BOEMRE 2010-048 

Beaufort Sea Marine Fish Monitoring 2008: 

Pilot Survey and Test of Hypotheses 

Final Report 

1

Alaska Fisheries Science Center 

NOAA National Marine Fisheries Service 

7600 Sand Point Way, NE Seattle, WA 98115-6349 

Report Authors: 

Elizabeth Logerwell1

 and Kimberly Rand1 

 

 

 

 

Sandra Parker-Stetter and John Horne 

School of Aquatic and Fishery Science 

University of Washington 

Box 355020, Seattle, WA 98115-0070

Tom Weingartner and Bodil Bluhm 

Institute of Marine Science 

School of Fisheries and Ocean Sciences 

University of Alaska Fairbanks 

Box 757220, Fairbanks, AK 99775-7220 

Prepared for 

Minerals Management Service 

U.S. Department of the Interior 

3801 Centerpoint Drive, Suite 500 

Anchorage, AK 99503-5823 

This study was funded by the U.S. Department of the Interior, Minerals Management Service now called the 

Bureau of Ocean Energy Management, Regualtion and Enforcement (BOEMRE) Alaska Outer 

Continental Shelf Region, Anchorage Alaska, through an Inter-agency Agreement between BOEMRE and the 

Alaska Fisheries Science Center, Agreement No. AKC-058, MMS Agreement No. M07PG13152, as part of the 

BOEMRE Alaska Environmental Studies Program. 

1
DISCLAIMER 

This report has been reviewed by the Bureau of Ocean Energy Management, Regulation and 

Enforcement (BOEMRE) and approved for publication. Approval does not signify that the contents 

necessarily reflect the views and policies of the Service, nor does mention of trade names or 

commercial products constitute endorsement or recommendation for use. 

Further analysis and interpretation of the ecological data collected in this study will be published in a 

future BOEMRE report. 

REPORT AVAILABILITY 

This document is available to the public through: 

National Technical Information Service 

5285 Port Royal Road 

Springfield, Virginia 22161 

FAX: (703) 605-6900 

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Table of Contents 

Abstract.......................................................................................................................................... 5 

Introduction................................................................................................................................... 6 

Methods.......................................................................................................................................... 7 

Survey area.................................................................................................................................. 7 

Fish, invertebrate, and habitat data collection .......................................................................... 11 

Demersal fish and invertebrate data collection.................................................................... 11 

Demersal fish and invertebrate sampling............................................................................. 13 

Pelagic fish sampling............................................................................................................ 15 

Demersal and pelagic trawl data entry ................................................................................ 15 

Zooplankton data collection ................................................................................................. 15 

Habitat characteristic data collection (physical oceanography) ......................................... 16 

Fish lengths and biological collections................................................................................ 16 

Special projects..................................................................................................................... 18 

Auxiliary studies....................................................................................................................... 18 

Marine mammals .................................................................................................................. 18 

Seabirds................................................................................................................................. 18 

Demersal fish data analysis....................................................................................................... 19 

Abundance............................................................................................................................. 19 

Cluster analysis..................................................................................................................... 19 

Coefficient of variation ......................................................................................................... 19 

Demersal fish-habitat associations....................................................................................... 20 

Pelagic fish data analysis.......................................................................................................... 22 

Acoustic data processing ...................................................................................................... 22 

Backscatter estimates............................................................................................................ 22 

Target strength...................................................................................................................... 23 

Density distribution, mean density, and abundance ............................................................. 24 

Comparing acoustic and bottom trawl surveys .................................................................... 25 

Pelagic fish-habitat associations.......................................................................................... 27 

Results.......................................................................................................................................... 31 

Demersal fish ............................................................................................................................ 31 

Demersal fish abundance...................................................................................................... 31 

Demersal fish cluster analysis.............................................................................................. 41 

Demersal fish distribution maps............................................................................................... 45 

Demersal fish biological collections..................................................................................... 55 

Demersal fish geographic comparisons................................................................................ 60 

Demersal fish historical comparisons .................................................................................. 63 

Benthic invertebrates ................................................................................................................ 65 

Benthic invertebrate abundance ........................................................................................... 65 

Pelagic fish data analysis.......................................................................................................... 76 

Pelagic fish midwater trawls ................................................................................................ 76 

Backscatter............................................................................................................................ 80 

Target strength...................................................................................................................... 82 

Density distribution, mean density, and abundance ............................................................. 84 

Comparing acoustic and bottom trawl surveys .................................................................... 89 

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4

Fish habitat (physical oceanography) ....................................................................................... 99 

Winds and sea ice.................................................................................................................. 99 

Temperature and salinity .................................................................................................... 103 

The spatial distribution of temperature and salinity........................................................... 104 

Results of the demersal fish habitat associations ............................................................... 114 

Pelagic fish habitat associations ........................................................................................ 158 

Discussion................................................................................................................................... 162 

Demersal fish and benthic invertebrates................................................................................. 162 

Pelagic fish.............................................................................................................................. 166 

Comparison of demersal trawl and pelagic acoustic methods........................................... 168 

Fish habitat (physical oceanography) ..................................................................................... 169 

Literature Cited ........................................................................................................................ 178 

Appendix I – Database table documentation.......................................................................... 186 

Appendix II – Review of Beaufort Sea Fish Studies.............................................................. 199 

Appendix III – CTD cast data.................................................................................................. 214 

Appendix IV – Net mensuration data and trawl design and rigging ................................... 216 

Appendix V – Sample size and final destination of biological samples................................ 219 

Appendix VI – Auxiliary studies ............................................................................................. 221 

Bitter crab syndrome in Beaufort Sea snow (Chionoecetes opilio) and Arctic lyre (Hyas 

coarctacus) crabs................................................................................................................ 221 

Platforms of Opportunity Program – Marine Mammals.................................................... 223 

Marine bird and mammal surveys conducted during AFSC marine fish surveys in the 

Beaufort Sea and transit routes, August 2008 .................................................................... 225 

Appendix VII – Under-ice sampling workshop ..................................................................... 241 

Appendix VIII – Recommendations for future monitoring methods .................................. 244 

Vessel...................................................................................................................................... 244 

Survey design and methods .................................................................................................... 246 

Station and transect spacing............................................................................................... 246 

Bottom trawl field methods and data analyses (demersal fish sampling) .......................... 247 

Acoustic field methods and data analysis (pelagic fish survey) ......................................... 249 

Fish habitat (phycial oceanography).................................................................................. 252 

Quality control and disposition of samples and/or data..................................................... 252 

Survey Planning...................................................................................................................... 253 

Scientific staffing................................................................................................................. 253 

Logistics.............................................................................................................................. 253 

Safety................................................................................................................................... 254 

Contigency planning ........................................................................................................... 255 

Necessary permits-Federal ................................................................................................. 257 

Necessary permits-Local..................................................................................................... 260 

Subsistence activities .......................................................................................................... 261 

Coordination with related projects..................................................................................... 261 

Funding............................................................................................................................... 261 

 
Abstract 

The Minerals Management Service (MMS), Alaska OCS Region funded a pilot survey in 2008 

of the offshore marine fishes of the Beaufort Sea. This was the first offshore marine fish survey 

to have taken place since an opportunistic survey in 1977 (Frost and Lowry 1983). This pilot 

survey provided recommendations for future monitoring methods in addition to baseline data 

against which to compare future anthropogenic and climate impacts. Because it was a pilot 

survey, different techniques were employed to assess fish abundance. It is important to note that 

density, abundance, and biomass estimates from the bottom trawl and acoustic/midwater trawl 

surveys targeted different sections of the water column, used different sampling gears, and 

followed disparate sampling strategies and analytic paths. Demersal fish and benthic 

invertebrates were assessed using standardized bottom trawl gear and methods. Pelagic fish 

abundance was assessed using hydroacoustics and midwater net tows. The distribution of 

zooplankton was sampled with small-meshed bongo nets and physical oceanographic data were 

collected with conductivity-temperature-depth instruments. Demersal fish made up 6% of the 

bottom trawl catch by weight, and invertebrates made up the remaining 94% of the catch. A 

total of 32 fish were identified to species, two were identified to genus and 1 to family, and 174 

species of invertebrates were identified. The four most abundant benthic fish taxa were Arctic 

cod (Boreogadus saida), eelpouts (Lycodes spp.), Bering flounder (Hippoglossoides robustus), 

and walleye pollock (Theragra chalcogramma). The most abundant invertebrates were notched 

brittle stars (Ophiura sarsi), opilio crab (Chionoecetes opilio), mollusks (Musculus spp.) and a 

seastar (Ctenodiscus crispatus). Comparison of our results with historic data suggests that 

climate change may have resulted in northward expansion of some species’ ranges, including 

commercially valuable species such as pollock and Pacific cod (Gadus macrocephalus). This 

survey was also the first to document commercial-sized opilio crab (Chionoecetes opilio) in the 

North American Arctic. Acoustics and midwater trawling were used to quantify density 

distributions of pelagic and semi-demersal fish in the survey area (20-500 m bottom depths) and 

to evaluate relationships between fish distribution and habitat descriptors. Year-plus Arctic cod 

were the dominant pelagic/semi-demersal fish species, with peak densities of 150,000 fish/ha at 

bottom depths of 100-350 m. Oceanographically, year-plus Arctic cod were associated with 

cold, saline waters. The density distribution of year-plus Arctic cod closely mirrored published 

foraging distributions for beluga whales (Delphinapterus leucas). Young of the year fish (Arctic 

cod, unidentified sculpin (Cottidae), and undentified eelblenny (Lumpenus sp.)), dominated the 

pelagic biomass at bottom depths of 20-75 m, with peak densities up to 160,000 fish/ha, but were 

also found in surface waters at bottom depths greater than 75 m. The age-0 fish were associated 

with warm, fresher water throughout the study area. Physical oceanographic data indicated the 

presence of Pacific Ocean-derived waters (modified on the Bering and Chukchi shelves) that 

likely exited the Chukchi shelf through Barrow Canyon and into the Beaufort Sea. In addition, 

evidence of recent ice melt was found in cold, low salinity waters in the upper few meters of the 

water column in the western portion of the study area. River outflow water influenced water 

column properties in the eastern portion of our study area, as evidenced by a lens of very low 

salinity, warm water near the surface. 

5
Introduction 

In August 2008 researchers from NOAA-NMFS Alaska Fisheries Science Center (AFSC), 

University of Washington (UW) and University of Alaska Fairbanks (UAF) conducted a survey 

of offshore marine fish, invertebrates, and physical and biological oceanography of the western 

Beaufort Sea in the vicinity of Cape Simpson to Cape Halkett. The most recent previous survey 

of Beaufort Sea offshore marine fish was conducted opportunistically from a US Coast Guard 

cutter during 1976-1977 (Frost and Lowry 1983). The majority of previous fish studies have 

focused on anadromous fish in estuaries, inlets, river deltas, or lagoons (Bond and Erickson 

1997, Gallaway et al. 1997, Jarvela and Thorsteinson 1997, Moulton et al. 1997, Underwood et 

al. 1997). A few studies have examined the occurrence of marine fish in nearshore waters (<20 

m deep), often in the transition zone between marine and brackish waters (Craig 1984, Craig et 

al. 1982, Jarvela and Thorsteinson 1999, Moulton and Tarbox 1987). The distribution and 

abundance of benthic invertebrates in the Beaufort Sea have only been documented in two 

previous publications, and the most recent was published over 20 years ago (Carey et al. 1984, 

Frost and Lowry 1983). The physical and biological oceanography of the Beaufort Sea shelf 

have been investigated more thoroughly and more recently (Aagaard 1984, Ashjian et al. 2009, 

Ashjian et al. 2006, Matthews 1981, Okkonen 2008, Pickart 2004, Pickart et al. 2005, 

Weingartner et al. 2005b), although no synchronous measures of marine fish distribution and the 

oceanographic characteristics of their habitat have been made prior to the survey reported here. 

Minerals Management Service (MMS) requires information on the species presence, distribution 

and abundance of marine fishes to assess and manage the potential environmental effects of 

offshore development. This information is used in National Environmental Protection Act 

(NEPA) analyses of lease sales, exploration plans, and development and production plans. The 

primary potential effects on fish that MMS analysts commonly evaluate in these NEPA 

documents are the effects 1) within the water column (e.g. from an unlikely but potentially wide 

spread oilspill or from seismic exploration), and 2) in benthic (e.g. from building and operating 

subsea pipelines) habitats. 

The overarching goal of the survey presented here is to generate a baseline against which to 

assess the effects of offshore development on marine fish and to provide information for 

designing mitigation measures. A related goal is to provide a baseline against which to assess 

the impact of climate change, the manifestation of which is particularly severe in the Arctic as 

evidenced by recent dramatic declines in sea ice cover (Maslanik et al. 2007, Stroeve et al. 2007, 

Stroeve et al. 2008) 

The specific objectives of the study are: 

1. Quantify the distribution of benthic and pelagic fish in a subset of the Beaufort Sea Outer 

 Continental Shelf (OCS) Planning Area 

2. Quantify the characteristics of marine habitats occupied by fish 

3. Recommend methods for future monitoring 

A suite of field methods was employed to accomplish these objectives. A standardized bottomtrawl survey was conducted to quantify the distribution and density of benthic fish and 

invertebrates. The distribution and density of pelagic fish was assessed with an acoustic6
midwater trawl survey. Marine habitats were characterized with data on water temperature and 

salinity. Data on the species distribution of zooplankton prey will be incorporated in the future. 

The diets of benthic and pelagic fish, a measure of habitat use, will be determined from stomach 

specimens. In addition, data on the density of seabirds was collected with standardized striptransects and opportunistic observations of marine mammals were recorded. Recommendations 

for future monitoring methods are based on these results and on the collective experience of the 

investigators during the survey. The results document the distribution and abundance of key 

ecological species that could be vulnerable to offshore development, such as Arctic cod 

(Boreogadus saida). Arctic cod are important prey for seabirds and marine mammals and are in 

turn important consumers of secondary production (Bradstreet et al. 1986, Frost and Lowry 1981 

and 1983, Jarvela and Thorsteinson 1999). The results also document potential northerly 

expansions in the known ranges of some species, a potential indicator of the impact of climate 

change. A brief literature review of past studies in the US and Canadian Beaufort Sea can be 

found in Appendix II of this report. 

Methods 

The survey was conducted on board the chartered fishing vessel F/V Ocean Explorer, a 155-foot 

(47.2 m) trawler, equipped with two net reels. The vessel departed from Dutch Harbor, Alaska 

on July 30, 2008 arriving on the survey grounds on August 6. The survey was completed on 

August 22, and the vessel returned to Dutch Harbor on August 27. Sunrise on August 5 (the day 

we arrived on the survey grounds) was at 03:45 and sunset was at 00:13. Sunrise on August 22 

(the day we finished the survey) was 05:22 and sunset was at 22:30. There was one full moon 

during the survey on August 16th. 

Oil and gas industry vessels conducted seismic surveys during August-September 2008 in the 

Beaufort Sea in both state (nearshore) and federal waters. Quantitative data on the distribution, 

timing and amount of seismic activity are proprietary and confidential. However, it is known 

that the seismic surveys that took place in state waters were over 50 nmi from our marine fish 

survey area. The seismic surveys that were conducted in federal waters were 93 nmi from the 

eastern boundary of the fish survey area and 140 nmi from the western boundary. These 

distances are greater than the spatial extent of fish response to seismic survey activity that has 

been documented in the literature (Engås, et al. 1996; Slotte et al. 2004). 

Survey area 

The survey area started at approximately 155°W and extended to 152°W (Figure 1); the south 

end of the transects started at approximately 71°N and continued north to 72°N, crossing the 

shelf break. 

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Figure 1. Bottom and midwater trawl locations and acoustic transects, Beaufort Sea, August 

2008. Bottom trawl numbers (only) are also shown. North-south lines (1-7) are systematic 

acoustic transect lines. The Outer Continental Shelf (OCS) Lease Area is shown in gray 

shading (Bathymetry data from IBCAO, 

http://www.ngdc.noaa.gov/mgg/bathymetry/arctic/arctic.html). 

8
9

Bottom trawl stations were occupied first, using a stratified sampling plan with a random start 

location. The survey design called for bottom trawl locations to be distributed evenly among 

three depth strata, 20-40 m, 40-100 m, and 100-500 m (Figure 1). However, due to the presence 

of sea ice during the first 6 days of the survey and untrawlable habitat for setting bottom gear 

(e.g. boulders, high relief), trawling was limited to areas that would minimize potential gear loss 

or damage. If a predetermined station was found to be unsuitable for trawling, the trawlable site 

closest to the station was used. If no suitable trawling site was located near the predetermined 

station, the site was eliminated and we moved to the next station. In addition, we were not able 

to do bottom trawls in the 20-40 m strata, due to untrawlable habitat. Table 1 summarizes all the 

bottom trawl locations, depth, distance fished and total catch weight (all species combined). 

After all the bottom trawl stations were sampled, a total of seven acoustic transects were 

surveyed spaced 18.42 km (10 nautical miles) apart with a random start location (Figure 1). 

Midwater tows were conducted opportunistically to identify the species composition and to 

collect other biological samples of the backscatter (Figure 1). 

Conductivity-temperature-depth (CTD) casts and zooplankton net (bongo) tows were conducted 

at nearly all bottom and midwater trawl locations, generally immediately after the trawl was 

brought on board (Figure 2). Additional CTD stations spaced 3-4 km apart were sampled on the 

westernmost transect 1, and eastern transect 5 to capture small-scale cross-shelf variability in 

water properties. 
Trawl 

No. 

Start 

Latitude 

(DD) 

Start 

Longitude 

(DD) 

Avg Bottom 

Depth (m) 

Qualitative 

Bottom 

Type 

Depth 

Classification 

Distance 

fished (km) 

Bottom temp 

°C 

Tow Time 

(minutes) 

Lined or 

Unlined net 

Total Catch 

Weight (kg) 

1 71.88 -154.97 428 mud Slope 3.6 0.5 30 lined No catch 2 71.89 -154.95 470 mud Slope 1.127 0.5 10 lined 694.93 3 71.74 -154.99 198 rocks Slope 1.355 -0.1 15 lined 751.34 

4 71.90 -153.91 347 Slope 1.288 0.6 15 lined 1881.89 

5 71.81 -153.92 143 rocks Slope 1.26 -1.2 15 lined 1846.51 

6 71.81 -154.46 158 mud Slope 1.454 -1.4 15 lined 9502.65 7 71.98 -154.41 322 Slope 1.64 0.5 15 lined 2028.50 

8 71.72 -152.84 318 mud Slope 1.393 0.5 15 lined 1382.47 

9 71.66 -152.49 302 mud Slope 1.513 0.6 15 lined 1984.08 

10 71.52 -152.25 175 mud Slope 1.52 -0.8 15 lined 2359.84 

11 71.75 -153.94 66 rocks Shelf 1.397 -0.7 15 lined 419.10 12 71.69 -154.52 50 rocks Shelf 1.51 1.8 15 lined 251.08 

13 71.48 -153.96 49 mud Shelf 1.346 1.5 15 lined 339.30 

14 71.39 -153.99 41 mud Shelf 1.363 1.8 15 unlined No catch 15 71.25 -153.13 41 rocks Shelf 1.425 1.0 15 unlined No catch 

16 71.25 -153.11 41 rocks Shelf 0.395 1.0 5 unlined 19.45 17 71.37 -153.07 75 rocks Shelf 0.459 0.3 5 unlined 256.35 18 71.46 -153.04 64 hard Shelf 0.561 0.7 5 unlined 87.81 

19 71.16 -152.23 30 mud Shelf 0.423 1.3 5 unlined No catch 

20 71.28 -152.31 50 rocks Shelf 0.572 -0.4 5 unlined 38.74 21 71.35 -151.99 83 rocks Shelf 0.624 -1.4 5 unlined 27.45 22 71.51 -152.20 178 Slope 0.708 -0.4 5 unlined 77.74 

23 71.58 -155.05 44 rocks Shelf 0.62 -0.1 5 unlined 43.05 24 71.68 -154.48 50 rocks Shelf 0.579 -0.9 5 unlined 52.78 

25 71.53 -152.89 59 hard Shelf 0.613 -0.9 5 unlined 35.52 

26 71.55 -153.48 52 hard Shelf 0.482 1.2 5 unlined 10.59 

Table 1. Bottom trawl locations (Lat/Long) in decimal degrees, bottom depth, qualitative bottom type, distance fistemperature and total catch weight for all bottom trawls conducted. “No catch” in the “Total Catch Weight” columgear was lost or damaged resulting in no catch sample. 

10
 

 

Figure 2. Bongo tow and CTD cast stations, Beaufort Sea, August 2008. The Outer 

Continental Shelf (OCS) Lease Area is shown in gray shading. 

Fish, invertebrate, and habitat data collection

Refer to “Recommendations for Future Monitoring” for a discussion of how sampling gears were 

selected, how they addressed the characteristics of Arctic benthic and pelagic fish and potential 

sources of bias. 

Demersal fish and invertebrate data collection 

All bottom trawls were conducted in concordance with standards set by the Alaska Fisheries 

Science Center’s Resource Assessment and Conservation Engineering (RACE) Division 

(Stauffer 2004). The net used for the bottom trawls was a standard 83-112 Eastern otter trawl 

(built at AFSC), which has a 25.3-m (83 ft) headrope and a 34.1-m (112 ft) footrope. The 

Eastern trawl has a 10.16 cm (4”) mesh in wings and body and 8.89 cm (3.5”) mesh in 

intermediate and codend. Bottom trawls 1 through 13 were conducted with a standard 83-112 

11
Eastern otter trawl net modified with a small-mesh liner in order to catch relatively small Arctic 

fish. The mesh liner was 3.8 cm (1.5”) and covered the entire bottom body of the net, both 

bottom wings and completely covered the top and bottom of the intermediate and cod end. The 

original field plan was to conduct the entire bottom trawl survey with the lined 83-112, but 

unfortunately, all three lined nets were irreparably damaged during the first half of the cruise. 

Trawls 14 through 26 were conducted with the backup nets, standard 83-112 nets with no liner. 

The result of this gear change was that with the exception of one station, all the rise stations 

(bottom depths 101-500 m) were sampled with the lined net and tows were 15 minutes long. 

Nearly all the shelf/slope stations (9 out of 12 stations in bottom depths 40-100 m) were sampled 

with the unlined net and were 5 minutes long. This confounding was not intentional but was the 

result of the fact that only the rise stations were free of ice early in the survey and so we sampled 

them first with the lined net. When the ice cleared out of the shelf/slope area we had damaged 

all the lined nets and were forced to complete the survey with the unlined net. Tow time was 

reduced to 5 minutes when we switched to the unlined net to minimize the chance of damaging 

our last remaining bottom trawl net. In summary, the sample collection order imposed by 

practical constraints during the cruise (ice cover and availability of nets) prevented collection of 

the data as originally planned. All trawls were towed behind 1.83 x 2.75-m (6x9 ft), 816 kg steel 

V-doors paired with 54.9-m dandylines (Appendix IV for net schematic, trawl door details, the 

footrope plan and frame lines). 

Due to the unexpected change in gear type half way through the bottom trawl survey, near the 

end of the survey we returned to two locations that had previously been trawled with the lined 

net and trawled again with the unlined 83-112 net. We refer to these two pair of trawls as 

“paired trawls”, because they occurred at the same location, with both gear types, however, they 

occurred at different times. Trawl 10 (lined net, 100-500 m depth) was paired with trawl 22 

(unlined net, 100-500 m depth) and they occurred four days apart; trawl 12 (lined net, 40-100 m 

depth) was paired with trawl 24 (unlined net, 40-100 m depth), also occurring four days apart. 

The trawl warps onboard the F/V Ocean Explorer were measured and calibrated at the start of 

the survey using Olympic 750-N in-line wire counters. To standardize trawl performance, a 

table of trawl wire out for optimal trawl performance at a particular depth was used for all 

bottom trawls (Stauffer 2004). After the wires were marked, a test tow was done to make sure 

the survey trawl was performing to standardized specifications found in Stauffer 2004. 

Net height and width were measured with Netmind net mensuration equipment during trawling 

operations (Northstar Technical Inc., St. John’s, Newfoundland). A hydrophone was lowered 

into the water and data were recorded from the net sensors during trawl operations. A sensor was 

placed on the headrope of the net that measured the distance to the bottom. This was monitored 

during trawl operations to insure the net opening remained consistent during the towing. A pair 

of spread sensors were connected to each of the dandylines and provided net width data. Net 

width was averaged over the duration of the trawl, based on the data recorded by the net 

mensuration sensors. The net width sensors failed during three trawls (6, 18 and 23). For these 

trawls, net width was estimated based on a regression equation that predicts net width from scope 

(amount of wire out). No regression has been developed specifically for the F/V Ocean Explorer 

so a regression developed for a similar-sized trawler (the F/V Northwest Explorer) was 

employed (Lauth and Acuna 2007). Trawl footrope contact with the seafloor was monitored at 1 

12
second intervals using a calibrated bottom contact sensor (BCS). The BCS consists of a tilt 

sensor and other electronics inside a stainless steel pipe and is attached at the center of the 

footrope. Bottom contact data were used to estimate distance fished. Net width and distance 

fished were then used to calculate area swept which was then used to determine catch-per-uniteffort (CPUE) (Appendix IV, Table IV.1). 

A bathythermograph (SBE-39 from Seabird Electronics Inc., Bellevue, Washington) was 

attached to the headrope of the trawl net. Temperature and depth were recorded at 3-second 

intervals from the time of net deployment from the vessel to net retrieval and instrument 

removal. 

Trawls were deployed at a constant vessel speed of approximately three knots. The first tow was 

deployed for 30 minutes of bottom time (the AFSC survey standard), but it was immediately 

obvious that tows of that duration would result in catch volumes that were too large to effectively 

sort and quantify. So tow times were reduced to 15 minutes. Even at these shorter tow times, 

several trawl nets were damaged due to large catches. When only one undamaged trawl net 

remained, tow times were further reduced to five minutes. Tow times and distances trawled are 

summarized in Table 1. Tows were conducted in whatever direction was optimal, based on wind 

and current conditions. 

Demersal fish and invertebrate sampling 

The entire catch for each bottom trawl (with the exception of trawl 6; see below) was weighed on 

a marine Marel scale (www.marel.com). The scale was calibrated daily. The preferred method 

for quantifying the bottom trawl catch was to sort, identify, count and weigh all individual fish 

and invertebrates. However, due to large catch sizes, and high species diversity, the most 

common method of sampling the bottom trawl catch was sub-sampling. A random sample of the 

catch was weighed and sorted for fish to the lowest taxonomic level possible. A sub-subsample 

(i.e. a sample of the subsample) was taken of the invertebrates due to the high species diversity 

and quantity of invertebrates caught. Within the sub-subsample of invertebrates, all species were 

sorted, counted and weighed to the lowest taxonomic level. As the survey progressed and 

bottom trawl times were reduced, we were able to count and weigh all species in the catch. 

When the total catch weight was <200 kg, the entire catch (fish and invertebrates) was sorted to 

the lowest possible taxonomic level, counted, and weighed. Trawls 2-13 and 17 were 

subsampled; subsample sizes ranged from 31 kg to 200 kg with the average at 79 kg. Trawls 16, 

18 and 20-26 were sampled entirely. 

We had one bottom trawl that was estimated to be between 9 and 10 metric tons (trawl 6), too 

large to weigh in baskets on the Marel scale. Several measurements were taken of the codend 

(length, height, and width in meters). Catch density was estimated by recording the weight, 

height and width of a square basket filled with unsorted catch. Using the mean codend 

measurements, and estimated unsorted catch density, a volumetric formula was used to estimate 

the entire weight of the unsorted codend. The volumetric formula, Frustum of a Cone, was used 

where h is the height of the cone, R is the radius at the lower base of the cone and r is the radius 

at the upper base of the cone: 

13
 ( ) 2 2 rRrR

3

πh

V ++=

The catch was then sub-sampled as described above. 

Pelagic fish data collection 

Acoustic data were collected using a Simrad ES60 split beam 38 kHz echosounder (model ES380) mounted on the vessel’s hull at a depth of 4.75 m. The transducer had an 8o, 3 dB beam 

width, an equivalent beam angle of 19.5 dB, and a power output of 2000 W. A ping rate of 1 

ping/second and a pulse duration of 0.512 msec were used. 

A preliminary calibration of the system was performed prior to the survey, but final calibration 

values were based on a full calibration after the survey. The calibration took place in Broad Bay, 

near Dutch Harbor, Alaska following standard sphere methods detailed in Foote et al. (1987). 

Transducer gain (Sv gain, 21.28 dB re 1 m-1, herein referred to as “dB”) and Sa correction (0.63 

dB re 1 m2/m2, herein referred to as “dB”) were determined using calibration data. The Sv gain 

and Sa correction are input values to quantitatively align the acoustic output with the standard 

calibration sphere. A CTD was deployed to provide estimates of temperature and salinity for the 

calculation of sound speed and absorption coefficient for the calibration conditions. 

 

Acoustic data were collected during three operations; during the acoustic-midwater trawling 

along transect lines, during the bottom trawl survey, and opportunistically after daytime survey 

operations had ended (e.g. while drifting). As opportunistic stationary data were not needed for 

our analysis, only the data collected during the acoustic-midwater trawling survey and during the 

bottom trawl survey are used in this report. 

 

Survey operations were conducted during daytime hours from approximately 07:00 to 

19:00 Alaska Daylight Time (ADT). Sunrise on August 5 (the day we arrived on the survey 

grounds) was at 03:45 and sunset was at 00:13. Sunrise on August 22 (the day we finished the 

survey) was 05:22 and sunset was at 22:30. Acoustic data was collected continuously along a 

series of parallel transects (Figure 1, Acoustic Transects). Data collection along transects was 

interrupted to conduct midwater trawling to verify the identity and obtain measurements from the 

species contained in aggregations observed on the acoustics. At each midwater trawl location a 

CTD was deployed to measure temperature and salinity to determine a mean sound speed 

(1452.3 m/sec) and absorption coefficient (0.009397 dB/m) for the study area. 

When trawling was complete, acoustic data collection resumed at the transect break point. 

During acoustic operations, the vessel maintained a speed of approximately 3.6-4.6 m/s (7-9 

knots), depending on weather conditions in the survey area. Data were logged using the ES60 

software. 

 

A Marinovich net was used for midwater trawling operations. The designed opening dimensions 

of the net are 6.10 m horizontal and 6.10 m vertical, but average fishing dimensions during the 

survey were 3-4 m vertical and 6 m horizontal based on third wire measurements (see below). 

The net was fished with the same doors used for bottom trawling. The vessel’s third wire net 

14
monitoring system (Simrad Mesotech FS903) was used to monitor net headrope depth and net 

dimensions during deployment. A bathythermograph was attached to the headrope to collect 

temperature and depth data. Vessel speed was maintained at 1.0-2.1 m/s (2-4 kt) during 

midwater trawling and the tows lasted 10-60 minutes depending on acoustic target density 

observed on the ES60 and third wire display. 

Pelagic fish sampling 

All midwater trawl catches were generally <50 kg and were sampled in one of two ways. For 

catches dominated by large (>60 mm fork length) Arctic cod, all fish were sorted to species, each 

species was weighed, and up to 50 fish from each species were measured for fork length. For 

catches dominated by fish <60 mm fork length, the entire catch was weighed and a subsample 

was selected and weighed. This subsample was then sorted to the lowest possible taxonomic 

level and up to 50 fish from each taxonomic group were measured. 

Demersal and pelagic trawl data entry 

All bottom and midwater trawl data were entered using the AFSC’s RACE Division data entry 

program in MS Access. For each trawl, the subsample was entered as a fraction of the trawl’s 

total catch weight. The subsample was considered to be a representative proportion of the entire 

catch, thus the counts and weights were used to obtain average weights for each species, and then 

each species was extrapolated to the total catch level. When there was no subsample, such as in 

the case of bottom trawls <200 kg and most midwater trawls, the entire catch was counted and 

weighed, requiring no extrapolation. When a sub-subsample was taken, species were 

extrapolated up to the subsample level (using counts and weights), and then to the total catch 

level. 

A database from the 2008 Beaufort Sea Survey is available through MMS. A metadata report 

associated with the database is located in Appendix I. All descriptions and limitations of the data 

are summarized in the metadata report. 

Zooplankton data collection 

Zooplankton tows typically occurred before or after a CTD cast (Figure 2) and were launched 

using the same winch system. The zooplankton net consisted of two bongo net frames. The top 

frame had two 20-cm aluminum hoops with 153-μm mesh nets. The bottom frame, one meter 

away, had two 60-cm aluminum hoops with 333-μm mesh nets. Flow meters were mounted in 

the center of the net mouth openings. The flow meters provided data used to estimate the 

volume of water sampled by the zooplankton nets. 

The nets were towed between 1.0 and 2.5 knots depending on weather conditions. This was 

done to insure the wire angle was as close as possible to 45 degrees, the angle which maximizes 

the fishing capacity of the gear, not necessarily to keep the speed of the net constant relative to 

the bottom. The wire out rate was 30-m per minute and the wire in rate was 20-m per minute. 

The wire out rate was determined by the deployment speed required for the CTD because both 

15
the CTD and the zooplankton nets were deployed from the same winch. The few tows not 

meeting specifications (i.e. hit bottom, poor wire angles, nets tangled, etc.) were repeated. 

When the nets were brought to the surface, the total tow time was recorded along with flow 

meter revolutions. The nets were rinsed with seawater starting at the mouth and working down 

towards the codend. All zooplankton samples from both mesh sizes were preserved in 5% 

formaldehyde (in seawater), buffered with a saturated sodium borate buffered solution and 

seawater. Numerical composition of plankton samples will be determined in Szczecin, Poland, 

by the Plankton Sorting and Identification Center following established AFSC protocols, pending 

availability of additional funds. 

Habitat characteristic data collection (physical oceanography) 

Conductivity-temperature-depth (CTD) data were collected at the stations shown in Figure 2. 

CTDs were deployed at all bottom trawl locations and most of the midwater trawl locations 

immediately following the trawl. Additional intensive sampling along transects 1 and 5 was 

conducted on 16-17 August and 19 August, respectively. The instrument was a calibrated SBE 

19plus CTD profiler (Seabird Electronics Inc., Bellevue, Washington) deployed with a portable 

winch installed on the vessel for this survey. The CTD was deployed at depths of 1 to 2 m off 

bottom and at a rate of no more than 30 meters/minute. 

A series of cross-sections were constructed from the CTD data collected along the various 

sampling transects that begin inshore at about the 20 m isobath and extend to the offshore end of 

the transect (500 m depth). The geostrophic velocity relative to the bottom was computed from 

the thermal wind shear. The spatial distribution of water masses were summarized in separate 

potential temperature-salinity (θ-S) plots composited for each line. 

Fish lengths and biological collections 

Several species of fish from both bottom and midwater trawls were sexed when feasible and the 

fork length (FL) was recorded (termed “sexed-length”). Small or juvenile fish were not sexed. 

Lengths were recorded on deck using an Allegro polycorder (www.junipersys.com) in 

conjunction with a barcode wand and barcoded length strips. All lengths for fish in the bottom 

trawls were recorded in centimeters. For small or juvenile fish (<7 cm) in the midwater trawls, 

lengths were recorded manually in millimeters. 

Lengths were collected for Arctic cod (Boreogadus saida), walleye pollock (Theragra 

chalcogramma), Greenland turbot (Reinhardtius hippoglossoides), Bering flounder 

(Hippoglossoides robustus) and from two Pacific cod (Gadus macrocephalus) caught in the 

bottom trawls. From the midwater trawls, lengths were recorded for Arctic cod, an unidentified 

sculpin (family Cottidae), and an unidentified eelblenny (family Lumpenus). 

Samples of fish for sexed-lengths were randomly collected if the number of fish in the trawl 

catch was greater than approximately 150 fish. This was the case only for Arctic cod. The 

16
number of pollock, turbot, flounder and Pacific cod was low, so we were able to measure all 

individuals in the catch or subsample. 

Biological collections included sex, length, weight, otoliths (age structures), stomachs, and 

ovaries. All specimens were weighed on a motion compensated Marel specimen scale (smaller 

than Marel scale mentioned above) to the nearest hundredth gram. The collections varied by 

species and depended on information necessary for future analysis (e.g. otoliths for stock 

assessment). Otoliths were preserved in a 70% solution of ethyl alcohol and seawater. Stomachs 

were preserved in a 10% solution of formaldehyde and seawater buffered with sodium 

bicarbonate. Due to the small sizes of fish encountered on the survey, it was not possible to 

excise stomachs or ovaries without significant damage to the specimen. Instead, the other data 

and samples were collected (otoliths, length, weight) and the remainder of the fish specimen was 

preserved. The same method applied to the collection of ovaries. The method of collection for 

each species is described below: 

Arctic cod. Within each bottom trawl, a subsample of approximately 25 fish was collected from 

the 150 sexed lengths. The fish’s length, weight, and age structures were collected. Ten females 

were selected for the ovary collection. In addition, 10-15 fish were randomly collected from 

sexed lengths for the stomach collection. Approximately fish fish from five trawls were frozen 

for stable isotope analysis; each of the five fish were frozen whole, in one bag per trawl. Stable 

isotope analysis does not require freezing of individual fish per trawl. Stomachs and ovaries 

were not collected at every trawl but collections were distributed so that they were made across 

the survey area. A summary table of total samples sizes and final destinations of the samples is 

located in Appendix V. 

Walleye pollock. All walleye pollock present in the bottom trawls were sexed, lengthed, 

weighed and the entire fish was frozen for processing at the AFSC. Freezing the fish allowed for 

future genetic analysis. 

Bering flounder. All Bering flounder were sexed, lengthed, weighed and the entire specimen 

was preserved for the stomach collection (no ovaries collected). 

Greenland turbot. All Greenland turbot were sexed, lengthed, weighed and the entire specimen 

was preserved for the stomach collection (no ovaries collected). 

Pacific cod. Only two specimens were caught in the bottom trawls. Both were sexed, lengthed, 

weighed and frozen for verifying species identification and future analysis at the AFSC. 

Collections from the micro- and macro- zooplankton Bongo tows (~20 samples) were also frozen 

for stable isotope analysis, to coincide with the fish stable isotope analysis. 

All species of fish were collected for species identification in the AFSC taxonomic laboratory. 

All specimens were photographed with the trawl number for proper assignment when species ID 

was verified or changed. Specimens were counted, weighed and preserved in a 10% 

formaldehyde and seawater solution buffered with sodium bicarbonate. Most specimens 

collected are stored at the University of Washington’s (UW) Fish Collection 

17
(http://www.washington.edu/burkemuseum/collections/ichthyology/). The UW Fish Collection 

laboratory will also work to provide specimens from several fish species to the University of 

Alaska’s Museum of the North (www.uaf.edu/museum/collections/aqua/). See Appendix V for 

more details. 

All invertebrate species were photographed, collected and preserved in 95% ethyl alcohol or 

10% formaldehyde and seawater solution buffered with hexamethylenetetramine. All 

invertebrates collected on the survey are currently stored at the University of Alaska Fairbanks, 

pending funding for species identification. See Appendix V for details. 

Special projects 

We were able to accommodate four special projects on the survey. A special project requested 

by the AFSC RACE Division entailed collecting two taxa of crab; Chionoecetes opilio and Hyas

sp. The crabs were examined for the presence of Bitter Crab Syndrome. The carapace 

length/width was recorded to the nearest 0.1 mm, the weight (g), sex, shell condition, and clutch 

size were recorded. Approximately 20-30 crabs were randomly selected from the catch, when 

large numbers of crab were caught (greater than 100 kg). See Appendix VI, Auxillary studies,

for preliminary results of the Bitter Crab Syndrome study. 

