Sonar estimation of fall chums salmon abundance in the Sheenjek River, 2004.

74 Pages·2008·2.17 MB·English

Fishery Data Series No. 08-34
Sonar Estimation of Fall Chum Salmon Abundance in
the Sheenjek River, 2004
by
Roger Dunbar

June 2008
Alaska Department of Fish and Game Divisions of Sport Fish and Commercial Fisheries
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FISHERY DATA SERIES NO. 08-34
SONAR ESTIMATION OF FALL CHUM SALMON ABUNDANCE IN THE
SHEENJEK RIVER, 2004
by
Roger Dunbar
Alaska Department of Fish and Game, Division of Commercial Fisheries, Fairbanks

Alaska Department of Fish and Game
Division of Sport Fish, Research and Technical Services
333 Raspberry Road, Anchorage, Alaska, 99518

June 2008
This investigation was partially financed by the U.S./Canada Salmon Research Cooperative under NOAA
Cooperative Agreement Award Number NA04NMF4380264.
The Division of Sport Fish Fishery Data Series was established in 1987 for the publication of technically oriented
results for a single project or group of closely related projects. Since 2004, the Division of Commercial Fisheries has
also used the Fishery Data Series. Fishery Data Series reports are intended for fishery and other technical
professionals. Fishery Data Series reports are available through the Alaska State Library and on the Internet:
http://www.sf.adfg.state.ak.us/statewide/divreports/html/intersearch.cfm. This publication has undergone editorial
and peer review.
Roger Dunbar,
Alaska Department of Fish and Game, Division of Commercial Fisheries,
1300 College Rd., Fairbanks, AK 99701, USA

This document should be cited as:
Dunbar, R. D. 2008. Sonar estimation of fall chum salmon abundance in the Sheenjek River, 2004. Alaska
Department of Fish and Game, Fishery Data Series No. 08-34, Anchorage.
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TABLE OF CONTENTS
Page
LIST OF TABLES.........................................................................................................................................................ii
LIST OF FIGURES.......................................................................................................................................................ii
LIST OF APPENDICES...............................................................................................................................................ii
ABSTRACT..................................................................................................................................................................1
INTRODUCTION.........................................................................................................................................................1
Inriver Fisheries.............................................................................................................................................................1
Escapement Assessment................................................................................................................................................2
Study Area.....................................................................................................................................................................3
OBJECTIVES................................................................................................................................................................4
METHODS....................................................................................................................................................................4
Hydroacoustic Equipment.............................................................................................................................................4
Site Selection and Transducer Deployment...................................................................................................................5
Sonar Count Adjustments..............................................................................................................................................5
Stationary Bottom Removal..........................................................................................................................................5
Tracking.........................................................................................................................................................................6
Final Editing..................................................................................................................................................................6
Test Fishing and Salmon Sampling...............................................................................................................................6
Climatological and Hydrological Observations.............................................................................................................6
DIDSON™ Deployment and Operation........................................................................................................................7
RESULTS......................................................................................................................................................................7
River and Sonar Counting Conditions...........................................................................................................................7
Abundance Estimation...................................................................................................................................................8
Temporal and Spatial Distribution.................................................................................................................................8
Age and Sex Composition.............................................................................................................................................8
Split-Beam and DIDSON™ Comparison......................................................................................................................8
DISCUSSION................................................................................................................................................................9
Escapement Estimate.....................................................................................................................................................9
Split-Beam and DIDSON™ Comparison....................................................................................................................10
ACKNOWLEDGMENTS...........................................................................................................................................10
REFERENCES CITED...............................................................................................................................................11
TABLES AND FIGURES...........................................................................................................................................13
APPENDIX A. ECHO SOUNDER SPECIFICATIONS............................................................................................27
APPENDIX B. JAVA PROGRAM CODE.................................................................................................................29
APPENDIX C. CLIMATOLOGICAL AND HYDROLOGIC OBSERVATIONS....................................................63
APPENDIX D. AGE COMPOSITION ESTIMATES................................................................................................67
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LIST OF TABLES
Table Page
1. Alaskan and Canadian total utilization of Yukon River fall chum salmon, 1970–2004................................14
2. Operational dates, and escapement estimates of fall chum salmon in the Sheenjek River, 1981–2004........15
3. Sonar-estimated passage of fall chum salmon in the Sheenjek River, 2004..................................................16
4. Sheenjek River test fishing (beach seine) results, 2004................................................................................17

