses
that provides insights into biological processes. Purging them from the sample universe scrubs
the data of this biological signal, particularly for small populations where siblings are
common. The effects that this has on subsequent analyses cannot be easily determined, but
could be substantial. This purging makes the remaining individuals more similar to what would
be expected from populations that are infinite in size and hence have no relatives. Purging of a
particular sample might be justified, if the sample has been collected non-randomly (that is, if it
is thought to represent progeny from only a few families). However, in that case the proper
amount of purging could only be determined if one knows exactly how non-random the
collection is. But this will seldom if ever be known in practice. Furthermore, even if this was
known and relatives were removed, the result still would not be a representative collection from
the population as a whole. Therefore, the solution to non-random sampling is not purging
relatives but to going back into the field and collecting a representative sample.
Page 13: "We will exclude juvenile collections from the baseline if they show significant allele
frequency differences from adult collections or show deviations from HWE when pooled with
adult collections." We note that age structure creates mini-Wahlund effects that could cause HW
departures even in mixed-age adult samples. Likewise the same thing could happen if you
combine juveniles and adults produced by different cohorts. That does not mean that combining
them won't produce a more robust overall estimate of population allele frequencies.
NMFS does not agree with using the Bonferroni correction for HWE tests; there are too many
overall tests and thus the criterion become too conservative. Bonferroni correction controls the
probability of false positives o:nly and the correction otOinarily oome8 at the cbst of iri.cieasing
the probability of producing false negatives, consequently reducing the statistical power of the
HWE tests. Instead, we suggest starting with unadjusted tests and evaluating what fraction are
significant for each locus (across all pops) and for each pop (across all loci). If the resulting
proportions do not deviate much from the expected proportion (dictated by the significance level
11
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of the test), there is no reason to reject HWE. Loci or pops that are outliers can be singled out
for more detailed analysis, perhaps using Bonferroni or FDR [false discovery rate].
Minor comments:
Page 1: The project "will modify the flow, thermal, and sediment regimes of the Susitna River ...
. " The project will also affect migration and fish passage, among a host of other important
effects. The description of project effects should be written to comprehensively describe all
major project effects.
Page 1: "If breeding isolation (lack of migration) among populations occurs over sufficient time
and population sizes are small enough, genetic drift will result in variation in allele frequencies at
neutral loci (loci not under natural selection) among populations." Genetic drift
will always result in some differences unless there is complete panmixia.
Analyses of genetic distance: it is fine to use Fst as an index of genetic distance, but it must
include a correction for sample size (like W&C theta). Otherwise, small samples will tend to
look like outliers.
Page 6: "For mixed stock collections, sample sizes of200 fish or 100 fish per collection are
adequate to provide stock composition estimates that are within 7% or 10% of the true estimate
95% of the time, respectively (Thompson 1987)." That might have been true for the particular
study cited, but how large a sample is required will depend on the number of markers and the
magnitude of divergence among populations, so this general statement is not valid.
Page 8, the numbering is off under "Sample Collection Targets."
Page 9, under "Sample Collection Targets" item #9, we understand the issues regarding sample
numbers, but an adequate adult Chinook salmon sample set from above the proposed dam is
needed at the end of the study to make the necessary conclusions. What happens if the goal of
100 adult Chinook salmon is not realized? This should be addressed in advance.
Page 10, Section 4.2.4.1, identifies a sample target of 200 juvenile Chinook salmon from 4
systems in or above Devils Canyon, but later in the report under section 4.5 "Data Retrieval and
Quality Control" it mentions that software will be used to identify siblings and exclude all but
one individual in the baseline for every set of siblings identified. As such, given the likely small
population sizes above the proposed dam site, 200 juveniles from each system is unlikely to be
sufficient.
Page 16, Section 4.6.5, where it says "Collections will be pooled when tests indicate no
difference between collections ( P>O.Ol)." While we agree that it is difficult to prove there is no
difference between collections, we recommend though using a p value greater than 0.05 as more
appropriate to reject the null hypothesis.
12
Appendix A Section 2.2 Regarding the radio telemetry studies, the potential impacts of the tag
on the migration pattern of the salmon, especially for a stock that has to migrate the farthest and
through a 7 -mile long Class 5+ canyon must be considered and discussed. Also please address
whether the tags let you know where the fish spawned (or if they spawned) or just indicate where
they were when relocated, including noting the spatial accuracy of the tag signal recoveries.
Appendix B -page 1, for the Black River: Were the Chinook that were sampled two juveniles
which were collected in 2013? Please confirm and identify them as juveniles if that's true.
Table BS, Is there an overall HWE test for all markers for each population?