Arctic cod were collected for the Marine Gene Probe Lab at Dalhousie University as part of a 

genetic analysis examining transarctic exchange between marine fish species in the Pacific and 

Atlantic oceans. Fish species (1-10 individuals per species) also were collected for genetic bar 

coding at the Point Stephens Research Lab in Auke Bay, Alaska. Finally, a small collection of 

juvenile Arctic cod was requested by Minerals Management Service, Anchorage, Alaska. See 

Appendix V for information on the destination of all the genetic specimens. 

Auxiliary studies

Marine mammals 

Opportunistic marine mammal sightings were recorded in collaboration with the Platforms of 

Opportunity Program (POP) at the National Marine Mammal Laboratory. The date, time, 

location, species and number of animals observed were recorded whenever possible. Taxonomic 

guides assisted in the proper identification of a marine mammal or it was recorded as 

“unidentified” if the observer was unsure or distance too far. See Appendix VI for a report 

summarizing the results. 

Seabirds 

Data on the distribution and abundance of seabirds were collected during the transit to and from 

Dutch Harbor and during the acoustic transects, when conditions allowed. This project was a 

collaboration with US Fish and Wildlife Service. Continuous strip transects up to 300 meters 

wide (depending on visibility) were conducted by a single observer, looking on one side of the 

vessel. Birds were identified to species, when possible, and counted. Observations were entered 

18
into a laptop computer using a program (Dlog2) that assigned time and position to each 

observation using a GPS receiver. See Appendix VI for a report summarizing the results. 

Demersal fish data analysis 

Abundance 

Mean catch-per-unit effort (CPUE) was estimated for all fish species and the top 24 invertebrate 

taxa. CPUE was calculated as both kilograms (kg/ha) and numbers per hectare (#/ha) from the 

weight or number of each species or taxon divided by the area swept for each trawl. Area swept 

was calculated as the distance fished multiplied by the mean net width. The CPUE (kg/ha or 

#/ha) for each trawl was averaged by depth and also by net type (lined vs. unlined). Zero catches 

were included in these calculations. 

Depth-specific estimates of fish and invertebrate biomass and abundance were calculated from 

mean CPUE in each depth and depth area (derived from GIS). Strata were defined by bottom 

depth (as opposed to vertical position in the water column). The estimated area for the 40-100 m 

depth is 370,399 ha and for the 100-500 m depth, it is 257,593 ha (Figure 1). All the bottom 

trawls that occurred in the 100-500 m depth range were conducted with the lined net (except 

one), by coincidence. The majority of trawls that occurred in the 40-100 m depth range were 

conducted with the unlined net, also by coincidence. However, three trawls were conducted with 

a lined net in the 40-100 m depth range (trawls 11, 12 and 13). These trawls were not used in 

calculating CPUE, biomass or abundance by depth, but were used in estimating mean CPUE and 

abundance for comparing catch of the lined vs.unlined nets. Trawl 22 was conducted in the 100-

500 m depth range with an unlined net and so was not included in calculations of CPUE, biomass 

or abundance by depth. 

Cluster analysis 

Cluster analysis was employed to identify co-occurring groups of fish species and their 

distribution within the study area. To reduce the potential bias in CPUE due to different gear 

types (lined vs. unlined nets), the analysis was conducted on species presence/absence data. A 

matrix of species presence/absence by trawl was constructed from the bottom trawl data. An 

agglomerative hierarchical clustering analysis was then conducted on a dissimilarity matrix 

calculated from the presence/absence matrix using the S-Plus group average method (Insightful 

Corporation, 2005), following methods detailed in Kaufman and Rousseeuw (1990). A 

euclidean metric was used for calculating dissimilarities and the measurements were not 

standardized beforehand. 

Coefficient of variation 

Coefficients of variation (CV) among trawl CPUE (#/ha) were calculated for each fish species, 

for lined and unlined net samples separately and both net types combined. In order to make 

recommendations for future monitoring, sample size approximations were calculated based on 

observed CV, zα=1.96, zβ=1.64 and a range of delta (% difference between estimated and true 

mean, Ott 1993). 

19
Demersal fish-habitat associations 

We examined the associations between demersal fish distribution and several environmental 

variables using linear regression, generalized linear models (GLM) and generalized additive 

models (GAM). Due to low sample sizes we chose a P-value of 0.10 as our significance 

threshold for all statistical analyses, this reduces the risk of making a Type II error (failing to 

observe a relationship when in truth there is one). Data collected with lined and unlined nets 

were analyzed separately. For all analyses, the data were log transformed. 

Linear regression 

As part of the exploratory data analysis, we examined the relationships between several 

environmental variables and fish distributions using simple linear regression. This allowed us to 

determine what, if any, relationships may exist between fish catch per unit effort (CPUE) 

distribution and the environment. We examined the distributions of several species and groups 

of species: 

1. All fish species; lined and unlined net trawl data analyzed separately 

2. All invertebrates; lined and unlined nets separately 

3. Arctic cod; lined and unlined nets separately 

4. Walleye pollock; lined and unlined nets separately 

5. All eelpouts; lined nets only (generalized linear model, GLM was used to examine 

correlations with unlined net catches) 

6. All sculpins; unlined nets only (GLM was used to examine correlations with lined net 

catches) 

7. Opilio crab; lined and unlined nets separately 

All regressions were done with a single independent variable, and stations were separated by 

gear type, as indicated above (lined and unlined net). Due to the low sample size and increasing 

variance with increasing means CPUE #/ha and CPUE kg/ha were log transformed for all seven 

species groups and both lined and unlined net gear types. In cases where there was a zero 

observation, 0.5 was added to all data observation points in that group, and then the values were 

log transformed. Due to the high number of zero catches for “All sculpins”, lined net, and “All 

eelpouts”, unlined net, it was not appropriate to do a linear regression; instead a generalized 

linear model (GLM) was formulated. In a GLM, the outcome of the dependent variable (e.g. 

CPUE) is assumed to be from a particular distribution (e.g. poisson) (see below). Alternatively, 

a GAM is a non parametric model that can incorporate both linear and nonlinear relationships. 

In many cases, it appeared that there was one observation that had significant leverage on the 

relationship. Therefore Cook’s Distance (Cook 1977) was calculated to determine if any of the 

data point(s) had a value greater than 1.0. A Cook’s Distance greater than 1.0 generally warrants 

further analysis (e.g., regression without the outlier). Cook’s Distance was calculated using 

transformed data. In many cases the transformation reduced the variance enough to result in a 

Cook’s Distance value less than 1.0. 

20
The dependent variables were CPUE #/ha and CPUE kg/ha (with the exception of invertebrates 

for which CPUE #/ha was not feasible to calculate). The independent variables were: 

1. Longitude of haul catch (in decimal degrees) 

2. Bottom temperature (°C) 

3. Temperature difference (°C) (difference between temperature at the seafloor bottom and 

temperature 1 m below the surface) 

4. Bottom depth (m) 

5. Bottom salinity (psu) 

6. Salinity difference (psu) (difference between salinity at the seafloor bottom and salinity 1 

m below the surface) 

7. Bottom density (sigma-t) 

8. Density difference (sigma-t) (difference between density at the seafloor bottom and 

density 1 m below the surface) 

Bottom temperature and bottom depth were obtained from the MBT attached to the survey net. 

Salinity and density data were obtained from the CTD casts. The differences between bottom 

and near surface temperature, salinity, and density are an indicator of the amount of water 

column stratification (a lesser difference indicates greater mixing due to upwelling or other 

processes). We examined percent ice cover as a potential variable, 

(http://www.natice.noaa.gov/index.htm); however, it was not included in any of the analyses 

because it was categorical with only two categories for each of the gear types. Because bottom 

temperature and temperature difference were correlated we only used bottom temperature in the 

GAM models. 

The variables that were chosen for generalized additive model (GAM) analysis and the order in 

which they were added to the model were based on the significance of the linear regressions. 

Variables with the most significant relationships were added first. Several of the independent 

variables were correlated. Because it is not appropriate to include correlated independent 

variables in a multivariate statistical analysis, one independent variable was selected from the 

correlated variables, as a representative in the GAM models. For stations sampled with the 

unlined net gear type, bottom depth was not included in the regression analysis due to the limited 

range of depths (i.e. there was only one observation in the 100-500 m depth range). 

GLM Analysis 

Due to the high frequency of zero catches for the group “All sculpins”, lined net, and “All 

eelpouts”, unlined net, it was more appropriate to examine the presence/absence of the species 

rather than CPUE. Possible relationships were examined with the same independent variables 

used in the linear regression. However, a generalized linear model (GLM), poisson distribution 

with a log link was used instead of linear regression. If the model showed a significant decrease 

from the null to residual deviance, that independent variable was considered significant in 

explaining the variance in the data. 

21
GAM Analysis 

The two to three independent variables that suggested a relationship with demersal fish CPUE 

(i.e. relatively low P-value) were initially selected for building a GAM model for each of the 

seven groups of fish and invertebrates (and each net type). To determine the best smoothing 

term (linear or non-linear) for each variable in the GAM analysis, scatterplots of each variable 

and CPUE were examined, linear and non-linear regressions were estimated, and the smoothing 

term with the lowest residual deviance was selected. In most cases, the relationship was linear 

and when not the case, a nonparametric b-spline linear smoothing term was used. The null 

deviance compared to the residual sum of squares (i.e. residual deviance) is reported. If the 

residual sum of squares is lower than the null deviance, this can support the use of the second or 

third variable in the model as an improvement in explaining the variance in the data. Mallow’s 

Cp value is also reported, which rescales the estimated mean square error, however, it adds a 

penalty for additional model parameters. Models with the smallest Cp have the smallest 

estimated mean square error and would be considered the better model for the data. 

Pelagic fish data analysis 

Acoustic data processing 

Vessel noise (Sv = -140 dB @ 1 m) was removed from backscatter (Sv) and target strength (TS) 

data using linear subtraction (Watkins and Brierley 1996, Korneliussen 2000). In addition, 

samples that did not meet a minimum 6 dB signal-to-noise (SNR) minimum threshold were 

removed from the analysis. 

Data from within 9.0 m of the surface were excluded to account for transducer depth (4.75 m) 

and twice the nearfield range (the zone where valid data cannot be obtained) for the 38 kHz 

transducer (2*2.04 m). The bottom was detected using the Echoview line pick function (-50 dB 

discrimination level) and manually corrected as needed. Data from within 0.5 m of the bottom 

(the acoustic deadzone) were excluded from analysis. 

Backscatter estimates 

Acoustic data files were scrutinized in Echoview 4.70 (Myriax Pty Ltd, 2009) and off-systematic 

acoustic transect regions were removed from the analysis (e.g. when the vessel left the 

systematic survey track during trawling). A minimum Sv threshold of -75 dB was applied to all 

data. This value represents the upper 95% confidence level for vessel noise estimates (-81 dB) 

for the Sv data along acoustic transects plus a 6 dB SNR threshold. 

Based on trawl results and visual inspection of echograms, a young-of-the-year fish (YOY) 

region was defined between the surface exclusion line (9.0 m from the surface) to 75 m depth. 

The YOY fish included Arctic cod, an unidentified sculpin (Family Cottidae) and an unidentified 

prickleback (Lumpenus sp.). In regions with bottom depths less than 75 m, the YOY region was 

defined down to the 0.5 m bottom exclusion line. All transects were inspected in the 

determination of the lower depth limit for the YOY region. A yearling-and-older Arctic cod 

(year-plus) region was between the 75 m line and the 0.5 m bottom exclusion line. As needed, 

22
the 75 m line was adjusted up or down to account for vertical fluctuations in YOY or year-plus 

distribution. 

Backscatter (Area Backscattering Coefficient, m2

/m2) data for YOY fish and year-plus Arctic 

cod regions were exported in 1 km horizontal bins. No additional vertical binning was used as 

we were interested in areal estimates of and year-plus backscatter. Young-of-the-year and yearplus data were separated into the 20-40, 40-100, and 100-500 m depth strata based on the mean 

bottom depth of the 1 km analytic bin. 

Target strength 

In situ target strengths of YOY and year-plus Arctic cod were examined using acoustic data 

collected during midwater trawl deployment. The data were chosen to horizontally span the 

region that was sampled by the trawl, which included a horizontal offset to account for trawl 

wire out, wire angle, and vessel speed. 

To minimize the probability of mistakenly detecting multiple fish as a single fish (and 

erroneously increasing estimated target strength), we applied the Nv index (fish per reverberation 

volume, Sawada et al. 1993). The Nv index used the noise-cleaned Sv data (see Acoustic data 

processing above) that were binned into 20 m horizontal by 2 m vertical bins. As target strength 

for Arctic cod in the U.S. portion of the Beaufort Sea is not known, we used an estimated mean 

target strength of -60 dB re 1 m2 (herein referred to as dB) for young-of-the-year and -55 dB for 

yearling-and-older in Nv calculations. Sv bins with Nv values greater than 0.10 fish per 

reverberation volume were excluded from single echo detection. 

In each trawl region, single in situ target echoes were detected using criteria recommended by 

Rudstam et al. (2009) and Parker-Stetter et al. (2009). As the target strength, and variability in 

target strength, of YOY Arctic cod were not known, we used a minimum target strength of -90 

dB for single echo detections. This value accounts for both potential off-axis location (-6 dB) 

and high directional variability in the swimbladder (c.f. Rudstam et al. 2009) that can reduce 

target strength. In situ targets were not detected above the 9.0 m surface exclusion line or below 

the 0.5 m bottom exclusion line. Schools within the 40-100 m depth and demersal and pelagic 

layers in the 100-500 m depth were not eligible for the detection of single targets due to 

estimated year-plus densities that exceeded our Nv cut-off. Our single target detections, for the 

development of the target strength to length relationship, were limited to regions around schools 

or in the top and bottom of layers. Mean target strength values for year-plus Arctic cod and 

YOY fish were used to convert backscatter values to areal density estimates. 

Preliminary analysis suggested that in situ target strength did not change with depth in water 

greather than 100 m deep (See Results). This observation, coupled with the fact that the nonclosing trawl likely fished during deployment and retrieval, lead us to set fixed vertical limits for 

data export regions rather than follow the exact trawl track. This approach also accounted for 

tow-yo net deployments, where the net was fished up and down through a layer, to sample the 

layer constituents. For trawls that were fished at depths 100 m in the water column, target 

strength data were restricted to between 100 m and the 0.5 m bottom exclusion line. For shallow 

trawls, or those in at depths <100 m, data were restricted to between the 9.0 m surface exclusion 

23
line and 50 m. The 50-100 m depth zone, from which no in situ target strength data were used, 

appeared to be a transition zone between YOY and year-plus Arctic cod and did not appear to 

represent the target strength of either group exclusively. 

For each trawl a mean in situ target strength, weighted by the number of single echo detections 

within 1.5 dB target strength bins, was calculated. Each mean target strength value from the 

trawls was paired with a mean fish length calculated from the midwater trawl data to generate a 

target strength to length relationship. For YOY fish, only trawls which contained greater than 

90% Arctic cod YOY were included in the in situ target strength to length relationship. 

The limited length range of year-plus Arctic cod captured in midwater trawls and the shallow 

slope of the target strength to length regression equation reduced variability in target strength 

estimates over the length range present in the midwater trawl catches. Expected mean target 

strengths of year-plus captured in the midwater trawl ranged from -54.3 dB (65 mm) to -50.5 dB 

(190 mm). Within the 40-100 m depth, the weighted mean target strength (n=2, 116.2 mm 

weighted mean length) was -52.2 dB. Comparatively, the weighted mean target strength (n=13, 

102.5 mm weighted mean length) was -52.7 dB in the 100-500 m depth. For YOY fish (assumed 

to be dominated by Arctic cod), the weighted mean target strengths were -55.8 dB (n=7, 42.2 

mm weighted mean Arctic cod length, 20-40 m depth), -55.7 dB (n=4, 42.8 mm weighted mean 

Arctic cod length, 40-100 m depth), and -55.8 dB (n=1, 42.3 mm Arctic cod length, 100-500 m 

depth). As stated, only those trawls with greater than 90% Arctic cod YOY were used to 

develop the target strength to length relationship. The weighted mean target strength for all 

YOY catches combined (n=12, 39.7 mm weighted mean length for all YOY species) was -56.0 

dB. 

A target strength (dB) to length (fork length, cm) relationship was developed for Arctic cod 

using samples from 23 trawl collections that contained year-plus Arctic cod (n=15 trawls) and 

greater than 90% YOY Arctic cod (n=8 trawls). Two outlying points (121 mm and -59.3 dB; 

111 mm and -58.3 dB) resulted when large year-plus schools were sampled with the midwater 

trawl, to provide length frequency estimates for year-plus Arctic cod, but the surrounding lowdensity acoustic targets, from which the target strength values were derived, were from YOY. In 

the resulting target strength to fork length regression equations, the equation that excluded the 

two outlying year-plus Arctic cod points and used a flexible intercept (Target 

Strength=8.03×log10(Length)-60.78) is considered the most appropriate equation for this study. 

Density distribution, mean density, and abundance 

Densities of YOY fish and year-plus Arctic cod were calculated for each 1 km analytic bin by 

scaling the exported backscatter values (Area Backscattering Coefficient, m2/m2) with estimates 

of and 1+ Arctic cod target strengths (σbs, m

2

/m2). When scaling to density, mean target 

strengths for YOY and year-plus Arctic cod within the 20-40, 40-100, and 100-500 m depth 

strata were calculated by converting the mean fork length (within the depth) to target strength 

using the target strength to length relationship. Density estimates were made for analytic bins 

along the north-south transects and the connecting east-west cross-transects. 

24
Cluster sampling (Schaeffer et al. 1996) was used to generate a mean density (#/ha) for YOY and 

year-plus within depth strata. To meet the statistical assumptions of cluster sampling (and to 

prevent oversampling of some depth regions), only those 1 km bins along the parallel northsouth transects were used in this analysis. Transects were treated as clusters and 1 km bins along 

the transects represented elements within the cluster. For each depth, a mean density and 

standard deviation of the mean were calculated. Zero values (i.e. 1 km bins in which YOY or 

year-plus density estimates were zero) were included in the analysis. 

Estimates of YOY and year-plus Arctic cod abundance and biomass were made for each depth 

using mean densities from cluster sampling. For each age-group and depth, the mean density 

(#/ha) was scaled to abundance (fish within the study area) using depth strata areas derived from 

ESRI’s ArcMap GIS software (20-40 m depth: 205,372 ha, 40-100 m depth: 370,399 ha, 100-

500 m depth: 257,593 ha). The standard deviations of the means were also scaled using the same 

area scalars. Finally, to estimate Arctic cod biomass (metric tons, t) within the study area, 

abundance was multiplied by the mean weight (g) of a YOY or year-plus (based on midwater 

trawl catches) within each depth and converted to metric tons (t). 

We used a Pearson’s Chi-Squared test to statistically evaluate differences in mean YOY fish 

densities among depth strata (<40, 40-100, 100-500 m). We used a Pearson’s Chi-Squared test 

to statistically examine whether there were differences in mean year-plus Arctic cod densities 

between depth strata (40-100, 100-500 m). 

Comparing acoustic and bottom trawl surveys 

We compared year-plus Arctic cod densities (#/ha) from the acoustic and bottom trawl surveys. 

The acoustic data covered from 9.0 m below the surface to 0.5 m above the bottom, while the 

bottom trawl covered from 2.0 m above the bottom to the bottom. Our analysis evaluated the 

relationship between the bottom trawl catch and several acoustic estimates that are described 

below. As no acoustic estimates of year-plus density were made for the 20-40 m depth, no 

bottom trawls from the 20-40 m depth were used in this analysis. 

Two acoustic data sets were used in the analysis: coincident (collected during the bottom trawl 

survey) and non-coincident (collected during the systematic acoustic survey ~1 week later). In 

both acoustic data sets, we selected the 1 km horizontal bin that was the nearest neighbor to the 

midpoint (latitude, longitude) of the bottom trawl path. Due to high vessel noise, which 

interfered with the acoustics during bottom trawling, we used the pre-trawl scouting pass that 

was closest to final trawl location. 

Within each acoustic bin (paired with individual bottom trawls), we utilized several indices of 

year-plus Arctic cod density (#/ha): 

1. Acoustic survey depths (9.0 m below surface to 0.5 m from bottom) 

2. Acoustic survey depths above bottom trawl region (9.0 m below surface to 2.0 m above 

bottom) 

3. Overlapped survey depths (2.0 m above bottom to 0.5 m above bottom) 

25
4. Corrected overlapped region - proportional correction (2.0 m above bottom to the bottom, 

with the 0.5 m above bottom to bottom region corrected proportional to density in the 2.0 

to 0.5 m above the bottom region) 

5. Corrected overlapped region - adjacent correction (2.0 m above bottom to the bottom, 

with the 0.5 m above bottom to bottom region corrected using the adjacent amount of 

density in the 2.0 to 0.5 m above the bottom region) 

6. Water column using the proportional correction (9.0 m below surface to bottom) 

7. Water column using the adjacent correction (9.0 m below surface to bottom) 

The deadzone corrections used in indices 4-7 (proportional and adjacent) are commonly used 

assumptions in acoustic studies of fish distribution. 

There were three components to this analysis: (1) Evaluating distribution of Arctic cod from 

acoustic and bottom trawl surveys; (2) Comparison of acoustic (coincident and noncoincident) 

density estimates and bottom trawl CPUE, and; (3) Evaluating systematic bias in acoustic or 

bottom trawl estimates with depth. 

Evaluating distribution of Arctic cod – As a simple visual comparison between acoustic and 

bottom trawl survey year-plus Arctic cod densities, we used the coincident data to calculate the 

density ratio:

( )

Acoustic density ( ) ha

Bottom CPUE ha Density ratio

/#

/# =

where Acoustic density (#/ha) is the density calculated between 9.0 m from the surface and 0.5 m 

from the bottom (index #1 above). Density ratio values were plotted at the station location. 

Comparison of acoustic density estimates and bottom trawl CPUE – Error structure in the data 

(bottom trawl, coincident acoustics, noncoincident acoustics) was evaluated using Shapiro-Wilk, 

Komogorov-Smirnov, QQ-Plots, and by examining histograms. The bottom trawl data were 

normalized using a log transformation (log(bottom trawl CPUE)) and the acoustic data 

(coincident and noncoincident) was normalized using either a fourth-root ((acoustic density)0.25) 

transformation to normalize the residuals or the data were left untransformed. In some cases, 

data points were identified as outliers by a Cook’s distance test (Cook’s distance greater than 

0.5). These points were removed from the analysis.

Simple linear regression models were used in this analysis. Both generalized linear models 

(GLM) and generalized additive models (GAMs) were also tested but provided similar, linear 

results. Two model groups were run: 

Model group 1 contained the variables: 

Acoustic density indices (1-7 above) as response (continuous) 

Bottom trawl CPUE as predictor (continuous) 

Lined versus unlined net as predictor (categorical) 

Bottom depth (categorical) 

+ interaction terms 

26
Model group 1 was performed using coincident data and noncoincident data that included all 

lined and unlined bottom trawl results. The global model for this analysis was: 

Acoustic index ~ Bottom trawl CPUE + net (lined/unlined) + depth (below/layer) + interactions 

Model group 2 contained the variables: 

Acoustic density indices (1-7 above) as response (continuous) 

Bottom trawl CPUE as predictor (continuous) 

Bottom depth (categorical) 

+interaction terms 

Model group 2 was performed using lined net only data from coincident and noncoincident 

datasets. This removed the potential dual-influence of the categorical bottom depth variable and 

the lined/unlined net variable. The global model for this analysis was: 

Acoustic index ~ Bottom trawl CPUE + depth (below/layer) + interaction 

In early model runs, depth was treated as a continuous variable, but this was deemed 

inappropriate as it did not represent the observed relationship between year-plus Arctic cod and 

bottom depth. Instead, we classified the bottom depth at each location relative to the year-plus 

Arctic cod layer. If the year-plus layer was in contact with the bottom, the depth was classified as 

“layer”. If the year-plus layer was above the bollow, the depth was classified as “below”.. 

Optimal models were selected using AIC criteria. This procedure produces a global model that 

includes all possible combinations of variables as a starting point, but variable deletions are used 

to find the model with the lowest AIC score. This form of model selection, which uses a model 

with the lowest AIC, may result in predictors which are present in the model but are not 

significant. 

Acoustic and bottom trawl potential bias with depth – Coincident acoustic and bottom trawl 

(lined and unlined) data were used in this analysis. Due to the possible nonlinear relationship 

with depth, generalized additive models (GAMs) were chosen. Acoustic indices of density (1-7 

above) were log transformed to help with heteroscedasticity. A plot of residuals and tests of 

normality suggested that the error structure for the acoustic data were normal. Transformations 

of the bottom trawl data did not make the residuals normal, so a quasipoisson error structure was 

used. GAMs were used to test the relationship between the acoustic indices or bottom trawl 

density (response variables) and depth (continuous predictor variable). The global models for 

this analysis were: 

Acoustic index ~ depth 

Bottom trawl density ~ depth 

Pelagic fish-habitat associations 

This analysis evaluated relationships between YOY fish or year-plus Arctic cod densities with 

oceanographic characterizations of the habitat. Due to spatial correlation in both the acoustic 

27
and oceanographic data, this analysis used individual CTD casts paired with collocated acoustic 

data. A 3 km radius around each CTD location was considered a “point” observation. 

To calculate mean YOY fish or year-plus Arctic cod densities (#/ha), we identified any 1 km 

horizontal bins from the systematic survey whose midpoint (median latitude, median longitude) 

fell within the 3 km radius around the CTD cast location. If more than one acoustic bin was 

identified within the 3 km radius, a mean YOY fish or year-plus Arctic cod density (#/ha) was 

calculated. 

To characterize the habitat, CTD data were processed by applying the manufacturer’s calibration 

curves to the raw data then binning to 1-dB pressure levels, using the Sea-Bird Electronics Inc. 

SBE Data Processing algorithms and all recommended processing steps. We used custom scripts 

developed on the MATLAB platform, all binned Temperature/Salinity profiles were visually 

inspected for egregious outliers, spikes, and density inversions, which were removed via 

interpolation (midwater column) or extrapolation (at surface). The threshold level for removal 

was at the ~0.01 oC (temperature) and ~0.02 PSU (for salinity). 

The following physical and oceanographic variables were available at each CTD deployment: 

Latitude (decimal degrees) 

Longitude (decimal degrees) 

Bottom depth (meters) 

Surface Temperature (oC) 

Surface Salinity (PSU) 

Surface Density (Sigma-T, kg/m3

-1000) 

Surface Turbidity (FTU) 

Bottom Temperature (oC) 

Bottom Salinity (PSU) 

Bottom Density (kg/m3

-1000) 

Bottom Turbidity (FTU) 

Surface-Bottom Temperature Difference (oC) 

Surface-Bottom Salinity Difference (PSU) 

Surface-Bottom Density Difference (kg/m3

-1000) 

Surface-Bottom Turbidity Difference (FTU) 

Mixed Layer Depth (MLD) via change of 0.1 kg/m3

 from surface (m) 

Depth of N2

 maximum (m; a.k.a. the Brunt-Vaisala frequency squared, a measure of vertical 

stratification) 

Mean Temperature above the mixed layer depth (MLD, oC) 

Mean Salinity above MLD (PSU) 

Mean Density above MLD (kg/m3

-1000) 

Mean Turbidity above MLD (FTU) 

Mean Temperature below MLD (oC) 

Mean Salinity below MLD (PSU) 

Mean Density below MLD (kg/m3

-1000) 

Mean Turbidity below MLD (FTU) 

28
Spearman rank correlation tests suggested that many of the variables were significantly 

correlated (P<0.05). Variables that were highly correlated with other variables were sequentially 

removed and re-tested, resulting in a list of twelve variables. We then considered which 

variables were potentially biologically-relevant given the distribution of YOY fish and year-plus 

Arctic cod and came up with our list of “biological predictors”: 

Longitude (decimal degrees) 

Bottom depth (meters) 

Mixed Layer Depth (MLD) via change of 0.1 kg/m3

 from surface (m) 

Depth of N2

 maximum (m) 

Mean Temperature above MLD (oC) 

Mean Salinity above MLD (PSU) 

Mean Temperature below MLD (oC) 

Mean Salinity below MLD (PSU) 

In order to compare pelagic fish results with the demersal fish-habitat models, we also used a set 

of “standard predictors” that were comparable to bottom trawl model predictors: 

Longitude (decimal degrees) 

Bottom depth (meters) 

Bottom Temperature (oC) 

Bottom Salinity (PSU) 

Bottom Density (kg/m3

-1000) 

Surface-Bottom Temperature Difference (oC) 

Surface-Bottom Salinity Difference (PSU) 

Surface-Bottom Density Difference (kg/m3

-1000) 

The response variables, YOY fish density and year-plus Arctic cod densities, were log 

transformed to reduce issues of heteroscedasticity in the regression models. Some variables 

(Bottom depth and Depth of the N2

 max) were also log transformed to help stabilize model 

variance. 

The YOY fish models (comparing density to biological and standard predictors) were run using a 

simple linear model (with normal error structure) and a GAM. The two model types were run for 

comparison. Model assumptions were checked using residual plots, QQ-plots, and a ShapiroWilk test of the residuals. For the linear model, the optimal model was selected using AIC 

criteria. This procedure produces a global model that includes all possible combinations of 

variables as a starting point, but variable deletions are used to find the model with the lowest 

AIC score. This form of model selection, which uses a model with the lowest AIC, may result in 

predictors which are present in the model but are not significant. The GAM was run on the same 

dataset, but the number of knots in the smoother was limited due to the small sample size. 

Year-plus Arctic cod densities were not estimated from the acoustic data in the nearshore 

because it was not possible to analytically separate them from the YOY layer in shallow depths. 

So for year-plus Arctic cod density models, the presence of these zero values in the nearshore 

complicated the analysis. When zero values were included in the model run, general linear 

29
30

models were used but when zero values were excluded from the model run, linear models were 

chosen. Model assumptions were checked using residual plots, QQ-plots, and a Shapiro-Wilk 

test of the residuals and, in one case a quasipoisson error structure was selected. Models 

comparing year-plus density to biological and standard predictors were performed using linear 

models (simple or general) and GAMs (for comparison) both including and excluding the 

nearshore zero values. We consider the models with zero values excluded to be the most 

appropriate given that zero values are artificial (i.e., analytic not biological), however we 

performed both model sets to compare results.
Results 

As detailed in the “Methods” section, the distribution and abundance of fish were assessed using 

two different techniques: standardized bottom trawls for the benthic fish and acoustics (verified 

with midwater trawls) for the pelagic fish. The data from these two surveys should not be 

combined into a comprehensive benthic-pelagic estimate because the bottom trawls assess fish 

from the bottom to 2-3 m off bottom, and the acoustics assess fish from 9.0 m below the surface 

to 0.5 m off bottom. Given this overlap in the vertical zones surveyed with each method, and 

potential differences in gear selectivity, it is not valid to simply add the two data sets to obtain a 

full water-column abundance or biomass estimate of fish. Also, seismic surveys witin 100 nm 

overlapped with the survey time period (see “Methods”). 

Demersal fish 

Demersal fish abundance 

There were a total of 26 bottom trawls of which 22 were successful (Table 1). The first bottom 

trawl was on August 6, 2008 and the last bottom trawl was completed on August 21, 2008. 

Bottom depths ranged from 40 to 478 m. Twelve successful trawls were made in the 40-100 m 

bottom depth (only nine were used in CPUE estimates with the unlined net), and ten in the 100-

500 m bottom depth. Bottom trawl durations ranged from approximately 7 to 19 minutes of 

bottom time. Distance fished for each bottom trawl ranged from 0.4 km to 3.6 km (Table 1). 

Fish comprised 6% of the total weight captured in the bottom trawls and 34 species of fish were 

identified (Table 2). Several taxa could only be identified to the genus or family level in the 

field. However, all specimens were verified and/or identified in the AFSC taxonomy lab after 

the survey (James Orr and Duane Stevenson, AFSC, pers. com.). In this survey, Arctic cod made 

up 92% of the total numbers of fish captured and eelpouts made up 3.5% of the total numbers of 

fish captured. Together Bering flounder and Greenland turbot made up only 0.3% of the total 

numbers of fish captured in the bottom trawls. Arctic cod occurred at all bottom trawl stations. 

Two species were identified in the AFSC taxonomic laboratory but not in the field, Lycodes 

marmoratus (festive snailfish), and Nautichthys pribilovius (eyeshade sculpin) and were 

subsequently reassigned to the appropriate trawl. However, because they were not identified in 

the field, no catch information was associated with either species (i.e. counts or weights). 

Three trawls occurred at bottom depths 40-50 m (Tables 3a and 3b). Tables 3a and 3b show 

CPUE #/ha and kg/ha for each of the three trawls. Trawl 13 was with a lined net and trawls 16 

and 23 were with an unlined net, thus we could not combine the three catch estimates. In Table 

3c, mean CPUE (± 1 SD) in numbers (#/ha) and weight (kg/ha) were calculated by depth (40-100 

m and 100-500 m). Trawl 13 was not included in Table 3c, the 40-100 m bottom depth, as it was 

with a lined net (all other hauls in this statum were with an unlined net). Trawls 16 and 23 were 

included in the table, as they were with an unlined net. 

31
Scientific Name Common Name Total numbers Total weight (kg)

Boreogadus saida Arctic cod 66,278 1241.95 

Lycodes raridens marbled eelpout 1,642 141.65 

Lycodes polaris Canadian eelpout 772 38.48 

Hippoglossoides robustus Bering flounder 231 34.62 

Theragra chalcogramma walleye pollock 1,082 34.00 

Reinhardtius hippoglossoides Greenland turbot 221 11.55 

Lycodes mucosus saddled eelpout 18 8.38 

Lycodes sp. unid. eelpout 72 8.03 

Liparis gibbus variegated snailfish 132 10.17 

Lycodes rossi threespot eelpout 66 7.75 

Liparis fabricii gelatinous seasnail 165 4.97 

Myoxocephalus verrucosus warty sculpin 67 1.39 

Triglops pingeli ribbed sculpin 219 1.29 

Gadus macrocephalus Pacific cod 5 1.02 

Careproctus sp. cf. rastrinus (Orr et al.) salmon snailfish 59 1.10 

Mallotus villosus capelin 9 0.86 

Gymnocanthus tricuspis Arctic staghorn sculpin 77 0.84 

Artediellus scaber hamecon 154 0.94 

Lumpenus medius stout eelblenny 136 0.49 

Liparis sp. unid. snailfish 36 0.34 

Aspidophoroides olriki Arctic alligatorfish 134 0.33 

Cottidae sculpin family 79 0.32 

Lumpenus maculatus daubed shanny 40 0.31 

Triglops nybelini bigeye sculpin 71 0.21 

Lumpenus fabricii slender eelblenny 41 0.18 

Lumpenus sp. unid. eelblenny 21 0.16 

Enophrys diceraus antlered sculpin 1 0.10 

Icelus spatula spatulate sculpin 20 0.14 

Eumesogrammus praecisus fourline snakeblenny 3 0.10 

Eleginus gracilis saffron cod 4 0.06 

Liparis marmoratus festive snailfish 2 0.01 

Nautichthys pribilovius eyeshade sculpin 1 0.01 

Eumicrotremus derjugini leatherfin lumpsucker 6 0.16 

Gymnelus viridis fish doctor 3 0.05 

Table 2. Fish taxa from the bottom trawl caught during the 2008 Beaufort Sea survey, total 

numbers and weights were extrapolated from subsampling. 

32
Scientific Nam Common Name 

CPUE (#/ha) Haul 13 (49 m) (lined net) 

CPUE (#/ha) Haul 16 (41 m) (unlined net) 

CPUE (k#/ha) Haul 23 (44 m) (unlined net) 

Boreogadus saida Arctic cod 1,294 22 32 Lycodes raridens marbled eelpout 0 0 0 Lycodes polaris Canadian eelpout 8 3 0 

Hippoglossoides robustus Bering flounder 3 0 2 

Theragra chalcogramma walleye pollock 6 3 7 Reinhardtius hippoglossoides Greenland turbot 0 0 0 

Lycodes mucosus saddled eelpout 0 0 0 

Lycodes sp. unid. eelpout 0 0 0 

Liparis gibbus variegated snailfish 0 0 0 

Lycodes rossi threespot eelpout 0 0 0 

Liparis fabricii gelatinous seasnail 0 0 0 Myoxocephalus verrucosus warty sculpin 13 0 < 1 

Triglops pingeli ribbed sculpin 15 0 0 

Gadus macrocephalus Pacific cod 0 0 0 

Careproctus sp. cf. rastrinus (Orr et al.) salmon snailfish 0 0 0 

Mallotus villosus capelin 4 0 0 Gymnocanthus tricuspis Arctic staghorn sculpin 23 0 0 

Artediellus scaber hamecon 6 3 3 Lumpenus medius stout eelblenny 2 0 0 

 Liparis sp. unid. snailfish 6 0 0 

Aspidophoroides olriki Arctic alligatorfish 0 0 0 

Cottidae sculpin family 0 0 0 Lumpenus maculatus daubed shanny 0 0 0 Triglops nybelini bigeye sculpin 0 0 0 Lumpenus fabricii slender eelblenny 8 0 0 

Lumpenus sp. unid. eelblenny 0 0 0 Enophrys diceraus antlered sculpin 0 0 0 

Icelus spatula spatulate sculpin 2 0 0 

Eumesogrammus praecisus fourline snakeblenny 0 0 < 1 

Eleginus gracilis saffron cod 2 0 0 

Liparis marmoratus festive snailfish 0 0 0 Nautichthys pribilovius eyeshade sculpin 0 0 0 Eumicrotremus derjugini leatherfin lumpsucker 0 1 0 Gymnelus viridis fish doctor 0 4 0 

Table 3a. CPUE in numbers (#/ha) of fish caught in 40-50 m bottom depths during the 2008 Beaufort Sea survey, bottom trawl. The haul depth is in parenthesis. Note: haul 13 was with a lined net and hauls 16 and 23 were with 

an unlined net, thus we were not able to combine them. 

33
Scientific Name Common Name 

CPUE (kg/ha) Haul 13 (49 m) (lined net) 

CPUE (kg/ha) Haul 16 (41 m) (unlined net) 

CPUE (kg/ha) Haul 23 (44 m) (unlined net) 

Boreogadus saida Arctic cod 7.82 0.19 0.24 Lycodes raridens marbled eelpout 0 0 0 Lycodes polaris Canadian eelpout 0.29 0.03 0 

Hippoglossoides robustus Bering flounder 0.15 0 0.19 

Theragra chalcogramma walleye pollock 0.11 0.13 0.16 Reinhardtius hippoglossoides Greenland turbot 0 0 0 Lycodes mucosus saddled eelpout 0 0 0 

Lycodes sp. unid. eelpout 0 0 0 

Liparis gibbus variegated snailfish 0 0 0 

Lycodes rossi threespot eelpout 0 0 0 Liparis fabricii gelatinous seasnail 0 0 0 Myoxocephalus verrucosus warty sculpin 0.06 0 < 0.01 

Triglops pingeli ribbed sculpin 0.05 0 0 Gadus macrocephalus Pacific cod 0 0 0 Careproctus sp. cf. rastrinus (Orr et al.) salmon snailfish 0 0 0 

Mallotus villosus capelin 0.42 0 0 

Gymnocanthus tricuspis Arctic staghorn sculpin 0.13 0 0 

Artediellus scaber hamecon 0.04 0.02 0.02 

Lumpenus medius stout eelblenny < 0.01 0 0 

 Liparis sp. unid. snailfish 0.05 0 0 

Aspidophoroides olriki Arctic alligatorfish 0 0 0 

Cottidae sculpin family 0 0 0 

Lumpenus maculatus daubed shanny 0 0 0 

Triglops nybelini bigeye sculpin 0 0 0 

Lumpenus fabricii slender eelblenny 0.03 0 0 

Lumpenus sp. unid. eelblenny 0 0 0 Enophrys diceraus antlered sculpin 0 0 0 Icelus spatula spatulate sculpin 0.01 0 0 

Eumesogrammus praecisus fourline snakeblenny 0 0 0.02 Eleginus gracilis saffron cod 0.03 0 0 Liparis marmoratus festive snailfish 0 0 0 Nautichthys pribilovius eyeshade sculpin 0 0 0 Eumicrotremus derjugini leatherfin lumpsucker 0 0.02 0 Gymnelus viridis fish doctor 0 0.07 0 

Table 3b. CPUE in fish weight (kg/ha) caught in 40-50 m bottom depths during the 2008 Beaufort Sea survey, bottom trawl. The haul depth is in parenthesis. Note: haul 13 was with a lined net and hauls 16 and 23 were with 

an unlined net, thus we were not able to combine them. 