LIST OF FIGURES
Figure Page
1. Yukon River drainage showing selected locations........................................................................................18
2. Sheenjek River drainage................................................................................................................................19
3. Sheenjek River sonar project site..................................................................................................................20
4. Aerial photographs of the Sheenjek River sonar project site taken August 16, 1999....................................21
5. Depth profile (downstream view) made August 10, 2004, at the Sheenjek River sonar project site.............22
6. Changes in daily water elevation relative to August 8 measured at the Sheenjek River sonar project
site, 2004.......................................................................................................................................................22
7. Adjusted fall chum salmon sonar counts by date, Sheenjek River, 2004......................................................23
8. Diel migration pattern of fall chum salmon observed on the right bank of the Sheenjek River, August
9–September 25, 2004...................................................................................................................................23
9. Split-beam, right bank upstream fall chum salmon distribution in the Sheenjek River, 2004.......................24
10. DIDSON™, right bank upstream fall chum salmon distribution in the Sheenjek River, 2004.....................24
11. Sonar-estimated escapement and BEG (horizontal lines) of fall chum salmon in the Sheenjek River,
1981–2004.....................................................................................................................................................25

LIST OF APPENDICES
Appendix Page
A1. Technical specifications for the Model 241 Portable Split-Beam Digital Echo Sounder..............................28

B1. Java program code used to remove stationary object (bottom) echoes from HTI .raw echo files.................30

C1. Climatological and hydrologic observations at the Sheenjek River project site, 2004..................................64

D1. Age composition estimates of Sheenjek River fall chum salmon, 1974–2004..............................................68
ii
ABSTRACT
Hydroacoustic Technology, Incorporated (HTI) fixed-location, split-beam, sonar was used to estimate chum salmon
Oncorhynchus keta escapement in the Sheenjek River August 8 to September 25, 2004. The sonar-estimated
escapement was 37,878 chum salmon, 24% below the low end of the Sheenjek River biological escapement goal
(BEG) of 50,000–104,000 chum salmon. Median passage was observed on September 13; peak single day passage
was September 21 when 3,124 fish were estimated passed the sonar site. A diel migration pattern showed most
chum salmon passed the sonar site during periods of darkness or suppressed light. Range of ensonification was
considered adequate for most fish which passed near shore. However, the passage estimate should be considered
conservative since it does not include fish migrating beyond the counting range (including along the left bank; left
and right bank refers to the bank on the left or right side of the river when looking downstream), fish present before
sonar equipment was in operation, or fish passing after counting ceased. Only 107 vertebrae samples for age
determination were collected because of low salmon passage. Analysis of vertebrae collections showed age-4 fish
dominated at 62%, age-5 fish represented 25%, age-3 fish 12%, and age-6 fish about 2% of all fish sampled. Male
chum salmon comprised 62% of the sample and 38% were female.
A new multi-beam, dual frequency identification sonar (DIDSON™) developed by Applied Physics Laboratory was
tested side-by-side with the currently used HTI sonar. The DIDSON™ system was used to estimate chum salmon
passage in the Sheenjek River from August 18 through September 24, 2004. Complete analysis of collected data will
be published in a future report.
Key words: Chum salmon, Oncorhynchus keta, sonar, hydroacoustics, escapement, enumeration, Yukon River,
Porcupine River, Sheenjek River.

