Susitna River Chinook salmon inriver abundance and spawning distribution, 2017.

91 Pages·2017·2.36 MB·English

Regional Operational Plan SF.2A.2017.09
Operational Plan: Susitna River Chinook Salmon
Inriver Abundance and Spawning Distribution, 2017
by
Pete Cleary
Johnathon Campbell
and
Nick Decovich
May 2017
Alaska Department of Fish and Game Divisions of Sport Fish and Commercial Fisheries
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REGIONAL OPERATIONAL PLAN SF.2A.2017.09
OPERATIONAL PLAN: SUSITNA RIVER CHINOOK SALMON INRIVER
ABUNDANCE AND SPAWNING DISTRIBUTION, 2017

by
Pete Cleary
Johnathon Campbell
and
Nick Decovich

Alaska Department of Fish and Game
Division of Sport Fish, Research and Technical Services
333 Raspberry Road, Anchorage, Alaska, 99518-1565
May 2017
The Regional Operational Plan Series was established in 2012 to archive and provide public access to operational
plans for fisheries projects of the Divisions of Commercial Fisheries and Sport Fish, as per joint-divisional
Operational Planning Policy. Documents in this series are planning documents that may contain raw data,
preliminary data analyses and results, and describe operational aspects of fisheries projects that may not actually be
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implementation of the operational plan described in this series may be subsequently finalized and published in a
different department reporting series or in the formal literature. Please contact the author if you have any questions
regarding the information provided in this plan. Regional Operational Plans are available on the Internet at:
http://www.adfg.alaska.gov/sf/publications/

Pete Cleary,
Alaska Department of Fish and Game, Division of Sport Fish,
1800 Glenn Hwy, Suite 2, Palmer, AK 99645-6736, USA

Johnathon Campbell,
Alaska Department of Fish and Game, Division of Sport Fish,
1800 Glenn Hwy, Suite 2, Palmer, AK 99645-6736, USA

and

Nick Decovich,
Alaska Department of Fish and Game, Division of Sport Fish,
1800 Glenn Hwy, Suite 2, Palmer, AK 99645-6736, USA

This document should be cited as follows:
Cleary, P., J. Campbell, and N. Decovich. 2017. Operational Plan: Susitna River Chinook salmon inriver
abundance and spawning distribution, 2017. Alaska Department of Fish and Game, Regional Operational
Plan ROP.SF.2A.2017.09, Anchorage.
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TABLE OF CONTENTS
Page
LIST OF TABLES........................................................................................................................................................iii
LIST OF FIGURES ......................................................................................................................................................iii
LIST OF APPENDICES ..............................................................................................................................................iii
ABSTRACT .................................................................................................................................................................. 1
INTRODUCTION ......................................................................................................................................................... 1
OBJECTIVES ................................................................................................................................................................ 2
Primary Objectives ........................................................................................................................................................ 2
Secondary Objectives .................................................................................................................................................... 2
METHODS .................................................................................................................................................................... 2
Study Design ................................................................................................................................................................. 2
Mainstem Susitna River ............................................................................................................................................ 3
Yentna River ............................................................................................................................................................. 6
Data Collection .............................................................................................................................................................. 6
Marking .................................................................................................................................................................... 6
Genetics .................................................................................................................................................................. 16
Recapture ................................................................................................................................................................ 16
Data Reduction ............................................................................................................................................................ 19
Data Analysis ............................................................................................................................................................... 20
Mark–Recapture Assumptions ................................................................................................................................ 20
Sample Sizes ........................................................................................................................................................... 22
Analysis of Abundances ......................................................................................................................................... 25
Analysis of Spawning Locations ............................................................................................................................ 27
Analysis of Spawning Distributions ....................................................................................................................... 28
SCHEDULE AND DELIVERABLES ........................................................................................................................ 29
RESPONSIBILITIES .................................................................................................................................................. 30
BUDGET SUMMARY ............................................................................................................................................... 30
REFERENCES CITED ............................................................................................................................................... 31
APPENDIX A: PIT–TAG METHODS ....................................................................................................................... 33
APPENDIX B: FIELD DATA FORMS ...................................................................................................................... 39
APPENDIX C: BIOLOGICAL SAMPLING PROCEDURES ................................................................................... 69
APPENDIX D: TESTS OF MARK–RECAPTURE ASSUMPTIONS AND SAMPLE SIZES ................................. 73
APPENDIX E: SPAWNING CODE ASSIGNMENTS AND INTERPRETATION .................................................. 81
ii
LIST OF TABLES
Table Page
1. Location and mark type for Susitna and Yentna rivers mark–recapture events, 2017. ................................... 3
2. Radiotagging schedule for Chinook salmon at the mainstem Susitna River fishwheels, 2017. ...................... 9
3. Radiotagging schedule for Chinook salmon at the mainstem Susitna River gillnets, 2017. ......................... 10
4. Radiotagging schedule for Chinook salmon at the Yentna River RM 6 fishwheels, 2017. ........................... 11
5. Radiotagging schedule for Chinook salmon at the Yentna River RM 6 gillnets, 2017. ................................ 12
6. Location of radiotracking stations. ................................................................................................................ 18