34
Scientific Name Common Name 

Mean CPUE (#/ha) 40-100 m depth (unlined net) 

Mean CPUE (#/ha) 100-500 m depth (lined net) 

Mean CPUE (k40-100 m depth (unlined net) 

Boreogadus saida Arctic cod 917 (± 2,532) 2,341 (± 3,472) 6.48 (± 17.60) Lycodes raridens marbled eelpout 0 72 (± 145) 0 Lycodes polaris Canadian eelpout < 1 (± 1) 33 (± 55) 0.01 (± 0.02) 

Hippoglossoides robustus Bering flounder < 1 (± 1) 10 (± 11) 0.09 (± 0.09) 

Theragra chalcogramma walleye pollock 8 (± 7.56) 35 (± 46) 0.14 (± 0.2) 

Reinhardtius hippoglossoides Greenland turbot 0 10 (± 15) 0 Lycodes mucosus saddled eelpout 0 1 (± 3) 0 

Lycodes sp. unid. eelpout 0 4 (± 8) 0 

Liparis gibbus variegated snailfish 0 6 (± 13) 0 

Lycodes rossi threespot eelpout < 1 (± 1) 3 (± 4) 0.01 (± 0.02) 

Liparis fabricii gelatinous seasnail 0 7 (± 12) 0 

Myoxocephalus verrucosus warty sculpin < 1 (± 1) 2 (± 5) < 0.01 (± 0.002Triglops pingeli ribbed sculpin < 1 (± 1)) 0 0.01 (± 0.01) 

Gadus macrocephalus Pacific cod 0 < 1 (± 1) 0 

Careproctus sp. cf. rastrinus (Orr et al.) salmon snailfish 0 3 (± 4) 0 

Mallotus villosus capelin 0 0 0 Gymnocanthus tricuspis Arctic staghorn sculpin < 1 (± 1) 0 < 0.01 (± 0.006Artediellus scaber hamecon 3 0 0.02 (± 0.03) 

Lumpenus medius stout eelblenny 0 6 (± 13) 0 

 Liparis sp. unid. snailfish < 1 (± 1) 0 < 0.01 (± 0.000

Aspidophoroides olriki Arctic alligatorfish < 1 (± 1) 6 (± 11) < 0.01 (± 0.000

Cottidae sculpin family 0 0 0 Lumpenus maculatus daubed shanny 0 2 (± 5) 0 

Triglops nybelini bigeye sculpin 0 3 (± 9) 0 

Lumpenus fabricii slender eelblenny 0 1 (± 3) 0 

Lumpenus sp. unid. eelblenny 0 0 0 

Enophrys diceraus antlered sculpin 0 0 0 Icelus spatula spatulate sculpin < 1 (± 1) 0 0.01 (± 0.02) 

Eumesogrammus praecisus fourline snakeblenny < 1 (± 1) 0 < 0.01 (± 0.007Eleginus gracilis saffron cod 0 0 0 

Liparis marmoratus festive snailfish 0 0 0 

Nautichthys pribilovius eyeshade sculpin 0 0 0 Eumicrotremus derjugini leatherfin lumpsucker < 1 (± 1) 0 0.01 (± 0.02) Gymnelus viridis fish doctor < 1 (± 1) 0 < 0.01 (± 0.02) 

Table 3c. Mean CPUE (± 1 SD) in numbers and weight of fish caught by bottom depth strata during the 2008 Beabottom trawl. Note: does not include hauls 11, 12 and 13 (lined net) for the 40-100 m depth and haul 22 in the 100-500 m depth (unli

and 23 are included in the 40-100 m statum from Tables 3a and 3b. 

35
Mean CPUE (± 1 SD) in numbers (#/ha) and weight (kg/ha) for all lined compared to all unlined 

trawls is summarized in Table 4. The CPUE (#/ha) for fish species found in the paired trawls are 

summarized in Table 5. For all species of fish, the CPUE is larger for the lined net catches than 

the unlined net catches. Species diversity also was lower in the unlined net catches (Table 6). 

For example, 11 of the 15 species that were captured in trawl 12 with a lined net, did not appear 

in trawl 24 using an unlined net. 

36
Scientific Name Common Name Mean CPUE (#/ha) lined net Mean CPUE (#/ha) unlined net Mean CPUE (kg/ha) lined net 

Boreogadus saida Arctic cod 1,953 (± 3,324) 849 (± 2,397) 39.64 (± 68.96) Lycodes raridens marbled eelpout 54 (± 135) 0 4.60 (± 10.88) 

Lycodes polaris Canadian eelpout 26 (± 52) < 1 (± 1) 1.41 (± 3.05) 

Hippoglossoides robustus Bering flounder 8 (± 11) 1 (± 1) 1.26 (± 1.66) Theragra chalcogramma walleye pollock 36 (± 45) 7 (± 12) 1.18 (± 1.77) 

Reinhardtius hippoglossoides Greenland turbot 8 (± 14) 0 0.41 (± 0.57) Lycodes mucosus saddled eelpout < 1 (± 2) 0 0.34 (± 1.2) 

Lycodes sp. unid. eelpout 3 (± 7) 0 0.34 (± 0.96) 

Liparis gibbus variegated snailfish 4 (± 12) 0 0.31 (± 1.09) Lycodes rossi threespot eelpout 2 (± 4) < 1 (± 1) 0.28 (± 0.59) 

Liparis fabricii gelatinous seasnail 5 (± 4) 0 0.16 (± 0.35) 

Myoxocephalus verrucosus warty sculpin 2 (± 5) < 1 (± 1) 0.04 (± 0.13) 

Triglops pingeli ribbed sculpin 8 (± 22) < 1 (± 1) 0.04 (± 0.14) 

Gadus macrocephalus Pacific cod < 1 (± 1) 0 0.03 (± 0.13) 

Careproctus sp. cf. rastrinus (Orr et al.) salmon snailfish 2 (± 4) < 1 (± 1) 0.03 (± 0.07) 

Mallotus villosus capelin < 1 (± 1) 0 0.03 (± 0.12) 

Gymnocanthus tricuspis Arctic staghorn sculpin 3 (± 7) < 1 (± 1) 0.03 (± 0.08) Artediellus scaber hamecon 5 (± 13) 3 (± 4) 0.02 (± 0.07) 

Lumpenus medius stout eelblenny 4 (± 12) 0 0.01 (± 0.05) Liparis sp. unid. snailfish 1 (± 3) < 1 (± 1) 0.01 (± 0.03) 

Aspidophoroides olriki Arctic alligatorfish 5 (± 11) < 1 (± 1) 0.01 (± 0.03) 

Cottidae sculpin family 3 (± 10) 0 0.01 (± 0.04) Lumpenus maculatus daubed shanny 1 (± 4) 0 0.01 (± 0.03) 

Triglops nybelini bigeye sculpin 2 (± 8) 0 < 0.01 (± 0.03) 

Lumpenus fabricii slender eelblenny 2 (± 4) 0 < 0.01 (± 0.02) Lumpenus sp. unid. eelblenny < 1 (± 3) 0 < 0.01 (± 0.02) 

Icelus spatula spatulate sculpin < 1 (± 2) < 1 (± 1) < 0.01 (± 0.01) 

Eumesogrammus praecisus fourline snakeblenny < 1 (± 1) < 1 (± 1) < 0.01 (± 0.01) Eleginus gracilis saffron cod < 1 (± 1) 0 < 0.01 (± 0.01) 

Liparis marmoratus festive snailfish < 1 (± 1) 0 < 0.01 (± 0.001) 

Nautichthys pribilovius eyeshade sculpin < 1 (± 1) 0 < 0.01 (± 0.001) 

Eumicrotremus derjugini leatherfin lumpsucker 0 < 1 (± 1) 0 

Gymnelus viridis fish doctor 0 < 1 (± 1) 0 

Enophrys diceraus antlered sculpin < 1 (± 1) 0 < 0.01 (± 0.001) 

Table 4. Mean CPUE (± 1 SD) in numbers and weight of fish caught in lined vs. unlined nets (includes all depths) Beaufort Sea survey, bottom trawl. 

37
Scientific Name Common Name 

CPUE (#/ha) lined net, 10 (100-500 m) 

CPUE (#/ha) unlined net, 22 (100-500 m) 

CPUE (#/ha) lined net, 12 (40-100 m) 

Cun(4

Boreogadus saida Arctic cod 825 234 556 8 Lycodes raridens marbled eelpout 0 0 0 0 

Lycodes polaris Canadian eelpout 58 1 4 0 Hippoglossoides robustus Bering flounder 14 3 1 0 Theragra chalcogramma walleye pollock 0 0 84 41 

Reinhardtius hippoglossoides Greenland turbot 43 0 0 0 Lycodes mucosus saddled eelpout 0 0 1 0 Lycodes sp. unid. eelpout 0 0 0 0 Liparis gibbus variegated snailfish 0 0 0 0 Lycodes rossi threespot eelpout 0 0 0 0 

Liparis fabricii gelatinous seasnail 0 0 0 0 

Myoxocephalus verrucosus warty sculpin 14 0 1 0 Triglops pingeli ribbed sculpin 0 0 78 0 Gadus macrocephalus Pacific cod 0 0 1 0 

Careproctus sp. cf. rastrinus (Orr et al.) salmon snailfish 0 3 0 0 Mallotus villosus capelin 0 0 1 0 Gymnocanthus tricuspis Arctic staghorn sculpin 0 0 13 1 Artediellus scaber hamecon 0 0 44 1 Lumpenus medius stout eelblenny 0 0 0 0 

Liparis sp. unid. snailfish 0 0 0.04 0 

Aspidophoroides olriki Arctic alligatorfish 29 0 1 0 

Cottidae sculpin family 0 0 36 0 

Lumpenus maculatus daubed shanny 14 0 0 0 Triglops nybelini bigeye sculpin 29 0 0 0 

Lumpenus fabricii slender eelblenny 0 0 0 0 

Lumpenus sp. unid. eelblenny 0 0 9 0 Enophrys diceraus antlered sculpin 0 0 0 0 Icelus spatula spatulate sculpin 0 0 0 0 

Eumesogrammus praecisus fourline snakeblenny 0 0 0 0 Eleginus gracilis saffron cod 0 0 0 0 

Liparis marmoratus festive snailfish 0 0 0 0 

Nautichthys pribilovius eyeshade sculpin 0 0 0 0 Eumicrotremus derjugini leatherfin lumpsucker 0 1 0 0 

Gymnelus viridis fish doctor 0 0 0 0 

Table 5. CPUE (#/ha) of fish caught in the paired lined and unlined comparison trawls during the 2008 Beaufort S

The two pairs were trawls 10 and 22; and trawls 12 and 24. The trawl number is listed after net type. 

38
Total numbers and biomass of all fish species were calculated from mean CPUE and area, by 

depth (Table 7). Arctic cod was the most abundant fish followed by several species of eelpouts, 

Bering flounder, walleye pollock, Greenland turbot, snailfish, and sculpins. The total dermersal 

fish number estimate for both strata combined was 1.0 × 109

 (18,841 t) of which 65% was in the 

100-500 m depth. Approximately 60% of the estimated total numbers of Arctic cod was in the 

100-500 m depth (84% of the biomass). The second most abundant fish (by numbers and 

weight) was Lycodes raridens. This species was only caught in the 100-500 m depth. Eelpouts 

(genus Lycodes and Gymnelus) had a density estimate of 2.90 × 107

 in the 100-500 m depth and 

3.17 × 105 in the 40-100 m depth (biomass was estimated at 2,390 t in the 100-500 m depth and 6 

t in the 40-100 m depth). Bering flounder and walleye pollock were the second and third most 

abundant species in the 40-100 m depth. 

15 min 5 min 15 min 5 min 

lined unlined lined unlined 

10 22 12 24 

No. species 8 5 15 4 

Fish Total catch weight 32.4 4.4 13.1 0.7 

CPUE (kg/ha) 13.3 3.3 5.9 0.8 

Total no. fish 2,506 315 1,846 52 

No. species 54 51 46 39 

Invertebrates Total catch weight 2327.4 73.3 238.0 52.0 

CPUE (kg/ha) 954.8 56.2 107.2 50.7 

Total no. invertebrates 1,777,752 1,889 20,347 1,250 

Table 6. A summary table of the paired tows: tow time, if net was lined or unlined and 

rawl number are column headings. The number of species caught, total catch weight (kg), 

PUE (kg/ha) and the total number of individuals caught for both fish and invertebrates 

ake up the row headings. 

t

C

m

39
Scientific Name Common Name 

Total no. 40-100 m depth (unlined net) 

Total no. 100-500 m depth (lined net) 

Biomass (t) 40-100 m depth (unlined net) 

Boreogadus saida Arctic cod 3.39 x 108 6.03 x 108 2,402 Lycodes raridens marbled eelpout 0 1.84 x 107 0 

Lycodes polaris Canadian eelpout 227,904 8.54 x 106 3 

Hippoglossoides robustus Bering flounder 328,419 2.61 x 106 32 Theragra chalcogramma walleye pollock 2.80 x 106 9.08 x 106 53 Reinhardtius hippoglossoides Greenland turbot 0 2.61 x 106 0 Lycodes mucosus saddled eelpout 0 242,356 0 

Lycodes sp. unid. eelpout 0 938,202 0 Liparis gibbus variegated snailfish 0 1.46 x 106 0 

Lycodes rossi threespot eelpout 89,814 809,043 3 Liparis fabricii gelatinous seasnail 0 1.88 x 106 0 Myoxocephalus verrucosus warty sculpin 36,306 410,960 0.3 

Triglops pingeli ribbed sculpin 246,462 833,661 2 Gadus macrocephalus Pacific cod 0 50,698 0 

Careproctus sp. cf. rastrinus (Orr et al.) salmon snailfish 0 693,827 0 

Mallotus villosus capelin 0 0 0 

Gymnocanthus tricuspis Arctic staghorn sculpin 40,119 0 1 Artediellus scaber hamecon 1.05 x 106 0 7 

Lumpenus medius stout eelblenny 0 1.46 x 106 0 

Liparis sp. unid. snailfish 0 0 0 Aspidophoroides olriki Arctic alligatorfish 35,781 1.57 x 106 0.04 Cottidae sculpin family 0 0 0 

Lumpenus maculatus daubed shanny 0 410,960 0 

Triglops nybelini bigeye sculpin 0 833,661 0 

Lumpenus fabricii slender eelblenny 0 316,659 0 Lumpenus sp. unid. eelblenny 0 0 0 Enophrys diceraus antlered sculpin 0 0 0 Icelus spatula spatulate sculpin 223,509 0 3 

Eumesogrammus praecisus fourline snakeblenny 36,306 0 1 

Eleginus gracilis saffron cod 0 0 0 Liparis marmoratus festive snailfish 0 0 0 

Nautichthys pribilovius eyeshade sculpin 0 0 0 

Eumicrotremus derjugini leatherfin lumpsucker 204,740 0 4 

Gymnelus viridis fish doctor 142,818 0 0.13 

Table 7. Biomass and total number estimates of fish taxa from the 2008 Beaufort Sea survey, bottom trawls, extra

depth strata area. Note: trawls 11, 12, and 13 are not included in these results as they were with a lined net in the 40-100 m depth and 

the 100-500 m depth, it was with an unlined net. 

40
Demersal fish cluster analysis 

Agglomerative hierarchical clustering identified five clusters of trawl stations based on species 

presence/absence (Figure 3). Arctic cod were present in all trawls, so were not included in the 

clustering analysis. 

Table 8 shows the predominant species in each cluster, and Figure 4 shows the distribution of 

trawls belonging to each cluster. Species are grouped for the purposes of summarizing the 

results in Table 8, but the cluster analysis was conducted on a species-basis. Walleye pollock 

were present in at least half the trawls for nearly all clusters. Clusters 1 and 5 were made up of 

trawls in the most offshore depth (100-500 m). Bering flounder, snailfish, eelpouts and 

Greenland turbot characterized Cluster 1. The species composition of Cluster 5 was similar 

except Greenland turbot was not present and eelblennies were found in more than half the trawls. 

The trawls in Clusters 2 and 3 were distributed primarily in the shallower (40-100 m) depth. 

Species distinguishing Cluster 2 were Bering flounder and sculpins. Sculpins were common in 

Figure 3. Clustering tree based on species presence/absence in the bottom trawl data. The 

vertical coordinate (“height”) of the place where two branches join equals the dissimiliarity 

between the corresponding cluster. Bottom trawls only shown. 

2

3

7456

89

10

11

1213

16

17

18

20

21

23

22

24

2526

Cluster 1 

Cluster 

3 

Cluster 

4 

Cluster 5 

Cluster 2 

0.0 0.2 0.4 0.6 0.8

Height

41
Cluster 3, but Bering flounder were not present. In addition, leatherfin lumpsucker and eelpouts 

were a presence in Cluster 3. The trawls making up Cluster 4 were found in the shallower depth 

and only in the western half of the survey area. This was a diverse cluster with several species 

occurring in all of the trawls. The presence of capelin and alligatorfish in more than half the 

trawls was a unique characteristic of this cluster. 

The clustering analysis was conducted with species presence/absence data in the hopes of 

avoiding the bias towards higher CPUE in the lined net catches, compared to the unlined net 

catches. Net type neverthelss may have influenced the trawl composition of some of the clusters. 

Clusters 1 and 4 were comprised exclusively of trawls conducted with the lined net, and Cluster 

3 was made of only un-lined trawls. The other clusters were comprised of a mix of lined and unlined trawls. 

Cluster leatherfin 

lump-sucker 

Bering 

flounder 

snailfish 

spp. 

eelblenny eelpout 

spp. capelin Greenland turbot 

walleye 

pollock 

alligatorfish sculpin 

spp. 

1 0 0.60 1 0.20 1 0 0.80 0.80 0 0 

2 0.17 1 0.17 0 0 0 0 1 0 0.50 

3 0.67 0 0.33 0 0.67 0 0 1 0.33 1 

4 0 1 1 1 1 0.67 0 1 0.67 1 

5 0.20 0.80 0.60 0.60 1 0 0.20 0.20 0.40 0.40 

Table 8. Proportion of trawls (both net types included) in which the species shown was 

present for each of five clusters identified with agglomerative hierarchical clustering. Only 

species that were present in at least 50% of the trawls in at least one cluster are shown. Arctic 

cod were present in all trawls and thus not included in the clustering analysis. Species are 

grouped for the purposes of summarizing results in this table, but the clustering analysis was 

conducted on a species-basis. Numbers in bold are proportions that are 0.50 or greater. 

Bottom trawls only shown. 

42
Figure 4. Distribution of trawls making up the five clusters identified with agglomerative 

hierarchical clustering based on species presence/absence in the bottom trawl data (see Table 5, 

Figure 3). The Outer Continental Shelf (OCS) Lease Area is shown in gray shading. 

Demersal fish coefficient of variation 

CVs among trawls of a single type (lined or unlined) were fairly high, ranging from 0.88 to 3.00, 

mostly likely due to small sample size: less than 10 for each net type (Table 9). CVs among all 

trawls, lined and unlined combined, were similarly high with a maximum value of 4.69, likely 

due to the substantial decrease in CPUE in unlined compared to lined nets. Sample size 

approximations for the highest and lowest CVs over a range of deltas (% difference between 

estimated and true mean, (Ott 1993) are shown in Table 10. 

43
Table 9. Coefficients of variation (CV) among bottom trawl CPUE (#/ha) for all fish species 

caught. CVs are shown for lined net trawls in the 100-500 m bottom depth (all towed for 15 

minutes) and unlined net trawls in 40-100 m bottom depth (all towed for 5 minutes), and for all 

trawl nets combined. 

Scientific name 

Common name CV lined net, 

100-500 m (n=9) 

CV unlined net, 

40-100 m (n=9) 

CV all 

trawls 

(n=22) 

Artediellus scaber hamecon 1.59 2.51 

Aspidophoroides olriki Arctic alligatorfish 1.99 3.00 2.92 

Boreogadus saida Arctic cod 1.57 2.76 1.98 

Careproctus sp. cf. rastrinus (Orr, et al.) salmon snailfish 1.56 2.33 

Cottidae sculpin unident. 4.69 

Eleginus gracilis saffron cod 4.69 

Enophrys diceraus antlered sculpin 4.69 

Eumesogrammus praecisus fourline snakeblenny 3.00 3.24 

Eumicrotremus derjugini leatherfin lumpsucker 1.68 2.47 

Gadus macrocephalus Pacific cod 3.00 3.81 

Gymnelus viridis fish doctor 2.28 3.65 

Gymnocanthus tricuspis Arctic staghorn sculpin 3.00 3.27 

Hippoglossoides robustus Bering flounder 1.14 0.88 1.76 

Icelus spatula spatulate sculpin 2.41 2.54 

Liparis fabricii gelatinous seasnail 1.73 3.00 2.85 

Liparis gibbus variegated snailfish 2.49 3.95 

Liparis marmoratus festive snailfish 4.69 

Liparis sp. unid. snailfish 2.66 

Lumpenus fabricii slender eelblenny 3.00 3.29 

Lumpenus maculatus daubed shanny 3.00 4.03 

Lumpenus medius stout eelblenny 2.49 3.80 

Lumpenus sp. unid. eelblenny 4.69 

Lycodes mucosus saddled eelpout 3.00 4.45 

Lycodes polaris Canadian eelpout 1.77 1.99 2.76 

Lycodes raridens marbled eelpout 2.15 3.46 

Lycodes rossi threespot eelpout 1.51 3.00 2.40 

Lycodes sp. unid. eelpout 2.30 3.33 

Mallotus villosus capelin 4.21 

Myoxocephalus verrucosus warty sculpin 3.00 3.00 2.92 

Nautichthys pribilovius eyeshade sculpin 4.69 

Reinhardtius hippoglossoides Greenland turbot 1.58 2.69 

Theragra chalcogramma walleye pollock 1.39 1.68 1.64 

Triglops nybelini bigeye sculpin 3.00 4.69 

Triglops pingeli ribbed sculpin 2.33 3.63 

44
delta zα zβ CV n 

0.2 1.96 1.64 0.88 501 

0.25 1.96 1.64 0.88 321 

0.3 1.96 1.64 0.88 223 

0.4 1.96 1.64 0.88 125 

0.5 1.96 1.64 0.88 80 

0.6 1.96 1.64 0.88 55 

0.2 1.96 1.64 4.69 14253 

0.25 1.96 1.64 4.69 9122 

0.3 1.96 1.64 4.69 6334 

0.4 1.96 1.64 4.69 3563 

0.5 1.96 1.64 4.69 2280 

0.6 1.96 1.64 4.69 1583 

Table 10. Sample size (n) approximations based 

on lowest and highest CVs of bottom trawl CPUE 

(#/ha) observed during the 2008 Beaufort Sea 

survey, for a range of delta values (% difference 

between estimated and true mean, Ott 1993).

Demersal fish distribution maps 

Arctic cod 

The distribution of Arctic cod CPUE by kg/ha is illustrated in Figure 5. The highest CPUE 

(kg/ha) for Arctic cod was found in the 100-500 m depth, in the westernmost half of the survey 

area. Arctic cod CPUE was consistent from west to east (25.83-58.64 kg/ha) along the deepest 

part of the survey area, 300-500 meters. Figure 6 illustrates the distribution of Arctic cod CPUE 

by #/ha and shows similar patterns as CPUE by kg/ha. 

Walleye pollock 

Walleye pollock CPUE distribution by kg/ha (Figure 7) was similar to that of Arctic cod, 

however CPUE (kg/ha) values were an order of magnitude smaller (0-6.47 kg/ha). The highest 

CPUE was found in the western part of the survey area, in the 100-500 m depth, with zero 

catches occurring in the 100-500 m depth in the eastern half of the survey area. Walleye pollock 

CPUE distribution by #/ha is shown in Figure 8, again the distribution is similar to CPUE by 

kg/ha. 

45
Figure 5. Arctic cod CPUE (kg/ha) distribution from the Beaufort Sea survey, 2008, bottom 

trawls only. The Outer Continental Shelf (OCS) Lease Area is shown in gray shading. 

46
Figure 6. Arctic cod CPUE (#/ha) distribution from the Beaufort Sea survey, 2008, bottom 

trawls only. The Outer Continental Shelf (OCS) Lease Area is shown in gray shading. 

47
Figure 7. Walleye pollock CPUE (kg/ha) distribution from the Beaufort Sea survey, 2008, 

bottom trawls only. The Outer Continental Shelf (OCS) Lease Area is shown in gray shading. 

48
Figure 8. Walleye pollock CPUE (#/ha) distribution from the Beaufort Sea survey, 2008, 

bottom trawls only. The Outer Continental Shelf (OCS) Lease Area is shown in gray shading. 

49
Eelpouts (all species combined) 

Eelpouts were the second most abundant species of fish captured in the 2008 Beaufort Sea 

survey. All species of eelpouts were combined and the CPUE (kg/ha) distribution is illustrated 

in Figure 9 and CPUE (#/ha) in Figure 10. Similar to Arctic cod and walleye pollock, the highest 

CPUE both both kg/ha and #/ha occurred in the 100-500 m depth and primarily in the western 

half of the survey area. Zero and low CPUE trawls (0.04-1.89 kg/ha) dominated the 40-100 m 

depth. 

Sculpins (all species combined) 

Sculpin species were combined and the CPUE (kg/ha) distribution over the survey area is shown 

in Figure 11 and CPUE (#/ha) in Figure 12. The trawls with the highest CPUE for sculpins 

(0.50-2.06 kg/ha), were primarily located in the 40-100 m depth. Several zero catches occurred 

in the 100-500 m depth, particularly in the western half of the survey area. Sculpins were found 

across the entire survey area, from west to east. 

50
Figure 9. Eelpouts (all species combined) CPUE (kg/ha) distribution from the Beaufort Sea 

survey, 2008, bottom trawls only. The Outer Continental Shelf (OCS) Lease Area is shown in 

gray shading. 

51
Figure 10. Eelpouts (all species combined) CPUE (#/ha) distribution from the Beaufort Sea 

survey, 2008, bottom trawls only. The Outer Continental Shelf (OCS) Lease Area is shown in 

gray shading. 

52
Figure 11. Sculpins (all species combined) CPUE (kg/ha) distribution from the Beaufort Sea 

survey, 2008, bottom trawls only. The Outer Continental Shelf (OCS) Lease Area is shown in 

gray shading. 

53
Figure 12. Sculpins (all species combined) CPUE (#/ha) distribution from the Beaufort Sea 

survey, 2008, bottom trawls only. The Outer Continental Shelf (OCS) Lease Area is shown in 

gray shading. 

54
Demersal fish biological collections 

Approximately 1,493 Arctic cod from bottom trawls were sexed and lengthed (701 males and 

792 females). In addition, 753 Arctic cod were sexed, lengthed and individually weighed (331 

males, 399 females, 30 unsexed). 

The mean length for both sexes and all trawls combined was 113 mm with both a median and 

mode at 110 mm. The mean length for males was 108 mm and 120 mm for females, for all 

trawls. The median for males was 110 mm and for females it was 120 mm, for all trawls. For 

the lined nets (trawls 1-13), the mean length for males was 112 mm and 128 mm for females. 

The mode for males in the lined trawls was 110 mm and for females, there were 2 modes at 80 

and 150 mm (Figure 13). For the unlined nets (trawls 16-26), the distribution of males and 

females size is similar with a mean of 102 mm for males and 107 mm for females. The mode for 

both males and females in the unlined trawls was 100 mm (Figure 14). Larger sized cod, along 

with the smaller sizes (~100 mm) appear to be distributed primarily in the 100-500 strata (lined 

net, Figure 13) whereas there were very few larger size cod found in the 40-100 mm strata 

(unlined net, Figure 14). 

0

10

20

30

40

50

60

70

80

90

50 70 90 110 130 150 170 190 210 230

fork length (mm)

frequency

male

female

Figure 13. Length frequencies for male and female Arctic cod captured in the lined net 

during the 2008 Beaufort Sea survey, bottom trawls. 

55
0

10

20

30

40

50

60

70

80

90

50 70 90 110 130 150 170 190 220

fork length (mm)

frequency

male

female

Figure 14. Length frequencies for male and female Arctic cod captured in the unlined net 

during the 2008 Beaufort Sea survey, bottom trawls. 

The overall mean individual weight for Arctic cod in bottom trawls was 12 g (both sexes 

combined). The mean individual weight of males was 10 g and of females was 15 g. Some 

differences in the spatial distribution of individual weights for Arctic cod were observed: cod 

were somewhat larger in deeper water (Figure 15), similar to the larger lengths observed in the 

lined nets (Figure 13). The average length and weight for Arctic cod in the 100-500 m depth was 

132 mm and 16 g, whereas the average length and weight for cod in the 40-100 m depth was 102 

mm and 7 g (both sexes combined). In addition, trawls 8 and 9 had the highest individual 

average weights and lengths of cod and the sex ratio was greater than 75% females. Note that 

most of the catch in the 100-500 m depth was from the lined net, and most of the catch in the 40-

100 m depth was from the unlined net. 

56
Figure 15. The average individual weight (g) of Arctic cod from each bottom trawl during the 

2008 Beaufort Sea survey, bottom trawls. Trawl numbers are indicated for each point. The 

Outer Continental Shelf (OCS) Lease Area is shown in gray shading. 

A length-weight relationship for Arctic cod was determined using Ricker’s (1973) model: weight 

(g) =1.47x10-5 × length (mm) 2.8313. Males and females were examined separately, however, 

there was no difference between the estimated model parameters, and therefore sexes were 

combined. These results are illustrated in Figure 16. 

In addition to Arctic cod lengths, lengths were collected from walleye pollock. There were 51 

males, 44 females, and 4 unsexed (Figure 17). The mean fork length for all walleye pollock was 

159 mm, with a median at 150 mm and mode at 130 mm. The mean for male pollock was 155 

mm and 170 mm for females. Walleye pollock from the 2008 Beaufort Sea survey were aged at 

the AFSC and length-at-age is illustrated in Figure 18. For comparison, the lengths of Bering 

Sea walleye pollock collected in 2007 are included in Figure 18. In the Beaufort Sea 2008 

survey, walleye pollock, age 2, occurred most frequently with a range of 110 to 203 mm in 

length. The Beaufort Sea pollock were similar in size to the Bering Sea pollock age 1 (2007 

data), but at ages 2 and older the Beaufort Sea pollock were smaller than Bering Sea pollock. 

57
0

10

20

30

40

50

60

70

80

0 50 100 150 200 250

length (mm)

weight (g)

observed

predicted

Figure 16. The length-weight relationship for Arctic cod from bottom trawls, 

both sexes combined. 

0

2

4

6

8

10

12

80 100 120 140 160 180 200 220 290 320

fork length (mm)

frequency

male

female

Figure 17. Length frequencies of male and female walleye pollock captured in the 

2008 Beaufort Sea survey, bottom trawls. 

58
0

100

200

300

400

500

600

0123456

age (years)

length (mm)

2008 Beaufort sea pollock

2007 Bering sea pollock

Figure 18. Length-at-age for walleye pollock captured in the 2008 Beaufort Sea 

survey (large, orange circles), and 2007 Bering Sea walleye pollock (small, blue 

circles), bottom trawls. Note the age 1 overlap. 

59
Demersal fish geographic comparisons 

The mean CPUE of species from current surveys of the Chukchi and Bering Seas is compared to 

CPUE of species from the Beaufort Sea survey (Table 11). All three surveys used the same 

standardized bottom trawl nets (unlined, 83-112 otter trawl). The Beaufort CPUE data shown are 

only from the unlined net stations. Arctic cod were the most prevalent fish species found in both 

the 2008 Beaufort, and the 1990 Chukchi Sea surveys (Barber et al. 1997). In the Bering Sea, 

walleye pollock was the most abundant fish species in terms of total CPUE, at 61.2 kg/ha 

compared to 0.13 kg/ha in the Beaufort Sea and 0.02 kg/ha in the Chukchi Sea. In addition, the 

flatfish species that were dominant in the Bering Sea (Arrowtooth/Kamchatka flounder, Bering 

flounder, flathead sole, Greenland turbot, northern rock sole, and yellowfin sole) were absent or 

found in low densities in the Chukchi and Beaufort Seas. Saffron cod was most abundant in the 

Chukchi Sea: it was absent from the Beaufort Sea 2008 survey and at very low densities in the 

Bering Sea. 

All fish species captured during the 2008 Beaufort Sea survey are listed in Table 12, along with 

the presence or absence of those species caught during the 1990 Chukchi Sea survey (Barber et 

al. 1997). Presence/absence of fish in the Bering Sea is based on AFSC surveys conducted in 

1984-2008 and taxonomy expertise (James Orr AFSC, pers. com.). Note: Species Liparis 

tunicatus and Lycodes seminudus occurred in the Beaufort Sea survey; however, there are no 

associated weights or numbers because they were not identified in the field, but in the laboratory 

from vouchers. They are listed in this table for ecosystem presences.

 

60
Beaufort Sea 20081 Chukchi Sea 19902 Bering Sea 20083 Species Common Name CPUE (kg/ha) CPUE (kg/ha) CPUE (kg/ha) 

Arctic cod 6.12 3.02 1.04 Arrowtooth/Kamchatka flounder * * 11.87 Bering Flounder 0.11 0.18 0.45 

Cottidae (sculpin family) 0.03 0.76 4.22 

Flathead sole * * 10.81 Greenland turbot * <0.01 0.27 

Northern rock sole * * 41 

Pacific cod * 0.12 8.65 Saffron cod * 0.39 <0.01 

Walleye pollock 0.13 0.02 61.2 Yellowfin sole * * 42.4 

Zoarcidae (eelpout family) 0.03 0.21 0.5 

1 Beaufort Sea 2008 Survey 2 Barber et al., 1997 3 Eastern Bering Sea 2008 survey (Jason Conner, AFSC, pers. com.) Table 11. Mean CPUE (kg/ha) of common species found in the Beaufort, Chukchi and Bering Seas. The CPUE reported for the Beaufort Sea is from the bottom trawl, unlined nets only. An asterisk indicates that 

there was no catch of that species. 

61
Scientific Name Common Name Beaufort Sea1 Chukchi Sea2 Bering 

Artediellus scaber hamecon * * * Aspidophoroides olriki Arctic alligatorfish * * * Boreogadus saida Arctic cod * * * Careproctus sp. cf. rastrinus (Orr et al.) salmon snailfish * * 

Cottidae sculpin family * * * 

Eleginus gracilis saffron cod * * * Enophrys diceraus antlered sculpin * * * Eumesogrammus praecisus fourline snakeblenny * * * Eumicrotremus derjugini leatherfin lumpsucker * 

Gadus macrocephalus Pacific cod * * * 

Gymnelus viridis fish doctor * * * Gymnocanthus tricuspis Arctic staghorn sculpin * * * Hippoglossoides robustus Bering flounder * * * Icelus spatula spatulate sculpin * * * Liparis fabricii gelatinous seasnail * * 

Liparis gibbus variegated snailfish * * * 

Liparis marmoratus festive snailfish * * 

Liparis tunicatus kelp snailfish * * * Liparis sp. unid. snailfish * * * Lumpenus fabricii slender eelblenny * * * Lumpenus maculatus daubed shanny * * 

Lumpenus medius stout eelblenny * * * Lumpenus sp. unid. eelblenny * * * Lycodes mucosus saddled eelpout * * * Lycodes polaris Canadian eelpout * * * Lycodes raridens marbled eelpout * * * Lycodes rossi threespot eelpout * * 

Lycodes seminudus longear eelpout * Lycodes sp. unid. eelpout * * * 

Mallotus villosus capelin * * * Myoxocephalus verrucosus warty sculpin * * * Nautichthys pribilovius eyeshade sculpin * * * 

Reinhardtius hippoglossoides Greenland turbot * * * Theragra chalcogramma walleye pollock * * * Triglops nybelini bigeye sculpin * Triglops pingeli ribbed sculpin * * * 

Table 12. Fish species presence/absence for the Beaufort, Chukchi and Bering Seas. An asterix represents spec

present and blank space represents species absent. Sources are: 1Beaufort Sea 2008 survey, 2Barber et al., 1997

3Eastern Bering Sea 1984-2008 surveys (Jason Conner and Jay Orr, AFSC, pers. com.)

62
Demersal fish historical comparisons 

The most recent previous survey of Beaufort Sea offshore marine fish was conducted during 

1976-1977 (Frost and Lowry 1983). The Frost and Lowry (1983) survey took place in 1977 

from August 2nd until September 3rd. There was a nearshore (<10 m water depth) marine fish 

survey that took place in the central/eastern Beaufort Sea in 1988-1990 (Jarvela and 

Thorsteinson 1999), but because the survey was in habitat shallower than the current survey the 

data are not useful for a historical comparison of the occurrence of fish species in the offshore 

habitat. Of the 34 species captured and identified from the 2008 Beaufort Sea survey, 17 of 

those species had also been documented in the 1976-77 survey (Table 13). Although CPUE was 

not calculated during the earlier survey, the number of fish caught was recorded at each station. 

Arctic cod (Boreogadus saida) was the most numerous fish species found in both surveys. 

Bering flounder (Hippoglossoides robustus) and walleye pollock (Theragra chalcogramma) 

were fairly abundant relative to other species in the 2008 survey but were not observed during 

the 1977 survey. Pacific cod (Gadus macrocephalus), festive snailfish (Liparis marmoratus), 

eyeshade sculpin (Nautichthys pribilovius) and bigeye sculpin (Triglops nybelini) were caught in 

small numbers compared to other species during the 2008 survey and were absent from the 1977 

survey. 

Eelpouts were common during both surveys, but different species were dominant: marbled 

eelpouts (Lycodes raridens) were the most abundant eelpout in the 2008 survey, whereas 

Canadian eelpouts (Lycodes polaris) and fish doctors (Gymnelus viridis) were most abundant in 

the 1977 survey. Snailfish were a fairly common species during both surveys. Variegated 

(Liparis gibbus) and gelatinous seasnail (Liparis fabricii) were the most abundant snailfish 

species in the 2008 survey, but unfortunately the snailfish were not identified to species in the 

1977 survey. Sculpins were caught during both surveys, but they appeared to be ranked higher 

in abundance during the 1977 survey. In addition, different species were apparantly caught: 

warty (Myoxocephalus verrucosus) and ribbed sculpin (Triglops pingeli) were most common 

during the 2008 survey and spatulate (Icelus spatula) and twohorn sculpin (Icelus bicornis) were 

the dominant species during the 1977 survey. In fact, the twohorn sculpin was the third most 

prevelant species in the 1977 survey and did not occur in the 2008 survey. Arctogadus glacialis

(polar cod) was likewise caught during the 1977 survey but not the 2008 survey. Only 1 polar 

cod was recorded in the 1977 survey. 