INTRODUCTION
Five species of anadromous Pacific salmon Oncorhynchus are found in the Yukon River
drainage. However, chum salmon O. keta are the most abundant and occur in genetically distinct
summer and fall runs (Wilmot et al. 1992; Seeb et al. 1995). Fall chum salmon are larger, spawn
later, and are less abundant than summer chum salmon. Spawning occurs in upper portions of the
drainage in spring fed streams, usually remaining ice-free during the winter (Buklis and Barton
1984). Major fall chum salmon spawning areas occur within the Tanana, Chandalar, and
Porcupine river systems, as well as portions of the upper Yukon River in Canada (Figure 1). The
Sheenjek River (66° 47.02 N 144° 27.82 W) is one of the most important producers of fall chum
salmon in the Yukon River drainage. Located above the Arctic Circle, it heads in glacial ice
fields of the Romanzof Mountains, a northern extension of the Brooks Range, and flows
southward approximately 400 km to its terminus on the Porcupine River (Figure 2).
INRIVER FISHERIES
Fall chum salmon are harvested for commercial and subsistence uses. Commercial harvest is
permitted along the entire Yukon River in Alaska and in the lower portion of the Tanana River.
No commercial harvest is permitted in any other tributaries of the drainage including the
Koyukuk and Porcupine river systems. Although commercial harvest occurs in the Canadian
portion of the Yukon River near Dawson, most fish are taken commercially in the lower river,
downstream of the village of Anvik. Subsistence use of fall chum salmon is greatest throughout
the upper river drainage, upstream of the village of Koyukuk.
Although the Alaskan commercial fishery for Yukon River fall chum salmon developed in the
early 1960s, annual harvests remained relatively low through the early to mid 1970s. Estimated
total inriver utilization (U.S. and Canada commercial and subsistence) of Yukon River fall chum
salmon was below 300,000 fish per year before the mid 1970s (JTC 2005). Inriver commercial
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fisheries became more fully developed during the late 1970s and early 1980s, total utilization
averaged 535,826 fish from 1979–1983 (Table 1). Harvest peaked in 1979 at 615,377 and in
1981 at 677,257 fish. Since the mid 1980s, management strategies have been implemented to
reduce commercial exploitation on fall chum stocks to improve low escapements observed
throughout the drainage during the early 1980s. In 1987, the commercial fall chum fishery was
completely closed in the Alaskan portion of the drainage. In 1992, commercial fishing in Alaska
was restricted to a portion of the Tanana River during the fall season. In addition to a commercial
fishery closure, 1993 marked the first year in state history that Alaska Department of Fish and
Game (ADF&G) instituted a total closure of subsistence fishing in the Yukon River. The closure
was in effect during the latter portion of the fall season in response to the extremely weak fall
chum salmon run.
Yukon River fall chum salmon runs improved somewhat from 1994 through 1996. In 1994,
limited commercial fishing was permitted in the Alaskan portion of the upper Yukon River, and
in the Tanana River. Commercial fishing was permitted in all districts throughout the Alaska
portion of the drainage in 1995. In 1996, limited commercial fishing was only permitted in
selected districts of the mainstem Yukon River, no commercial fishing was permitted in the
Tanana River. Poor salmon runs to Western Alaska from 1997 to 2003 resulted in partial or total
closures to commercial and subsistence fishing in Alaskan and Canadian portions of the
drainage. Commercial fishing was only permitted in the Tanana River and Canada in 1997. A
total commercial fishery closure and limited subsistence fishing was required in 1998. Limited
commercial harvest was permitted in 1999, and a total commercial fishery closure and severe
subsistence fishing restrictions were required in 2000, 2001, and 2002. Limited commercial
fishing for fall chum was allowed in 2003 and 2004. Subsistence harvest of fall chum in 2003
was also limited while the subsistence harvest in 2004 was unrestricted except within the
Canadian portion of the Porcupine River.
ESCAPEMENT ASSESSMENT
During the period of 1960–1980, only some segments of Yukon River fall chum salmon runs
were estimated from mark–recapture studies (Buklis and Barton 1984). Excluding these tagging
studies, and apart from aerial assessment of selected tributaries since the early 1970s,
comprehensive escapement estimation studies were sporadic and limited to only 2 streams, the
Delta River (Tanana River drainage) and Fishing Branch River (Porcupine River drainage). In
the early 1980s, comprehensive escapement assessment studies intensified on major spawning
tributaries throughout the drainage.
The Sheenjek River is one of the most intensely monitored fall chum salmon spawning streams
in Yukon River drainage. Escapement observations date back to 1960 when USFWS reported
chum salmon spawning in September. From 1974 to 1981, escapement observations in the
Sheenjek River were limited to aerial surveys flown in late September and early October (Barton
1984). Subsequent to 1980, escapements were monitored annually using fixed-location, single-
beam, side-looking sonar systems (Dunbar 2004). However, an early segment of the fall chum
salmon run was not included by sonar counting operations from 1981 through 1990 because late
project startups centered around August 25. By comparison, average startup during the period of
1991–2003 was August 8, more than 2 weeks earlier than previous years. The sonar-estimated
escapements for the years of 1986–1990 were subsequently expanded to include fish passing
before sonar operations (Barton 1995). Termination of sonar counting was consistent during the
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period of 1981–2003, averaging September 25, except in 2000 when the project was terminated
early because of extremely low water (Barton 2002).
The Sheenjek River sonar project has estimated fall chum salmon escapement since 1981 and has
undergone a number of changes in recent years. The project originally operated Bendix1 single-
beam sonar equipment and, although the Bendix sonar functioned well, the manufacturer ceased
production in the mid 1990s and no longer supports the system. In 2000, ADF&G purchased an
HTI model 241 split-beam digital echosounder system for use on the Sheenjek River to continue
providing the best possible data to fishery managers. In 2000 and 2002, the new system was
deployed alongside the existing single-beam sonar and produced results comparable to the
Bendix equipment (Dunbar 2004). In 2003 and 2004 the split-beam sonar system was used
exclusively to enumerate chum salmon in the Sheenjek River.
Annual escapement estimates averaged 100,533 spawners for the period 1991–2000 and
approximately 34,787 spawners for the most recent 5-year period of 1999–2003 (Table 2). From
1992 to 2000, the Sheenjek River minimum biological escapement goal (BEG) was 64,000 fall
chum salmon, based upon 1974–1990 aerial indices and hydroacoustic assessment (Buklis 1993).
In 2001, ADF&G completed a review of the escapement goal for Yukon River fall chum stocks
of which the Sheenjek River assessment is a component. Based on this review of long term
escapement, catch, and age composition data, the BEG for the Sheenjek River was set at a range
of 50,000–104,000 fall chum salmon (Eggers 2001).
STUDY AREA
The sonar project site is located approximately 10 km upstream from the mouth of the Sheenjek
River. Although created by glaciers, the Sheenjek River has numerous clearwater tributaries.
Water clarity in the lower river is somewhat unpredictable, but is generally clearest during
periods of low water. The water level normally begins to drop in late August and September.
Upwelling ground water composes a significant proportion of the river flow volume, especially
in winter. It is in these spring areas that fall chum salmon spawn, particularly within the lower
160 km.
Historically, because of unfavorable conditions for transducer placement on the left bank2, only
the right bank of the Sheenjek River has been used to estimate fish passage. Drift gillnet studies
in the early 1980s suggested that distribution of the upstream migrant chum salmon was
primarily concentrated on the right bank of the river at the sonar site, with only a small but
unknown proportion passing on the left bank (Barton 1985). In 2002, ADF&G began testing a
new Dual Frequency Identification Sonar (DIDSON™) for counting salmon in small rivers.
Based on the results of these tests, which showed this equipment to be easier to use, more
accurate, and capable of operating with substrate profiles that are unacceptable for split-beam
systems (Maxwell and Gove 2004), the Sheenjek River was selected as an ideal candidate for
this system. In an effort to estimate the proportion of fish passing on the left bank, a DIDSON™
was deployed there in 2003. Results indicated that approximately 33% of the fish were migrating
up the left bank. Due to large numbers of fish observed on the left bank, ADF&G anticipates
operating DIDSON™ on both banks in the future. In 2004, the DIDSON™ was tested side-by-side