LIST OF FIGURES
Figure Page
1. Sampling design for the mainstem Susitna and Yentna rivers mark–recapture experiments. ......................... 4
2. Locations of fish wheels, fixed telemetry stations, and weir site on the Susitna River, Alaska. ..................... 5
3. Tagging sites and river miles for the Susitna RM 34 and Yentna RM 6 operations. ...................................... 8

LIST OF APPENDICES
Appendix Page
A1. PIT–tag detection methods. ........................................................................................................................... 34
B1. Fish wheel catch and effort field data form for deployment. ......................................................................... 40
B2. Gillnet catch and effort field data form for deployment. ............................................................................... 41
B3. Detailed radiotag deployment form for mainstem Susitna River Fish Wheel 1. ........................................... 42
B4. Detailed radiotag deployment form for mainstem Susitna River Fish Wheel 2. ........................................... 46
B5. Detailed radiotag deployment form for mainstem Susitna River gillnets. ..................................................... 50
B6. Detailed radiotag deployment form for Yentna River Fish Wheel 1. ............................................................ 54
B7. Detailed radiotag deployment form for Yentna River Fish Wheel 2. ............................................................ 58
B8. Detailed radiotag deployment form for Yentna River gillnets. ..................................................................... 62
B9. Example of radiotag deviation log. ............................................................................................................... 66
B10. Fish wheel catch and effort field data form for recovery. ............................................................................. 67
B11. Gillnet catch and effort field data form for recovery. .................................................................................... 68
C1. Genetic tissue sample collection procedures. ................................................................................................ 70
C2. Location of axillary process. ......................................................................................................................... 71
C3. Measuring salmon for length from mid eye to tail fork. ................................................................................ 72
D1. Detection and mitigation of selective sampling during a 2-event mark–recapture experiment. .................... 74
D2. Possible results of selectivity testing, interpretation, and action. .................................................................. 75
D3. Composition estimation for stratified estimates. ........................................................................................... 76
D4. Tests for consistency of the Petersen estimator ............................................................................................. 77
D5. Tables describing anticipated sampling rates and sample sizes..................................................................... 79
E1. Spawning code assignments and interpretation of spawning codes for radiotagged fish in 2017 using
aerial survey and stationary telemetry data. .................................................................................................. 82
iii
iv
ABSTRACT
The goals of this study are to estimate the abundance and distribution of spawning Chinook salmon in the entire
Susitna River in 2017. An independent, 2-event, mark–recapture experiment will be conducted on the mainstem
Susitna River and the Yentna River. For the mainstem Susitna River experiment, fish wheels and gillnets will be
operated at river mile (RM) 34 to capture Chinook salmon for marking with dart-PIT tags (a dart tag with an
imbedded passive integrated transponder [PIT]). Recapture event sampling will occur at the Deshka River weir at
RM 7 where a PIT array will be used and at Sunshine (RM 83) with fish wheels and gillnets. In the Yentna River,
fish wheels and gillnets will be used at RM 6 to capture Chinook salmon for marking with dart tags (no PIT-tag
component). Recapture event sampling will occur at Yentna RM 18 using fish wheels and gillnets. Radio tags will
be applied to a subsample of Chinook salmon in the mainstem Susitna and Yentna rivers to determine spawning
distribution and handling effects. Aerial telemetry surveys every 2 weeks and stationary telemetry receiver-loggers
will be used to track movements of radiotagged salmon.
Key words: Chinook salmon, abundance, mark–recapture, Susitna River, Yentna River, spawning distribution,