63
Scientific Name Common Name 2008 survey mean CPUE (#/ha) 2008 survey no. of stations 1977 survey No. individual

Arctogadus glacialis polar cod 1 Artediellus scaber hamecon 6 9 30 

Aspidophoroides olriki Arctic alligatorfish 2 6 19 Boreogadus saida Arctic cod 1,303 22 194 

Careproctus sp. cf. rastrinus (Orr et al.) salmon snailfish 1 6 

Cottidae sculpin family 3 1 

Eleginus gracilis saffron cod 1 1 

Enophrys diceraus antlered sculpin 1 1 

Eumesogrammus praecisus fourline snakeblenny 1 2 4 

Eumicrotremus derjugini leatherfin lumpsucker 1 4 29 Gadus macrocephalus Pacific cod 1 2 

Gymnelus viridis fish doctor 1 2 23 

Gymnocanthus tricuspis Arctic staghorn sculpin 3 3 2 

Hippoglossoides robustus Bering flounder 4 16 

Icelus bicornis twohorn sculpin 74 

Icelus spatula spatulate sculpin 1 4 14 Liparis fabricii gelatinous seasnail 2 5 

Liparis gibbus variegated snailfish 2 1 

Liparis marmoratus festive snailfish 1 1 

Liparis sp. unid. snailfish 1 4 29 Lumpenus fabricii slender eelblenny 1 2 11* 

Lumpenus maculatus daubed shanny 1 2 1 

Lumpenus medius stout eelblenny 2 3 1 Lumpenus sp. unid. eelblenny 1 1 

Lycodes mucosus saddled eelpout 1 2 2 

Lycodes polaris Canadian eelpout 12 8 81 

Lycodes raridens marbled eelpout 24 5 7 Lycodes rossi threespot eelpout 1 4 2* 

Lycodes sp. unid. eelpout 2 3 

Mallotus villosus capelin 1 2 

Myoxocephalus verrucosus warty sculpin 2 5 

Nautichthys pribilovius eyeshade sculpin 1 1 

Reinhardtius hippoglossoides Greenland turbot 3 5 

Theragra chalcogramma walleye pollock 23 17 

Triglops nybelini bigeye sculpin 1 1 

Triglops pingeli ribbed sculpin 8 6 2 

Table 13. Fish species from the 2008 Beaufort Sea survey, bottom trawls, (CPUE in #/ha from all nets combined) compared to the previous Beaufort Sea survey in 1977 by Frost and Lowry (1983). * found in 1976 survey but not in 1977 survey 

64
Benthic invertebrates

Benthic invertebrate abundance 

Invertebrates made up 94% of the total weight in the bottom trawls and 174 taxa were identified. 

Similar to fish, all invertebrates were identified to the lowest taxonomic level possible in the 

field (family, genus or species). Species identifications are preliminary and will be confirmed in 

the laboratory pending further funding. Not all invertebrate species are typically enumerated 

(such as corals and ascidians) so the summary table only shows total catch weight and not 

number. Of the invertebrates, Ophiura sarsi (notched brittle star) made up 41% and 

Chionoecetes opilio (opilio crab) made up 10% of the total weight (kg). The catch of the 24 taxa 

that comprised 94% of the total invertebrate weight is shown in Table 14. 

Species Name Common name Total weight (kg) 

Ophiura sarsi notched brittle star 9775.93 

Chionoecetes opilio opilio crab 3916.96 

Musculus spp. mussels 1424.95 

Ctenodiscus crispatus mud star 940.07 

Actiniaria sea anenomes 488.22 

Strongylocentrotus sp. sea urchin 418.61 

Psolus fabricii sea cucumber 352.89 

Buccinum polare polar whelk 213.27 

Pyrulofusus spp. whelk 204.23 

Gorgonocephalus arcticus basket starfish 168.16 

Neptunea spp. whelk 154.28 

Golfingia margaritacea worm 149.47 

Gersemia rubiformis soft coral 125.35 

Psolus phantapus sea cucumber 123.21 

Halocynthia aurantium ascidian 114.99 

Stomphia sp. anemone 110.07 

Pagurus rathbuni hermit crab 83.03 

Naticidae moon snails 70.74 

Buccinum glaciale glacial whelk 67.68 

Margarites spp. snail 67.00 

Hyas coarctatus lyre crab 58.42 

Buccinum spp. whelk 56.62 

Pagurus trigonocheirus hermit crab 49.44 

Brada spp. polychaete 49.29 

Table 14. The 24 most abundant invertebrate taxa captured in the bottom trawls 

during the 2008 Beaufort Sea survey, ranked by total weight (all trawls 

combined). Species identifications are preliminary.

65
The CPUE for the 24 most abundant invertebrate taxa are shown in Table 15. The top three taxa 

by CPUE weight in the 40-100 m depth were Halocynthia arurantium (ascidian), Psolus fabricii

(sea cucumber), and Ctenodiscus crispatus (mud star). In the 100-500 m depth, the top three 

species by CPUE weight were Ophiura sarsi (notched brittle star), Chionoecetes opilio (opilio 

crab), and Musculus spp. (mussels). 

Mean CPUE in both numbers and weight (± 1 SD) was greater for catches made with the lined 

versus the unlined survey net (Table 16). The mean CPUE by weight for only a few taxa 

captured in the unlined net was higher or similar to the CPUE in the lined net: Halocynthia 

aurantium (ascidian), Pagurus trigonocheirus (hermit crab), and Hyas coarctatus (lyre crab). 

The CPUE by numbers of the two crab species was much lower in the unlined net, suggesting 

larger organisms were caught with the unlined net. 

The CPUE of invertebrates for the paired trawls are summarized in Table 17. The difference in 

CPUE between the lined and unlined survey nets was even more dramatic for invertebrates than 

it was for fish catches. For virtually all species, the CPUE was higher at the same location fished 

with a lined net compared to an unlined net. For example, the CPUE for Ophiura sarsi (notched 

brittle star) sampled with a lined net was 696.47 kg/ha compared to using an unlined net at the 

same location, <0.01 kg/ha. 

Total invertebrate biomass estimated for both depths combined was 247,639 t, with 23,660 t in 

the 40-100 m depth and 223,979 t in the 100-500 m depth. The invertebrate with the largest 

estimated biomass was Ophiura sarsi (notched brittle star) (Table 18). The most prevalent 

invertebrate in the 40-100 m depth was Halocynthia aurantium (ascidian) and this species did 

not occur in the 100-500 m depth. In the 100-500 m depth, Chionoecetes opilio (opilio crab) had 

the second highest biomass. 

66
Species Name Common name 

Mean CPUE (#/ha) 40-100 m depth (unlined net) 

Mean CPUE (#/ha) 100-500 m depth (lined net) 

Mean CPUE (kg/ha) 40-100 m depth (unlined net) 

M((

Ophiura sarsi notched brittle star 67 343,266 0.17 4

Chionoecetes opilio opilio crab 6 1,127 0.31 

Musculus spp. mussels 0 10,461 0 6

Ctenodiscus crispatus mud star 497 2,989 2.96 3Actiniaria sea anemones 0 135 0 2

Strongylocentrotus sp. sea urchin 47 414 1.43 

Buccinum polare polar whelk 0 1,051 0 9

Pyrulofusus spp. whelk 2 172 0.08 9

Gorgonocephalus arcticus basket starfish 0 32 0 

Golfingia margaritacea worm < 1 4,447 < 0.01 6Neptunea spp. whelk 9 156 0.42 5Psolus phantapus sea cucumber 0 81 0 5

Stomphia sp. anemone 23 143 0.93 4

Psolus fabricii sea cucumber 131 181 4.44 3

Pagurus rathbuni hermit crab 5 889 0.06 3

Naticidae moon snails 0 516 0 3Buccinum glaciale glacial whelk 1 139 0.03 2

Buccinum spp. whelk < 1 289 < 0.01 2

Margarites spp. snail < 1 1,350 < 0.01 2

Gersemia rubiformis. soft coral * * 0.04 2

Brada spp. polychaete 0 839 0 2Hyas coarctatus lyre crab 41 99 1.24 

Pagurus trigonocheirus hermit crab 90 6 1.73 0

Halocynthia aurantium ascidian * * 11.85 0 

Table 15. Mean CPUE in numbers and weight of the top 24 invertebrate taxa that were caught during the 2008 Be

by bottom depth strata. Species identifications are preliminary. (Note: trawls 11, 12, and 13 are not included in these results 

lined net in the 40-100 m stratum). 

* = species typically not counted 

67
Species Name Common name Mean CPUE (#/ha) lined net Mean CPUE (#/ha) unlined net Mean CPUE (kg/ha) lined net Mean 

(kg/ha

Ophiura sarsi notched brittle star 286,277 61 337.61 0.16 

Chionoecetes opilio opilio crab 996 8 86.54 0.47 

Musculus spp. mussel 8,718 < 1 50.12 < 0.01 Ctenodiscus crispatus mud star 4,122 454 34.73 2.7 Actiniaria sea anemones 112 0 15.76 0 

Strongylocentrotus sp. sea urchin 281 122 12.23 4.95 

Psolus fabricii sea cucumber 526 118 11.97 4.0 Buccinum polare polar whelk 872 6 7.36 0.06 

Pyrulofusus spp. whelk 144 2 6.28 0.07 Neptunea spp. whelk 178 9 5.32 0.40 

Gorgonocephalus arcticus basket starfish 26 < 1 5.28 < 0.01 

Golfingia margaritacea worm 3,706 < 1 4.78 < 0.01 

Gersemia rubiformis soft coral * * 4.66 0.04 

Psolus phantapus sea cucumber 69 0 3.88 0 Stomphia sp. anemone 125 26 3.25 1.13 Pagurus rathbuni hermit crab 800 8 2.92 0.07 

Naticidae moon snails 432 1 2.50 0.01 Margarites spp. snail 1,254 < 1 2.36 < 0.01 

Buccinum glaciale glacial whelk 115 3 2.20 0.06 

Buccinum spp. whelk 241 < 1 2.08 < 0.01 

Brada spp. polychaete 699 < 1 1.83 < 0.01 

Hyas coarctatus lyre crab 155 37 1.69 1.52 Pagurus trigonocheirus hermit crab 255 83 1.32 1.57 

Halocynthia aurantium ascidian * * 0.56 10.69 

Table 16. Mean CPUE numbers and weight of the top 24 invertebrate taxa caught in lined vs. unlined nets during Beaufort Sea survey. Species identifications are preliminary.

* = species typically not counted 

68
Species Name Common name 

CPUE (kg/ha) lined trawl 10 (100-500 m) 

CPUE (kg/ha) unlined trawl 22 (100-500 m) 

CPUE (kg/ha) lined trawl 12 (40-100 m) 

Ophiura sarsi notched brittle star 696.47 < 0.01 0.77 Strongylocentrotus sp. sea urchin 142.97 36.68 1.81 Pyrulofusus spp. whelk 21.78 0 0 

Margarites spp. snail 18.87 0.01 0.05 

Ctenodiscus crispatus mud star 15.29 0.38 0 

Chionoecetes opilio opilio crab 14.82 1.96 0.06 Stomphia sp. anemone 9.41 2.89 1.49 

Pagurus rathbuni hermit crab 6.6 0.23 0.05 

Buccinum polare polar whelk 4.11 0.6 0 

Buccinum glaciale glacial whelk 3.01 0.33 0 Naticidae moon snails 1.18 0.11 0 

Brada spp. polychaet 0.49 < 0.01 0 Gersemia rubiformis soft coral 0.34 0.05 1.01 Hyas coarctatus lyre crab 0.17 0 3.85 Neptunea spp. whelk 0.14 0.15 9.29 Musculus spp. black mussel 0.08 < 0.01 0 

Pagurus trigonocheirus hermit crab 0.08 0.19 7.46 

Actiniaria sea anemones 0 0 0 Psolus fabricii sea cucumber 0 0.02 41.92 Gorgonocephalus arcticus basket starfish 0 0 0 

Golfingia margaritacea worm 0 0 0 

Psolus phantapus sea cucumber 0 0 0.53 

Buccinum spp. whelk 0 0 0.06 

Halocynthia aurantium ascidian 0 0.31 6.42 

Table 17. CPUE for the top 24 invertebrate taxa caught in the paired comparison trawls. The two pairs were traw

trawls 12 and 24. Species identifications are preliminary. 

* = species typically not counted 

69
Species Name Common name Biomass estimate (t) 

40-100 m depth 

Biomass estimate (t) 

100-500 m depth 

Ophiura sarsi notched brittle star 70 127,332 

Chionoecetes opilio opilio crab 124 32,580 

Musculus spp. mussels 0 18,935 

Ctenodiscus crispatus mud star 1,207 8,911 

Actiniaria sea anemones 0 5,596 

Strongylocentrotus sp. sea urchin 581 4,533 

Buccinum polare polar whelk 0 2,781 

Pyrulofusus spp. whelk 34 2,772 

Gorgonocephalus arcticus basket starfish 0 2,348 

Golfingia margaritacea worm 2 1,806 

Neptunea spp. whelk 172 1,530 

Psolus phantapus sea cucumber 0 1,450 

Stomphia sp. anemone 380 1,174 

Psolus fabricii sea cucumber 1,808 1,080 

Pagurus rathbuni hermit crab 23 970 

Naticidae moon snails 0 939 

Buccinum glaciale glacial whelk 11 822 

Buccinum spp. whelk 1 783 

Margarites spp. snail 0 766 

Gersemia rubiformis. soft coral 15 722 

Brada spp. polychaete 0 692 

Hyas coarctatus lyre crab 505 311 

Pagurus trigonocheirus hermit crab 703 12 

Halocynthia aurantium ascidian 4,826 0 

Table 18. Biomass of invertebrate taxa caught during the 2008 Beaufort Sea survey, 

extrapolated to bottom depth area. Species identifications are preliminary. (Note: trawls 11, 

12, and 13 are not included in these results as they were with a lined net at the 40-100 m depth). 

70
Benthic invertebrate distribution 

Notched brittle star (Ophiura sarsi) 

A distribution map of CPUE for Ophiura sarsi (notched brittle star), showed the highest CPUE 

in the 100-500 m depth range with a fairly similar CPUE from west to east across the study area 

(Figure 19). 

Opilio crab 

The highest CPUE for Chionoecetes opilio (opilio crab) was likewise found in the 100-500 m 

depth (Figure 20). However, the largest catches (kg/ha) occurred in the western portion of the 

study area. In contrast, CPUE varied little by longitude in the 40-100 m depth (0.01-14.82 

kg/ha). 

The legal size for opilio crab fished in the Bering Sea is 78 mm carapace width, and a map of the 

distribution of crab above this limit would be of interest. However, individual crab were not 

measured and weighed from all trawls. Eighty-six Chionoecetes opilio (both males and females 

with eggs) from three trawls and 50 Hyas coarctatus (both males and females) from two trawls 

were weighed, measured and collected as part of a special project on Bitter Crab Syndrome 

(BCS). Because individual opilio crab were not lengthed and weighed from every trawl, a 

length-weight relationship dervied from the BCS project data was used to deduce the expected 

weight of a crab above 78 mm carapace width. Female crab carapace width ranged from 58-78 

mm (n=16), and male carapace width ranged from 55-119 mm (n=70). Average individual crab 

weight for all trawls was calculated from total crab catch weight and numbers. The carapace 

width vs. weight of Chionoecetes opilio (male and female combined) is shown in Figure 21. 

Using this relationship, it was estimated that most crabs with a weight above 0.11 kg would have 

been greater than 78 mm. The distribution for average individual weight of crab is shown in 

Figure 22. The crabs with average weights greater than 0.11 kg were found only in the 100-500 

m depth. In addition, the depth range can be narrowed to trawls that occurred between 306-478 

m. In the 40-100 m depth, crab average weight varied little and ranged between 0.02-0.10 kg. 

71
 

Figure 19. Distribution of Ophiura sarsi (notched brittle star) CPUE (kg/ha) from the 

Beaufort Sea survey, 2008, bottom trawls. The Outer Continental Shelf (OCS) Lease Area is 

shown in gray shading. 

72
Figure 20. Distribution of Chionoecetes opilio (opilio crab) CPUE (kg/ha) from the Beaufort 

Sea survey, 2008, bottom trawls. The Outer Continental Shelf (OCS) Lease Area is shown in 

gray shading. 

73
0

0.1

0.2

0.3

0.4

0.5

0.6

0.7

0.8

0 20 40 60 80 100 120 140

carapace width (mm)

weight (kg)

Commercial size 

n=86 

Legal size

Figure 21. Chionoecetes opilio (opilio crab) weight (kg) vs. carapace 

width (mm). Legal crab size is 78 mm (red line) and commercial size 

starts at 101 mm (red line). This figure includes males and females. 

Female width ranged from 58-78 mm and male carapace width ranged 

from 55-119 mm. 

74
75

Figure 22. Distribution map of Chionoecetes opilio (opilio crab) average individual weight 

from the Beaufort Sea survey, 2008, bottom trawls. The Outer Continental Shelf (OCS) 

Lease Area is shown in gray shading. 
Pelagic fish data analysis

Pelagic fish midwater trawls 

Twenty-eight midwater trawls were completed during the acoustic survey (Figure 1 and Table 

19). Depth terminology used in the pelagic fish data analysis is analogous to the bottom depth 

terminology used in the demersal trawl data analysis section. Of the twenty-eight trawls, seven 

were completed in the 20-40 m depth (referring to bottom depth), six in the 40-100 m depth 

(referring to bottom depth), and 15 in the 100-500 m depth (referring to bottom depth). All but 

two midwater trawl catches weighed <50 kg total. Midwater trawls were used to identify fish 

species within aggregations observed on echograms, to sample species-specific length 

frequencies, and to proportion the backscattered energy by species or age group for echo 

integration. Net catch composition was considered representative of the fish community but not 

quantitative. Midwater trawls were therefore not used as quantitative estimates of biomass and 

no measures of CPUE were calculated for midwater trawl catches. 

Midwater 

trawl no. 

Latitude 

(DD) 

Longitude 

(DD) 

Bottom depth 

(m) 

Headrope depth 

(m) 

101 71.88 -154.97 263 232 

102 71.89 -154.95 316 219 

103 71.74 -154.99 193 178 

104 71.90 -153.91 191 41 

105 71.81 -153.92 190 35-55 

106 71.81 -154.46 190 175 

107 71.98 -154.41 45 20 

108 71.72 -152.84 30 25 

109 71.66 -152.49 25 15 

110 71.52 -152.25 40 34 

111 71.75 -153.94 210-300 180-230 

112 71.69 -154.52 24 15 

113 71.48 -153.96 56 35-55 

114 71.39 -153.99 52 41 

115 71.25 -153.13 230-310 198 

116 71.25 -153.11 47 40 

117 71.37 -153.07 25 17 

118 71.46 -153.04 224-442 23 

119 71.16 -152.23 200 185 

120 71.28 -152.31 35 26 

121 71.35 -151.99 62 15 

122 71.51 -152.20 225 215 

123 71.58 -155.05 400 271 

124 71.68 -154.48 385 300 

125 71.53 -152.89 25 17 

126 71.55 -153.48 20 17 

127 71.66 -155.00 100 47 

128 71.82 -154.98 330 240-320 

Table 19. Midwater trawl number, latitude and longitude (decimal degrees), 

and headrope depth (m). 

76
Arctic cod dominated midwater trawl catches in all depth strata (Figure 23). Yearling-and-older 

(year-plus) Arctic cod catches contained <1% “other” fish species which were identified 

snailfish, unidentified poacher, and capelin (Mallotus villosus). Arctic cod young-of-the-year 

(YOY) dominated midwater trawl catches in the 20-40 m depth, were a large (>20%) component 

of the catch within the 40-100 m depth, and were present (12%) in the single near-surface tow 

within the 100-500 m depth. Unidentified sculpin (Family Cottidae) constituted <20% of the 

catch in the 20-40 m depth, 10-70% of the catch in the 40-100 m depth, and dominated (77%) the 

single near-surface tow in the 100-500 m depth. Eelblenny (Lumpenus sp.) were <5% of the 

catch in all trawl catches except a single trawl within the 20-40 m depth and the single nearsurface tow in the 100-500 m depth. 

 

Figure 23. Midwater trawl location and catch composition for young-of-the-year (YOY) Arctic 

od, yearling-and-older (YAO) Arctic cod, YOY Cottidae (sculpin family), YOY Lumpenus sp.

unidentified eelblenny), and other species. The Outer Continental Shelf (OCS) Lease Area is 

hown in gray shading. 

c

(

s

77
Fork lengths of the three most abundant YOY species (Arctic cod, Cottidae, and Lumpenus sp.) 

ranged from 25 mm to 60 mm (n=671) with a weighted mean length of 39.7 mm. Of these, 

Arctic cod lengths ranged from 30-60 mm (n=316, Figure 24), Cottidae from 25-50 mm (n=286, 

Figure 25), and Lumpenus sp. from 30-60 mm (n=69, Figure 26). When YOY Arctic cod length 

samples were stratified by depth, mean lengths were 42.2 mm in the 20-40 m depth, 42.8 mm in 

the 40-100 m depth, and 42.3 mm in the 100-500 m depth. As the fork length-to-weight 

relationship for Arctic cod (developed in this study) did not include data from YOY fish, we 

calculated a mean weight of 0.37 g for YOY using midwater trawl subsamples. 

Yearling-and-older Arctic cod fork lengths from midwater trawl catches ranged from 65 to 190 

mm (n=1474, Figure 24). The overall weighted mean length for year-plus Arctic cod was 104.3 

mm. Fish caught within the 40-100 m depth were larger (116.2 mm weighted mean fork length) 

compared to the 100-500 m depth (102.5 mm weighted mean fork length). Using the fork length 

to weight relationship, the mean weight for year-plus Arctic cod in the 40-100 m depth was 

10.35 g and 7.27 g in the 100-500 m depth. 

0

10

20

30

40

20 40 60 80 100 120 140 160 180 200

Fork length (mm)

Percent frequency

 

Figure 24. Young-of-the-year (YOY) Arctic cod length 

frequencies collected in midwater trawls (n=316), measured to 

a 1 mm resolution (light blue bars). Yearling-and-older 

(YAO) Arctic cod length frequencies collected in midwater 

trawls (n=1474). YAO were measured to a 1 cm resolution 

(dark blue bars). 

78
0

10

20

30

40

50

60

70

20 40 60 80 100 120 140 160 180 200

Fork length (mm)

Percent frequency

Figure 25. Young-of-the-year (YOY) sculpin (Cottidae) length 

frequencies collected in midwater trawls (n=286). YOY were 

measured to a 1 mm resolution. 

0

10

20

30

40

20 40 60 80 100 120 140 160 180 200

Fork length (mm)

Percent frequency

Figure 26. Young-of-the-year (YOY) eelblenny (Lumpenus sp.) 

length frequencies collected in midwater trawls (n=69). YOY 

were measured to a 1 mm resolution. 

79
Backscatter 

Young-of-the-year (YOY) fish (varying proportions of Arctic cod, Cottidae, and Lumpenus sp.) 

and year-plus Arctic cod were detected throughout the study area. Midwater trawl catches used 

for target identification confirmed that year-plus Arctic cod were found in large schools in water 

<75 m deep (Figure 27a) and in bottom-associated layers that extended as a pelagic layer into the 

midwater in water depths greater than 75 m (Figure 27c). Young-of-the-year (YOY) were 

observed throughout the water column in water depths <75 m (Figure 27b) and in surfaceassociated layers in water depths 75 m (Figure 27c). 

80
a) YAO Arctic cod schools in shallow water (60 m) 

b) YOY Arctic cod in shallow water (25 m) (likely with small numbers of Cottidae and 

Lumpenus sp.) in shallow water (25 m),

c) YOY Arctic cod in surface water (<75 m), and yearling-and-older Arctic cod 

extending off bottom into the pelagic zone in water >300 m. 

Figures 27a-c. Example acoustic echograms (Sv threshold = -80 dB) for young-of-year. Backscatter 

is shown as high (red) to low (grey). Vertical lines occur at 1 km intervals and horizontal lines at 50 

m intervals. The bottom and below is shown in black and includes 0.5 m “deadzone” that cannot be 

accurately used in the acoustic analysis. 

81
Target strength 

Target strength results suggested that year-plus Arctic cod are often found in dense aggregations 

(see “Methods” Nv index). . Single target detections for the 100-500 m depth depth suggested 

that target strength did not change with depth (Figure 28). 

-90 -80 -70 -60 -50 -40

200

150

100

Target strength (dB)

Target depth (m)

-90 -80 -70 -60 -50 -40

200

150

100

Target strength (dB)

Target depth (m)

Figure 28. Depth distribution (m) and target strength 

(dB) of single targets detected between 100 m and the 0.5 

m bottom exclusion line for midwater trawl no. 24. 

Target strength minimum threshold was -90 dB (see 

Methods). 

In the target strength to fork length regression equations, the equation that excluded the two 

outlying year-plus Arctic cod points and used a flexible intercept (Target 

Strength=8.03×log10(Length)-60.78) is considered the most appropriate equation for this study 

(Figure 29). Figure 29 also illustrates how the relationship used in this study compares with 

other general and Arctic cod-specific target strength to length relationships. It is likely that 

regression equations in the literature were developed with year-plus -sized individuals only. 

82
g g g

Length (cm)

-65

-60

-55

-50

-45

Target Strength (dB)

Crawford & Jorgenson 

Anon. 1988 

Gjosaeter 

Mamylov <15 cm

Mamylov >15 cm 

YAO TS

YOY TS

20log(L)-71.8

5.27log(L)-58.95

8.03log(L)-60.78

20log(L)-71

2 4 6 8 10 12 14 16 18 20

Figure 29. Target strength to length (cm) relationship for Arctic cod. Year-plus 

target strength (YAO TS) and YOY TS data are from this study. The equations for 

Crawford and Jorgenson, Anon (1988), and Gjosaeter are presented in Crawford 

and Jorgenson (1996). The Mamylov (for polar cod) equation is from Mamylov 

(2003). All points and equations derived from this study are shown in black. 

83
Density distribution, mean density, and abundance 

Densities of year-plus Arctic cod and YOY fish varied throughout the study area. Arctic cod 

year-plus densities ranged from 0 to 155,052 #/ha, with the highest densities found along the 

continental slope observed during the east-west cross-transects (Figure 30). Using only alongtransect data from cluster sampling estimates, year-plus Arctic cod densities ranged from 0 

to10,693 #/ha in the 40-100 m depth and 0 to 155,052 #/ha in the 100-500 m depth (Figure 30). 

No year-plus Arctic cod were estimated in the 20-40 m depth (Figure 30) as they were not visible 

on the acoustics and trawling confirmed little to no year-plus Arctic cod in this depth depth. 

Little to no year-plus Arctic cod were detected with either acoustics or trawls in 20-40m depths. 

Yearling-and-older Arctic cod densities were highest at depths greater than 100 m wi th the 

highest values in the 150-300 m depth range (Figure 31). 

Figure 30. Density distribution of yearling-and-older (YAO) Arctic cod along acoustic 

transects and cross-transects. Density is shown as #/ha. The Outer Continental Shelf (OCS) 

Lease Area is shown in gray shading. 

84
0

100

200

300

400

500

0 60,000 120,000 180,000

Density (fish/ha)

Bottom depth (m)

Figure 31. Yearling-and-older (YAO) Arctic cod density 

(#/ha) versus bottom depth (m) for 1 km analytic bins 

(n=209 analytic bins with non-zero values) used in cluster 

sampling and abundance estimates. 

Young-of-the-year (YOY) fish densities ranged from 4 to 160,553 #/ha (Figure 32). The highest 

densities were detected inshore along the east-west cross-transects (Figure 32). Along-transect 

estimates of YOY densities used in cluster sampling estimates were 119 to 25,170 #/ha in the 20-

40 m depth, 38 to 22,086 #/ha in the 40-100 m depth, and 4 to 21,830 in the 100-500 m depth 

(Figure 32). As mean lengths of Arctic cod YOY were larger than those of Cottidae or 

Lumpenus sp., expected mean target strengths of Arctic cod would also be larger, and therefore 

resulting density estimates of YOY using the YOY Arctic cod mean target strength are 

conservative estimates of Cottidae or Lumpenus sp. densities. Densities of YOY fish were 

highest in water depths <100 m, but some high density values were observed in surface layers in 

regions with bottom depths greater than 150 m (Figure 33). 

85
Figure 32. Density distribution of young-of-the-year (YOY) fish (assumed to be dominated 

by Arctic cod) along acoustic transects and cross-transects. Density is shown as #/ha. The 

Outer Continental Shelf (OCS) Lease Area is shown in gray shading. 

86
0

100

200

300

400

500

0 10,000 20,000 30,000

Density (fish/ha)

Bottom depth (m)

Figure 33. Young-of-the-year (YOY) fish density (#/ha), 

versus bottom depth (m) for for 1 km analytic bins (n=489 

analytic bins with non-zero values) used in cluster sampling 

and abundance estimates. 

Cluster sampling estimates of mean fish densities suggest that year-plus Arctic cod and YOY 

fish (assumed to be dominated by Arctic cod) had different distributions in the study area. The 

highest mean density (Table 20, 9580 ± 926 #/ha, mean ± 1 SD) for YOY fish was found within 

the 20-40 m depth depth. Mean YOY fish densities were similar between the 40-100 m depth 

(4342 ± 649 #/ha) and the 100-500 m depth (4706 ± 1296 #/ha), with the higher standard 

deviation in the 100-500 m depth attributed to patchiness in the near-surface distribution (Table 

20). Yearling-and-older (year-plus) Arctic cod had the highest mean density (9387 ± 1768 #/ha) 

in the 100-500 m depth, with a lower and more variable density (2354 ± 1436 #/ha) within the 

40-100 m depth depth (Table 20). The higher standard deviation can be explained by the fact 

that year-plus Arctic cod within the 40-100 m depth were generally found within patchilydistributed schools (Figures 27a-c) and therefore many zero (i.e. no year-plus fish detected) 

values were included in estimates of mean density for the 40-100 m depth. No estimate of yearplus Arctic cod was made for the 20-40 m depth as no year-plus were observed on the acoustic 

echograms. Midwater trawling confirmed that year-plus Arctic cod were present in low numbers 

in the 20-40 m depth depth. Six large year-plus Arctic cod schools were observed in the 40-100 

m depth depth (Figure 32) during the systematic acoustic survey, but we can only speculate that 

this region is important for feeding and/or has desirable physical characteristics. Our survey and 

sampling effort was not sufficient to allow the fine-scale sampling needed to evaluate why yearplus Arctic cod were schooled in the 40-100 m depth. 

87
Age-class Bottom 

Depth 

(m) 

# Clusters Range 

elements

Mean density 

(#/ha) 

Standard 

deviation 

CV 

YOY 20-40 7 14-38 9580 926 0.10 

40-100 7 12-50 4342 648 0.15 

100-

500 

7 11-27 4706 1296 0.28 

year-plus 20-40 n/a 

40-100 7 12-50 2354 1436 0.61 

100-

500 

7 11-27 9387 1768 0.19 

Table 20. Cluster sampling (Scheaffer et al. 1996) results for acoustic estimates of 

young-of-the-year (YOY) fish and yearling-and-older (year-plus) Arctic cod in thre 

depth strata (20-40, 40-100, and 100-500 m). # Clusters is the number of clusters 

(i.e. transects) used in the analysis and Range elements is the range of elements (i.e. 1 

km bins) included in the analysis. Mean density, standard deviation, and CV for each 

estimate are given. No estimate of year-plus density was made in the 20-40 depth 

stratum. 

Scaling cluster sampling estimates of mean density to the entire survey area provides an 

abundance (fish within the study area) estimate for year-plus Arctic cod and YOY fish (assumed 

to be dominated by Arctic cod). Young-of-the-year abundance estimates were high in all strata, 

with the highest estimate occurring in the 20-40 m depth (1.967 × 109

 ± 0.190 × 109, abundance 

± 1 SD). The two deeper strata within the study area had similar YOY fish abundance estimates, 

with an estimated 1.608 × 109

 ± 0.240 × 109 fish (± 1 SD) present in the 40-100 m depth, and 

1.212 × 109

 ± 0.334 × 109 fish in the 100-500 m depth. These abundance estimates scale to 

biomass estimates of 734 ± 71 t (20-40 m strata), 600 ± 90 tonnes (40-100 m strata), and 452 ± 

125 t (100-500 m strata) using an average YOY fish weight of 0.37 g. 

Estimates of year-plus Arctic cod abundance from cluster sampling mean densities also illustrate 

a strong presence of year-plus Arctic cod in deeper water. Within the 40-100 m bottom depth, 

year-plus Arctic cod abundance is estimated to be 0.872 × 109

 ± 0.532 × 109 fish (± 1 SD). This 

abundance corresponds to a biomass estimate of 9034 ± 5510 t (± 1 SD) using an average yearplus Arctic cod weight of 10.35 g. In the 100-500 m depth, abundance of year-plus Arctic cod is 

estimated to be 2.418 × 109

 ± 0.455 × 109 fish (± 1 SD). Converting this number to biomass 

using an average year-plus Arctic cod weight of 7.26 g resulted in a biomass estimate of 17,559 

± 3308 t (± 1 SD) of year-plus Arctic cod in the 100-500 m depth depth. 

Likely due to the low sample size (n=7 systematic acoustic transects) and high variability in the 

data, there was no statistically significant (P > 0.10) differences in mean YOY fish densities 

among the depth strata (<40, 40-100, 100-500 m). 

88
89

There was no statistically significant (P > 0.10) difference in mean year-plus Arctic cod densities 

between the depth strata (40-100, 100-500 m). This is likely due to the low sample size (n=7 

systematic acoustic transects) and high variability in the data. 

Comparing acoustic and bottom trawl surveys 

By examining the ratio of bottom trawl to acoustic density estimates for year-plus Arctic cod, we 

can draw inferences on the “picture” of distribution that the two approaches provide. Inshore of 

the 100 m depth contour bottom trawl estimates of year-plus Arctic cod were greater than 

acoustic estimates for 3 out of 4 stations (Figure 34). Deeper than the 100 m contour, only one 

out of nine bottom trawl estimates was higher than the concurrent acoustic estimate. . 

Figure 34. Density ratio for yearling-and-older (year-plus) Arctic cod, calculated as (bottom 

trawl density / acoustic density) where acoustic density is from 9.0 m from the surface to 0.5 

m from the bottom. A value of 1 indicates that bottom trawl = acoustic estimates. The Outer 

Continental Shelf (OCS) Lease Area is shown in gray shading. 
Model results are presented for coincident acoustic density estimates and bottom trawl CPUE 

with combined lined and unlined trawls (Table 21), coincident data using lined bottom trawls 

only (Table 22), and noncoincident data using lined bottom trawls only (Table 23). 

When a predictor was found to be significant, the relationship between the acoustic response 

variable (A) and significant variables (i.e. logBT, dep, net, and interactions) are listed in the 

“Relationship” column (i.e. A = b0 + b1*logBT), and categorical variable conditions are listed in 

parentheses (Tables 21-23). When bottom trawl CPUE (BT) and depth (dep) or the interaction 

term (logBT:dep) were significant, the relationship was tested for bottom trawls in water depths 

both below (below) and within (layer). When depth (dep) was a significant predictor but bottom 

trawl CPUE (BT) was not, the model estimate of the mean ± 1 standard error is given (Tables 

21-23). 

In the comparison between coincident acoustic data and combined lined and unlined bottom 

trawl data, several patterns emerge (Table 21). Depth (dep), the categorical predictor of whether 

the year-plus Arctic cod aggregations were in contact with the bottom at the site, was a 

significant predictor of acoustic density for all comparisons (Table 21). Within models that used 

the acoustic density only within overlap regions (indices 3-5), depth was the only significant 

predictor of year-plus Arctic cod density (P = 0.03, Table 21). In the overlap regions (variable 3-

5), there was no relationship between bottom trawl CPUE and acoustic densities (Table 21). In 

the four water column models (variable 1, 2, 6, 7), bottom trawl CPUE (logBT), depth (dep), and 

the interactions between bottom trawl CPUE and depth (logBT:dep) were significant in all 

models and the overall models were also significant (P = 0.03-0.05, Table 21). Figure 35 is 

shown as an example of this relationship – within year-plus Arctic cod aggregation layer, there is 

a positive relationship between acoustic density and bottom trawl catch but below the layer there 

is a negative (or no) relationship between the acoustics and bottom trawl (Table 21). 

90
91

Acoustic density response variable n Predictor F df P Adj.R2 Relatio

i.e. A = b0 + 

A survey depth (1) 14 logBT* 3.803 4,9 0.04 0.46 10e4 - 14e3•log9.0 m from surface to 0.5 m from bottom dep* 10e2 + 600.5•lo

net 

logBT:dep*

A above BT (2) 14 logBT* 4.395 4,9 0.03 0.51 10e4 - 14e3•log

9 m from surface to 2.0 m from bottom dep* -2900 + 630•log

net 

logBT:dep*

A & BT overlap region (3) a 13 logBT 4.306 3,10 0.03 0.43 1.7 ± 0.8 (layer) 

2.0 m from bottom to 0.5 m from bottom dep* 

net 

A & BT overlap region A corrected (4) a 14 logBT 4.305 3,10 0.03 0.43 1.9 ± 0.8 (layer) 

2.0 m from bottom to bottom dep* 

net 

A & BT overlap region A corrected (5) a 14 logBT 4.305 3,10 0.03 0.43 1.8 ± 0.8 (layer) 

2.0 m from bottom to bottom dep* 

net 

A to bottom corrected (6) 14 logBT 3.639 4,9 0.05 0.45 10e4 ± 41e3 (be

9.0 m from surface to bottom dep* 1037.0 + 636.7•

net 

logBT:dep*

A to bottom corrected (7) 14 logBT* 3.692 4,9 0.05 0.45 10e4 - 14e3•log

9.0 m from surface to bottom dep* 991.7 + 655.5•lo

net 

logBT:dep*

Table 21. Model results for coincident acoustic and bottom trawl (lined and unlined nets) data. A=acoustics, BT=

net=lined or unlined categorical predictor, dep=depth categorical predictor (below or within the layer), and “:” deninteraction term. Acoustic density response variable and numbers in parentheses ( ) refer to the list of acoustic p

found in the text, a denotes a fourth root transformation of the response variable, n is the number of data points, P

list of predictors in the model with the lowest AIC value (* denotes a significant predictor), F is the F statistic for 

are the number of degrees of freedom for the F distribution (# parameters, remaining degrees of freedom for test), 

value for the model fit, Adj.R2 is the fit to the model accounting for the number of predictors in the model, and Rel

model output. e# is an abbreviation for •10#.
15000 

Acoustic density estimate 

10000 

5000 

3 5 7 9 

Log Bottom trawl (CPUE) 

Figure 35. Model results for coincident data comparing acoustic 

density estimates for YAO Arctic cod (9.0 m from the surface to 

0.5 m from the bottom) to bottom trawl density estimates below 

(solid circles, solid line) and within (hollow circles, broken line) 

the YAO Arctic cod layer. 