13
U00040Enclosure3:NMFSInitialCommentstoAEAregardingthe2014PilotStudyforCookInletBelugaWhalesandEulachon00SUMMARY:oBeginninginearlyMay2014,NNFSstaffwerecontactedandaskedtomeetwithAEAandtheircontractors(hereinafterreferredtocollectivelyasAEA)todiscussAEA’splanstomodifythe[RSPasmodifiedbyFERC’sdetermination]fortheCookInletBelugaWhaleStudy(Studyo9.17).AEAinformedNMFSstaffoftheirintenttoconductaboat-basedpilotstudyinvolving0bothaCookInletbelugawhaleresearcheffortandaeulachonresearcheffort.Despitethevery0shortnoticefromtheintendedstartdateoftheresearchactivities,NMFSagreedtoprovidesomeoinitialcommentsandpreliminaryrecommendationstoAEA.Theseinitialcommentswere0primarilyprovidedtohelpreducethehighharassmentandharmpotentialthispilotprojectcouldhaveontheendangeredCookInletbelugawhales,andtohelpABAavoidviolatingboththeMarineMammalProtectionActandtheEndangeredSpeciesAct.ThesecommentswerenotanC.endorsementofthepilotstudy,noranacknowledgementthatthepilotstudywouldconstitutetheC)secondyearoftherequiredFERC-approvedstudyplans.ThesecommentsweresenttoABAby0emailonMay14,2014,andarereproducedinEnclosure3.AsaresultoftheseNMFSocomments,ABAdidmakemodificationstothepilotstudyinanefforttoreducetheharassmentopotentialtoCookInletbelugawhales.NMFShashadmultiplemeetingswithABAtodiscussOtheprogressandstatusofthe2014pilotstudysinceearlyMay.Duringseveralmeetings,AEAhasprovidedinconsistentinformationregardingtheirplansfor2015CookInletbelugaostudies.Atthistime,itisunclearwhichaspectsoftheFERC-approvedstudyplansforCook0InletbelugawhalesABAintendstoimplementin2015,ifany.Additionally,ABAhasapatternoofprovidinginformationtoNMFSimmediatelypriortoameeting(e.g.,onehourinadvance)or0afterthemeeting,buthasanexpectationthatNMFSwillprovideofficialcommentsduringthemeeting.ThisprocesshassubstantiallylimitedtheabilityofNMFStoprovidemeaningfulcommentstoABA.Finally,whilethefocusofStudy9.17isonCookInletbelugawhales,NMFSreiteratesthattheMarineMammalProtectionActpertainstoallmarinemammals,0regardlessofanyadditionalprotectionsundertheEndangeredSpeciesAct.Thus,harassmentofC)anymarinemammalresultingfromABA’sactivitiesisprohibited.0COMMENTSPROVIDEDTOABA:Theseinitialcommentsareintendedtoprovideearlyguidanceandpreliminaryrecommendationsregardingthispilotstudy.NMFSintendstosubmitformalcommentsonthisstudyproposaltoFERC.oNMFSreceivedadraftcopyoftheABA’s“PilotStudyofCookInletBelugaWhaleandPrey0SpeciesintheSusitnaRiverDelta”onMondayMay12,2014.ABAandtheircontractorsintendC)toimplementthepilotstudybeginningtheweekafterNMFSreceivedthedraftstudyplanforreview,andcontinuethroughallofJune.ThepilotstudyissubmittedinlieuoftheFERCapprovedbelugastudies(aerialsurveys,videocameras,stillcameras,andwatersurfaceUUU
elevation model) for 2014. Although NMFS agreed to try and get these preliminary comments
back to ABA prior to implementation of the pilot study, NMFS advises that these are not official
comments, and as such do not indicate NMFS's support for or rejection of the pilot
study. Furthermore, NMFS does not consider any 2014 study to be the second year of study
under the ILP process. This is because the Initial Study Report is not complete, and licensing
participants have not been able to recommend any changes to the study or make new study
requests based on a review of the completed Initial Study Report. Our initial comments
regarding the draft pilot study after an abbreviated review period are as follows:
We understand neither ABA nor its contractors will be obtaining authorizations under the federal
Marine Mammal Protection Act (MMP A) for the unintentional take by harassment of marine
mammals. Thus no harassment or take of any marine rnamrna1 under NMFS' jurisdiction is
authorized under either the MMP A or the Endangered Species Act (ESA) and AEA and/or its
contractors would be responsible for any violation of these federal laws.
The draft pilot study references LGL Alaska Research, Inc.'s ongoing boat-based surveys for
Cook Inlet belugas as good documentation of Cook Inlet belugas as a result of closer proximity
and longer encounter durations with the whales than by aerial surveys. While we agree that a
boat survey has the potential to get closer to and spend more time with a group of marine
mammals than an airplane, we do note that the referenced LGL studies have a NMFS-issued
MMP A research permit and ESA authorization to allow harassment and close approaches. The
level of information collected by these two different boat-based studies will not be
comparable. Furthermore, we note that the LGL researchers associated with the NMFS
permitted photo-identification study are not indicated as participating in this pilot study.