1 Product names used in this report are included for scientific completeness, but do not constitute a product endorsement.
2 Left and right bank refers to the bank on the left or right side of the river when looking downstream.
3
with the split-beam sonar on the right bank to examine differences in the estimates produced by
the 2 types of sonar and whether escapement goals will need to be reevaluated.

OBJECTIVES
Goals for the 2004 Sheenjek River fall chum salmon study were to estimate the timing and
magnitude of adult salmon escapement, characterize age and sex composition, and to deploy,
test, and compare chum salmon passage estimates of the new DIDSON™ to those of the split-
beam sonar system. To accomplish these tasks, these specific objectives were identified:
• Estimate timing and magnitude of chum salmon escapement using fixed-location, split-
beam, side-looking hydroacoustic techniques.
• Estimate age and sex composition of the spawning chum salmon population from a
minimum of 30–35 vertebrae samples per week up to 180 for the season, such that
simultaneous 95% confidence intervals of age composition are no wider than 0.20 (α=0.05
and d=0.10).
• Monitor selected climatological and hydrologic parameters daily at the project site for use
as baseline data.
• Deploy and operate the DIDSON™ side by side with the split-beam system on the right
bank, and compare the DIDSON™ passage estimates with the split-beam system.

METHODS
HYDROACOUSTIC EQUIPMENT
A fixed-location, split-beam, fisheries hydroacoustic system developed by HTI was used to
estimate chum salmon abundance in the Sheenjek River in 2004. Fish passage was monitored
with a model 241 digital echo sounder (Appendix A1) and a 2° by 10° 200 kHz split-beam
transducer deployed from a right-bank point bar at the historic sonar site (Figures 3 and 4). The
transducer was attached to an HTI model 662H dual-axis rotator, with an HTI model 660 remote
controller to facilitate aiming. The HTI system is capable of distinguishing upstream fish from
downstream fish and debris, determining fish velocity, discriminating between random
reverberation and fish targets, and providing a less biased estimate of target strength (HTI 2000).
The HTI digital echo sounder is a state-of-the-art system designed for fisheries research.
Accurate time-varied gains (TVG’s) and stable transmit and receive sensitivities are possible.
Short pulse widths can be used to improve resolution between targets. A Digital Echo Processor
(DEP) is integrated into the system. A laptop computer paired with the sounder provides access
to all DEP settings and permits saving settings for future use. An oscilloscope can be linked to
the sounder for diagnostic use, such as in-situ system calibration or transducer aiming. After all
parameters are determined for data acquisition, the system operates 24 hours a day. Files are
created by the DEP and edited by the field crew to produce an estimate of fish passage. The crew
of 3 technicians monitors the sonar and interprets the data during three 7 hour shifts per day.
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