92
Depth was a strong predictor (P < 0.01) of acoustic density within the overlap region for acoustic 

data and lined bottom trawl only data (variables 3-5, Table 22), as was found in the previous 

comparison (using combined lined and unlined bottom trawl data). For the water column models 

(variables 1, 2, 6, 7), depth and the interaction between bottom trawl CPUE and depth 

(logBT:dep) were significant predictors in variables 1, 6, and 7 but variable 2 had no significant 

predictors (Table 22). No water column model results were significant (P = 0.10-0.18). 

Finally, Table 23 presents model results for the noncoincident acoustic data using only lined 

bottom trawl data. Within overlap regions (variables 3-5), there were no significant predictors (P

= 0.35-0.45, Table 23) of acoustic density. In the water column models (variables 1, 2, 6, 7), 

depth (dep) was the only significant predictor but overall water column model results were not 

significant (P = 0.6-0.10). 

Acoustic and bottom trawl potential bias with depth – For the acoustic variables of year-plus 

Arctic cod density, only water column predictors (1, 2, 6, 7) were significantly positively related 

to depth (P = 0.01-0.02, Table 24). An example of this relationship is shown in Figure 36 for 

acoustic index #1 which shows that Arctic cod acoustic density is positively related to bottom 

depth. General additive models for bottom trawl densities were run using all data (lined and 

unlined combined), lined only, and unlined only. No significant relationships were found 

between bottom trawl densities and depth (Table 24). Figure 37 presents the bottom trawl 

results, showing lined and unlined nets, with the model fit for the combined dataset. 

93
Acoustic density response variable n Predictor F df P Adj.R2 Relationsh

i.e. A = b0 + b1

A survey depth (1) 9 logBT 3.661 3,5 0.10 0.50 -18e3 + 35e2•logB9.0 m from surface to 0.5 m from bottom dep* 

logBT:dep*

A above BT (2) 10 logBT 2.301 3,6 0.18 0.30 

9 m from surface to 0.5 m from bottom dep 

logBT:dep 

A & BT overlap region (3) a 9 dep* 40.560 1,7 <0.01 0.83 2.7 ± 0.3 (below) 

2.0 m from bottom to 0.5 m from bottom 5.7 ± 0.5 (layer) 

A & BT overlap region A corrected (4) a 9 dep* 40.560 1,7 <0.01 0.83 2.9 ± 0.3 (below) 

2.0 m from bottom to bottom 6.1 ± 0.5 (layer) A & BT overlap region A corrected (5) a 9 dep* 45.810 1,7 <0.01 0.85 2.9 ± 0.3 (below) 

2.0 m from bottom to bottom 6.2 ± 0.5 (layer) 

A to bottom corrected (6) 9 logBT 3.512 3,5 0.11 0.49 -18e3 + 36e2•logB

9.0 m from surface to bottom dep* 

logBT:dep*

A to bottom corrected (7) 9 logBT 3.520 3,5 0.10 0.49 -18e3 + 37e2•logB

9.0 m from surface to bottom dep* 

logBT:dep*

Table 22. Model results for coincident acoustic and bottom trawl (lined nets only) data. A=acoustics, BT=bottom dep=depth categorical predictor (below or within the layer), and “:” denotes an interaction term. Acoustic density 

variable and numbers in parentheses ( ) refer to the list of acoustic predictors found in the text, a denotes a fourth 

transformation of the response variable, n is the number of data points, Predictor is the list of predictors in the m

lowest AIC value (* denotes a significant predictor), F is the F statistic for the model, df are the number of degree

for the F distribution (# parameters, remaining degrees of freedom for test), P is the p-value for the model fit, Adj.R

the model accounting for the number of predictors in the model, and Relationship is the model output. e# is an ab

for •10#. 

94
Acoustic density response variable n Predictor F df P Adj.R2 Relationship i.e. A = b0 + b1*log

A survey depth (1) a 11 logBT 3.18 2,8 0.10 0.30 -5.8 ± 2.1 (layer) 9.0 m from surface to 0.5 m from bottom dep* 

A above BT (2) a 11 logBT 3.966 2,8 0.06 0.37 -6.3 ± 2.0 (layer) 

9 m from surface to 0.5 m from bottom dep* 

A & BT overlap region (3) a 11 logBT 1.283 3,7 0.40 0.08 

2.0 m from bottom – 0.5 m from bottom dep 

logBT:dep

A & BT overlap region A corrected (4) a 11 logBT 0.989 3,7 0.45 0.00 

2.0 m from bottom to bottom dep 

logBT:dep

A & BT overlap region A corrected (5) a 11 logBT 1.004 3,7 0.45 0.00 

2.0 m from bottom to bottom dep 

logBT:dep

A to bottom corrected (6) a 11 logBT 3.598 2,8 0.08 0.34 -6.6 ± 2.1 (layer) 

9.0 m from surface to bottom dep* 

A to bottom corrected (7) a 11 logBT 3.16 2,8 0.10 0.30 -5.8 ± 2.1 (layer) 

9.0 m from surface to bottom dep* 

Table 23. Model results for noncoincident acoustic and bottom trawl (lined nets only) data. A=acoustics, BT=botttrawl, dep=depth categorical predictor (below or within the layer), and “:” denotes an interaction term. Acoustic d

index and numbers in parentheses ( ) refer to the list of acoustic predictors found in the text, a denotes a fourth root 

transformation of the response variable, n is the number of data points, Predictor is the list of predictors in the mo

with the lowest AIC value (* denotes a significant predictor), F is the F statistic for the model, df are the number of 

degrees of freedom for the F distribution (# parameters, remaining degrees of freedom for test), P is the p-value for 

model fit, Adj.R2 is the fit to the model accounting for the number of predictors in the model, and Relationship is th

model output. 

95
Response variable n Predictor F P Adj.R2 Relationship 

A survey depth (1) 14 Depth 5.598 0.02* 0.46 positive GAM 9.0 m from surface to 0.5 m from bottom 

A above BT (2) 14 Depth 6.311 0.01* 0.49 positive GAM 

9 m from surface to 0.5 m from bottom 

A & BT overlap region (3) 14 Depth 3.127 0.07 0.40 GAM 

2.0 m from bottom to 0.5 m from bottom

A & BT overlap region A corrected (4) 14 Depth 3.127 0.07 0.40 GAM 

2.0 m from bottom to bottom 

A & BT overlap region A corrected (5) 14 Depth 3.314 0.06 0.42 GAM 

2.0 m from bottom to bottom 

A to bottom corrected (6) 14 Depth 5.391 0.02* 0.46 positive GAM 

9.0 m from surface to bottom 

A to bottom corrected (7) 14 Depth 5.389 0.02* 0.46 positive GAM 

9.0 m from surface to bottom

Bottom trawl density (2.0 m to bottom) 22 Depth 0.887 0.56 0.15 flat GAM, quasipoisson 

Combined lined and unlined nets 

Bottom trawl density (2.0 m to bottom) 10 Depth 3.783 0.07 flat GAM Unlined nets only 

Bottom trawl density (2.0 m to bottom) 12 Depth 1.354 0.32 flat GAM Lined nets only 

Table 24. Relationship of acoustic (indices 1-7) and bottom trawl yearling-and-older (YAO) Arctic cod densities depth for coincident data. A=acoustics, BT=bottom trawl, Depth=depth continuous predictor. Response variable 

numbers in parentheses ( ) refer to the list of acoustic predictors found in the text except for the bottom trawl data

the number of data points, F is the F statistic for the model, P is the p-value for the model fit (* denotes a significa

relationship), Adj.R2 is the fit to the model accounting for the number of predictors in the model, and Relationship 

model that was used. 

96
97

100 200 300 400 

-4 

-2 

0 

2 

4 

Arctic cod acoustic density (#/ha) 

Bottom depth (m) 

Figure 36. GAM model showing what bottom depth (m) is 

contributing to the model of yearling-and-older (YAO) Arctic cod 

density (#/ha, 9.0 m below the surface to 0.5 m above the bottom). 

Dashed lines indicate the 95% confidence interval. 
-40 

-20 

0 

20 

40 

60 

80 

Arctic cod bottom trawl CPUE (#/ha) 

100 200 300 400 

Bottom depth (m) 

Figure 37. General additive model showing what bottom depth 

(m) is contributing to the model of yearling-and-older (YAO) 

Arctic cod density (CPUE, #/ha) from the bottom trawl. Hollow 

circles are unlined nets, solid circles are lined nets. Dashed lines 

indicate the 95% confidence interval. 

98
Fish habitat (physical oceanography)

A total of fifty-six CTD casts and thirty-eight bongo tows were successfully completed during 

the survey (Appendix II, Table II.1). 

Winds and sea ice 

Figures 38a-c show the regional wind fields obtained from evening passes of the QuikSCAT 

satellite for the period of August 2-19, 2008. The satellite resolves wind vectors on a 25 km 

grid. Data contamination, due to the presence of land or sea ice within a grid, is indicated by 

black in the figures. 

Moderate concentrations of sea ice persisted over the Northeast Chukchi Sea and the shelfbreak 

of the western Beaufort Sea in early August and then gradually melted or receded from the 

sampling area. By the end of the field season only small patches of ice remained over the 

Northeast Chukchi shelf. 

99
Figure 38a. Beaufort/Chukchi regional wind fields from August 2-7, 2008. The date is 

given in the lower right corner of each panel. The red dot indicates Pt. Barrow. Black 

areas indicate sea ice or contaminated data. North is toward the top of each panel. 

100
Figure 38b. Beaufort/Chukchi regional wind fields from August 8-13, 2008. The date is 

given in the lower right corner of each panel. The red dot indicates Pt. Barrow. Black 

areas indicate sea ice or contaminated data. North is toward the top of each panel. 

101
Figure 38c. Beaufort/Chukchi regional wind fields from August 14-19, 2008. The date is 

given in the upper left hand corner of each panel. The red dot indicates Pt. Barrow. Black 

areas indicate sea ice or contaminated data. North is toward the top of each panel. 

102
Temperature and salinity 

Before presenting the spatial distribution of temperature and salinity along the CTD transects we 

first describe the various water masses that occur in the region with the aid of Figure 39, which 

shows 

The temperature and salinity characteristics at each one-meter averaged CTD sample from all 

casts. These data are plotted as a scatter plot in potential temperature-salinity (θ/S) space and 

color-coded according to depth range (figure 39). Potential temperature is the temperature that a 

parcel of water would acquire if brought to a standard reference pressure, usually 1000 millibars. 

Less scatter among points of a similar color indicates less variability in water mass 

characteristics at that depth. The plot includes isopleths (gray) of sigma-θ (density based on 

potential temperature) and the freezing point curve. 

The temperature and salinity data distribution indicates considerable variability amongst the 

warmer and fresher water types, while colder and saltier waters show less scatter. 

Upper ocean waters are considerably more variable than deeper waters. For example, 

temperatures and salinities in the upper 15 m of the water column range between 1 and 5o

C and 

26-30. The sources of low-salinity water in the study area include: ice melt, Alaskan Coastal 

Water (ACW), and local runoff modified by mixing with ambient shelf waters. 

Our analyses cannot unequivocally discriminate easily amongst the three, but ACW and runoffmodified waters are generally warmer (due to solar heating) than ice melt water. However, 

shallow ice melt lenses can easily warm rapidly under relatively calm and sunny conditions. 

Below, in discussion we will indicate areas which we believe are likely due to ice melt, based on 

their distance offshore. 

The bulk of the remaining waters (where ice melt waters are not found), between 16 and 80 m 

depth, have temperatures between 2 and -1o

C and salinities between 30 and 32. The colder and 

saltier fractions are waters formed in winter on the Bering, Chukchi and Beaufort Sea shelves 

whereas the warmer and fresher water types are likely mixtures consisting of deeper winter water 

and surface waters (Mountain et al. 1976, Weingartner et al. 2005). 

103
Figure 39. Potential temperature-salinity scatter plot composed of all 

data collected during the survey. The grey lines are isopleths of 

potential density and the straight black line denotes the freezing point 

curve. 

The spatial distribution of temperature and salinity 

Transect 1 (Figure 2) extends ~60 km northward from about the 20 m isobath inshore, across the 

eastern wall of Barrow Canyon and terminates at the mouth of the canyon in about 400 m water 

depth. 

 Properties along transect 1 are shown in Figures 40-xxx. The geostrophic velocity in these 

figures is relative to the unknown velocity at the reference depth, which could not be measured. 

Hence the velocity contours represent the velocity field relative to the (unknown) velocity at the 

reference depth. The velocity at the reference depth is assumed to be0 cm s-1. Geostrophy refers 

to the force balance the Coriolis and horizontal pressure gradient forces and it assumes that these 

are the only two forces affecting the fluid motion. The pressure gradient is estimated from 

horizontal density gradients. Salinities in the upper 20 meters are relatively fresh (<30) over the 

entire line with the freshest (<29) water at the four outermost stations over the mouth of the 

canyon. 

Transect 1 near-surface temperatures range between 3.5 and 4.5o

C offshore to about the 140 m 

isobath (~35 km offshore), but relatively cold (<2o

C) surface waters occur farther offshore, with 

the coldest temperatures coincident with the freshest surface waters. Seaward of the 30 m 

104
isobath the surface waters are separated from cold (<2o

C) sub-surface waters by a strong 

seasonal halocline in which salinities increase rapidly from 30-32 from ~20-30 m depth. Below 

30 m, salinities increase more gradually and reach a maximum of ~33.5 at 140 m. Temperatures 

at depths below 30 m are colder than 0o

C, and temperatures at depths greater than 40 m are all 

below -1o

C. There are three prominent fronts in the section. The first is relatively shallow 

surface haline front associated with fresh, ice melt water that lies approximately at the 40 km 

point along the transect, from the surface to 20 m depth in the water column. The second front is 

primarily a thermal front that is inshore of, but abuts, the salinity front associated with the ice 

melt, also found from the surface to approximately 20 m depth. The third front is trapped to the 

bottom between the 30 and 40 m isobaths. This is a thermohaline front, in which salinity 

(temperature) increases (decreases) seaward. Although this front includes strong salinity and 

temperature gradients, the density contrast is primarily associated with the salinity change. 

Figure 40. Transect 1 (labeled “line1”). The distribution of temperature (upper 

left), salinity (upper right), sigma-t (density; lower left), and the relative 

geostrophic velocity (lower right) along the transect. Black dots at the top of e

plot indicate station locations used in the contouring. 

ach 

The geostrophic velocity relative to the bottom as computed from the thermal wind shear, 

indicates a strong eastward jet over the eastern side of the canyon, at 10 to 20 m water depth, 

with weaker westward flow to either side of the jet. The jet is most likely part of the 

105
106

northeasterly outflow from Barrow Canyon that extends eastward along the shelfbreak of the 

Beaufort Sea shelfbreak (Pickart 2004, Pickart et al. 2005). The bulk of this outflow consists of 

cold (-1.5o

C), salty (~32.5) water formed in winter on the Chukchi shelf (Itoh et al., in press; 

Pickart et al. 2005; Weingartner et al. 2005). 

Although the stations along Transects 2 and 3 have coarser horizontal station spacing (Figure 2), 

he water property distributions along transects 2 and 3both (Figures 41 and 42) have several 

features in common with those along Transect 1. Relatively warm (~ 4.5 oC) , fresh (<30) water 

occupies the upper 20 m inshore, while ice melt waters occupy the upper 20 m seaward of the 50 

m isobath. Ice melt fronts overlie the 40 and 50 m isobaths and cold, salty water occupies the 

outermost stations below 50 m depth along both transects. On Transect 2 warm (~4.5o

C) surface 

waters are found inshore of a strong surface thermal that lies adjacent to and inshore of the ice 

melt front. The front is at 20 m water depth to the surface is located about 30 km from shore. 

Inshore surface waters are cooler (<2o

C) along Transect 3 and the inshore surface thermal front 

is weaker. Bottom-trapped thermohaline fronts spanning the 30.5-32 isohalines are also evident 

on both transects but these are more diffuse than the subsurface front on Transect 1. 
107

Figure 41. Transect 2 (labeled “line2”). The distribution of temperature (upper 

left), salinity (upper right), sigma-t (density; lower left), and the relative g

velocity (lower right) along the transect. Black dots at the top of each plot indicate 

station locations used in the contouring. 

eostrophic 
Figure 42. Transect 3 (labeled “line3”). The distribution of temperature (upper 

left), salinity (upper right), sigma-t (density; lower left), and the relative 

geostrophic velocity (lower right) along transect. Black dots at the top of each 

plot indicate station locations used in the contouring. 

A insufficient number of stations were occupied along Transect 4 to construct profiles. 

Most of the Transect 5 (Figure 42) stations were occupied following the August 13-15 upwelling 

wind event and the effects of this event are unknown. 

108
Figure 43. Transect 5 (labeled “line5”). The distribution of temperature (upper 

left), salinity (upper right), sigma-t (density; lower left), and the relative 

geostrophic velocity (lower right) along the transect. Black dots at the top of 

each plot indicate station locations used in the contouring.

Other points of difference between this section (transect 5) and those to the west are that there is 

a lens of very fresh (27.5) and warm (~4.5o

C) water approximately 20 km seaward of the 20 m 

isobath along Transect 5 (Figure 43). 

The final transect shown is comprised of the deeper stations along the slope (Figure 44). These 

are composed of the deepest stations along the shelfbreak in water depths greater than 250 m 

(Figure 2). Here we present water properties deeper than 50 m depth, since the surface waters 

were described for the cross-shelf sections. Two prominent features are evident in the plot. The 

first is the very cold (-1.5 to -1.0o

C) water with salinities between 32.5 and ~34 between 50 and 

150 m. 

109
Figure 44. The distribution of temperature (upper left), salinity (upper right), and 

sigma-t (density; lower panel) from west to east based on measurements along the 

continental slope (see Figure 2). Black dots at the top of each plot indicate station 

locations used in the contouring. 

Potential temperature-salinity (θ-S) plots composited for each line (Figure 45) show that the 

coldest waters (near the freezing point and with salinities of between 30 and 33.1) are found 

along Transects 1 and 2 with the coldest stations found offshore of the shelfbreak. 

110
Figure 45. Potential temperature (θ) versus salinity (S) plots for each 

CTD transect The black vertical bars delineate the region between 30 a

32 in salinity. 

nd 

111
The θ-S plots also show a considerable range in temperature for low salinity waters. In general 

the cooler temperatures are associated with ice melt (although shallow ice melt lens can warm 

rapidly under calm conditions and sufficient solar heating). Other sources of low-salinity water 

include contributions from the Chukchi Sea shelf, local rivers, such as the Colville and Meade 

that empty into or near the study region. In addition, Mackenzie shelf waters might also have 

contributed to the region during the survey, with these relatively warm waters found offshore and 

over the shelfbreak (e.g. Figure 43). These waters do spread eastward and have been reported 

over the basin(Guay and Falkner 1998, Macdonald et al. 1999) and continental slope (Macdonald 

et al., 1999) west of the Mackenzie shelf. The westward spreading of Mackenzie shelf waters in 

2008 is suggested by the AVHRR image from July 25 -28, 2009, which shows relatively warm 

water emanating from the Mackenzie shelf and spreading westward over the 4-day image 

sequence (Figure 46). The westward penetration of the plume is presumably due to the generally 

eastward winds that prevailed throughout July 2008 (not shown). Note that the position of the 

plume varies rapidly through the sequence, which is likely a result of changing winds and or 

dynamic instabilities associated with density fronts that delimit the plume boundaries. We were 

unable to obtain additional AVHRR during the survey period because of pervasive cloud cover 

from the end of July through August. 

112
113

Figure 46. A July 25 – 28 sequence of MODIS SST images of 

the Beaufort Sea showing the eastward spreading over the 

Alaskan Beaufort Sea of relatively warm Mackenzie shelf plume 

waters. 
Results of the demersal fish habitat associations 

Lined net stations environmental variable correlation resulted in the following:- Bottom 

temperature was correlated with all of the salinity and density variables (P ≤ 0.10) (Table 25). 

Predictably, salinity and density were highly correlated (R2 > 0.90 and P < 0.01). Temperature 

difference and density difference were also correlated (P = 0.09). 

Unlined net stations environmental variable correlation indicate that- Longitude was 

significantly correlated with density and salinity difference (P = 0.03) (Table 26). Similar to the 

results for the lined net stations, salinity and density variables were correlated (P < 0.01) and 

temperature difference and density differences were correlated (P = 0.09). 

114
Lined Net 

Percent ice removed 

Density 

Difference 

(sigma-t) 

Salinity 

Difference 

(psu) 

Bottom 

Density 

(sigma-t) 

Bottom 

Salinity 

(psu) 

Bottom 

Depth (m) 

Temperature 

Difference 

 (°C) 

Bottom 

Temperature 

(°C) 

Lon

(d

de

Longitude (decimal degrees) 

R2 0.02 0.03 0.05 0.05 <0.01 <0.01 <0.01 

P-value 0.63 0.61 0.50 0.50 0.98 0.97 0.97 

Bottom Temperature (°C) 

R2 0.09 0.08 0.01 <0.01 <0.01 0.49 

P-value 0.37 0.37 0.76 0.86 0.82 0.01 

Temperature Difference (°C) 

R2 0.26 0.22 0.02 0.01 0.04 

P-value 0.09 0.12 0.69 0.76 0.54 

Bottom Depth (m) 

R2 0.67 0.68 0.73 0.74 

P-value <0.01 <0.01 <0.01 <0.01 

Bottom Salinity (psu) 

R2 0.67 1.0 

P-value <0.01 <0.01 

Bottom Density (sigma-t) 

R2 0.71 

P-value <0.01 

Salinity Difference (psu) 

R2 1.0 

P-value <0.01 

Density Difference (sigma-t) 

R2

P-value 

Table 25. Correlation matrix of all the environmental variables at the lined net stations. Values in bold indicate sigcorrelated relationships (P < 0.10). The variable name, R2, and P-values are listed. 

115
Unlined Net

Bottom depth removed 

Density 

Difference 

(sigma-t) 

Salinity 

Difference 

(psu) 

Bottom 

Density 

(sigma-t) 

Bottom 

Salinity 

(psu) 

Temperature 

Difference 

 (°C) 

Bottom 

Temperature 

(°C) 

Longitude 

(decimal 

degrees) 

Longitude (decimal degrees) 

R2 0.46 0.49 0.19 0.18 0.04 0.02 

P-value 0.03 0.03 0.21 0.21 0.56 0.69 

Bottom Temperature (°C) 

R2 0.04 0.03 0.2 0.17 0.36 

P-value 0.56 0.61 0.2 0.23 0.07 

Temperature Difference (°C) 

R2 0.32 0.28 0.26 0.23 

P-value 0.09 0.12 0.13 0.16 

Bottom Salinity (psu) 

R2 0.67 1.0 

P-value <0.01 <0.01 

Bottom Density (sigma-t) 

R2 0.67 

P-value <0.01 

Salinity Difference (psu) 

R2 1.0 

P-value <0.01 

Density Difference (sigma-t) 

R2

P-value 

Table 26. Correlation matrix of all the environmental variables at the unlined net stations. Values in bold indicate significantly correlated relationships (P < 0.10). The variable name, R2, and P-values are listed. 

Bottom depth was not part of this analysis, see above. 

116
Results for all fish species – lined net

Linear regression and generalized additive model (GAM) 

CPUE #/ha 

There were no significant correlations between CPUE #/ha and environmental variables. 

CPUE kg/ha 

The only significant correlation was CPUE kg/ha and bottom temperature (P = <0.01), and the 

correlation was negative (Figure 47 and Table 27). The Cook’s Distance less than 1.0, therefore 

none of the observations were outliers. 

-1.6 -1.1 -0.6 -0.1 0.4 0.9 1.4 1.9

MBTBotTemp

1

2

3

4

5

6

Log Transformed CPUE kg/ha

R2 = 0.53

P-value = <0.01

Figure 47. All fish species log transformed CPUE kg/ha and bottom temperature 

(°C), lined net stations. 

Based on linear regression results, the first term in the GAM was bottom temperature (P < 0.01). 

The second term with the lowest P-value from the linear regression analysis was density 

difference (P = 0.17). Adding the second term to the GAM lowered the residual deviance but the 

Cp value increased (Table 28). Adding a third term to the model, longitude (P = 0.32), lowered 

both the residual deviance and Cp values (F = 16.52, P = 0.01). 

117
All Fish Species 

Lined Net 

Longitude 

(decimal 

degrees) 

Bottom 

Temperature 

(°C) 

Temperature 

Difference 

(°C) 

Bottom 

Depth (m) 

Bottom 

Salinity 

(psu) 

Bottom 

Density 

(sigma-t) 

Salinity 

Difference 

(psu) 

Den

Diffe

(sig

CPUE #/ha – R2 0.13 0.10 0.05 0.01 < 0.01 < 0.01 < 0.01 < 0CPUE #/ha – P-value 0.25 0.33 0.50 0.75 0.99 0.96 0.92 0

CPUE kg/ha – R2 0.10 0.53 (-) 0.12 0.03 0.07 0.09 0.18 0

CPUE kg/ha – P-value 0.32 <0.01 0.27 0.57 0.40 0.35 0.17 0

GAM Terms Smoothing Term Residual deviance Cp DF F P Bottom Temperature b-spline linear 2.77 6.72 7 Bottom Temperature + Density Difference linear 2.73 7.48 6 0.07 0.8 

Bottom Temperature + Density Difference + Longitude linear 0.64 7.01 5 16.52 0.10 

Table 28. Results for all fish species, lined net. Results of GAM between environmental variables and all fish 

species, from the lined net stations. The GAM terms are listed in the order of which they went into the model. 

Response: CPUE kg/ha. Significant values are in bold. 

Table 27. Results for all fish species, lined net. Results of linear regression between environmental variables an

fish species combined, from the lined net stations. Data were log transformed, CPUE #/ha and CPUE kg/ha. R2 a

values for each regression are shown. Significant P-values and the corresponding R2 are in bold designating if it i

positive (+) or negative (-) correlation. Variables shaded in gray are correlated with each other; the variables shadlight green are also correlated with one another. In addition, temperature difference and density difference are correlated. 

118
Results for all invertebrate species – lined net 

Linear regression and generalized additive model (GAM) 

CPUE kg/ha (no CPUE #/ha for invertebrates) 

A significant correlation was found between CPUE kg/ha and bottom temperature, P = 0.02 and 

the correlation was negative (Figure 48 and Table 29) for all invertebrates species, lined net. 

There was also a significant positive correlation between CPUE kg/ha and the variable 

temperature difference, P = 0.08 (Figure 49 and Table 29). The Cook’s Distance on CPUE kg/ha 

and both bottom temperature and temperature difference was less than 1.0 for all observations. 

-1.6 -1.1 -0.6 -0.1 0.4 0.9 1.4 1.9

Average Bottom Temperature (°C)

4

5

6

7

8

Log Transformed CPUE kg/ha

R2 = 0.42

P-value = 0.02

Figure 48. All invertebrate species log transformed CPUE kg/ha and bottom 

temperature (°C), lined net. 

119
120

01234

Temperature Difference (°C)

4

5

6

7

8

Log Transformed CPUE kg/ha

R2 = 0.28

P-value = 0.08

Figure 49. All invertebrate species log transformed CPUE kg/ha and temperature 

difference (°C), lined net. 

Based on linear regression results, the first term in the GAM analysis of “all invertebrates, 

unlined net” was bottom temperature (P = 0.02). The second term with the lowest P-value from 

the linear regression analysis that was not correlated with bottom temperature was bottom 

density (P = 0.14). The third term in the GAM model was longitude (P = 0.34). Although 

bottom depth, bottom salinity, salinity difference and density difference had lower P-values than 

longitude, all of those variables were correlated with bottom density. Adding the second and 

third terms to the GAM model further reduced the residual deviance and the Cp statistic 

decreased (Table 30). The three term GAM model was significant in explaining over half the 

variability in the data (F = 5.75, P = 0.06). 

 
All Invertebrate Species 

Lined Net 

Longitude 

(decimal 

degrees) 

Bottom 

Temperature 

(°C) 

Temperature 

Difference 

(°C) 

Bottom 

Depth (m) 

Bottom 

Salinity 

(psu) 

Bottom 

Density 

(sigma-t) 

Salinity 

Difference 

(psu) 

Densi

Differe

(sigma

CPUE kg/ha – R2 0.09 0.42 (-) 0.28 (+) 0.12 0.19 0.21 0.18 0.19 CPUE kg/ha – P-value 0.34 0.02 0.08 0.26 0.16 0.14 0.16 0.15 GAM Terms Smoothing Term Residual deviance Cp DF F P Bottom Temperature b-spline linear 2.10 5.09 7 Bottom Temperature + Bottom Density linear 0.84 4.43 6 8.91 0.02 Bottom Temperature + Bottom Density + Longitude linear 0.39 2.36 5 5.75 0.06 

Table 30. Results for all invertebrate species, lined net. Results of GAM between environmental 

variables and all invertebrate species, from the lined net stations. The GAM terms are listed in the order of which they went into the model. Response: CPUE kg/ha. Significant values are in bold. 

Table 29. Results for all invertebrate species, lined net. Results of linear regression between environmental va

and all invertebrate species combined, from the lined net stations. Data were transformed, by CPUE kg/ha only (invertebrates are not typically counted). R2 and P-values for each regression are shown. Significant P-values and 

corresponding R2 are in bold designating if it is a positive (+) or negative (-) correlation. Variables shaded in gray 

correlated; the variables shaded in light green are also correlated with one another. In addition, temperature differand density difference are correlated. 

121
Results for Arctic cod – lined net

Linear regression and generalized additive model (GAM) 

CPUE #/ha 

There were no significant correlations bewteen CPUE #/ha and environmental variables. 

CPUE kg/ha 

There was a significant correlation between CPUE kg/ha and bottom temperature (P = 0.03), and 

the correlation was negative between Arctic Cod Lined net CPUE #/ha and environmental 

variable (Figure 50 and Table 31). The Cook’s Distance on all data points was less than 1.0, 

indicating there are no outliers. 

-1.6 -1.1 -0.6 -0.1 0.4 0.9 1.4 1.9

Average Bottom Temperature (°C)

1

2

3

4

5

Log Transformed CPUE kg/ha

R2 = 0.40

P-value = 0.03

Figure 50. Arctic cod log transformed CPUE kg/ha and bottom temperature 

(°C), lined net. 

Based on linear regression results, the first term in the GAM analysis was bottom temperature (P 

= 0.03). The second term with the lowest P-value from the linear regression analysis was density 

difference (P = 0.25). The third term in the GAM model was longitude (P = 0.33). Although 

salinity difference had a lower P-value than longitude, that variable was correlated with density 

difference. Adding the second term to the GAM model lowered the residual deviance but the Cp 

value increased (Table 32). Adding a third term to the model lowered both the residual deviance 

and Cp values (F = 13.64, P = 0.01). 

122
Arctic cod 

Lined Net 

Longitude 

(decimal 

degrees) 

Bottom 

Temperature 

(°C) 

Temperature 

Difference 

(°C) 

Bottom 

Depth (m) 

Bottom 

Salinity 

(psu) 

Bottom 

Density 

(sigma-t) 

Salinity 

Difference 

(psu) 

Densi

Differe

(sigma

CPUE #/ha – R2 0.11 0.05 0.05 <0.01 < 0.01 <0.01 < 0.01 < 0.0CPUE #/ha – P-value 0.29 0.47 0.47 0.95 0.80 0.77 0.95 0.99 

CPUE kg/ha – R2 0.09 0.40 (-) 0.08 0.02 0.06 0.07 0.13 0.13 

CPUE kg/ha – P-value 0.33 0.03 0.38 0.63 0.45 0.40 0.25 0.25 

GAM Terms Smoothing Term Residual deviance Cp DF F P Bottom Temperature b-spline linear 5.21 12.66 7 Bottom Temperature + Density Difference linear 5.02 13.96 6 0.22 0.65 

Bottom Temperature + Density Difference + Longitude linear 1.34 13.07 5 13.64 0.01 

Table 32. Results for Arctic cod, lined net. Results of GAM between environmental variables and Arctic cod, 

from the lined net stations. The GAM terms are listed in the order of which they went into the model. Response: 

CPUE kg/ha. Significant values are in bold. 

Table 31. Results for Arctic cod, lined net. Results of linear regression between environmental variables and A

cod, from the lined net stations. Data were log transformed, CPUE #/ha and CPUE kg/ha. R2 and p-values for eac

regression are shown. Significant P-values and the corresponding R2 are in bold designating if it is a positive (+) o

negative (-) correlation. Variables shaded in gray are correlated; the variables shaded in light green are also correwith one another. In addition, temperature difference and density difference are correlated. 

123
Results for walleye pollock – lined net

Linear regression and generalized additive model (GAM) 

CPUE #/ha 

There was a significant correlation between CPUE #/ha (P = 0.02) and the independent variable 

longitude (Figure 51 and Table 33). The relationship was negative, decreasing from west to east 

in the study area. There were no data points that had a Cook’s Distance value greater than 1.0, 

confirming that there were no outlier observations. 

-155.0 -154.5 -154.0 -153.5 -153.0 -152.5 -152.0

Longitude (decimal degrees)

-1

0

1

2

3

4

5

Log Transformed CPUE #/ha

R2 = 0.43

P-value = 0.02

Figure 51. Walleye pollock log transformed CPUE #/ha and longitude (decimal 

degrees), lined net. 

 

Based on linear regression results, the first term in the GAM analysis was longitude (P = 0.02). 

The second term with the lowest P-value from the linear regression analysis was temperature 

difference (P = 0.42). The third term was salinity difference (P = 0.88),. The three term GAM 

model did not significantly explain the variance in the data (F = 0.08, P = 0.79). 

 

124
walleye pollock cont.-

CPUE kg/ha 

A significant correlation was found for CPUE kg/ha walleye pollock and the independent 

variable longitude (P = 0.02), and the relationship was negative, CPUE kg/ha decreasing from 

west to east (Figure 52 and Table 33). There were no data points that had a Cook’s Distance 

greater than 1.0. 

-155.0 -154.5 -154.0 -153.5 -153.0 -152.5 -152.0

Longitude (decimal degrees)

-1.0

-0.5

0.0

0.5

1.0

1.5

2.0

Log Transformed CPUE kg/ha

R2 = 0.41

P-value = 0.02

Figure 52. Walleye pollock log transformed CPUE kg/ha and longitude 

(decimal degrees), lined net. 

Based on linear regression results, the first term in the GAM analysis was longitude (P = 0.02). 

The second term with the lowest P-value from the linear regression analysis was temperature 

difference (P = 0.42). The third term in the GAM model was salinity difference (P = 0.43). The 

three term GAM model did not significantly explain the variance in the data (F = 1.74, P = 0.22). 

125
Table 33. Results for walleye pollock, lined net. Results of linear regression between environmental variables a

walleye pollock, from the lined net stations, CPUE #/ha and CPUE kg/ha. R2 and p-values for each regression are 

shown. Significant P-values and the corresponding R2 are in bold designating if it is a positive (+) or negative (-) 

correlation. Variables shaded in gray are correlated; the variables shaded in light green are also correlated with onanother. In addition, temperature difference and density difference are correlated. 

Pollock 

Lined Net 

Longitude 

(decimal 

degrees) 

Bottom 

Temperature 

(°C) 

Temperature 

Difference 

(°C) 

Bottom 

Depth (m) 

Bottom 

Salinity 

(psu) 

Bottom 

Density 

(sigma-t) 

Salinity 

Difference 

(psu) 

Densi

Differe

(sigma

CPUE #/ha – R2 0.43 (-) 0.02 0.06 0.01 <0.01 <0.01 <0.01 <0.0CPUE #/ha – P-value 0.02 0.68 0.42 0.71 0.82 0.81 0.88 0.92 CPUE kg/ha – R2 0.41 (-) <0.01 0.07 <0.01 0.02 0.02 0.06 0.05 

CPUE kg/ha – P-value 0.02 1.0 0.42 0.99 0.64 0.64 0.43 0.47 

GAM Terms Smoothing Term Residual deviance Cp DF F P Longitude linear 27.33 38.26 10 Longitude + Temperature Difference linear 24.36 40.76 9 1.10 0.32 

Longitude + Temperature Difference + Salinity Difference linear 24.13 45.78 8 0.08 0..79 

GAM Terms Smoothing Term Residual deviance Cp DF F P Longitude linear 3.95 5.53 10 Longitude + Temperature Difference linear 3.53 5.90 9 1.07 0.33 Longitude + Temperature Difference + Salinity Difference linear 2.90 6.04 8 1.74 0.22 

Table 35. Results for walleye pollock, lined net. Results of GAM between environmental variables and walleye 

pollock, from the lined net stations. The GAM terms are listed in the order of which they went into the model. Response: CPUE kg/ha. Significant values are in bold. 

Table 34. Results for walleye pollock, lined net. Results of GAM between environmental variables and walleye 

pollock, from the lined net station. The GAM terms are listed in the order of which they went into the model. Response: CPUE #/ha. Significant values are in bold. 

126
Results for all eelpouts – lined net

Linear regression and generalized additive model (GAM) 

CPUE #/ha 

Bottom temperature was significantly correlated with CPUE #/ha All Eelpouts – Lined Net

 (P <0.01), and the correlation was negative, decreasing CPUE #/ha with increasing bottom 

temperature (Figure 53 and Table 36). The Cook’s Distance was less than 1.0, indicating there 

were no outliers. 

-1.6 -1.1 -0.6 -0.1 0.4 0.9 1.4 1.9

Average Bottom Temperature (°C)

1

2

3

4

5

6

Log Transformed CPUE #/ha

R2 = 0.58

P-value = <0.01

Figure 53. All eelpouts log transformed CPUE #/ha and average bottom 

temperature (°C), lined net. 

Based on linear regression results, the first term in the GAM analysis was bottom temperature (P 

< 0.01). The second term with the lowest P-value from the linear regression analysis was density 

difference (P = 0.61). Temperature difference had a lower P-value than density difference, but 

the former variable was correlated with bottom temperature. The third term in the GAM model 

was longitude (P = 0.64). Although salinity difference had a lower P-value than longitude, that 

variable was correlated with density difference. 

Adding the second term and third terms, bottom temperature and density, to the GAM model 

slightly lowered the residual deviance but the Cp values increased with each added term (Table 

127
128

37), indicating the model was not improved by adding density difference and longitude. The 

three term GAM model did not significantly explain the variance in the data (F = 0.63, P = 0.45). 
all eelpouts cont.-

CPUE kg/ha 

The dependent variable, CPUE kg/ha was also significantly correlated with bottom temperature 

(P = 0.02), and the relationship was negative, CPUE kg/ha decreasing with increasing 

temperature (Figure 54 and Table 36). 

-1.6 -1.1 -0.6 -0.1 0.4 0.9 1.4 1.9

Average Bottom Temperature (°C)

-5

-3

-1

1

3

Log Transformed CPUE kg/ha

R2 = 0.42

P-value = 0.02

Figure 54. All eelpouts log transformed CPUE kg/ha and average bottom 

temperature (°C), lined net. 

Based on linear regression results, the first term in the GAM analysis was bottom temperature (P 

= 0.02). The second term with the lowest P-value from the linear regression analysis was density 

difference (P = 0.18). The third term in the GAM model was longitude (P = 0.68). Although 

bottom depth, bottom salinity, bottom density and salinity difference had lower P-values than 

longitude, those variables were all correlated with density difference. Adding the second term 

and third terms to the GAM model slightly lowered the residual deviance but the Cp values 

increased with each added term (Table 38), indicating the model was not improved by adding 

density difference and longitude. The three term GAM model did not significantly explain the 

variance in the data (F = 0.17, P = 0.69). 

