HomeMy WebLinkAboutSuWa264Alaska Resources Library & Information Services
Susitna-Watana Hydroelectric Project Document
ARLIS Uniform Cover Page
Title:
SuWa 264
Fish distribution and abundance in the upper and middle/lower Susitna
River (Studies 9.5 and 9.6), draft chinook and coho salmon identification
protoco
Author(s) – Personal:
Author(s) – Corporate:
R2 Resource Consultants, Inc.
AEA-identified category, if specified:
November 14, 2014 technical memorandum filings
AEA-identified series, if specified:
Series (ARLIS-assigned report number): Existing numbers on document:
Susitna-Watana Hydroelectric Project document number 264
Published by: Date published:
[Anchorage, Alaska : Alaska Energy Authority, 2014] November 2014
Published for: Date or date range of report: Alaska Energy Authority
Volume and/or Part numbers:
Final or Draft status, as indicated:
Attachment J
Document type: Pagination:
Technical memorandum ii, 3 p.
Related work(s): Pages added/changed by ARLIS:
Cover letter to this report: Susitna-Watana Hydroelectric
Project, FERC Project no. 14241-000; Filing of Initial Study Plan
Meetings transcripts and additional information in response to
October 2014 Initial Study Plan Meetings. (SuWa 254)
Attachments A-I (SuWa 255-263) and K-N (SuWa 265-268)
Added cover letter (4 pages)
Notes:
All reports in the Susitna-Watana Hydroelectric Project Document series include an ARLIS-
produced cover page and an ARLIS-assigned number for uniformity and citability. All reports
are posted online at http://www.arlis.org/resources/susitna-watana/
November 14, 2014
Ms. Kimberly D. Bose
Secretary
Federal Energy Regulatory Commission
888 First Street, N.E.
Washington, D.C. 20426
Re: Susitna-Watana Hydroelectric Project, Project No. 14241-000
Filing of Initial Study Plan Meetings Transcripts and Additional Information in
Response to October 2014 Initial Study Plan Meetings
Dear Secretary Bose:
By letter dated January 28, 2014, the Federal Energy Regulatory Commission
(Commission or FERC) modified the procedural schedule for the preparation and review
of the Initial Study Report (ISR) for the proposed Susitna-Watana Hydroelectric Project,
FERC Project No. 14241 (Project).1 As required by the Commission’s January 28 letter,
the Alaska Energy Authority (AEA) filed the ISR with the Commission on June 3, 2014
and conducted ISR meetings on October 15, 16, 17, 21, 22, and 23, 2014. Attached as
Attachments A-1 through F-2 are the written transcripts (along with the agenda and
PowerPoint presentations) for these ISR meetings.
During the October ISR meetings, AEA and licensing participants identified
certain technical memoranda and other information that AEA would file with the
Commission by November 15, 2014. In accordance, AEA is filing and distributing the
following technical memoranda and other information:
• Attachment G: Glacier and Runoff Changes (Study 7.7) and Fluvial
Geomorphology (Study 6.5) - Assessment of the Potential for Changes in
Sediment Delivery to Watana Reservoir Due to Glacial Surges Technical
Memorandum. This technical memorandum documents AEA’s analysis of the
potential changes to sediment delivery from the upper Susitna watershed into
the Project’s reservoir from glacial surges.
• Attachment H: Riparian Instream Flow (Study 8.6) and Fluvial
Geomorphology (Study 6.6) - Dam Effects on Downstream Channel and
Floodplain Geomorphology and Riparian Plant Communities and Ecosystems
− Literature Review Technical Memorandum. This literature review technical
1 Letter from Jeff Wright, FERC Office of Energy Projects, to Wayne Dyok, Alaska Energy Authority,
Project No. 14241-000 (issued Jan. 28, 2014).
2
memorandum synthesizes historic physical and biologic data for the Susitna
River floodplain vegetation (including 1980s studies), studies of hydro project
impacts on downstream floodplain plant communities, and studies of un-
impacted floodplain plant community successional processes.
• Attachment I: Susitna River Fish Distribution and Abundance Implementation
Plan, Appendix 3. Protocol for Site-Specific Gear Type Selection, Version 5.
In accordance with the fish distribution and abundance studies, as described in
Revised Study Plan (RSP) Sections 9.5 and 9.6 and in the Fish Distribution
and Abundance Implementation Plan, this appendix establishes the protocol
for site-specific gear type selection for fish surveys. Throughout study plan
implementation, AEA has updated this appendix as needed to provide
consistent direction to all field teams. Version 1 of Appendix 3 was originally
filed with the Fish Distribution and Abundance Implementation Plan in March
2013. That version was updated twice (Versions 2 and 3) during the 2013
field season to accommodate protocol changes that related to FERC’s April 1,
2013 Study Plan Determination, field permits, and lessons learned during
study implementation. Version 4 was the protocol used for the 2014 field
season and was updated with respect to the prioritization of gear use and
based on 2013 data collected. This version herein, Version 5, will be followed
during the 2015 field season.