PIT tag, dart tag, gillnet, fish wheel, radio telemetry
INTRODUCTION
Recent downturns in productivity and abundance of Chinook salmon (Oncorhynchus
tshawtyshca) stocks across Alaska have created social and economic hardships within many
communities. There is a fundamental need to accurately describe productivity and abundance
trends of Chinook salmon stocks across Alaska, gather essential information necessary to
understand root causes of these widespread declines, and track population trends into the future
(ADF&G Chinook Salmon Research Team 2013). The Susitna River was selected by the Alaska
Department of Fish and Game (ADF&G) as a Chinook salmon indicator stock, with estimation
of the inriver run size in both the mainstem Susitna and Yentna rivers recommended as stock
assessment projects. Use of radio tags in these abundance estimation projects also allows
estimation of spawner distribution.
In 2017, the ADF&G plans to estimate the inriver abundance and spawner distribution for
Chinook salmon for both the Yentna and mainstem Susitna rivers. Data collected from these
studies will supplement similar data collected in 2012–2016. The 2015 mainstem Susitna River
Chinook salmon abundance estimate upstream of the Yentna River confluence was 88,600 (CI
77,500–101,100) fish. The estimated abundance in the Yentna River in 2015 was 48,400 (CI
39,500–60,400) fish.
Data collected in 2017 from the Yentna and mainstem Susitna river stocks will also enhance
knowledge of the spawning distribution and habitat use of each species and quantify the annual
variation in distribution and use. The 2017 experiment will be the fifth such study providing an
estimate of Chinook salmon for the entire Susitna River (mainstem Susitna River plus Yentna
River) since estimates were made during the 1984 Susitna hydroelectric project environmental
assessment. The data generated by these studies will help interpret present and past stock
assessments, choose future assessments that are efficient and effective, provide new knowledge
to fishery managers and users, advise the Alaska Board of Fisheries regulatory process, and be
useful in land use planning and permitting.
1
OBJECTIVES
PRIMARY OBJECTIVES
1) Estimate the abundance of Chinook salmon greater than or equal to 500 mm mid eye to
tail fork (METF) length in the mainstem Susitna River upstream of the mouth of the
Yentna River at river mile (RM) 341, such that the estimate is within 20% of the true
value 90% of the time.
2) Estimate the abundance of Chinook salmon greater than or equal to 500 mm METF
length in the Yentna River above RM 62, such that the estimate is within 25% of the true
value 90% of the time.
3) Identify Chinook salmon spawning locations in the mainstem Susitna River by tagging
site (fish wheel or gillnet) so that any spawning location used by at least 5% of the
Chinook salmon spawners captured in a particular fish wheel or by drift gillnet will be
detected (≥ 1 radio tag) with probability of at least 98%, and if spawners are distributed
uniformly among 20 locations, the probability of detecting all 20 locations is at least
55%.
4) Identify Chinook salmon spawning locations in the Yentna River by tagging site (fish
wheel or gillnet) so that any spawning location used by at least 5% of the Chinook
salmon spawners captured with a gillnet or in a particular fish wheel will be detected (≥ 1
radio tag) with probability of at least 98%, and if spawners are distributed uniformly
among 20 locations, the probability of detecting all 20 locations is at least 75%.
5) Estimate the proportions of the Chinook salmon inriver run ≥500 METF length spawning
in the 6 major tributaries (or groupings of minor tributaries) of the mainstem Susitna
River, such that each proportion is within 7 percentage points of the true value 90% of
the time3.
6) Estimate the proportions of Chinook salmon inriver run ≥500 METF length spawning in
the 7 major tributaries (or groupings of minor tributaries) of the Yentna River, such that
each proportion is within 7 percentage points of the true value 90% of the time.
SECONDARY OBJECTIVES
1) Collect a tissue sample for genetic analysis from all Chinook salmon marked with a radio
tag.
2) Evaluate the effectiveness of the passive integrated transponder (PIT) tag reader at the
Deshka River weir.
METHODS
STUDY DESIGN
The Susitna River downstream of the confluence of the Yentna River becomes braided, shallow,
and subject to tidal influence, where migrating salmon are not concentrated in any particular

1 Defined by Alaska Energy Authority, Watana Hydroelectric Studies
2 Defined by the ADF&G Anadromous Waters Catalog
3 Absolute precision: Estimate of within d units of the true value 100(1-α)% of the time implies
θ 𝑃𝑃�𝜃𝜃−𝑑𝑑≤𝜃𝜃�≤𝜃𝜃+𝑑𝑑�=1−𝛼𝛼
2