129
Eelpouts (several species 

combined) 

Lined Net 

Longitude 

(decimal 

degrees) 

Bottom 

Temperature 

(°C) 

Temperature 

Difference 

(°C) 

Bottom 

Depth (m) 

Bottom 

Salinity 

(psu) 

Bottom 

Density 

(sigma-t) 

Salinity 

Difference 

(psu) 

Densi

Differe

(sigma

CPUE #/ha – R2 0.02 0.58 (-) 0.10 <0.01 <0.01 0.01 0.03 0.03 CPUE #/ha – P-value 0.64 <0.01 0.33 0.96 0.81 0.74 0.62 0.61 

CPUE kg/ha – R2 0.02 0.42 (-) 0.15 0.13 0.12 0.14 0.17 0.18 

CPUE kg/ha – P-value 0.68 0.02 0.22 0.25 0.27 0.24 0.18 0.18 

GAM Terms Smoothing Term Residual deviance Cp DF F P Bottom Temperature linear 11.21 15.69 10 Bottom Temperature + Density Difference linear 11.08 18.47 9 0.10 0.76 

Bottom Temperature + Density Difference + Longitude linear 10.27 20.12 8 0.63 0.45 

GAM Terms Smoothing Term Residual deviance Cp DF F P Bottom Temperature linear 27.23 38.12 10 Bottom Temperature + Density Difference linear 24.67 41.10 9 0.93 0.36 

Bottom Temperature + Density Difference + Longitude linear 24.16 46.08 8 0.17 0.69 

Table 38. Results for all eelpouts, lined net. Results of GAM between environmental variables and all 

eelpouts, from the lined net stations. The GAM terms are listed in the order of which they went into the model. 

Response: CPUE kg/ha. Significant values are in bold. 

Table 37. Results for all eelpouts, lined net. Results of GAM between environmental variables and all 

eelpouts, from the lined net stations. The GAM terms are listed in the order of which they went into the model. 

Response: CPUE #/ha. Significant values are in bold. 

Table 36. Results for all eelpouts, lined net. Results of linear regression between environmental variables and al

eelpouts, from the lined net stations, CPUE #/ha and CPUE kg/ha. R2 and p-values for each regression are shown. 

Significant P-values and the corresponding R2 are in bold designating if it is a positive (+) or negative (-) correlatio

Variables shaded in gray are correlated; the variables shaded in light green are also correlated with one another. In addition, temperature difference and density difference are correlated. 

130
Results for all sculpins – lined net

Generalized linear model (GLM) 

The GLM analysis found bottom depth explained over half the deviance in the presence or 

absence of sculpins, sampled with the lined net (P = 0.005) (Table 39). Bottom salinity, bottom 

density, salinity difference and density difference were also significantly correlated with the 

presence/absence of sculpins, however, these independent variables were correlated with bottom 

depth. Adding longitude to the GLM model accounted for almost all of the variance observed in 

the presence/absence of sculpins. The null deviance was 8.79 and residual deviance was 0.85 (F 

= 30.23, P = 0.0004) with both bottom depth and longitude in the model. Although the residual 

deviance and P-value indicate the two term model was statistically significant it is very likely 

that the results are due to interactions between independent variables and over fitting the model. 

Both of these problems are related to the small sample size (n = 11) and thus the two term GLM 

model is probably not biologically significant.

131
Sculpins (several species 

combined) 

Presence / Absence 

Longitude 

(decimal 

degrees) 

Bottom 

Temperature 

(°C) 

Temperature 

Difference 

(°C) 

Bottom 

Depth (m) 

Bottom 

Salinity 

(psu) 

Density 

(sigma-t) 

Salinity 

Difference 

(psu) 

D

Di

(s

Residual Deviance (Null Deviance: 8.789) 8.547 8.013 8.000 3.293 5.833 5.807 4.840 F statistic 0.31 0.93 0.92 12.97 3.90 3.93 7.57 

P-value 0.59 0.36 0.36 0.005 0.08 0.08 0.02 

Table 39. Results for all sculpins, lined net. Results of generalized linear models (GLM) of environmental vari

and all sculpins, from the lined net stations. The dependent variable is species presence/absence (not CPUE). Msignificance compares the residual deviance for each variable to the null deviance and reports a t-value. Numberbold are significant. All variables in shaded gray are correlated; the variables shaded in light green are also correwith one another. In addition, temperature difference and density difference are correlated. 

132
Results for opilio crab – lined net

Linear regression and generalized additive model (GAM) 

CPUE #/ha 

CPUE #/ha was negatively correlated with bottom temperature (P <0.01; Figure 55 and Table 

40), and positively correlated with temperature difference (P = 0.06; Figure 56 and Table 40). 

CPUE #/ha was also significantly positvely correlated with the group of correlated independent 

variables: bottom salinity, bottom density, salinity difference and density difference (Table 40). 

The Cook’s Distance for each observation was less than 1.0, indicating there were no outlier 

observations. 

-1.6 -1.1 -0.6 -0.1 0.4 0.9 1.4 1.9

Average Bottom Temperature (°C)

0

2

4

6

8

Log Transformed CPUE #/ha

R2 = 0.53

P-value = <0.01

Figure 55. Opilio crab log transformed CPUE #/ha and average bottom 

temperature (°C), lined net. 

Based on linear regression results, the first term in the GAM analysis was bottom temperature (P 

<0.01). Temperature difference was not used in the model because it was correlated with bottom 

temperature. The second term with the lowest P-value from the linear regression analysis was 

bottom depth (P = 0.12). Although salinity and density differences had lower P-values, they 

were correlated with one another and also with temperature difference which was in turn 

correlated with bottom temperature; therefore bottom depth was used as the second term. The 

third term in the GAM model was longitude (P = 0.49). Adding the second term and third terms 

to the GAM model lowered both the residual deviance and Cp values with each added term 

(Table 41). However, the three term GAM model did not significantly explain the variance in 

133
134

the data (F = 3.20, P = 0.11). The two term GAM was significant in describing most of the 

variance in the data (F = 13.02, P = 0.005) (Table 41), indicating the model was improved by 

adding bottom depth but not longitude. 

01234

Temperature Difference (°C)

0

2

4

6

8

Log Transformed CPUE #/ha

R2 = 0.32

P-value = 0.06

Figure 56. Opilio crab log transformed CPUE #/ha and temperature difference 

(°C), lined net. 
opilio crab cont.-

CPUE kg/ha 

CPUE kg/ha was positively correlated with bottom depth (Figure 57) and the suite of salinity, 

and density variables (Table 40). The Cook’s Distance on all observations was less than 1.0, 

indicating there were no outliers. 

0 100 200 300 400 500

Average Bottom Depth (m)

-4

-2

0

2

4

6

Log Transformed CPUE kg/ha

R2 = 0.70

P-value = <0.01

Figure 57. Opilio crab log transformed CPUE kg/ha and bottom depth (m), 

lined net. 

Based on linear regression results, the first term in the GAM analysis was bottom depth (P 

<0.01). Because bottom depth was correlated with bottom salinity, density, salinity difference 

and density difference, we only used bottom depth in the GAM. The second term used in the 

GAM model was bottom temperature (P = 0.26). Although, temperature difference had a lower 

P-value, it was correlated with density difference which was, in turn, correlated with bottom 

depth. The third term in the GAM model was longitude (P = 0.99). Adding the second term and 

third terms to the GAM model lowered the residual deviance and the Cp (Table 42). However, 

the three term GAM model did not significantly explain the variance in the data (F = 0.007, P = 

0.93; Table 42). The two term GAM with bottom depth and bottom temperature as explanatory 

variables was significant in describing most of the variance in the data (F = 11.94, P = 0.007; 

Table 42). 

135
Opilio crab 

Lined Net 

Longitude 

(decimal 

degrees) 

Bottom 

Temperature 

(°C) 

Temperature 

Difference 

(°C) 

Bottom 

Depth (m) 

Bottom 

Salinity 

(psu) 

Bottom 

Density 

(sigma-t) 

Salinity 

Difference 

(psu) 

Densi

Differen

(sigma

CPUE #/ha – R2 0.05 0.53 (-) 0.32 (+) 0.23 0.31 (+) 0.35 (+) 0.55 (+) 0.56 (+CPUE #/ha – P-value 0.49 <0.01 0.06 0.12 0.06 0.04 <0.01 <0.01 

CPUE kg/ha – R2 <0.01 0.12 0.17 0.70 (+) 0.73 (+) 0.75 (+) 0.75 (+) 0.74 (+

CPUE kg/ha – P-value 0.99 0.26 0.19 < 0.01 <0.01 <0.01 < 0.01 < 0.0

GAM Terms Smoothing Term Residual deviance Cp DF F P Bottom Temperature linear 19.66 27.52 10 Bottom Temperature + Bottom Depth linear 7.89 19.68 9 13.42 0.005 Bottom Temperature + Bottom Depth + Longitude linear 5.64 12.65 8 3.20 0.11 GAM Terms Smoothing Term Residual deviance Cp DF F P Bottom Depth linear 23.73 33.22 10 Bottom Depth + Bottom Temperature linear 10.20 24.44 9 11.94 0.007 

Bottom Depth + Bottom Temperature + Longitude linear 10.19 19.26 8 0.007 0.93 

Table 41. Results for opilio crab, lined net. Results of GAM between environmental variables and opilio 

crab, from the lined net stations. The GAM terms are listed in the order of which they went into the model. 

Response: CPUE #/ha. Significant values are in bold. 

Table 42. Results for opilio crab, lined net. Results of GAM between environmental variables and opilio 

crab, from the lined net stations. The GAM terms are listed in the order of which they went into the model. 

Response: CPUE kg/ha. Significant values are in bold. 

Table 40. Results for opilio crab, lined net. Results of linear regression between environmental variables and 

opilio crab, from the lined net stations, CPUE #/ha and CPUE kg/ha. R2 and P-values for each regression are sho

Significant P-values and the corresponding R2 are in bold designating if it is a positive (+) or negative (-) 

correlation. Variables shaded in gray are correlated; the variables shaded in light green are also correlated with oanother. In addition, temperature difference and density difference are correlated. 

136
Results for all fish species – unlined net

Linear regression and generalized additive model (GAM). 

CPUE #/ha 

CPUE #/ha was significantly correlated with temperature difference (P = 0.01), and the 

correlation was negative (Figure 58 and Table 43). The Cook’s Distance on an outlier was 

greater than 2.0, indicating that there is a high leverage data point or points. After removing the 

outlier, the relationship between CPUE #/ha and temperature difference becomes non-significant 

(P = 0.28). In Figure 59, the high leverage data point is circled in red. 

Despite the presence of a potential outlier, all data points were used for the GAM analysis 

because of the low sample size (n=10). Due to the many correlations between independent 

variables (Table 43), only two rather than three term GAM models were possible. The two 

GAM terms used in the analysis for CPUE #/ha, in order, were temperature difference with the 

lowest P-value from the linear regression (P = 0.01) and longitude with the P = 0.74 from the 

linear regression. Although density difference and salinity difference had lower P-values than 

longitude, those variables are correlated with temperature difference. A linear b-spline smoother 

Figure 58. All fish species log transformed CPUE #/ha and temperature 

difference (°C), unlined net. Note: when removing the data point circled in 

red (high Cooks’ Distance), the relationship becomes non-significant. 

123456

Temperature Difference (°C)

1

3

5

7

9

R2 = 0.55

P-value = 0.01

Log Transformed CPUE #/ha

137
was used for both terms. The residual deviance was slightly lowered with the addition of 

longitude, however, the Cp value increased and the relationship was non-significant (F = 0.50, P 

= 0.51; Table 44). 

CPUE kg/ha 

CPUE kg/ha was significantly correlated with temperature difference (P = 0.01) and the 

correlation was negative (Figure 59 and Table 43). The Cook’s Distance on an outlier was 

greater than 2.0, indicating that there is a high leverage data point or points. After removing the 

outlier, the relationship between CPUE kg/ha and the independent variable, temperature 

difference, becomes non-significant (P = 0.28). In Figure 60, the high leverage data point is 

circled in red. 

123456

Temperature Difference (°C)

-2

-1

0

1

2

3

4

Log Transformed CPUE kg/ha

R2 = 0.55

P-value = 0.01

Figure 59. All fish species log transformed CPUE kg/ha and temperature 

difference (°C), unlined net. The relationship is significant and negatively 

correlated, CPUE kg/ha decreasing with increasing temperature difference 

(stratification). Note: when removing the data point circles in red (high 

Cook’s Distance), the relationship becomes non-significant. 

Despite the presence of a potential outlier, all data points were used for the GAM analysis 

because of the low sample size (n=10). Due to the many correlations between independent 

variables, only two rather than three term GAM models were possible. The two terms in the 

138
139

GAM model were, in order, temperature difference, with the lowest P-value from the linear 

regression (P = 0.01) and longitude, with the P = 0.82 from the linear regression. Although 

density difference and salinity difference had lower P-value than longitude, those variables are 

correlated with temperature difference. A linear b-spline smoother was used for both terms. The 

GAM model was not significant (F = 0.23, P = 0.65), even though the residual deviance 

decreased, the Cp value increased (Table 45). 
All Fish Species 

Unlined Net 

Longitude 

(decimal 

degrees) 

Bottom 

Temperature 

(°C) 

Temperature 

Difference 

(°C) 

Bottom 

Salinity 

(psu) 

Bottom 

Density 

(sigma-t) 

Salinity 

Difference 

(psu) 

Density 

Difference 

(sigma-t) 

CPUE #/ha – R2 0.01 0.07 0.55 (-) <0.01 <0.01 0.03 0.04 CPUE #/ha – P-value 0.74 0.47 0.01 0.86 0.80 0.65 0.57 

CPUE kg/ha – R2 <0.01 0.05 0.55 (-) <0.01 <0.01 0.02 0.03 

CPUE kg/ha – P-value 0.82 0.56 0.01 0.97 0.91 0.69 0.61 

GAM Terms Smoothing Term Residual deviance Cp DF F P Temperature Difference b-spline linear 3.83 7.11 7 Temperature Difference + Longitude b-spline linear 3.53 7.91 6 0.50 0.51 GAM Terms Smoothing Term Residual deviance Cp DF F P Temperature Difference b-spline linear 4.07 7.56 7 Temperature Difference + Longitude b-spline linear 3.92 8.57 6 0.23 0.65 

Table 45. Results for all fish species, unlined net. Results of GAM between environmental 

variables and all fish species, from the unlined net station. The GAM terms are listed in the order of which they went into the model. Response: CPUE kg/ha. Significant values are in bold. 

Table 44. Results for all fish species, unlined net. Results of GAM between environmental 

variables and all fish species, from the unlined net station. The GAM terms are listed in the order of which they went into the model. Response: CPUE #/ha. Significant values are in bold. 

Table 43. Results for all fish species, unlined net. Results of linear regression between environmental 

variables and all fish species combined, from the unlined net stations. Data were log transformed, CPUE #/ha 

and CPUE kg/ha. R2 and P-values for each regression are shown. Significant P-values and the corresponding 

R2 are in bold designating if it is a positive (+) or negative (-) correlation. Results below include all data 

points. Variables shaded in gray are correlated; the variables shaded in light green are also correlated with one another. In addition, longitude is correlated with salinity and density difference and temperature difference is correlated with density difference. 

140
Results for all invertebrate species – unlined net

There were no significant linear relationships between environmental variables and CPUE kg/ha 

of all invertebrate species combined, at the unlined net stations (Table 46). CPUE #/ha was not 

analyzed because not all invertebrate taxa were practical to innumerate. We used GAM to 

explore nonlinear relationships between CPUE kg/ha and the non-correlated independent 

variables; however, there were no significant relationships. 

141
All Invertebrate Species 

Unlined Net 

Longitude 

(decimal 

degrees) 

Bottom 

Temperature 

(°C) 

Temperature 

Difference 

(°C) 

Bottom 

Salinity 

(psu) 

Bottom 

Density 

(sigma-t) 

Salinity 

Difference 

(psu) 

Density 

Difference 

(sigma-t) 

CPUE kg/ha – R2 < 0.01 0.03 0.10 0.04 0.03 0.03 0.02 CPUE kg/ha – P-value 1.00 0.64 0.38 0.60 0.64 0.64 0.70 

Table 46. Results for all invertebrate species, unlined net. Results of linear regression between 

environmental variables and all invertebrate species combined, from the unlined net stations. Data were log transformed, unlined nets, shown by CPUE #/ha and CPUE kg/ha, R2 and P-values for each variable. 

Significant P-values and the corresponding R2 are in bold designating if it is a positive (+) or negative (-) 

correlation. Variables shaded in gray are correlated; the variables shaded in light green are also correlated with one another. In addition, longitude is correlated with salinity and density difference and temperature 

difference is correlated with density difference. 

142
Results for Arctic cod – unlined net

Linear regression and generalized additive model (GAM) 

CPUE #/ha 

There was a significant correlation between CPUE #/ha and temperature difference (P = 0.05), 

and the correlation was negative (Figure 60 and Table 47). The Cook’s Distance on one data 

point (Figure 61, circled in red) exceeded 2.0 using the log transformed data. After removing 

this one data point (i.e. outlier), the relationship becomes non-significant (P = 0.63). 

Despite the presence of a potential outlier, all data points were used for the GAM analysis 

because of the low sample size (n=10). Due to the many correlations between independent 

variables, only two rather than three term GAM models were possible. The two terms in the 

CPUE #/ha GAM model, in order, were temperature difference with the lowest P-value from the 

linear regression (P = 0.05) and longitude with the next lowest P-value from the linear regression 

(P = 0.51). Although bottom temperature had a lower P-value than longitude, this variable was 

correlated with temperature difference. A linear b-spline smoother was used for temperature 

difference and a linear smoother was used for longitude. The residual deviance decreased with 

Figure 60. Arctic cod log transformed CPUE #/ha and temperature difference 

(°C), unlined net. Note: when removing the data point circled in red (high 

Cooks’ Distance), the relationship becomes non-significant. 

123456

Temperature Difference (°C)

1

3

5

7

9

Log Transformed CPUE #/ha

R2 = 0.51

P-value = 0.05

143
the addition of the second term but the Cp value increased (Table 48). The GAM model did not 

significantly explain the variance (F = 0.66, P = 0.62).

144
145

CPUE kg/ha 

Temperature difference was negatively correlated with CPUE kg/ha (P = 0.05; Figure 61 and 

Table 47). The Cook’s Distance on one observation exceeded 2.0 and when this data point was 

removed, the significant level dropped (P = 0.62), becoming a non-significant correlation. 

Despite the presence of a potential outlier, all data points were used for the GAM analysis 

because of the low sample size (n=10). Due to the many correlations between independent 

variables, only two rather than three term GAM models were possible. The two terms in the 

CPUE kg/ha GAM model, in order, were temperature difference with the lowest P-value from 

the linear regression (P = 0.05) and longitude with the next lowest P-value from the linear 

regression (P = 0.48). Although bottom temperature had a lower P-value than longitude, this 

variable was correlated with temperature difference. A linear b-spline smoother was used for 

temperature difference and a linear smoother was used for longitude Similar to CPUE #/ha, the 

residual deviance decreased but the Cp value increased with the addition of the second term 

(Table 49), and the GAM was not significant in accounting for the variance observed (F = 1.51, 

P = 0.27).

Figure 61. Arctic cod log transformed CPUE kg/ha and temperature 

difference (°C), unlined net. Note: when removing the data point circled in 

red (high Cooks’ Distance), the relationship becomes non-significant. 

123456

Temperature Difference (°C)

-4

-2

0

2

4 R2

 = 0.39

P-value = 0.05

/ha Log Transformed CPUE k

g
Arctic cod 

Unlined Net 

Longitude 

(decimal 

degrees) 

Bottom 

Temperature 

(°C) 

Temperature 

Difference 

(°C) 

Bottom 

Salinity 

(psu) 

Bottom 

Density 

(sigma-t) 

Salinity 

Difference 

(psu) 

Density 

Difference 

(sigma-t) 

CPUE #/ha – R2 0.06 0.10 0.51 (-) <0.01 <0.01 <0.01 <0.01 CPUE #/ha – P-value 0.51 0.38 0.05 0.92 0.97 0.97 0.88 CPUE kg/ha – R2 0.06 0.08 0.39 (-) 0.01 0.01 <0.01 <0.01 CPUE kg/ha – P-value 0.48 0.44 0.05 0.79 0.84 0.94 0.98 GAM Terms Smoothing Term Residual deviance Cp DF F P Temperature Difference b-spline linear 11.64 21.61 7 Temperature Difference + Longitude linear 9.44 22.74 6 0.66 0.62 GAM Terms Smoothing Term Residual deviance Cp DF F P Temperature Difference b-spline linear 12.94 24.03 7 Temperature Difference + Longitude linear 10.34 25.13 6 1.51 0.27 

Table 49. Results for Arctic cod, unlined net. Results of GAM between environmental variables 

and Arctic cod, from the unlined net station. The GAM terms are listed in the order of which they went into the model. Response: CPUE kg/ha. Significant values are in bold. 

Table 48. Results for Arctic cod, unlined net. Results of GAM between environmental variables 

and Arctic cod, from the unlined net station. The GAM terms are listed in the order of which they went into the model. Response: CPUE #/ha. Significant values are in bold. 

Table 47. Results for Arctic cod, unlined net. Results of linear regression between environmental 

variables and Arctic cod, from the unlined net stations. Data were log transformed, CPUE #/ha and CPUE 

kg/ha. R2 and P-values for each regression are shown. Significant P-values and the corresponding R2 are in 

bold designating if it is a positive (+) or negative (-) correlation. Results below include all data points. Variables shaded in gray are correlated; the variables shaded in light green are also correlated with one. In addition, longitude is correlated with salinity and density difference and temperature difference is 

correlated with density difference. 

146
Results for walleye pollock – unlined net

Linear regression and generalized additive model (GAM) 

CPUE #/ha 

A significant correlation was found between CPUE #/ha and the independent variable, longitude 

(P = 0.07), and the relationship was negative, CPUE #/ha decreasing from west to east in the 

study area (Figure 62 and Table 50). The salinity and density difference independent variables 

were also correlated with CPUE #/ha (P = 0.08; P = 0.10, respectively). The Cook’s Distance on 

the data observations did not exceed 1.0, suggesting there are no outlier data points. 

-155.6 -155.1 -154.6 -154.1 -153.6 -153.1 -152.6 -152.1

Longitude (decimal degrees)

-1

0

1

2

3

4

Log Transformed CPUE #/ha

R2 = 0.35

P-value = 0.07

Figure 62. Walleye pollock log transformed CPUE #/ha and longitude 

(decimal degrees), unlined net. 

Because longitude and salinity and density difference were correlated only longitude was used in 

the GAM analysis. Due to the many correlations between independent variables, only 2 rather 

than three term GAM models were possible. The two terms in the CPUE #/ha GAM model, in 

order, were longitude with the lowest P-value from the linear regression (P = 0.07) and bottom 

temperature with the one of the next lowest P-value from the linear regression (P = 0.51). 

Bottom salinity and density were not chosen for the GAM because they were correlatied with 

salinity and density differences which were in turn correlated with longitude. A linear smoother 

147
148

was used for both terms in the GAM. The residual deviance decreased but the Cp value 

increased (Table 51), and the GAM model was not significant (F = 1.36, P = 0.28)

CPUE kg/ha 

CPUE kg/ha was negatively correlated (P = 0.06) with longitude, CPUE decreasing from west to 

east in the study area (Figure 63 and Table 50). The Cook’s Distance on a log transformed data 

observation exceeded 1.0, indicating it was an outlier (Figure 64). When that observation was 

removed the relationship became non-significant (P = 0.17). 

Despite the presence of a potential outlier, all data points were used for the GAM analysis 

because of the low sample size (n=10). Due to the many correlations between independent 

variables, only two rather than three term GAM models were possible. The two terms in the 

CPUE kg/ha GAM model, in order, were also longitude with the lowest P-value from the linear 

regression (P = 0.06) and bottom temperature with one of the next lowest P-value from the linear 

regression (P = 0.43). None of the salinity or density variables were used in the GAM because 

they are correlated with each other and with longitude. A linear smoother was used for both 

terms in the GAM. The residual deviance stayed the same with the addition of longitude, but the 

Cp increased (Table 52). The GAM was not significant (F = 2.02, P = 0.20).

Figure 63. Walleye pollock log transformed CPUE kg/ha and longitude 

(decimal degrees), unlined net. Note: when removing the data point circled 

in red (high Cooks’ Distance), the relationship becomes non-significant. 

-155.6 -155.1 -154.6 -154.1 -153.6 -153.1 -152.6 -152.1

Longitude (decimal degrees)

-0.8

-0.6

-0.4

-0.2

0.0

0.2 R2

 = 0.35

P-value = 0.06

Log Transformed CPUE kg/ha
Pollock 

Unlined Net 

Longitude 

(decimal 

degrees) 

Bottom 

Temperature 

(°C) 

Temperature 

Difference 

(°C) 

Bottom 

Salinity 

(psu) 

Bottom 

Density 

(sigma-t) 

Salinity 

Difference 

(psu) 

Density 

Difference 

(sigma-t) 

CPUE #/ha – R2 0.35 (-) 0.06 0.03 0.18 0.16 0.34 (-) 0.31 (-) CPUE #/ha – P-value 0.07 0.51 0.63 0.23 0.24 0.08 0.10 

CPUE kg/ha – R2 0.37 (-) 0.08 <0.01 0.12 0.14 0.29 0.27 

CPUE kg/ha – P-value 0.06 0.43 0.99 0.32 0.23 0.11 0.13 

GAM Terms Smoothing Term Residual deviance Cp DF F P Longitude linear 9.67 14.51 8 Longitude + Bottom Temperature linear 8.1 15.36 7 1.36 0.28 GAM Terms Smoothing Term Residual deviance Cp DF F P Longitude linear 0.33 0.49 8 Longitude + Bottom Temperature linear 0.25 0.50 7 2.02 0.20 

Table 51. Results for walleye pollock, unlined net. Results of GAM between environmental 

variables and walleye pollock, from the unlined net stations. The GAM terms are listed in the order of which they went into the model. Response: CPUE #/ha. Significant values are in bold. 

Table 52. Results for walleye pollock, unlined net. Results of GAM between environmental 

variables and walleye pollock, from the unlined net stations. The GAM terms are listed in the order of which they went into the model. Response: CPUE kg/ha. Significant values are in 

bold. 

Table 50. Results for walleye pollock, unlined net. Results of linear regression between environmental 

variables and walleye pollock, from the unlined net stations, CPUE #/ha and CPUE kg/ha. R2 and P-values 

for each regression are shown. Significant P-values and the corresponding R2 are in bold designating if it is a 

positive (+) or negative (-) correlation. Variables shaded in gray are correlated; the variables shaded in light green are also correlated with one another. In addition, longitude is correlated with salinity and density 

difference and temperature difference is correlated with density difference. 

149
Results for all eelpouts – unlined net

Generalized linear model (GLM) 

The GLM analysis showed that none of the independent variables alone were significantly 

correlated with the presence/absence of eelpouts (Table 53). However, the two independent 

variables, bottom temperature and longitude, together explained approximately 38% of the 

variance in the presence or absence of eelpouts, unlined net, in the survey area (F = 5.68, P = 

0.05). The null deviance was 6.931 and residual deviance with both bottom depth and longitude 

was 4.0. 

150
Eelpouts (several species 

combined) 

Presence / Absence 

Longitude 

(decimal 

degrees) 

Bottom 

Temperature 

(°C) 

Temperature 

Difference 

(°C) 

Bottom 

Salinity 

(psu) 

Density 

(sigma-t) 

Salinity 

Difference 

(psu) 

Density 

Difference 

(sigma-t) 

Residual Deviance 

(Null Deviance: 6.931) 5.317 6.793 6.080 6.790 6.822 6.562 6.656 

F statistic 3.19 0.22 1.34 0.22 0.17 0.59 0.44 

P-value 0.11 0.65 0.28 0.65 0.69 0.46 0.53 

Table 53. Results for all eelpouts, unlined net. Results of Generalized Linear Models (GLM) of 

environmental variables and all eelpouts, from the unlined net stations. The dependent variable is species 

presence/absence (not CPUE). Model significance compares the residual deviance for each variable to the null deviance and reports a t-value. Numbers in bold are significant. All variables in shaded gray are correlated; the variables shaded in light green are also correlated with one another. In addition, longitude is correlated with salinity and density difference and temperature difference is correlated with density difference. 

151
Results for all sculpins – unlined net

Linear regression and generalized additive model (GAM) 

CPUE #/ha 

CPUE #/ha was significantly correlated with temperature difference (P = 0.07 and Table 54); the 

relationship was negative, CPUE #/ha decreasing with increasing temperature difference (more 

stratification) (Figure 64 and Table 54). Density difference was also correlated with CPUE #/ha, 

however, this is most likely due to density difference and temperature difference being 

correlated. 

123456

Temperature Difference (-°C)

-1.0

-0.5

0.0

0.5

1.0

1.5

2.0

Log Transformed CPUE #/ha

R2 = 0.35

P-value = 0.07

Figure 64. All sculpins log transformed CPUE #/ha and temperature 

difference (°C), unlined net. 

The two GAM terms, in order, are temperature difference with the lowest P-value from the linear 

regression (P = 0.07) and salinity difference with one of the next lowest P-value from the linear 

regression (P = 0.11). Although density difference had a lower P-value, this variable was 

correlated with temperature difference. A linear smoother was used for both terms. Due to the 

many correlations between independent variables, only two rather than three term GAM models 

were possible. The residual deviance decreased with the addition of bottom salinity but the Cp 

value increased (Table 55). The GAM model was not significant (F = 0.17, P = 0.70). 

152
153

CPUE kg/ha 

There were no significant relationships between CPUE kg/ha and any of the environmental 

variables.
Sculpins (several species 

combined)

Unlined Net 

Longitude 

(decimal 

degrees) 

Bottom 

Temperature 

(°C) 

Temperature 

Difference 

(°C) 

Bottom 

Salinity 

(psu) 

Density 

(sigma-t) 

Salinity 

Difference 

(psu) 

Density 

Difference 

(sigma-t) 

CPUE #/ha – R2 <0.01 <0.01 0.35 (-) 0.15 0.16 0.29 0.32 (-) CPUE #/ha – P-value 0.98 0.97 0.07 0.23 0.26 0.11 0.09 CPUE kg/ha – R2 <0.01 0.02 0.24 0.04 0.04 0.19 0.20 

CPUE kg/ha – P-value 0.83 0.74 0.15 0.59 0.56 0.21 0.19 

Table 54. Results for all sculpins, unlined net. Results of linear regression between environmental 

variables and all sculpins, from the unlined net stations, CPUE #/ha and CPUE kg/ha. R2 and P-values for 

each regression are shown. Significant P-values and the corresponding R2 are in bold designating if it is a 

positive (+) or negative (-) correlation. Variables shaded in gray are correlated; the variables shaded in light green are also correlated with one another. In addition, longitude is correlated with salinity and 

density difference and temperature difference is correlated with density difference. 

Table 55. Results for all sculpins, unlined net. Results of GAM between environmental variables 

and all sculpins, from the unlined net stations. The GAM terms are listed in the order of which they went into the model. Response: CPUE #/ha. Significant values are in bold. 

GAM Terms Smoothing Term Residual deviance Cp DF F P Temperature Difference linear 4.46 6.69 8 Temperature Difference + Salinity Difference linear 3.97 7.31 7 0.87 0.38 

154
Results for opilio crab – unlined net

Linear regression and generalized additive model (GAM) 

CPUE #/ha 

There were no correlations between CPUE #/ha and any of the environmental variables. 

CPUE kg/ha 

There were positive correlations between CPUE kg/ha and bottom salinity (P = 0.04) and bottom 

density (P = 0.05) (Figure 65 and Table 56). The Cook’s Distance on one observation exceeded 

1.0, indicating it was an outlier (Figure 66). When the data point was removed, the relationship 

became non-significant for both bottom salinity (P = 0.62) and bottom density (P = 0.61). 

25.0 25.2 25.4 25.6 25.8 26.0 26.2 26.4

Bottom Density (sigma-t)

-1.0

-0.5

0.0

0.5

Log Transformed CPUE kg/ha

Figure 65. Opilio crab log transformed CPUE kg/ha and bottom density 

(sigma-t), unlined net. Note: when removing the data point circled in red 

(high Cooks’ Distance), the relationship becomes non-significant 

Despite the presence of a potential outliers, all data points were used for the GAM analysis 

because of the low sample size (n=10). Due to the many correlations between independent 

variables, only two rather than three term GAM models were possible. The two terms in the 

GAM model, in order, were bottom salinity with the lowest P-value from the linear regression (P 

= 0.04) and longitude with the one of the next lowest P-values from the linear regression (P = 

155
156

0.47) (linear). Because bottom salinity and bottom density were correlated only one of the two 

variables was used in the GAM. Similarly salinity difference and density difference were not 

chosen for the second term because they were correlated with bottom salinity and density. Both 

the residual deviance and Cp values decreased with the addition of the second term (Table 57). 

The GAM model was significant (F = 12.66, P = 0.01). 
Opilio crab 

Unlined Net 

Longitude 

(decimal 

degrees) 

Bottom 

Temperature 

(°C) 

Temperature 

Difference 

(°C) 

Bottom 

Salinity 

(psu) 

Bottom 

Density 

(sigma-t) 

Salinity 

Difference 

(psu) 

Density 

Difference 

(sigma-t) 

CPUE #/ha – R2 0.19 <0.01 0.11 0.20 0.20 0.06 0.08 CPUE #/ha – P-value 0.21 0.89 0.34 0.19 0.20 0.48 0.44 CPUE kg/ha – R2 0.07 <0.01 0.03 0.42 (+) 0.40 (+) 0.16 0.16 CPUE kg/ha – P-value 0.47 0.79 0.65 0.04 0.05 0.26 0.26 GAM Terms Smoothing Term Residual deviance Cp DF F P Bottom Salinity linear 1.56 2.45 7 Bottom Salinity + Longitude linear 0.50 1.84 6 12.66 0.01 

Table 57. Results for opilio crab, unlined net. Results of GAM between environmental 

variables and opilio crab, from the unlined net stations. The GAM terms are listed in the order of which they went into the model. Response: CPUE kg/ha. Significant values are in bold. 

Table 56. Results for opilio crab, unlined net. Results of linear regression between environmental 

variables and opilio crab, from the unlined net stations, CPUE #/ha and CPUE kg/ha. R2 and P-values for 

each regression are shown. Significant P-values and the corresponding R2 are in bold designating if it is a 

positive (+) or negative (-) correlation. Variables shaded in gray are correlated; the variables shaded in light green are also correlated with one another. In addition, longitude is correlated with salinity and density difference and temperature difference is correlated with density difference. 

157
Pelagic fish habitat associations 

For young-of-the-year (YOY) fish and yearling-and-older (year-plus) Arctic cod, we tested both 

biological and standard oceanographic predictors. YOY fish density was not related to any 

biological oceanographic parameters under the linear or GAM model scenarios (Table 58). 

Using standard predictors, five variables were significant (bottom temperature, bottom salinity, 

salinity difference, density, and density difference) in the GAM model (Table 58), but there were 

concerns about this dataset given heterogeneous variance that was unimproved by data 

transformation. 

Year-plus Arctic cod models run with biological predictors provided different results depending 

on whether zero values were included for nearshore areas where year-plus estimates were not 

made. When zero values were included, the general linear model found no significant biological 

predictors of year-plus Arctic cod density (Table 59) and the GAM found a significant 

relationship with only temperature below the mixed layer depth (Table 59). When zero values 

were excluded, the linear model suggested a significant relationship between year-plus Arctic 

cod density and bottom depth, mixed layer depth (MLD), mean temperature below the MLD, and 

mean salinity below the MLD (Table 59). Using standard predictors, the general linear model 

found no significant standard predictors of year-plus Arctic cod density when zero values were 

excluded (Table 59). The GAM found a significant relationship with bottom temperature and 

salinity difference (Table 59) but there were concerns about data variance that could not be 

normalized by data transformation. When zero values were removed, the general linear model 

found no relationship between year-plus Arctic cod density and the standard predictors (Table 

59). Due to the low sample size (n=10) relative to the number of predictors (n=8), it was not 

appropriate to run the GAM on the zero -excluded datasets. 

158
Table 58. Model fits for YOY density versus oceanographic parameters. n is the number of data points, Predic

the “biological” or “standard” oceanographic variables listed in the text (* denotes a significant relationship), F i

statistic for the model, df are the number of degrees of freedom for the F distribution (# parameters, remaining defreedom for test), P is the p-value for the model fit, Adj.R2 is the fit to the model accounting for the number of pre

model, and Relationship is the model that was used and/or comments on the fit. 

Response variable n Predictor F df P Adj. R 2 Rela

YOY Density 19 Mean.Temperature.below.MLD 2.597 1,17 0.13 0.08 LineBiological predictors LowYOY Density 19 log(Bottom.Depth) > 0.05 0.38 GAMBiological predictors Mixed.Layer.Depth

log(Depth.N.2.max)Mean.Temperature.above.MLDMean.Salinity.above.MLDMean.Temperature.below.MLDMean.Salinity.below.MLDLongitude

YOY Density 19 log(Bottom.Depth) 1,17 0.16 0.06 LineStandard predictors LowYOY Density 19 Longitude 0.37 GAMStandard predictors Bottom.Temperature* 0.04

Delta.Surface.Bottom.TemperatureBottom.DepthBottom.Salinity* 0.05Delta.Surface.Bottom.Salinity* 0.03Bottom.Sigma.T* 0.04Delta.Surface.Bottom.Density* 0.04

159
Response variable n Predictor F df P Adj. R 2 Relations

YAO Density 19 log(Bottom.Depth) > 0.05 0.32 General l

Includes 0 values Mixed.Layer.Depth Quasipoi

Biological predictors log(Depth.N.2.max) AIC cann

Mean.Temperature.above.MLDMean.Salinity.above.MLDMean.Temperature.below.MLDMean.Salinity.below.MLDLongitude

YAO 19 log(Bottom.Depth) 0.42 GAM

Includes 0 values Mixed.Layer.DepthBiological predictors log(Depth.N.2.max)

Mean.Temperature.above.MLDMean.Salinity.above.MLDMean.Temperature.below.MLD* 0.04 ConcaveMean.Salinity.below.MLDLongitude

YAO 10 Bottom.Depth* 16.12 4,5 0 0.87 General l

Excludes 0 values Mixed.Layer.Depth* Lowest A

Biological predictors Mean.Temperature.below.MLD*

Mean.Salinity.below.MLD*

Table 59. Model fits for YAO density versus oceanographic parameters. n is the number of data points, Predic

“biological” or “standard” oceanographic variables listed in the text (* denotes a significant relationship), F is th

the model, df are the number of degrees of freedom for the F distribution (# parameters, remaining degrees of fre

P is the p-value for the model fit, Adj.R2 is the fit to the model accounting for the number of predictors in the modRelationship is the model that was used and/or comments on the fit. 