• Attachment J: Fish Distribution and Abundance in the Upper and
Middle/Lower Susitna River (Studies 9.5 and 9.6): Draft Chinook and Coho
Salmon Identification Protocol. This document established a Chinook and
coho salmon identification protocol to support accurate and consistent field
identification across field teams. It will allow for additional quality control
and assurance of field identification calls and for estimation and reporting of
any field identification error that may occur in future sampling efforts.
• Attachment K: Characterization and Mapping of Aquatic Habitats (9.9),
Errata to Initial Study Report Part A - Appendix A, Remote Line Mapping,
2012. This errata provides a corrected version of map book for Remote Line
Mapping, 2012. The version filed with the ISR (June 3, 2014) used a data
query to build the maps in geomorphic reaches MR-1 to UR-5 that mistakenly
did not include side slough habitat, so that no side sloughs were depicted on
the Appendix A maps 1 through 21. This version was corrected by including
side slough habitat in the data query for geomorphic reaches MR-1 to UR-5.
This version now includes side sloughs.
• Attachment L: Characterization and Mapping of Aquatic Habitats Study 9.9,
Revised Map Book for 2012 Remote Line Mapping. This map book represents
an update to the version published on June 3, 2014 with the Study 9.9 Initial
Study Report and the errata provided concurrently with this filing (see
Attachment K). The maps presented include all macrohabitat and mesohabitat
line identifications available in the 2012 Remote Line Mapping ArcGIS
3
shapefile. This map book should be considered a full replacement for
previous versions and represents the final product for the 2012 remote line
habitat mapping effort.
• Attachment M: Study of Fish Passage Barriers in the Middle and Upper
Susitna River and Susitna Tributaries (Study 9.12), Fish Passage Criteria
Technical Memorandum. This technical memorandum presents a proposed
final list of fish species that will be included in the fish barrier analysis as well
as depth, leaping and velocity passage criteria for selected fish species. AEA
previously consulted with the federal agencies and other licensing participants
regarding the information within the technical memorandum during a March
19, 2014 Fisheries Technical Meeting.
In addition to the technical memoranda and other information identified above,
AEA is filing a short errata (Attachment N) to the Mercury Assessment and Potential for
Bioaccumulation Study (Study 5.7), Evaluation of Continued Mercury Monitoring
Beyond 2014 Technical Memorandum. This technical memorandum, which was
originally filed on September 30, 2014, evaluates the need for continued monitoring of
mercury data beyond 2014 and whether the existing data collection efforts are sufficient
to satisfy objectives for characterizing baseline mercury conditions in the Susitna River
and tributaries (RSP Section 5.7.1). Since the filing of this TM and based upon the
ongoing QA/QC of the data reported in that TM, AEA discovered errors in the TM. The
attached TM corrects those errors. Additionally, the errata corrects corresponding errors
in the Mercury Assessment and Potential for Bioaccumulation presentation presented
during the October 16, 2014 ISR meeting.
Finally, AEA notes that data collected during the Study Plan implementation, to the
extent they have been verified through AEA’s quality assurance and quality control (QAQC)
procedures and are publicly available, can be accessed at http://gis.suhydro.org/isr_mtg. On
November 14, 2014, AEA posted the following data to this website:
• Baseline Water Quality Data (Study 5.5), 2013 QAQC water quality data
and DVRs per the Quality Assurance Project Plan.
• Breeding Survey Study of Landbirds and Shorebirds (Study 10.16),
cumulative 2013-2014 data.
• Characterization and Mapping of Aquatic Habitats (Study 9.9), ArcGIS
shapefile “ISR_9_9_AQHAB_RemoteLineMapping_2012.shp” used to
generate the maps in Attachment L.
4
AEA appreciates the opportunity to provide this additional information to the
Commission and licensing participants, which it believes will be helpful in determining
the appropriate development of the 2015 study plan as set forth in the ISR. If you have
questions concerning this submission please contact me at wdyok@aidea.org or (907)
771-3955.
Sincerely,
Wayne Dyok
Project Manager
Alaska Energy Authority
Attachments
cc: Distribution List (w/o Attachments)
Susitna-Watana Hydroelectric Project
(FERC No. 14241)
Fish Distribution and Abundance in the Upper and
Middle/Lower Susitna River (Studies 9.5 and 9.6):
Draft Chinook and Coho Salmon Identification
Protocol
Prepared for
Alaska Energy Authority
Prepared by
R2 Resource Consultants, Inc.