The pilot study has the potential to disturb or harass marine mammals due to the presence of the
boat and operation of the split-beam sonar. The pilot study does suggest the implementation of
the "Marine Mammal Viewing Guidelines and Regulations" as found on our website
(http://alaskafisheries.noaa.gov/protectedresources/mmv/WJide.htm) as an effort to reduce the
potential for harassment or take. We note that many of the steps of the viewing guidelines are
stated in the ''2014 Pilot Study Methods" section of the draft pilot study, but add that whales
should not be encircled or trapped between boats or boats and shore, and that the study needs to
ensure that when approaching the whales the boat stays fully clear of whales' path of travel (i.e.,
the boat doesn't approach belugas ''head-on"). These guidelines are intended to reduce the
likelibQQ<I ~ttrulriite mammals woulcl 'be affected by this study, but do not guarantee no
harassment or take will occur. This is a directed research project targeting Cook Inlet beluga
whales, and a research permit may be necessary if the project may result in take or harassment of
this endangered species or other marine mammals.
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The pilot study is designed for repeated approaches to Cook Inlet beluga whales, albeit
theoretically no less than lOOm away. This study design increases the potential for harassment,
including behavioral modifications or displacement that may not be evident from the boat,
despite one of the pilot study's goals being to not cause any disturbance to the whales
themselves. Given the repeated approaches, and potential for belugas or other marine mammals
to not be visible below the water, implementation of the Marine Mammal Viewing Guidelines
may be insufficient for preventing harassment or take. This potential for disturbance or
harassment is of concern to NMFS, not only in general, but specifically during the first two
weeks of June when we will be conducting our aerial surveys to assess official population
abundance and distribution. Any disturbance or behavioral modification of the beluga whales
associated with the pilot study may result in a reduction of our ability to accurately conduct our
aerial surveys. The Susitna delta area is an important foraging area to the Cook Inlet belugas in
late spring/early summer, after limited food during the winter. Any disturbance to the whales
may result in reduced foraging success, and thus have population-level adverse effects.
The draft pilot study plan indicates that "if whales move away from the area where they were
initially detected, an attempt will be made to obtain a depth reading and prey information at that
location", but there is no information regarding how much time must pass without a beluga
sighting before the survey crew moves to that location to attempt to obtain depth and prey
information. There are confirmed reports that some stressed, chased, or harassed Cook Inlet
beluga whales do not swim away, but rather submerge and remain on the bottom of the seafloor,
which can be very shallow in Cook Inlet. If the observers do not wait a sufficient length of time,
the potential exists for a beluga exhibiting this behavior to be struck by the vessel or propellers
as the boat approaches the area where belugas were observed.
Given the topography and mudflats surrounding the Susitna Delta, as well as the potential that
belugas will be traveling and not staying still, it is unclear how accurately or consistently the
fine-scale surveys could be implemented. Should the belugas be traveling, it is possible the boat
may inadvertently chase the whales group while trying to accomplish the fine scale sampling
scheme as depicted in Figure 3. This could result in increased stress or harassment to the belugas
or other marine mammals (i.e., seals) in the vicinity.
The draft pilot study does not provide much detail about the acoustic component of the split-
beam sonar, but we understand some split-beam sonars have the potential for operating at
multiple frequencies. Frequencies below 200kHz are within the·hearing range of Cook Inlet
belugas, and thus noises associated with the sonar with frequencies below 200 kHz have the
potential to harass belugas and other marine mammals. Noise has been identified as one of the
highest threats to Cook Inlet belugas. Based on the information in the draft pilot study plan, it
appears there may only be a single frequency during operation, at 206 kHz. It is unclear whether
the split-beam sonar will be operated when conducting the "fine-scale sampling" triggered by
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Cook Inlet beluga sightings or if it will only be operated when no belugas are sighted, or if it will
be in constant operation.
In general, the pilot study plan is unclear about the primary goal of the study; is this a beluga
study that has a fish component or a fish study that will record beluga sightings? The study plan
states that data on prey and belugas will be "collected simultaneously", however, fish data can
only be recorded after the whales leave the area, and the split-beam sonar is unlikely to be able to
collect adequate fish data from over 100 m away (the minimum distance the boat will stay from
the belugas and other marine mammals). Overall, while it appears this pilot study attempts to
combine information regarding the distribution of beluga whales and their prey, we do have
initial concerns about the harassment potential to the belugas. Although there is information on
the data collection protocol sheets and software, there is no information regarding protocols
should the vessel be closer to 100m of the Cook Inlet beluga whales, or if the presence of the
boat or use of the split-beam sonar results in a change of behavior, disturbance, or displacement
of the whales. These are indications of harassment and take, and are currently not authorized by
NMFS. NMFS requests to be provided a survey schedule in advance of the first survey.
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