160
161

Response variable n Predictor F df P Adj. R 2 Relations

YAO Density 19 Longitude > 0.05 0.29 General l

Includes 0 values Bottom.Temperature Lowest AStandard predictors Delta.Surface.Bottom.Temperature

Bottom.DepthBottom.SalinityDelta.Surface.Bottom.SalinityBottom.Sigma.TDelta.Surface.Bottom.Density

YAO Density 19 Longitude 0.68 GAMIncludes 0 values Bottom.Temperature* 0.02

Standard predictors Delta.Surface.Bottom.Temperature

Bottom.DepthBottom.SalinityDelta.Surface.Bottom.Salinity* 0.01Bottom.Sigma.TDelta.Surface.Bottom.Density

YAO 10 Longitude 10.1 8,1 0.24 General lExcludes 0 values Bottom.Temperature Lowest A

Standard predictors Delta.Surface.Bottom.Temperature

Bottom.DepthBottom.SalinityDelta.Surface.Bottom.SalinityBottom.Sigma.TDelta.Surface.Bottom.Density

Table 59 cont.- Model fits for YAO density versus oceanographic parameters. n is the number of data points, P

to the “biological” or “standard” oceanographic variables listed in the text (* denotes a significant relationship), 

statistic for the model, df are the number of degrees of freedom for the F distribution (# parameters, remaining d

freedom for test), P is the p-value for the model fit, Adj.R2 is the fit to the model accounting for the number of pre

model, and Relationship is the model that was used and/or comments on the fit. 
Discussion 

Our 2008 survey was the first dedicated survey of the offshore marine fish and invertebrates of 

the Beaufort Sea. The most recent previous offshore survey of any kind was an opportunistic 

bottom trawl survey conducted in 1976-77 (Frost and Lowry 1983). Our survey was thus a pilot 

survey to provide recommendations for future monitoring methods in addition to baseline data 

against which to compare future anthropogenic and climate impacts. Because it was a pilot 

survey, different techniques were employed to assess fish abundance. It is important to note that 

density, abundance, and biomass estimates from the bottom trawl and acoustic/midwater trawl 

surveys targeted different sections of the water column, used different sampling gears, and 

followed disparate sampling strategies and analytic paths. 

 

Demersal fish and benthic invertebrates

We report fish density (catch-per-unit-effort, CPUE) and abundance by depth but not for all 

depths combined. This is because, by coincidence, the deeper depth (100-500 m) was sampled 

with the lined 3.8 cm (1.5”) mesh net and the shallower depth (40- 100 m) was sampled 

primarily with the unlined net with 10.16 cm (4”) mesh in the wings and body and 8.89 cm 

(3.5”) mesh in the sidewings. The gear type was changed because all the lined nets were 

damaged by the time the ice cleared out of the survey area and we could access the shallower 

waters. A qualitative comparison of CPUE for all lined vs. unlined trawls does show that both 

the total volume of fauna captured and the number of species observed was greater for the lined 

net. However, this pattern could also be due to geographic location (shallow vs. deep strata). As 

an insight into gear performance, we conducted two sets of paired trawls, one with the lined net 

and one with the un-lined net in approximately the same location (but separated by several days). 

The catch was higher for the lined net for both fish and invertebrates, dramatically so for the 

invertebrates. So, the abundance and density of fish and invertebrates in the deeper 100-500 

meter depth is probably biased high, compared to the catch in the shallower 40-100 meter depth. 

Not surprisingly, Arctic cod were the most abundant fish caught during this survey, both 

numerically and by weight. Arctic cod are known to be a major component of the Beaufort Sea 

fish community and important prey for higher trophic levels such as seabirds (Hobson 1993) and 

marine mammals (Bradstreet and Cross 1982, Bradstreet et al. 1986, Welch 1992). They are also 

the dominant consumer of zooplankton (Atkinson and Percy 1992) and are thus an important 

conduit for secondary production (Welch 1992). One of the earliest documented records of 

Arctic cod in the Alaskan Beaufort Sea is from 1951 (University of British Columbia, N.J. 

Wilimovsky, H.A. Fehlmann) and they were the most abundant fish during the 1976-77 

opportunistic trawl survey (Frost and Lowry 1983). Previous studies in nearshore, often brackish 

waters have documented the distribution of Arctic cod (Craig 1984, Craig et al. 1982, Jarvela and 

Thorsteinson 1999, Moulton and Tarbox 1987), but our study is the first to thoroughly map the 

distribution of Arctic cod in offshore marine waters. Yearling-and-older (year-plus) Arctic cod 

were most abundant offshore of the shelf-break (100 m). It is possible that the apparent off-shelf 

distribution of year-plus demersal Arctic cod was an artifact of bottom trawl net type. However, 

the acoustic data (confirmed by midwater trawls) similarly showed that year-plus cod were most 

162
abundant and widespread off-shelf and three bottom trawls conducted with the lined net on the 

shelf caught less cod than the offshore trawls. 

Arctic cod lengths indicated that most of the fish were likely sub-adults, although there was a 

second mode of larger, likely adult fish. Analysis of Arctic cod otoliths is underway and will 

allow us to confirm the age distribution of the fish. Larger Arctic cod were distributed primarily 

in the deeper depth and the smaller cod primarily in the shallower depth. (Frost and Lowry 

1983) documented a similar distribution pattern from their 1976-77 survey. They report that 

Arctic cod found in water deeper than 100 m had a mean length of 11.4 cm (in this study, fork 

length was 13.2 cm in the bottom trawl and 10.3 cm in the midwater trawl). Whereas cod in 

water less than 100 m had a mean length of 8.1 cm (10.2 cm in the bottom trawl and 11.6 cm in 

the midwater trawl in this study). 

Other numerically abundant species in the bottom trawls included eelpouts (seven species) and 

sculpins (eight species), although sculpins made up a small fraction of the total weight of fish 

captured. Eelpouts and sculpins were also numerically abundant in the catches from the 1976-77 

survey (Frost and Lowry 1983), although there appears to have been a shift in the relative species 

composition of the two groups of fish. Similar species of eelpouts was found in both the 1976-

77 survey and our 2008 survey. However, marbled eelpout (Lycodes raridens) was the most 

abundant during the present survey and Canadian eelpout (Lycodes polaris) was the most 

abundant during the previous survey. Common sculpin species during the 2008 survey were 

warty sculpin (Myoxocephalus verrucosus) and ribbed sculpin (Triglops pingeli). The most 

common sculpin species caught during the 1976-77 survey were twohorn sculpin (Icelus 

bicornis) and spatulate sculpin (Icelus spatula). In fact, twohorn sculpin was the second most 

abundant species overall in the 1976-77 survey and we did not catch any of that species in 2008. 

It is not impossible that some of these species were mis-identified in the field, however all our 

species identifications were confirmed by examination of voucher specimens and/or genetic 

barcoding (J. Orr and D. Stevenson, AFSC; and K. Mecklenburg pers. com.). 

The density (CPUE) of eelpouts, from the bottom trawls, was greater offshore of 100 m than 

inshore. Some of this difference could have been due to the bias resulting from trawling 

exclusively with the lined net offshore. However, three stations sampled with the lined net 

inshore showed low CPUE of eelpouts. As eelpouts are found within the 0.5 m acoustic 

deadzone, no inferences on eelpout inshore-offshore distributions can be made from the pelagic 

survey. Sculpins are the only group of species that show a distribution pattern that may be 

unrelated to net type (lined vs. unlined). Nearly all of the trawls in the offshore depth (lined net) 

had zero catches of sculpins, whereas the inshore depth (unlined net) had catches with a 

consistently higher CPUE. The expectation is that catches of these small fish would be greater in 

the lined net, not less. Furthermore, the three stations that were sampled with the lined net 

inshore had the highest sculpin CPUE. 

Agglomerative clustering analysis highlighted five clusters of co-occurring species. Some of 

these species groups had distinctive inshore vs. offshore distributions. Eelpouts, Bering flounder 

snailfish, walleye pollock and Greenland turbot co-occurred and this cluster was found only in 

the deeper depth. These species could co-occur as a result of shared prey or as a result of 

predator-prey relations. The association of Greenland turbot and walleye pollock is likely a result 

163
of the latter. Walleye pollock is the dominant prey of Greenland turbot in the Bering Sea (Lang 

et al. 2005). The other three species in this cluster (eelpouts, Bering flounder and snailfish) 

likely co-occur as a result of shared prey. In the Bering Sea, they typically consume benthic 

invertebrate prey such as shrimp, polychaetes and mysids (Aydin et al. 2008). Unfortunately, 

food habits data for these species do not exist for the Beaufort Sea region such that further study 

is needed to confirm these relationships. Clusters in which sculpins were dominant were 

primarily distributed in the shallow depth. Sculpins of the Arctic burrow into sand and sand-mud 

bottoms with salinities of 32-35 ppt, sometimes as low as 16-30 ppt, feeding on small benthic 

amphipods and polychaetes (Fedorov 1986). The nearshore distribution of this cluster, 

dominated by sculpins, may be driven by a preference for muddy substrate, small benthic prey 

and a preference/tolerance for low salinity water. More detailed study of substrate type and the 

distribution of small benthic invertebrates is needed to test this hypothesis. The cluster that was 

comprised of the only three shallow trawls that occurred with a lined net had the highest 

diversity of species and occurred only in the western half of the study area. This could be an 

indication that the areas closer to shore are characterized by a greater diversity of habitat 

(substrate and prey). However, it is important to note that the spatial distribution of lined vs. 

unlined trawl stations could have influenced the results, in spite of the fact that the cluster 

analysis was conducted on species presence/absence data (as opposed to CPUE or catch 

abundance). 

Invertebrates dominated the bottom trawl catches both in terms of abundance and species 

diversity. The possible inflation of catch due to the lined net was greater for invertebrates than 

for fish. Notched brittle stars (Ophiura sarsi) were the most abundant species captured, followed 

closely by opilio crab (Chionoecetes opilio). In the 1977 survey, notched brittle stars were also 

reported to be the most abundant invertebrate captured (Frost and Lowry 1983) and dominated 

the catch west of longitude 154°. The top 24 species in our survey had significantly higher 

biomass in the offshore depth than the inshore depth, but this could have been an artifact of 

sampling the offshore depth with the lined net. Interestingly, three of the top 24 species caught 

in our 2008 survey (Halocynthia aurantium, Pagurus trigonocheirus, and Hyas coarctatus) had 

higher biomass and CPUE estimates in the 40-100 m depth (unlined net) than in the deeper depth 

(lined net), indicating habitat differences or depth preference for these species of invertebrates 

that were independent of the expected bias due to net type. 

 

The size and depth distribution of opilio crab (Chionoecetes opilio) were unexpected, based on 

previous studies in the Bering and Chukchi Seas. In 1990 and 1991, 48 stations were sampled in 

the northeast Chukchi Sea to examine the distribution and abundance of opilio crab (Paul et al. 

1997). Opilio crabs were found at all stations, with the highest abundance and mean crab weight 

occurring in the stations directly west of Pt. Barrow. However, carapace width of these crabs 

ranged from 20-74 mm, as compared to the measured opilio crab in our Beaufort survey that 

ranged from 55-119 mm. Opilio crab were caught in the 1977 Beaufort Sea survey (Frost and 

Lowry 1983), however, maximum carapace width was 75 mm. The legal minimum carapace 

width for the commercial opilio crab fishery in the Bering Sea is 78 mm, and the minimum 

commercially viable width is 101 mm. So, our survey is the first to document opilio crab of 

commercial size in the North American Arctic. Recently, Chionoecetes opilio have been 

observed in the northeast Atlantic’s Barents Sea (Alvsvåg et al. 2008). Evidence of juveniles 

below 50 mm carapace width confirms that the population is established and reproductive with 

164
adult crabs ranging in size from 50 mm to 136 mm (Alvsvåg et al. 2008). The presence of 

female crabs with egss during the 2008 Beaufort Sea Survey is further evidence that this 

population also is reproductive. The main population of crab found in the Barents Sea survey 

was located in waters less than 2°C, with depth ranges from 80 to 350 m (Alvsvåg et al. 2008). 

The fact that Frost and Lowry (1983) only caught small opilio crab may be due to the fact that 

only one tow was made in water deeper than 200 m. We found the highest CPUE and the largest 

crabs by carapace width and weight in water depths greater than 300 m. This result was also 

unexpected as surveys in the Bering and Chukchi Seas indicate that opilio crabs are found 

predominatly in waters less than 200 m in depth. 

Changes in the species composition of the fish community since 1977 may have occurred. 

Bering flounder (Hippoglossoides robustus), walleye pollock (Theragra chalcogramma), and 

Pacific cod (Gadus macrocephalus) were caught in our 2008 survey but not the earlier Frost and 

Lowry (1983) survey. These are species that are abundant in the Bering Sea and are 

commercially valuable. In addition, our 2008 survey was the first to document commercial-sized 

opilio crab (Chionoecetes opilio) in the North American Arctic. Previous surveys caught 

smaller-sized crab (Barber et al. 1997, Frost and Lowry 1983). We also document or confirm 

extensions to the known ranges of four species of fish: walleye pollock (Theragra 

chalcogramma), Pacific cod (Gadus macrocephalus), festive snailfish (Liparis marmoratus), and 

eyeshade sculpin (Nautichthys pribilovius). The Chukchi Sea survey in 1990 reported Pacific 

cod at 3 stations located between 68°N and 69°N. Festive snailfish are a relatively rare species, 

only 1 specimen has been recorded in the NE Bering Sea near St. Lawrence Island at 63°00’N, 

169°20’W (Busby and Chernova 2001). Previous to this record, the species had only been 

documented in the Sea of Okhotsk. The northernmost record of the eyeshade sculpin previous to 

our survey was in the north Chukchi Sea, west of Point Barrow (Barber et al. 1997). 

We caught walleye pollock as far north as 71°59’N, 154°25’W. The domestic groundfish fishery 

off Alaska is the largest fishery by volume in the U.S. and walleye pollock make up the 

dominant portion of that catch (Hiatt et al. 2008). Pollock were recorded as far north as 71°23’N 

during a 2004 survey of the Chukchi Sea (Mecklenburg et al. 2007) and a specimen was 

collected at 69°26’N, during a 1990 survey of the Chukchi Sea on the Ocean Hope III

(unpublished data; cruise 90-2). Two specimens were collected in the Beaufort Sea near the 

mouth of the Elson lagoon, east of Point Barrow at approximately 71°31’N, 156°32’W in 1951 

and 1954 (University of British Columbia: N. J. Wilimovsky, J. E. Bohlke; D. Wohlschlag, and 

W. C. Freihofer). However, the specimens are missing and identification as walleye pollock is 

uncertain (K. Mecklenburg, pers.com). We found pollock in moderate densities (compared to 

other species) throughout the survey area, so if the Elson lagoon samples collected in 1954 were 

correctly identified as pollock our results confirm the range extension and document that the 

species may be widespread in the Beaufort Sea. Analysis of pollock otoliths showed that most of 

the fish caught during our 2008 survey were sub-adults, age 2. In 1990, an ichthyoplankton 

survey in the Chukchi Sea (Echeverria 1995) found juvenile walleye pollock northwest of 

Barrow. During the RUSALCA survey of the Chukchi Sea in 2004, Mecklenburg et al. (2007) 

recorded lengths of pollock ranging from 102-168 mm total length (TL), indicating that these 

fish were likely sub-adults. So, although pollock are occurring in Arctic seas, fish of spawning 

age or size have not yet been documented and the origins of the juvenile fish are not known. The 

fact that the pollock we caught in the Beaufort Sea were smaller at age than pollock in the Bering 

165
Sea may provide evidence that the fish were spawned in cold Arctic waters or were transported 

into such waters shortly after spawning. The size difference is manifested first at age-2: age-1 

pollock from the Bering and Beaufort Seas were similar in size. This lends support to the latter 

hypothesis, that fish were spawned in north Pacific waters and transported into the Arctic 

sometime during their first year of life. 

The summer of 2007 saw the largest recession of sea ice since recording began (Boe et al. 2009, 

Greene et al. 2008, Stroeve et al. 2007, Stroeve et al. 2008). Trends of ocean warming and 

declines in Arctic sea ice increase the potential for the northward migration of fish and 

invertebrate species. Several factors have contributed to shifts in observed trends in Arctic ice 

cover over the last few decades. Both lengthened periods of open water, and an increase in sea 

surface temperatures have contributed to delays in the Arctic autumn and winter ice growth 

(Stroeve et al. 2007). Longer periods of open water may offer opportunities for a more northerly 

migration of fish species during the autumn months. Northerly extensions of fish ranges have 

been predicted to result from ocean warming (IASC 2004, Mueter et al. 2009, Mueter and 

Litzow 2008). For example, walleye pollock were predicted to expand northward in a warming 

climate, primarily due to the lessening extent of ice and more favorable temperatures over longer 

time periods (Strickland and Sibley 1984). Similarly, many Atlantic and North Sea fish 

communities have shown a northward trend in distributions over the last several decades (Beare 

et al. 2004, Perry et al. 2005). Despite the potential northward shift in the distribution of some 

species, the fish community of the Beaufort and Chukchi Seas is still distinct from the Bering 

Sea. Arctic cod are a dominant component of the Beaufort and Chukchi Sea fish communities, 

whereas pollock, Pacific cod and flatfish dominate the Bering Sea. We document the presence 

of pollock and commercial-sized opilio crab in the Beaufort Sea, but their densities are far lower 

than in the Bering Sea. 

 

Pelagic fish 

Although previous acoustic assessments of yearling-and-older (year-plus) Arctic cod have 

occurred in the both the Canadian and American portions of the Beaufort Sea (Benoit et al. 2008, 

Crawford and Jorgenson 1996, Crawford and Jorgenson 1993, Moulton and Tarbox 1987), these 

previous studies have focused primarily on overwintering or schooling fish in semi-protected 

bays. This study is, to our knowledge, the first systematic, open water assessment of year-plus 

Arctic cod. This study also appears to be the first summertime systematic assessment of youngof-the-year (YOY) fish including Arctic cod. 

The most abundant species observed during the pelagic survey was Arctic cod. With the 

exception of a few rare species (mostly near-bottom) captured in the midwater trawl, year-plus 

Arctic cod dominated the pelagic region. Similarly, YOY Arctic cod were captured more 

frequently and in higher numbers than either YOY fish from the sculpin family, Cottidae, or 

YOY Lumpenus sp., a species of eelblenny. For that reason, we infer that YOY Arctic cod was 

the dominant YOY species. Both YOY fish and year-plus Arctic cod had identifiable acoustic 

patterns on echograms that were combined with targeted trawling to classify backscatter in 

species and age-group categories. 

166
Young-of-the-year fish dominated areas with water depths less than 75 m and were observed in 

near surface waters throughout the survey area. The observation of high densities along the 

entire easternmost transect is consistent with YOY presence over the continental shelf as the 

shelf widened at the eastern end of the survey area. Unidentified sculpins (Cottidae) were more 

frequently captured in the 40-100 m depth and dominated the single near-surface trawl in the 

100-500 m depth. Additional trawling effort in near-surface waters would clarify whether these 

sculpins are consistently found in the offshore region. Density distribution plots for YOY fish 

suggested that near-surface densities in the 100-500 m depth may increase from west to east. 

Yearling-and-older (year-plus) Arctic cod densities were highest at water depths greater than 100 

m, with peak densities occurring at approximately 200 m depth. However, some high year-plus 

Arctic cod densities were detected in the 40-100 m depth due to the presence of dense year-plus 

schools. Interestingly, year-plus within these schools had higher mean lengths than year-plus 

found in layers within the 100-500 m depths. Diet analysis of Arctic cod found in these large 

schools compared to those found in deeper water would clarify whether they were using the 40-

100 m depth to feed on YOY fish. The concentration of year-plus Arctic cod in the vicinity of 

the shelf break between the 100 and 300 m contours was striking as it coincides with observed 

foraging patterns by beluga whales (Delphinapterus leucas) along the continental slope (Moore 

2000, Suydam et al. 2001). 

The highest densities of both YOY fish and year-plus Arctic cod were found at the ends of 

transects (shallow southern end for YOY, deeper northern end for year-plus) and on crosstransects, at depths of 200 – 400 m. This observation suggests that acoustic transects did not 

extend far enough in either northern or southern directions to capture the entire extent of YOY 

fish or year-plus Arctic cod distributions. Since nearshore regions may be important nursery 

habitat for YOY, a dedicated nearshore survey of YOY fish is needed. Additional effort is also 

needed to examine the potential importance of offshore near-surface regions for YOY fish and to 

quantify the relative contribution of offshore regions to YOY recruitment. 

Density estimates of YOY fish and year-plus Arctic cod are based on expected mean target 

strengths derived from this study. At each analytic step used to determine the target strength to 

length relationship, conservative choices were made to ensure that the resulting density estimates 

would also be conservative. As an example, a larger mean target strength was used in the 

calculation of YOY total fish density as it was based exclusively on YOY Arctic cod, which 

were longer than either Lumpenus sp. or Cottidae YOY. A smaller mean target strength would 

have resulted if the value was calculated using all three species, which would have increased the 

total YOY fish density estimate. Additional studies of YOY and year-plus Arctic cod, YOY 

Lumpenus sp., and YOY Cottidae target strength are needed to increase accuracy and precision 

of density, abundance, and resulting biomass estimates. The limited information available that 

describes methods used for single target detections in other studies of Arctic cod restricts our 

ability to compare reported target strength measurements and corresponding density estimates. 

The use of Sawada’s Nv index (Sawada et al. 1993) to avoid detecting multiple fish targets as 

single echoes in this study may be unique among acoustic studies of Arctic cod. The detection of 

multiple fish as single echoes would bias target strength estimates high, leading to the false 

conclusion that any estimated fish length, based on target strength to length relationships, was 

167
larger than it actually was. In that case, resulting density estimates, using inflated target strength 

values, would be biased low. 

Previous acoustic surveys of year-plus Arctic cod in the Beaufort Sea focused on characterizing 

schools or overwintering aggregations, so direct comparison with the current study are limited. 

In a 2004 survey of overwintering Arctic cod in the Canadian Beaufort (Franklin Bay), Benoit et 

al. (2008) reported that year-plus Arctic cod densities ranged from 72 × 103

 to 19,610 × 103 #/ha. 

The Benoit et al. (2008) data characterized a small spatial location between February and April. 

Fish lengths used to estimate densities by Benoit et al. (2008) included larger fish than those 

sampled in this study. In a second set of studies, Crawford and Jorgenson (1993, 1996) 

examined year-plus Arctic cod densities in two locations: Resolute Bay (Crawford and Jorgenson 

1993; Canadian Beaufort Sea, surveyed 1986) and in Allen Bay (Crawford and Jorgenson 1996, 

Canadian Beaufort Sea, surveyed 1989-1990). Sampling for both studies was conducted during 

August and targeted schooling aggregations of year-plus Arctic cod. In Resolute Bay, year-plus 

densities ranged from 6 × 103

 to 159 × 103 #/ha (Crawford and Jorgenson 1993). In Allen Bay, 

within school year-plus densities were between 20 × 103

 and 83,250 × 103 #/ha (Crawford and 

Jorgenson 1996). Finally Moulton and Tarbox (1987) quantified year-plus Arctic cod densities 

near Prudhoe Bay (American Beaufort Sea, surveyed 1978-1979) in water <10 m deep. 

Converting their volumetric estimates to areal estimates, Moulton and Tarbox (1987) found yearplus densities that ranged between 0 and 22,691 × 103

 #/ha. Echograms presented in Moulton 

and Tarbox (1987) suggest that fish were present in small schools. As a caveat, echo counting 

methods used in Moulton and Tarbox (1987) may have resulted in the potential detection of 

multiple YOY targets as single year-plus fish, thereby biasing their year-plus Arctic cod density 

estimates high. As a comparison, our maximum year-plus Arctic cod density (155 × 103

 #/ha) 

occurred in a dense region of the year-plus layer within the 100-500 m depth. This density 

corresponds to the maximum density within schools measured by Crawford and Jorgenson 

(1993) in Resolute Bay but is far less than maximum densities reported by Benoit et al. (2008) 

and Moulton and Tarbox (1987). 

Although results from the acoustic/midwater trawling survey are assumed to be representative of 

YOY fish and year-plus Arctic cod distributions within the 20-500 m depth range in the Beaufort 

Sea, three caveats are noteworthy. First, the extent of the survey area was limited relative to the 

entire Beaufort Sea shelf. Given the limited extent of the survey, it is not possible to detect and 

describe large-scale patterns in distribution. Second, our observations of year-plus Arctic cod 

distribution may indicate an association with oceanographic conditions (e.g. Chukchi Sea water 

inflow). If this is true, spatial distribution of year-plus Arctic cod may be influenced more by 

oceanographic than by bathymetric characteristics. 

Comparison of demersal trawl and pelagic acoustic methods 

Relationships between acoustic estimates of yearling-and-older (year-plus) Arctic cod density 

and bottom trawl estimates were related to whether the year-plus Arctic cod layer was in contact 

with the bottom (categorical bottom depth predictor). When the year-plus Arctic cod layer was 

168
in contact with the bottom (generally <300 m bottom depth) there was a positive relationship 

between acoustic and bottom trawl estimates. Bottom trawl estimates of year-plus Arctic cod 

sometimes were higher than acoustic estimates, but a positive relationship existed. In contrast, in 

regions greater than 300 m bottom depth where the layer was located off bottom there was a 

negative, or no, relationship between the acoustic and bottom trawl survey estimates. This 

finding suggests that while the bottom trawl may be an appropriate assessment tool for year-plus 

Arctic cod in regions where the year-plus layer is in contact with the bottom, it cannot provide 

quantitative estimates of density in deep offshore regions. Further, the acoustic survey results 

suggested that within the study area the maximum densities of year-plus Artic cod were located 

in regions that were not effectively surveyed by the bottom trawl gear. GAM models suggested 

that there was an increasing, nonlinear trend in year-plus Arctic cod density with depth. Had our 

survey extended into deeper water, the line may have hit an asymptote and decreased after the 

300-350 m depth mark. In contrast, GAM results suggested that there was no relationship 

between bottom trawl CPUE and bottom depth and delineating trawls into lined and unlined nets 

did not suggest separate relationships. 

Fish habitat (physical oceanography)

Winds during the field program were generally variable with moderate speeds of 3-7 m s-1. In 

general the wind conditions favored a relatively steady outflow of Chukchi Sea shelf water to the 

northeast through Barrow Canyon and along the Beaufort Sea shelfbreak and the inner shelf 

north and east of Pt. Barrow (Okkonen In press). These winds likely resulted in the distribution 

of cold Chukchi Sea water in the deeper areas of the study area (greater than 100m depth) 

described below. However, there were two periods of relatively strong northeasterly winds 

including August 7 (7-12 m s-1) and August 13-15 (12-15 m s-1). Pickart et al. (2010), found on 

average, that an easterly wind speed of 6-7 m s-1 results in a significant upwelling event in the 

Beaufort shelfbreak current, as measured by salinity changes, which lags the winds by about 18 

hours, whereas the current response lags the winds by about 8 hours. These time scales are 

similar to those reported by (Weingartner et al. 1998) for the Northeast Chukchi Sea. In 

particular they noted that flow in Barrow Canyon reversed to southward (upcanyon) when 

northeasterly winds exceeded about 6 m s-1. Winds were substantially strong and persistent 

enough during the August 13-15 wind event to possibly reduce or even reverse the flow in 

Barrow Canyon and induce upwelling along the Beaufort Sea shelfbreak. 

Evidence for this Chukchi Sea outflow is found in the cold and high salinity water that was 

observed offshore of the shelf break on the western transects. Although winds were generally 

from the southwest during the survey, there was a period of sufficiently strong and prolonged 

northeasterly winds that caused an upwelling event. The effects of the upwelling were evident 

along the transects sampled after the wind event. The bottom-trapped thermohaline front was 

more diffuse and was shifted shoreward and cold and high salinity water was observed inshore 

and towards the surface. 

The prevailing winds in the Beaufort Sea are from the northeast and force a westward winddriven flow over the shelf and an onshore and westward drift of first- and multi-year sea ice from 

the basin onto the shelf. On average, the wind-field promotes upwelling onto the shelf of 

nutrient laden sub-surface waters from the shelfbreak with this process probably being critical to 

maintaining the shelf nutrient supply on an annual basis. There is however substantial seasonal 

169
variation in the alongshore wind stress as summarized in the form of monthly statistics using the 

archived National Weather Service wind record in Barrow from 1949-2005. The statistics 

plotted in Figure 66 are based on the alongshore component of the winds, which accounts for 

most of the variance in the winds and which are primarily responsible for forcing shelf 

circulations. On a monthly basis the majority of the alongshore winds are westward (upwelling 

favorable) with the westward wind stress being stronger than eastward (downwelling-favorable) 

winds. Westward winds are strongest in late fall and early winter and occur most frequently in 

October and November and in March. The frequency of eastward winds, such as those that 

dominated during our survey, peaks in August, although westward wind stress is stronger than 

eastward stress in summer. 

Figure 66. Mean monthly wind statistics of the alongshore winds based on 

the 1949 – 2005 National Weather Service observations from Barrow 

Alaska. Upper left panel shows the percentage of days in a month in w

there are westward (upwelling-favorable; black circles) and eastwar

(downwelling-favorable; red circles) winds. The upper right panel show

the mean monthly wind stress for eastward and westward winds. The 

bottom panel shows the mean monthly wind stress (which is westward in 

all months). 

hich 

d 

s 

170
The occurrence of Pacific Ocean-derived waters (modified on the Bering and Chukchi shelves) 

that exit the Chukchi shelf through Barrow Canyon and into the Beaufort Sea has been 

documented previously (Aagaard and Roach 1990, Mountain et al. 1976, Pickart et al. 2005, 

Weingartner et al. 1998, Weingartner et al. 2005b, Woodgate et al. 2005b). Some of this outflow 

continues eastward (in the surface layer in summer) and/or as a subsurface current along the 

Beaufort shelfbreak and slope and contributes to the upper halocline of the Canada Basin 

(Aagaard 1984, Mountain et al. 1976, Pickart 2004, Pickart et al. 2005) and some appears to 

spread westward and/or offshore in the polar mixed layer (Shimada et al. 2001). However, some 

of the canyon outflow rounds Pt. Barrow and continues onto the inner portion of the Beaufort 

shelf, although the frequency and the extent to which this occurs are unknown. 

The differences between transects 2 and 3 may be because portions of these lines were sampled 

after the strong upwelling event of August 13-15. Note in particular that along both transects the 

31 isohaline extends to within about 10 km of the 20 m isobath, whereas along Transect 1, this 

isohaline is approximately 20 km seaward of the 20 m isobath. are readily apparent, e.g. note the 

upward bowing of the isohalines and isotherms beginning within 30 km of the 20 m isobath 

which has brought cold (2o

C), salty (31) water inshore and to within 10 m of the surface at the 

innermost station (Figure 43). 

Curiously, however, the saltier (31.5-32.5) isohalines that comprise the shelfbreak front along 

transect 5 intersect the bottom along the 60 m (or deeper) isobaths. These depths are 

approximately 40 m deeper than the depths in which the same isohalines intersect the bottom 

along Transect 1 (e.g. Figure 40). The data suggest that the upwelling event has split the 

shelfbreak front such that the shallower isohalines have migrated inshore and upward following 

classic upwelling behavior, whereas the deeper isohalines have moved deeper. The reasons for 

this apparent split are unclear; however, we note that while the salinities of the water masses 

comprising the shelfbreak front along Transect 5 are identical to those along the front in Transect 

1. The temperatures within the shelfbreak front along Transect 1 are, however, colder 

(approximately-1o

C) than those along Transect 5 suggesting that these water masses have 

different mixing histories as they flow along the shelfbreak. 

We suspect that the lens of very fresh (27.5) and warm (approximately 4.5o

C) water 

approximately 20 km seaward of the 20 m isobath along Transect 5 (Figure 43).this might be a 

filament or eddy of riverine water that was formed to the east of this section, since it is not found 

along any other line. Finally, as with the other sections, the near-surface waters at the offshore 

end of the line are also quite fresh and suggest the influence of ice melt waters in this area. 

These very cold (-1.5 to -1.0o

C) water with salinities between 32.5 and approximately 34 

between 50 and 150 m (figure 20 waters were formed in winter on the Bering-Chukchi shelves 

and comprise the cold upper halocline of the Canada Basin. Below approximately 150 m depth, 

salinity and temperature increase rapidly over the next 50 m and such that below 200 m salinities 

are 34.5 – 34.7 and temperatures are between 0 and 0.5o

C. These relatively warm, salty waters 

are derived from the Atlantic Ocean. 

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The cold, salty water along Transects 1 and 2 with the coldest stations found offshore of the 

shelfbreak was most likely formed on the Chukchi Sea shelf during the previous winter 

(Weingartner et al. 2005b) during the formation of sea ice. These winter-origin waters continue 

to drain offshore throughout spring and summer (Pickart et al. 2005, Weingartner et al. 2005b) 

with the most likely points of egress being Barrow Canyon in the northeast Chukchi Sea and 

Herald Valley on the western shelf (Russian EEZ). Some of this water flows eastward along the 

slope and apparently warms since the temperatures in this salinity range have increased slightly 

as evident in the θ-S panels for Transects 3, 5, and 6. The source of the heat must be through 

vertical mixing, either with warmer and fresher water at shallower depths or with saltier and 

warmer water from deeper depths. The figure also indicates that water types in the 30 - 32 

salinity range (delineated by vertical bars in Figure 45) span a broad temperature range (-1.3 to 

4o

 C). The coldest waters in this salinity range occur over and seaward of the shelfbreak, while 

the warmer waters are inshore of the shelfbreak. Nevertheless these water types have similar 

densities so that they can mix laterally along isopycnal (constant density) surfaces. 

Note that the coldest waters (near the freezing point) range between 32.5 and 33.3. These are 

associated with the Arctic Ocean’s permanent halocline, which in the study area can vary in 

depth from between 80 and 150 m. Beneath the halocline, salinities and temperatures both 

increase and this is indicative of the warmer and saltier waters of Atlantic Ocean origin that 

occupy the Arctic Ocean basin. 

For the most part shelf waters (<~60 m) have salinities <32.3 and range in temperature from ~-

1°C - <6°C.A more refined analysis of water mass origin would require an in-depth elucidation 

and analyses of geochemical properties of each water type. 

In addition to winds, sea ice and river outflow influenced water mass properties during our study. 

Evidence of recent ice melt was found in cold, low salinity waters in the upper few meters of the 

water column. Along the western transects there was a pronounced shallow surface haline front 

at the 40-50 m depth contour, separating offshore ice melt waters from warmer, saltier waters 

nearshore. River outflow water influenced water column properties in the eastern portion of our 

study area. There was a lens of very low salinity, warm water 20 km seaward of the 20 m 

isobath along the easternmost oceanographic transect. This apparent river water was not 

observed along the transects to the west and could have originated from local rivers such as the 

Colville or the Meade. The Meade River enters into Dease Inlet, whose mouth is about 25 km 

from the innermost station on Line 1. The Colville River delta and Harrison Bay is 

approximately 90 km east of Transect 7, and the Mackenzie delta is approximately 600 km east 

of the sampling area. The water could also have been the result of westward transport of 

Mackenzie River water. Satellite-derived surface temperature images from July 2008 showed 

the Mackenzie River plume penetrating into our study area. 

Alaskan Beaufort Sea water properties are known to be controlled by the annual freeze-thaw 

cycle and inflows from the oceanic and coastal boundaries. In winter temperatures are at or near 

the freezing point (except perhaps after upwelling events that bring warm water from the Atlantic 

layer onto the outer shelf). Near-freezing waters remain on the shelf year-round, although in the 

near-shore, highly stratified plume temperatures can be 5-10°C above the freezing point. 

172
Salinities (hence density) vary widely in space and time. Shelf salinities are between 32 and 33 

in winter, with higher values (33-40) in some of the coastal lagoons. During the spring freshet, 

river waters spread offshore beneath the landfast ice in highly stratified, thin (1 -2 m) plumes, 

although it is not known how far offshore the plumes spread. Plume salinities are greater than 5, 

whereas the salinity in the waters offshore or beneath the plume is 32-33. Once the landfast ice 

detaches from the coast, plume and ambient waters mix. The freshwater is carried offshore 

during upwelling events or in filaments generated by instabilities, or it is advected alongshore in 

a coastal current under downwelling favorable winds. The hydrographic and circulation 

structure of the Alaskan Beaufort Sea are poorly understood but probably complicated because 

of the diverse water sources feeding this shelf. For example, the different water sources applied 

at the lateral boundaries (Pacific waters in the west and Mackenzie shelf waters in the east) 

suggest that there are alongshelf gradients in both density and nutrients that affect circulation and 

biological production patterns. Similarly, cross-shelf differences are probably quite large. In 

summer and fall, these gradients are established by river runoff, ice melt, and shelfbreak 

processes, while in winter the shelfbreak processes and the landfast/pack ice boundary likely lead 

to spatial heterogeneity. How these gradients affect biological production patterns remains 

unknown. 

Although there are few measurements in this area, the year-round discharge from the Mackenzie 

River may profoundly influence the eastern Alaskan Beaufort Sea (Carmack et al. 1989, 

Macdonald and Carmack 1991, Macdonald et al. 1999). Mackenzie shelf waters have been 

detected throughout much of the Canada basin, including the continental slope of the Chukchi 

and western Beaufort Sea as far as 160o

W longitude (Guay and Falkner 1998, Macdonald et al. 

1999). It is likely that the prevailing northeasterly winds force Mackenzie shelf waters onto the 

Alaskan Beaufort Sea. 

Much of the oceanographic data were collected at the same stations that demersal and midwater 

fish were sampled with nets, thus providing a high degree of spatial and temporal coherence 

between the two physical and biological data sets. Additional CTD data along transects 1 and 5 

were collected independent of the fish trawling, and the assembled data show consistent and 

realistic across shelf gradients despite the temporal lag between adjacent CTD stations. 

Fish distribution and habitat associations

Habitat associations were evaluated for both bottom trawl (demersal) and acoustic (pelagic) 

datasets. Several of the environmental variables we chose to examine with regard to benthic and 

pelagic fish distribution were correlated with each other. Not surprisingly the salinity and density 

variables were correlated and these were all in turn correlated with bottom depth. Bottom 

temperature and temperature difference (surface to bottom) were also correlated. In addition, 

temperature difference and density difference were correlated. 

Finally, at the benthic stations sampled with the unlined net longitude was correlated with 

salinity and density variables. Because it is not statistically valid to include correlated 

independent variables in multivariate analyses such as GAM, these correlations among 

environmental variables resulted in only a limited number of variables being available for the 

GAMs. None of the two- or three-term GAMs for the benthic fish species were statistically 

173
significant. This is not surprising given the small sample size, the potential for over-fitting the 

models and possible interactions between independent variables. For example, temperature 

difference for “all fish species - lined net” in the linear regression had a lower P-value than 

longitude, that variable was correlated with bottom temperature and so was not used in the 

GAM. Although the Cp and P-values indicate the three term model was statistically significant it 

is very likely that the results were due to interactions between independent variables and over 

fitting the model. Both of these problems are related to the small sample size and thus the three 

term GAM model is probably not biologically significant. The three term GAM model for “all 

invertebrates - lined net” was significant in explaining over half the variability in the data. The 

two term GAM model also explained a significant amount of the spatial variability in density of 

opilio crab. 

Small sample sizes were also of concern in the analysis of YOY fish and year-plus Arctic cod. 

In the GAM for YOY pelagic fish, there were concerns about this dataset as there was 

heterogeneous variance that was unimproved by data transformation. Similarly the year-plus 

Arctic cod GAM had variance that could not be normalized by data transformation. 

Density by weight of all benthic fish was significantly negatively correlated with bottom 

temperature at the lined net stations. The same was true for benthic Arctic cod, which is not 

unexpected given that approx. 94% of the total weight and numbers of fish caught were Arctic 

cod. 

For pelagic yearling-and-older (year-plus) Arctic cod, the linear model using the zero-excluded 

dataset (in our opinion the most robust given that zero values in the nearshore were analyticallynot biologically-derived) suggested that year-plus Arctic cod are significantly associated with 

offshore regions with a fully-formed below- mixed layer depth (MLD) region and cold, saline 

water. Given visual observations of the data, this was our original interpretation of year-plus 

Arctic cod distribution. Interestingly, although surface and bottom parameters (i.e. temperature 

and salinity) were correlated with MLD attributes, the model run using the standard predictors 

did not find a significant relationship between year-plus distribution and oceanography. This 

suggests that the attributes of the below-MLD water mass may not have been well-captured by 

the surface and bottom descriptors. 

