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Susitna‐Watana Hydroelectric Project Document
ARLIS Uniform Cover Page
TK
1425
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S92
no.305
Title:
SuWa 305
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
[Title devised by cataloger.]
Author(s) – Personal:
James W. Balsiger (writer of cover letter)
Author(s) – Corporate:
National Marine Fisheries Service. Alaska Regional Office
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 305 20140923-5026 (FERC posting)
Published by: Date published:
National Marine Fisheries Service. Alaska Regional Office September 22, 2014
Published for: Date or date range of report:
Wayne Dyok, Alaska Energy Authority
Volume and/or Part numbers: Final or Draft status, as indicated:
Document type: Pagination:
Letter with enclosures 17 pages
Related work(s): Pages added/changed by ARLIS:
Comments 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/
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
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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
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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
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Enclosure 1: Details regarding Data Integrity, Model Integration/Proof-of-Concept and
Decision Support Systems.
DATA ISSUES:
Data Collection: Quality Assurance and Quality Contro~ and Methodologies
NMFS is concerned with the current status and implementation of aquatic studies and believes
that, unless these issues are addressed, many study objectives will not be met. Our primary
concerns are as follows:
1) Habitat classification has not been completed;
2) Fish passage criteria have not been developed;
3) Fish sampling study plans were not followed; sampling units were inappropriately
subsampled;
4) Fish sampling locations did not incorporate FERC recommendations;
5) Because the fish sampling did not follow the sampling plan, this resulted in an inability to
estimate relative fish abundance;
6) Fish seem to have been identified incorrectly;
7) Data were collected and reported at inappropriate mesohabitat scales;
8) Sampling sites among studies were not co-located;
9) Tagging goals were not met;
10) Fish targets for HSC sampling were not met;
11) The mainstem upper river migrant fish trap was not installed;
12) A fish wheel was not installed, and fish were not tagged near the entrance to Devils Canyon;
13) Additional problems associated with late installation and operation of migrant traps were
likely influenced by environmental conditions associated with late breakup; and
14) Juvenile salmon distribution and abundance in 2013 were likely affected by the record fall
floods in 2012.
We are providing some additional clarification on some of these concerns.
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 (different gears, different effort, different order of gears, different total
area sampled, etc). Sampling error in the fish diStribution and reliltive 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
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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.
Data collection and analysis
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.
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:
• large numbers of unidentified salmonid juveniles (some of which were PIT
tagged);
• anomalous length distributions and habitat associations (e.g., juvenile Chinook
150 mm fork-length;
• the large abundance of juvenile Chinook in beaver ponds;
• the absence of pink salmon in any samples; and
• the disappearance of sockeye salmon from Indian River between the February
draft Initial Study Report and the June draft Initial Study Report).
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.
There is an absence of quantitative analysis of habitat sampling, fish distribution and relative
abundance, and early life history data collected to date. Deviations from the Revised Study Plan
(RSP) and FERC staff recommendations make developing estimates from these data difficult or
f!V~PimPQs&ible. Th~.~ta.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
5
science on these species and their life stages as known through data previously collected and past
studies conducted in the Susitna River and environs.
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
Scale
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.
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
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.)
, 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.
Co-location of sampling sites
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
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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 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.
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.
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.
These issues of data integrity and data collection are based in part on studies being conducted
with significant differences from the FERC-modifi.ed 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.
MODEL INTEGRATION/PROOF-OF-CONCEPT:
Biological relevance
During the Riverine Modeling Integration 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.
NMFS has identified a need to develop and incorporate biological input and output parameters
and eyaluate 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)
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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.
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.
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.
DECISION SUPPORT SYSTEMS:
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.
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 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 da~ 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 tnbutary collectors
for outmigratingjuvenile fish but don't know if the model will provide that information. An
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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.
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Enclosure 2: NMFS Comments on the 2014 Fish Genetics Implementation Plan
SUMMARY:
NMFS Fisheries geneticists; Dr. Jeff Guyon, Supervisory Research Geneticist and the
Fisheries Genetics Program Manager at the Ted Stevens Marine Research Laboratory of
NOAA's Alaska Fisheries Science Center and Dr. Robin Waples, Senior Scientist at NOAA's
Northwest Fisheries Science Center, reviewed the "Implementation Plan for the Genetic Baseline
Study for Selected Fish Species in the Susitna River, Alaska." NMFS appreciates that AEA and
the Alaska Department of Fish & Game (ADF&G) incorporated most of the comments and
suggestions provided to AEA in our review, and included the topics discussed with ADF&G,
U.S. Fish and Wildife Service and NMFS at the technical meeting in March in the final2014
implementation plan.
COMMENTS PROVIDED TO AEA:
This report reflects a carefully thought-out approach to sampling from natural populations to
provide baseline data prior to a proposed hydroelectric project. As proposed, the project would
no doubt produce a great deal of very useful information. Comments below are intended to help
improve certain aspects of the experimental design and/or data analysis.
Hypotheses for Chinook salmon:
Page 3: NMFS agrees that departures from HWE [Hardy-Weinberg Equilibrium] could support
hypothesis lb (fish above Devils Canyon are derived from spawners above and below), but only
if the departures are in the direction of a deficit of heterozygotes, as expected under the W ahlund
effect (population mixture). However, Hypothesis 2 would not necessarily produce any such
departures if all the fish above the canyon were derived from a single lower population.
Page 3: "On the other hand, low genetic divergence between fish spawning above Devils Canyon
and fish spawning in aggregates below the canyon would indicate that a large proportion of the
fish ascending Devils Canyon are strays or colonizers, and have not established a self-sustaining
population (support for Hypothesis 2)." This conclusion cannot be supported simply from
failing to find a difference. It would be necessary to conduct a power analysis to determine how
large a difference (e.g., Fst value) could exist and not be detected as statistically
significant Then, it would be necessary to translate the genetic data into estimates of gene flow
to evaluate what levels of connectivity are consistent with the observed data.
Sampling design:
NMFS concurs that that samples from multiple years are essential to be able to make sense of the
relative magnitude of spatial and temporal differences. Three years of samples may be
inadequate for this purpose, especially considering that Chinook and perhaps some of the other
species have generation lengths much longer than three years.
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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
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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.
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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?
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Enclosure 3: NMFS Initial Comments to AEA regarding the 2014 Pilot Study for Cook
Inlet Beluga Whales and Eulachon
SUMMARY:
Beginning in early May 2014, NMFS staff were contacted and asked to meet with ABA and their
contractors (hereinafter referred to collectively as AEA) to discuss AEA's plans to modify the
[RSP as modified by PERC's determination] for the Cook Inlet Beluga Whale Study (Study
9.17). ABA 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 PERC-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 with ABA 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 PERC-approved study plans for Cook
Inlet beluga whales AEA intends to implement in 2015, if any. Additionally, ABA 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 ABA' s activities is prohibited.
COMMENTS PROVIDED TO ABA:
These initial comments are intended to provide early guidance and preliminary recommendations
regarding this pilot study. NMFS intends to submit formal comments on this study proposal to
FERC.
NMFS received a draft copy of the AEA's ''Pilot Study of Cook Inlet Beluga Whale and Prey
Species in the Susitna River Delta" on Monday May 12, 2014. ABA and their contractors intend
to implement the pilot study beginning the week after NMFS received the draft study plan for
review, and continue through all of June. The pilot study is submitted in lieu of the PERC-
approved beluga studies (aerial surveys, video cameras, still cameras, and water surface
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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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