November 2014
TECHNICAL MEMORANDUM DRAFT CHINOOK AND COHO SALMON IDENTIFICATION PROTOCOL
TABLE OF CONTENTS
1. Introduction ........................................................................................................................1
2. Field Training .....................................................................................................................1
3. Genetic Verification ...........................................................................................................2
4. Meristic Analysis ................................................................................................................2
5. Photograph Quality Control .............................................................................................2
6. References ...........................................................................................................................3
Susitna-Watana Hydroelectric Project Alaska Energy Authority
FERC Project No. 14241 Page i November 2014
TECHNICAL MEMORANDUM DRAFT CHINOOK AND COHO SALMON IDENTIFICATION PROTOCOL
LIST OF ACRONYMS AND SCIENTIFIC LABELS
Abbreviation Definition
ADF&G Alaska Department of Fish and Game
AEA Alaska Energy Authority
FDA Fish distribution and abundance
GRTS Generalized Random Tessellation Stratified
IP Implementation Plan
ISR Interim Study Report
PIT Passive integrative transponder
PRM Project river mile
QAQC Quality assurance quality control
Susitna-Watana Hydroelectric Project Alaska Energy Authority
FERC Project No. 14241 Page ii November 2014
TECHNICAL MEMORANDUM DRAFT CHINOOK AND COHO SALMON IDENTIFICATION PROTOCOL
1. INTRODUCTION
During the first study year of the Susitna-Watana Hydro Fish Distribution and Abundance
Studies, sampling occurred along over 200 miles of the Susitna River including many salmon-
bearing tributaries. As in other larger glacial river systems in Alaska, Chinook and coho salmon
in the Susitna River exhibit a wide variety of phenotypic variation and can appear very different
among reaches, rearing habitats (e.g., turbid mainstem vs. tannic upland slough), and stages of
smoltification. There is little data available regarding the accuracy of field identification of
juvenile salmonids as most field biologists do not collect voucher specimen or samples with
which they could verify field identifications and/or estimate a rate of error associated with their
field identification, yet differentiating between these two species in some Alaska rivers can be
challenging. This issue has been noted both historically in the Taku River (Meehan and Vania
1961) and, more recently, in the Copper River (Phil Joy, ADF&G, personal communication,
October, 2014) and in the Susitna River where AEA field crews, including ADF&G Chinook
salmon experts, incorrectly identified coho salmon when collecting Chinook salmon genetic
samples in 2013 (Chris Habicht, ADF&G, personal communication, August, 2014). A QAQC
review of the Chinook and coho salmon field calls from the 2013 Susitna River data set indicates
that the primary phenotypic characteristics that are used to distinguish between the two species
(e.g., anal fin shape and coloration, adipose fin pigmentation, parr mark shape/width, etc.) are
highly variable across sub-populations of juveniles within each species and that the range of
variation overlaps across species making field identification of juveniles of these two species
more challenging.
In light of this, AEA has enhanced the ongoing fish sampling under the Susitna-Watana
Hydroelectric Project’s Study Program by developing a protocol and accompanying Susitna
River specific field identification guide that will be used by all field crews. This standardized
protocol will support accurate and consistent field identification across field teams. It will allow
for additional quality control and assurance of field identification calls and for estimation and
reporting of any field identification error that may occur in future studies. In addition, for the
fish that were sampled for genetics, it will be possible to correct any erroneous field
identification in the database. Furthermore, if systematic error is evident from the genetics
analysis, for example all samples collected from salmon at one location or within a specific size
category are identified as one species, it may be possible to make species identification
adjustments to the data base for non-sampled individuals from that same group. Such
corrections would be done by adding a genetic identification to the database to preserve the
original field data.
2. FIELD TRAINING
The pre-sampling orientation of field crews will be expanded to include site specific information
of phenotypic variation in juvenile Chinook and coho salmon. During orientation and training of
field staff, Susitna-experienced Senior Fish Scientists will review with field crew a Susitna-
specific identification guide that is developed in collaboration with ADF&G as well as the other
field identification guides provided in Section 5.1.4 of the Implementation Plan (R2 Resource
Consultants 2013). Field teams, led by senior staff, will then visit locations where both Chinook
Susitna-Watana Hydroelectric Project Alaska Energy Authority
FERC Project No. 14241 Page 1 November 2014
TECHNICAL MEMORANDUM DRAFT CHINOOK AND COHO SALMON IDENTIFICATION PROTOCOL
and coho salmon phenotypic overlap has been found in the past and will use the field guide to
identify individual fish.
3. GENETIC VERIFICATION
AEA will standardize the collection of genetic samples across habitats and sampling events.
Field crews will be instructed to collect genetic samples on all Chinook salmon collected
upstream of Impediment 1 in Devils Canyon (PRM 154.8) and to subsample for genetics
downstream of Impediment 1. To determine the appropriate sample size for genetics sub-
sampling, a power analyses will be conducted using the 2012 and 2013 data. Genetic
identification data will be used to estimate the variation in field identification error rate across
species and habitats. The power analysis will be used to estimate the appropriate sample size
necessary to ensure that the fish identification error is within +/-5% of the true error rate. This
analysis will be conducted in the spring of 2015.
Once the total sample size is determined, the first X Chinook and coho salmon collected at each
site (GRTS or transect macrohabitat or check of a rotary screw trap) will be sampled for genetics
using the omniswab technique. After that, one out of every Y individuals identified will be
swabbed for genetics in order to meet pre-determined sample sizes in a way that is representative
across habitats and time. The number of genetic samples collected will be tracked during the
study season and the number of samples collected at each site may be adjusted as necessary to
meet our desired sample size.
4. MERISTIC ANALYSIS
Because of the time required for transfer and analysis of genetics samples, it may be weeks or
months until the samples are analyzed. To help improve field identification, more rapid and
direct feedback to field crews is needed. Thus, vouchers will be taken for quick meristic analysis
and specimens will be used as a teaching tool. Up to 20 juvenile Chinook, coho, and
undifferentiated Pacific salmon may be taken as voucher specimens from each hydrologic
segment: Lower and Middle. No meristics are needed in the Upper River as 100 % of all
juvenile salmon collected are sampled for genetics analysis. Dissection and meristic analysis of
pyloric caeca and branchiostegal counts will occur after collection, and specimens will be kept in
viewable containers at a central location (field camp) for staff to review. Voucher specimens
will focus on those individuals that are especially difficult to identify in the field or have unique
characteristics leading to uncertainty in identification.
5. PHOTOGRAPH QUALITY CONTROL
In the next study year, undifferentiated Pacific salmon that are handled, fish used for genetic
analysis, PIT-tagged fish, and PIT-tag recaptures will be photographed. Based on data from
2013 and 2014, there is photo documentation of approximately 4,000 PIT-tagged Chinook and
coho salmon as well as undifferentiated fish and those selected for genetic samples but not PIT-
tagged.
Susitna-Watana Hydroelectric Project Alaska Energy Authority
FERC Project No. 14241 Page 2 November 2014
TECHNICAL MEMORANDUM DRAFT CHINOOK AND COHO SALMON IDENTIFICATION PROTOCOL
A Senior Fish Biologist with experience identifying Susitna River juvenile salmon will review
photographs of all Chinook, coho, and undifferentiated Pacific salmon as a part of the AEA’s
data QAQC process. The reviewer will have the option to 1) confirm species call made in the
field, 2) override the species call made in the field by assigning a new species and providing
justification, or 3) determine that neither confirmation nor reassignment can be made based on
photograph. Results from meristic and genetic analysis may also be used to establish a photo
review error rate for those individuals for which species calls are confirmed or reassigned.
Photographic reviews will be conducted as soon as possible after field data is collected and
during the sampling season to provide feedback to field crews. A final review will be done and
at the culmination of the field season prior to data analysis.
6. REFERENCES
McConnel, R.J. and G.R. Snyder. 1972. Key to Field Identification of Anadromous Juveniles
Salmonids in the Pacific Northwest. NOAA Technical Report NMFS CIRC-366. 8 pp.
Meehan, W.R. and J.S. Vania. 1961. An external characteristic to differentiate between King
and Silver Salmon juveniles in Alaska. Informational Leaflet 1. Alaska Department of
Fish and Game. 9 pp.
Morrow, J.E. 1980. The freshwater fishes of Alaska. Alaska Northwest Publishing Co.,
Anchorage.
Pollard, W.R., G.F. Hartman, C. Groot, and P. Edgell. 1997. Field Identification of Coastal
Juvenile Salmonids. Harbor Publishing, Madeira Park, BC Canada. 32 pp.
R2 Resource Consultants, Inc. 2013. Susitna River Fish Distribution and Abundance
Implementation Plan: Susitna-Watana Hydroelectric Project FERC Project No. 14241.
March 31, 2013 including HDR prepared Appendix 2, Initial Results Aerial Video
Habitat Mapping of Susitna River Tributaries from the Upper Extent of Devils Canyon to
the Oshetna River, January 2013. http://www.susitna-watanahydro.org/wp-
content/uploads/2013/09/SuWa-FSP-2013-Section-09.05-FDAUP.pdf
Weiss, E. 2003. Juvenile and Small Fish Identification Aid. Alaska Department of Fish and
Game Habitat and Restoration Division.
.
Susitna-Watana Hydroelectric Project Alaska Energy Authority
FERC Project No. 14241 Page 3 November 2014