All benthic fish and Arctic cod densities (both by weight and number) at the unlined net stations 

were significantly negatively correlated with surface to bottom temperature difference, greater 

fish densities occurring in more mixed waters. All but one of the unlined net stations were at 

bottom depths less than 100 m, so this result may indicate that Arctic cod prefer well-mixed 

water on the shelf. Mixing of the water column can bring nutrients to the surface resulting in 

increased primary and secondary production and potentially increased fish prey density. 

Adult Arctic cod in both benthic and pelagic habitats apparently prefer the very cold winter 

water that emanates from the Chukchi Sea. This is the region of the cold halocline that 

characterized Chukchi Sea outflow through Barrow canyon and fish distributions and model 

results suggest that the fish prefer these low temperatures. The Chukchi Sea outflow of cold, 

winter-formed waters are also rich in dissolved and particulate organic carbon, with this water 

carried offshore into the halocline (Mathis et al. 2007, Pickart et al. 2005). Previous studies in 

the marine coastal habitat have similarly shown that arctic cod prefer waters that are cold (-1 to 3 

174
°C) and of high salinity (27-32 ppt; Craig 1984). However, information about cod in this habitat 

is scarce compared to information on their use of nearshore, brackish water habitats. Arctic cod 

are also one of the dominant fish species found in brackish nearshore waters, along with other 

marine fish such as fourhorn sculpin and anadromous fish such as cisco and char (Craig 1984; 

Craig et al 1987; Moulton and Tarbox 1987). Arctic cod winter under nearshore ice (where not 

frozen to the seafloor) and in brackish waters of river deltas (Craig 1984). The numbers of cod 

in nearshore waters increases as the open-water season progresses, with fish moving offshore 

between July and August (Craig 1984, Frost and Lowry 1983 Moulton and Tarbox 1987). Our 

observations of arctic cod throughout the marine offshore habitat (deeper than 40m) are 

consistent with this pattern. Our study and the previous studies cited above support the idea that 

fishes in coastal waters of the Beaufort Sea are euryhaline – “freshwater” species sometimes 

enter marine waters and “marine” species such as arctic cod sometimes enter brackish waters 

(Craig 1984). 

Based on both linear and GAM models, YOY pelagic fish (Arctic cod, sculpins, and eelblenny) 

were not found in association with particular oceanographic or physical attributes, suggesting 

that they are relatively ubiquitous throughout the study area. In the nearshore regions <50-75 m, 

they occupy the entire water column while in water greater than 75 m they are found in the nearsurface (i.e. <50-75 m from the surface) water. 

Our observations of Arctic cod distribution relative to water temperature and water column 

mixing may reflect foraging habitat selection. Differences in nearshore brackish and offshore 

marine habitats have been shown to be reflected in Arctic cod diets. In the nearshore habitat, cod 

prey on epibenthic mysids and amphipods (Craig 1984). In offshore marine waters, they prey on 

copepods and amphipods (Frost and Lowry 1983). Arctic cod are also common along sea ice 

margins, feeding on ice-associated invertebrates (Cobb et al. 2008). Whether the distribution of 

cod prey among nearshore, offshore and ice-edge habitats drives the seasonal movement and 

distribution of arctic cod is not known at this time, but would be a fruitful area of future study. 

Moulton and Tarbox (1987) found that cod were distributed shoreward of a transition zone 

between brackish and marine water where prey organisms may have been concentrated. In the 

Chukchi Sea arctic cod densities were greatest in Bering Shelf water perhaps due to a higher 

abundance of zooplankton, compared to Alaska coastal water and Chukchi water (Gillespie et al. 

1997). So there is some evidence that arctic cod may select habitat based on prey abundance. 

The density of walleye pollock was significantly related to longitude throughout the survey area 

(i.e. at both lined and unlined net stations), with fish density decreasing from west to east. This 

pattern would be consistent with a relatively recent introduction of pollock into the Beaufort Sea 

from the south and west (Bering and Chukchi Seas). The most recent previous confirmed 

northerly expansion of the range of pollock was documented during a 2004 survey of the 

Chukchi Sea (Mecklenburg et al. 2007). If this hypothesis is true, then future surveys of the 

Beaufort Sea could show further expansion of the range of pollock to the east. 

Eelpout density at the lined net stations was negatively correlated with bottom temperature. 

Similar to Arctic cod, these species apparently prefer cold water in the off-shelf portion of the 

study area. The GLM for eelpouts from the unlined net stations (primarily on the shelf) showed 

significant relationships with temperature and longitude. On the shelf, eelpouts were more likely 

175
to be present in warmer water in the eastern part of the study area. These apparent habitat 

preferences could be driven by the distribution of their prey. Eelpouts in the Bering Sea 

typically consume benthic invertebrate prey such as shrimp, polychaetes and mysids (Aydin et 

al. 2008). Unfortunately, food habits data for eelpouts do not exist for the Beaufort Sea region. 

Further study of the prey preferences of eelpouts and the distribution of their prey is needed to 

interpret these patterns. 

Sculpins were more likely to be present in shallower water as indicated by the GLM from the 

lined net station data. In fact, virtually no sculpins were caught where bottom depth exceeded 

100 m. In addition, sculpin density on the shelf (the unlined net stations) was significantly 

related to temperature and density difference, being more numerous in relatively mixed water. 

Mixing can bring nutrients towards the surface and fuel primary production which would 

eventually result in increased fish prey productivity. Sculpins of the Arctic burrow into sand and 

sand-mud bottoms feeding on small benthic amphipods and polychaetes (Fedorov 1986). The 

nearshore distribution of sculpins may be driven by a preference for muddy substrate and small 

benthic prey. More detailed study of substrate type and the distribution of small benthic 

invertebrates is needed to test this hypothesis. 

Benthic invertebrate density (all species combined) was significantly related to bottom 

temperature, bottom density and longitude, as indicated by the GAM. Invertebrates were more 

abundant in colder and denser water in the western portion of the survey area. The density of 

Opilio crab (by weight and number) at the lined net stations was significantly associated with 

bottom temperature and bottom depth, as indicated by the GAM. Crab densities were greater in 

cold waters and deeper depths. The distribution of Opilio on the shelf, sampled with the unlined 

nets, was apparently driven by bottom salinity and longitude, with more crabs associated with 

higher salinity waters towards the west. These patterns in the distribution of benthic 

invertebrates may reflect increased productivity of cold Chukchi Sea waters transported up 

Barrow Canyon into the Beaufort Sea (Mathis et al. 2007, Pickart et al. 2005). The diversity of 

invertebrate species sampled makes it difficult to form more specific hypotheses about particular 

prey or habitat selection processes driving the patterns. However, previous studies have 

suggested a metabolic explanation for the distribution of Oplio crab. Opilio crab on the Scotian 

Shelf are similarly most abundant in relatively cold water (Tremblay 1997), and the authors 

suggest that this is because at warmer temperatures metabolic costs are greater than consumption 

(Foyle et al. 1989). Further study of the metabolic and consumption rates of Beaufort Sea Opilio

are required to test this hypothesis. 

An additional explanation for the high catches of benthic fish and invertebrates offshore of 100 

m depth is that the inner shelf may suffer from ice grounding in winter, which could reduce 

habitat area for benthos. Sea ice may cover the shelf throughout the year, although over the last 

decade most of the shelf has been ice-free from late July through early October. The Beaufort 

Sea ice cover consists of two components; drifting pack ice over the middle and outer shelf and 

the virtually immobile landfast ice on the inner shelf. Landfast ice first forms in October and is 

anchored to the coast. It then rapidly extends some 20-40 km offshore to eventually cover ~25% 

of the shelf area and remains in place through June (Barnes et al. 1984a). Landfast ice is 

relatively smooth adjacent to the coast but can be highly deformed offshore and ridging increases 

throughout winter (Tucker-III et al. 1979). Deformation can, however, vary considerably along 

176
177

the shelf and it appears that the landfast ice zone on the Mackenzie shelf is less deformed than on 

the Alaskan Beaufort shelf (Tucker-III et al. 1979). Ice keels can gouge the seafloor (Barnes et 

al. 1984a) and form piles of grounded ice, stamukhi, along the seaward edge of the landfast ice. 

Stamukhi can be described according to this process. Landfast ice is anchored to the coast at the 

bottom along the 2 m isobath. Grounded ice may occur anywhere on the shallower portions of 

the shelf, but frequently grounding occurs along the 20 m isobath. Here ice ridging frequently 

develops and the ice keels often encounter the bottom and become immobile or scour the seabed. 

As the ridges develop at the edge of the landfast ice, they tend to build as more pack ice collides 

and deforms with previous grounded ridges and the landfast ice limit. The result is a complex 

series of grounded ice and ridges that forms the stamuhki zone. The stamukhi may be important 

in protecting the inner shelf from forcing by the drifting pack ice (Reimnitz and Kempema 

1984). It seems likely that persistent gouging by ice in shallow water could disturb, and thus 

affect, the composition of benthic communities. However, little is known about the direct effects 

of sea ice gouging on benthic habitat. 

Recommendation for Future Monitoring Methods 

“Based on results of the survey, recommend methods for future monitoring that could provide 

time-series and data trend information necessary to support offshore development decisions and 

serve as a proto-type fisheries component of future MMS or other ocean observing systems.” 

(from the Memorandum of Understanding). 

Recommendations are to use the same methods as used in this pilot. In order to facilitate the use of 

the same methods in future studies, the detailed review of the methods used in this study can be found in 

Appendix VIII 

As stated in the earlier discussion, additional effort is also needed to examine the potential 

importance of offshore near-surface regions for YOY fish and to quantify the relative 

contribution of offshore regions to YOY recruitment. 
Literature Cited 

Aagaard, K., and Roach, A.T. 1990. Arctic ocean-shelf exchange: Measurements in Barrow 

Canyon. . Journal of Geophysical Research 95: 18163-18175. 

Aagaard, K. 1984. The Beaufort undercurrent. In The Alaska Beaufort Sea. Edited by P.W. 

Barnes, D.M. Schell and E. Reimnitz. Academic Press, Orlando. pp. 47-72. 

Acuna, E., and Kotwicki, S. 2004. 2003 Bottom trawl survey of the eastern Bering Sea 

continental shelf. U.S. Department of Commerce NOAA-NMFS-AFSC Processed Report 2004-

02. 

Alverson, D.L., and W.T. Pereyra. 1969. Demersal fish explorations in the northeastern 

Pacific Ocean -- An evaluation of exploratory fishing methods and analytical approaches to stock 

size and yield forecasts. Journal of the Fisheries Research Board of Canada 26:1985-2001. 

Alvsvåg, J., Agnalt, A.L., and Jørstad, K.E. 2008. Evidence for a permanent establishment of the 

snow crab (Chionoecetes opilio) in the Barents Sea. Biological Invasasions 11: 587-595. 

Ashjian, C.J., Okkonen, S.R., and Campbell, R.G. 2009. Mooring and broad-scale oceanography. 

In Bowhead Whale Feeding Ecology Study (BOWFEST) in the western Beaufort Sea; 2008 

Annual Report. MMS-4500000120. Edited by D. Rugh. National Marine Mammal Laboratory, 

Alaska Fisheries Science Center, NMML, NOAA, 7600 Sand Point Way NE Seattle WA, 

Seattle. pp. 38-48. 

Ashjian, C.J., Sherr, E.B., Campbell, R.G., Sherr, B.F., Plourde, S., Hill, V.J., and Cota, G.F. 

2006. Mesozooplankton-microbial food web interactions in western Arctic shelf and basin 

regions. EOS Transaction of the American Geophysical Union 87(36, suppl.). 

Atkinson, E.G., and Percy, J.E. 1992. Diet comparison among demersal marine fish from the 

Canadian Arctic. Polar Biology 11(8): 567-573. 

Aydin, K., S. Gaichas, I. Ortiz, D. Kinzey, and N. Friday 2008. A comparison of the Bering Sea, 

Gulf of Alaska, and Aleutian Islands large marine ecosystems through food web modeling. U.S. 

Department of Commerce NOAA Tech. Memo. NMFS-AFSC-178. 

Barber, W.E., Smith, R.L., Vallarino, M., and Meyer, R.M. 1997. Demersal fish assemblages of 

the northeastern Chukchi Sea. Alaska. Fishery Bulletin 95: 195-209. 

Barnes, P.W., Rearic, D.M., and Reimnitz, E. 1984a. Ice gouging characteristics and processes. 

Academic Press, New York. 

Beare, D.J., Burns, F., Greig, A., Jones, E.G., Peach, K., Kienzle, M., McKenzie, E., and Reid, 

D.G. 2004. Long-term increases in prevalence of North Sea fishes having southern 

biogeographic affinities. Marine Ecology Progress Series 284: 269-278. 

178
Benoit, D., Simard, Y., and Fortier, L. 2008. Hydroacoustic detection of large winter 

aggregations of Arctic cod (Borgeogadus saida) at depth in ice-covered Franklin Bay (Beaufort 

Sea). Journal of Geophysical Research 113: C06S90, doi:10.1029/2007JC004276 

Boe, J., Hall, A., and Qu, X. 2009. September sea-ice cover in the Arctic Ocean projected to 

vanish by 2100. Nature Geoscience Letters advanced online publication. 

Bond, W.A., and Erickson, R.N. 1997. Coastal migration of arctic ciscoes in the eastern Beaufort 

Sea. In Fish ecology in arctic North America. American Fisheries Society, Bethesda. pp. 155-

164. 

Bradstreet, M.S.W., and Cross, W.E. 1982. Trophic relationships at high arctic ice edges. Arctic 

35: 1-12. 

Bradstreet, M.S.W., Finley, K.J., Sekerak, A.D., Griffiths, W.B., Evans, C.R., Fabijan, F.F., and 

Stallard, H.E. 1986. Aspects of the biology of Arctic cod (Boreogadus saida) in arctic marine 

food chains. Canadian Technical Report of Fisheries and Aquatic Sciences 1491. 

Britt, L., and Martin, M. 2001. 1999 Gulf of Alaska bottom trawl survey. U.S. Department of 

Commerce NOAA Tech. Memo. NMFS-AFSC-121. 

Busby, M.S., and Chernova, N.V. 2001. Redescription of the festive snailfish, Liparis 

marmoratus (Scorpaeniformes: Liparidae), with a new record from the northern Bering Sea. 

Ichthyological Research 48: 187-191. 

Carey, A.G., Boudrias, M.A., Kern, J.C., and Ruff, R.E. 1984. Selected ecological studies on 

continental shelf benthos and sea ice fauna in the southwestern Beaufort Sea In U.S. Department 

of Commerce, NOAA/OCSEAP Final Reports of Principal Investigators 23: 1-164. 

Carmack, E.C., Macdonald, R.W., and Papdakis, J.E. 1989. Water mass structure and boundaries 

in the Mackenzie Shelf Estuary. Journal of Geophysical Research 94: 18043-18055. 

Cobb, D., H. Fast, et al. (2008). Beaufort Sea Large Ocean Management Area: Ecosystem 

Overview and Assessment Report. DFO. Canadian Technical Report of Fisheries and Aquatic 

Sciences 2780. 

Cook, D. R. 1977. Detection of influential observation in linear regression. Technometrics 19(1): 

15-18. 

Craig, P.C. 1984. Fish use of coastal waters of the Alaska Beaufort Sea: a review. Transactions 

of the American Fisheries Society 113(3): 265-282. 

Craig, P.C., Griffiths, W.B., Haldorson, L., and McElderry, H. 1982. Ecological studies of Arctic 

cod (Boreogadus saida) in Beaufort Sea coastal waters, Alaska. Canadian Journal of Aquatic and 

Fisheries Sciences 39: 395-406. 

179
Crawford, R.E., and Jorgenson, J.K. 1996. Quantitative studies of Arctic cod (Boreogadus saida) 

schools: important energy stores in the Arctic food web. Arctic 49: 181-193. 

Crawford, R.E., and Jorgenson, J.K. 1993. Schooling behavior of Arctic cod, Boreogadus saida, 

in relation to drifting pack ice. Environmental Biology of Fishes 36: 345-357. 

Echeverria, T.W. 1995. Sea-ice conditions and the distribution of walleye pollock (Theragra 

chalcogramma) on the Bering and Chukchi Shelf In Climate change and northern fish 

populations. Edited by R.J.B. (Ed.), Victoria. pp. 131-136. 

Engås, A., Løkkeborg, S., Ona, E., and Soldal, A.V. 1996. Effects of seismic shooting on local 

abundance and catch rates of cod (Gadus morhua) and haddock (Melanogrammus aeglefinus). 

Candian Journal of Fisheries and Aquatic Sciences 53: 2283-2249. 

Engås, A., and Godø, O.R. 1989. The effect of different sweep lengths on the length composition 

of bottom-sampling trawl catches. ICES Journal of Marine Science 45: 269-276. 

Fedorov, V.V. 1986. Cottidae. In Fishes of the Northeastern Atlantic and the Mediterranean. 

Edited by M.-L.B. P.J.P. Whitehead, J-C. Hureau, J. Nielsen, and E. Tortonese, UNESCO, Paris. 

Foote, K.G., Knudsen, H.P., Vestnes, G., MacLennan, D.N., and Simmonds, E.J. 1987. 

Calibration of acoustic instruments for fish density estimation: a practical guide. ICES 

Cooperative Research Report Number 144. 

Foyle, T. P., R. K. O'Dor, and R. W. Elner. 1989. Energetically defining the thermal limits of the 

snow crab. Journal of Experimental Biology 145: 371–393. 

Frost, K.J., and Lowry, L.F. 1981. Distribution, growth, and foods of Arctic cod (Boreogadus 

saida) in the Bering, Chukchi and Beaufort Seas. Canadian Field Naturalist 95: 186-191. 

Frost, K.J., and Lowry, L.F. 1983. Demersal fishes and invertebrates trawled in the northeastern 

Chukchi and western Beaufort Seas 1976-1977, U.S. Department of Commerce NMFS-SSRF764. 

Gallaway, B.J., Felchhelm, R.G., Griffiths, W.B., and Cole, J.G. 1997. Population dynamics of 

broad whitefish in the Prudhoe Bay region, Alaska. In Fish Ecology in Arctic North America. 

Edited by J.B. Reynolds. American Fisheries Society Symposium 19, Bethesda. pp.194-207. 

Gillespie, J. G., Smith, R.L., Barbour, E., and Barber, W.E. 1997. Distribution, abundance, and 

growth of Arctic cod in the Northeastern Chukchi Sea. In Fish Ecology in Arctic North America. 

Edited by J. B. Reynolds. American Fisheries Society Symposium 19, Bethesda. pp.81-89. 

Greene, C.H., Pershing, A.J., Cronin, T.M., and Ceci, N. 2008. Arctic climate change and its 

impacts on the ecology of the north Atlantic. Ecology 89(11): S24-S38. 

180
Guay, C.K., and Falkner, K.K. 1998. A survey of dissolved barium in the estuaries of major 

Arctic rivers and adjacent seas. Continental Shelf Research 8: 859-882. 

Gunderson, D.R. 1993. Surveys of Fisheries Resources. New York: Wiley and Sons, Inc. 

Hiatt, T., Felthoven, R., Dalton, M., Gaber-Yonts, B., Haynie, A., Lew, D., Sepez, J., Seung, C., 

and Staff of Northern Economics, I. 2008. Stock assessment and fishery evaluation report for the 

groundfish fisheries of the Gulf of Alaska and Bering Sea/Aleutian Islands area: economic status 

of the groundfish fisheries off Alaska, 2007, Seattle, WA. 

Hobson, K.A. 1993. Trophic relationships among high Arctic seabirds: insights from tissuedependent stable-isotope models. Marine Ecology Progress Series 95: 7-18. 

IASC. 2004. Arctic Climate Impact Assessment, Cambridge University Press, Cambridge, UK. 

Itoh, M.K., Shimada, T., McLaughlin, F., Carmack, E., and Nishino, S. In press. Interannual 

variability of Pacific winter water inflow through Barrow Canyon from 2000 to 2006. Journal of 

Geophysical Research. 

Jarvela, L.E., and Thorsteinson, L.K. 1999. The epipelagic fish community of Beaufort Sea 

coastal waters, Alaska. Arctic 52(1): 80-94. 

Jarvela, L.E., and Thorsteinson, L.K. 1997. Movements and temperature occupancy of sonically 

tracked dolly varden and arctic ciscoes in Camden Bay, Alaska. In Fish ecology in Arctic North 

America. Edited by J.B. Reynolds. American Fisheries Society, Bethesda. pp. 165-174. 

Kaufman, L., and Rousseeuw, P.J. 1990. Finding Groups in Data. John Wiley and Sons, Inc., 

New York. 

Lang, G. M., Livingston, P. A., and Dodd, K. A. 2005. Groundfish food habits and predation on 

commercially important prey species in the eastern Bering Sea from 1977 through 2001. NOAA 

Tech. Memo. NMFS-AFSC-158. 

Lauth, R., and Acuna, E. 2007. Results of the 2006 eastern Bering Sea continental shelf bottom 

trawl survey of groudfish and invertebrate resources. NOAA-AFSC Tech Memo-176. pp 176. 

Macdonald, R.W., Carmack, E.C., McLaughlin, F.A., Falkner, K.K., and Swift, J.H. 1999. 

Connections among ice, runoff, and atmospheric forcing in the Beaufort Gyre. Geophysical 

Research Letters 26: 2223-2226. 

Macdonald, R.W., and Carmack, E.C. 1991. The role of large-scale under-ice topography in 

separating estuary and ocean on an arctic shelf. Atmosphere-Ocean 29: 37-51. 

Main, J., and Sangster, G.I. 1981. A study of the fish capture process in a bottom trawl by direct 

observations from a towed underwater vehicle. Scottish Fishery Research Report 23. pp 21. 

181
Mamylov, V.S. 2003. About the Comparison of fish distribution densities estimated using trawl 

and acoustic methods. Report on Improvement of instrumental methods for stock assessment of 

marine organisms, Russian-Norwegian Workshop, 11-14 November 2003, PINRO, Murmansk, 

Russia. 

Maslanik, J.A., Fowler, C., Stroeve, J., Drobot, S., Zwally, J., Yi, D., and Emery, W. 2007. A 

younger, thinner Arctic ice cover: Increased potential for rapid, extensive sea-ice loss. 

Geophysical Research Letters 34(L24501). 

Mathis, J.T., Pickart, R.S., Hansell, D.A., Kadko, D., and Bates, N.R. 2007. Eddy transport of 

organic carbon and nutrients from the Chukchi Shelf: Impact on the upper halocline of the 

western Arctic Ocean. Journal of Geophysical Research 112: C05011, doi: 

05010.01029/02006JC003899. 

Matthews, J.B. 1981. Observations of surface and bottom currents in the Beaufort Sea near 

Prudhoe Bay, Alaska. Journal of Geophyisical Research 86(C7): 6653-6660. 

Mecklenburg, C.W., Stein, D.L., Sheiko, B.A., Chernova, N.V., Mecklenburg, T.A., and 

Holladay, B.A. 2007. Russian-American long term census of the Arctic: benthic fishes trawled in 

the Chukchi Sea and Bering Strait, August 2004. Northwest Naturalist 88: 168-187. 

Moore, S.E. 2000. Variability of cetacean distribution and habitat selection in the Alaskan 

Arctic, autumn 1982-91. Arctic 53: 448-460. 

Moulton, L.L., Philo, L.E., and George, J.C. 1997. Some reproductive characteristics of least 

ciscoes and humpback whitefish in Dease Inlet, Alaska. In Fish ecology in arctic North America. 

Edited by J.B. Reynolds. American Fisheries Society, Bethesda. pp. 119-126. 

Moulton, L.L., and Tarbox, K.E. 1987. Analysis of arctic cod movements in the Beaufort Sea 

nearshore region, 1978-79. Arctic 40(1): 43-49. 

Mountain, D.G., Coachman, L.K., and Aagaard, K. 1976. On the flow through Barrow Canyon. 

Journal of Physical Oceanography 6: 461-470. 

Mueter, F.J., Broms, C., Drinkwater, K.F., Friedland, K.D., Hare, J.A., Hunt Jr., G. L., Melle, 

W., and Taylor, M. 2009. Ecosystem responses to recent oceanographic variability in highlatitude Northern Hemisphere ecosystems. Progress in Oceanography 81: 93-110. 

Mueter, F.J., and Litzow, M.A. 2008. Sea ice retreat alters the biogeography of the Bering sea 

continental shelf. Ecological Applications 18(2): 309-320. 

Nakashima, B. S. 1990. Escapement from a Diamond IX midwater trawl during acoustic surveys 

for capeplin (Mallotus villosus) in the Northwest Atlantic. J. Cons. Inst. Explor. Mer. 47: 76-82. 

Okkonen, S.R. 2008. Exchange between Elson Lagoon and the nearshore Beaufort Sea and its 

role in the aggregation of zooplankton. OCS Study MMS 1008-010. 

182
Ott, R.L. 1993. An introduction to statistical methods and data analysis. Duxbury Press, 

Belmont, California. 

Parker-Stetter, S.L., Rudstam, L.G., Sullivan, P.J., and Warner, D.M. 2009. Standard operating 

procedures for fisheries acoustic surveys in the Great Lakes. Great Lakes Fisheries Commission 

Special Publication (2009-01). 

Paul, J.M., Paul, A.J., and Barber, W.E. 1997. Reproductive biology and distribution of the snow 

crab from the northeastern Chukchi Sea. American Fisheries Society Symposium 19: 287-294. 

Perry, A.L., Low, P.J., Ellis, J.R., and Reynolds, J.D. 2005. Climate change and distribution 

shifts in marine fishes. Science 308: 1912-1915. 

Pickart, R.S. 2004. Shelfbreak circulation in the Alaskan Beaufort Sea: mean structure and 

variability. Journal of Geophyisical Research 109: 1-14. 

Pickart, R.S., Weingartner, T., Pratt, L.J., Zimmermann, S., and Torres, D.J. 2005. Flow of 

winter-transformed Pacific water into the western Arctic. . Deep-Sea Research, Pt. II 52: 3175 - 

3198. 

Pickart, R.S., Pratt, L.J., Torres, D.J., Whitledge, T.E., Proshutinsky, A.Y., Aagaard, K., Agnew, 

T.A., Moore, G.W.K., and Dail, H.J. 2010. Evolution and dynamics of flow through Herald 

Valley in the western Chukchi Sea. Deep-Sea Research II 57(1-2): 5-26. 

Reimnitz, E., and Kempema, E.W. 1984. Pack ice interaction with stamukhi shoal. In The 

Alaskan Beaufort Sea: Ecosystems and Environment. Edited by D.M.S. P. W. Barnes, and E. 

Reimnitz (ed.). Academic Press, New York. pp. 159-184. 

Ricker, W.E. 1973. Linear regressions in fishery research. Journal of Fisheries Research Board 

Canada 30: 409-434. 

Rudstam, L.G., Parker-Stetter, S.L., Sullivan, P.J., and Warner, D.M. 2009. Towards a standard 

operating procedure for fishery acoustic surveys in the Laurentian Great Lakes, North America. 

ICES Journal of Marine Science 66: 1391-1397. 

Sawada, K., Furusawa, M., and Williamson, N.J. 1993. Conditions for the precise measurement 

of fish target strength in situ. Journal of the Marine Acoustical Society of Japan 20: 73-79. 

Scheaffer, R.L., III, W.M., and Ott, R.L. 1996. Elementary Survey Sampling 5th Edition. 

Duxbury Press, London, U. K. . 

Shimada, K., Carmack, E.C., Hatakeyama, K., and Takizawa, T. 2001. Varieties of shallow 

temperature maximum waters in the western Canadian Basin of the Arctic Ocean. Geophysical 

Research Letters 28: 3441-3444. 

183
Slotte, A., Hansen, K., Dalen, J., and Ona, E. 2004. Acoustic mapping of pelagic fish distribution 

and abundance in relation to a seismic shooting area off the Norwegian west coast. Fisheries 

Research 67: 143-150. 

Stauffer, G. 2004. NOAA protocols for groundfish bottom trawl surveys of the nation's fishery 

resources. U.S. Departmen of Commerce NOAA Tech. Report NMFS-F/SPO-65: 205. 

Strickland, R., and Sibley, T. 1984. Projected effects of CO2-induced climate change on the 

Alaska pollock (Theragra chalcogramma) fishery in the Bering Sea and the Gulf of Alaska., 

Report prepared for U.S. Department of Energy, Carbon Dioxide Indirect Effects Program. 

Stroeve, J., Serreze, M., Drobot, S., Gearheard, S., Holland, M., Maslanik, J.A., Meier, W., and 

Scambos, T. 2008. Arctic sea ice extent plummets in 2007. EOS Transaction of the American 

Geophysical Union 89: 13-14. 

Stroeve, J., Holland, M.M., Meier, W., Scambos, T., and Serreze, M. 2007. Arctic sea ice 

decline: Faster than forecast. Geophysical Research Letters 43(L09501). 

Suydam, R. S., Lowry, L.F., Frost, K.J., O'Corry-Crowe, G.M., and Jr., D.P. 2001. Satellite 

tracking of eastern Chukchi Sea beluga whales into the Arctic Ocean. Arctic 54: 237-243. 

Tremblay, M. J. 1997. Snow Crab (Chionoecetes opilio) Distribution Limits and Abundance 

Trends on the Scotian Shelf. Journal of Northwest Atlantic Fishery Science 21: 7-22. 

Tucker-III, W. B., Weeks, W.F., and Frank, M. 1979. Sea Ice ridging over the Alaskan 

continental shelf. Journal of Geophysical Research 84: 4885-4897. 

Underwood, T. J., Palmer, D.E., Thorpe, L.A., and Osborne, B.M. 1997. Weight-length 

relationships and condition of dolly varden in coastal waters of the Arctic National Wildlife 

Refuge, Alaska. In Fish ecology in arctic North America. Edited by J.B. Reynolds. American 

Fisheries Society, Bethesda. pp. 295-309. 

Wardle, C.S. 1986. Fish behavior and fishing gear In The Behavior of Teleost Fishes. Edited by

T.J. Pitcher. John Hopkins University Press, Baltimore. pp. 463-495. 

Walsh, S.J. 1991. Diel variation in availability and vulnerability of fish to a survey trawl. Journal 

of Applied Ichthyology 7: 147-159. 

Weingartner, T., Okkonen, S.R., and Danielson, S.L. 2005 and 2005b. Circulation and Water 

Property Variations in the Nearshore Alaskan Beaufort Sea, Final Report. OCS Study MMS 

2005-028. 

Weingartner, T., Cavalieri, D.J., Aagaard, K., and Sasaki, Y. 1998. Circulation, dense water 

formation, and outflow on the northeast Chukchi shelf. Journal of Geophysical Research 103: 

7647-7661. 

184
Welch, H.E., Bergmann, M.A., Siferd, T.D., Martin, K.A., Curtis, M.F., Crawford, R.E., 

Conover, R.J., and Hop, H. 1992. Energy flow through the marine ecosystem of the Lancaster 

Sound Region, Arctic Canada. Arctic 45(4): 343-357. 

Woodgate, R.A., Aagaard, K., and Weingartner, T. 2005b. A Year in the Physical Oceanography 

of the Chukchi Sea: moored measurements from autumn 1990-91. Deep-Sea Research II 52: 

3116-314

185
186

Appendix I – Database table documentation 

Database: BSS_Database2008 

Beaufort Sea Offshore Marine Fish Survey, 2008 

Alaska Fisheries Science Center (AFSC) and Minerals Management Service (MMS) 

OCS Study MMS 2008-062 

 

*All table and field descriptions found in this document are also stored within the 

BSS_Database2008. 

Questions / Inquiries contact: 

Libby Logerwell 

Libby.logerwell@noaa.gov

206-526-4231 

Kimberly Rand 

Kimberly.rand@noaa.gov

206-526-6303 
Table: tblAllStationLocations 

Description: Bottom, midwater, CTD, and Bongo basic haul information; vessel, station, haul number, latitude (DD) and longitude (DD). All 

postitions are at start of event (start of net fishing, CTD cast, start of Bongo tow). 

 

Field Name (PK) Primary Key Description Type

Length

Cruise 200801, year 2008, 1 leg Long Integer 4

Vessel Ocean Explorer was used for the 2008 Beaufort sea Long Integer 4

survey (148)

(PK) Station Location where event took place Long Integer 4

(PK) Haul Bottom hauls were from 1-26. Midwater hauls from Text 50

101 - 128; CTD and bongo events have descriptive 

haul fields

LatDD Latitude is in decimal degrees. This latitude Double 8

represents the EQ location (start location) for all 

events - North

LongDD Longitude is in decimal degrees. This longitude Double 8

represents the EQ location (start location) for all 

events - West

EventDescription Bottom tow, midwater tow, CTD cast or bongo Text 50

Data Quality: 

This table only contains location information for all “events” that took place during the 2008 Beaufort Sea 

survey. The locations are “start” locations for each event. For bottom hauls, this location (lat/long) 

corresponds to the “Event” field, code “4” in the “tblBotEvent”. 

Table: tblBotCatch 

Description: Bottom haul; total catch weight and numbers of fish and invertebrates from bottom hauls

Field Name (PK) Primary Key Description Type

Length

Cruise 200801, year 2008, 1 leg. Long Integer 4

Vessel Ocean Explorer was used for the 2008 Beaufort sea Integer 2

survey (148).

Haul Bottom hauls were from 1-26. If a haul does not Text 50

appear in this table, there was no catch associated 

with it.

SpeciesCode Corresponds to the species in the "tblSpeciesList" Long Integer 4

table.

SpeciesLatinName Latin name for species; corresponds to the species Text 50

in the "tblSpeciesList" table

VoucherNumber Number that corresponds to specimens that were Integer 2

vouchered in formalin for future identification.

FishInvert Whether the species is an invertebrate or fish. Text 50

NonSubSubWeight This is a subsample of the subsample. It only Double 8

applies to invertebrates and trawl 3, this was not 

187
done with fish any other haul. These are the 

measured weights from field.

NonSubSubNumber This is a subsample of the subsample. It only Double 8

applies to invertebrates and trawl 3, this was not 

done with fish in any other haul. These are actual 

numbers from field.

NonSubsampleWeight Weight of the sample that was not counted and Double 8

weighed. For example count and weigh 50 Arctic 

cod for average weight and weigh the rest of the 

Arctic cod (because there are 1,000 in sample, takes

 too long to count.

SubSampleWeight Weight of the subsample. Everything that was Double 8

weighed was also counted. Corresponds to 

SubSampleNumbers. If there is an entry in 

"NonSubSubWeight", this is an extrapolated 

weight from that.

SubSampleNumbers Count of the subsample. Everything that was Double 8

counted was also weighed. Corresponds to 

SubSampleWeight. If there is an entry in 

"NonSubSubNumber", this is an extrapolated 

number from that.

CalculatedWeight Calculated weight from NonSubsample Weight. Double 8

Extraplates subsample nonsub weight up to the 

subsample level.

CalculatedNumbers Calculated numbers from NonSubsample Numbers. Double 8

Extraplates subsample nonsub numbers up to the 

subsample level.

TotalWeight Total weght of the species in the catch. Calculated Double 8

from the the subsample weight.

TotalNumbers Total numbers of the species in the catch. Double 8

Calculated from the subsample numbers.

SampledAll "Y" for yes if the species was entirely counted and Text 4

weighed in the total catch (no extrapolations) and 

"N" for no if the species was extrapolated from the 

subsample.

AverageWeight Calculated from the counts and weights. Double 8

Comment Comments about the catch/species. Text 255

Data Quality: 

This is where the catch information for the bottom trawls is stored. The location information for these hauls is 

found in both the “tblBotEvent” and the “tblAllStationLocations” only. There are a few hauls that appear in 

“tblBotHaul” and “tblAllStationLocations” that do not appear in the “tblBotCatch” table which means no catch 

was associated with that haul, either due to gear loss or damage. This table should be examined with the 

“tblBotHaul” so the reader is aware of gear type differences and gear performance codes associated with all the 

bottom catches. In particular, haul 3 was very large and highly diverse. In addition to collecting a random 

“subsample”, we “subsampled” the “subsample”. For example for the fish species Boreogadus saida (Arctic 

cod) in haul 3, the number of fish listed in the “SubSampleNumber” field is 5,163. This number was 

extrapolated from a “subsample” of a “subsample”. Situations in which high counts appear (>300) in the 

“SubSampleNumbers” field implies that is an extrapolated number from a “subsample” of a “subsample”, 

which is most common for invertebrate species (only appears in haul 3 for Arctic cod). The remaining data 

entries that appear in the fields “SubSampleWeight” and “SubSampleNumbers” are actual counts and weights 

from randomly selected subsamples of the entire catch. Also the reader should note that if a species did not 

appear in a particular haul, it does not appear in this table. This is important in estimating fish abundance and 

densities (e.g. zero catches). NOTE: All invertebrate data is preliminary. The vouchered invertebrate 

specimens (excluding crab) have not been verified as of August, 2009. 

188
Table: tblBotEvent 

Description: Bottom haul; all events recorded in wheelhouse and their associated lat/long. Includes, EQ (net starts fishing), HB (haul 

back), etc. 

Field Name (PK) Primary Key Description Type

Length

Cruise 200801, year 2008, 1 leg Long Integer 4

Vessel Ocean Explorer was used for the 2008 Beaufort sea Long Integer 4

survey

Haul Bottom hauls were from 1 - 26. Each haul has an Text 50

event associated with it. See "tblBotEvent".

DateTime Date and Time event began Date/Time 8

Event See "tblBotEventCode" for a list of codes Long Integer 4

PositionMethod GPS - USGlobalsat MR-350 Text 255

LatDD Latitude is in decimal degrees Text 255

LongDD Longitude is in decimal degrees Text 255

Comment Comments about the haul Text 255

Data Quality: 

This table describes events that take place during a single bottom trawl and the associated location and time the 

event took place. In conjunction with this table, “tblBotEventCode” should also be viewed for code definitions. 

This table and the “tblAllStationLocations” are the only 2 tables that have the haul location information 

(latitude/longitude). To assign a location to a bottom trawl using this table, the reader for example can choose 

event code “4” for the start of the haul or event code “6” for the end location of the haul. Event codes “4” and 

“6” are the ones most commonly used. 

Table: tblBotEventCode

 

Description: Bottom haul; code table for the "tblEvent" table

Field Name (PK) Primary Key Description Type

Length

ID Primary key Auto Number 4

Event Number code that corresponds to the code in field Long Integer 4

"Event" in "tblBotHaul"; recording begins at the 

start of a haul and ends when the trawl doors are on 

deck

Definition "Event" code definition Text 100

 

Data Quality: 

Corresponds to the “tblBotEvent”. 

189
Table: tblBotHaul

 

Description: Bottom haul; all information pertaining to haul and net mensuration; includes area swept (no location information stored in this 

table).

Field Name (PK) Primary Key Description Type

Length

Cruise 200801, year 2008, 1 leg Long Integer 4

Vessel Ocean Explorer was used for the 2008 Beaufort sea Long Integer 4

survey (148)

(PK) Station Location where an event took place (can be bottom Long Integer 4

tow or midwater tow)

(PK) Haul Bottom hauls ranged from 1 - 26 Text 50

Date Date the haul occurred (Alaska daylight time -8 from Date/Time 8

GMT)

Time Time the haul started - NOT the time net was on Date/Time 8

bottom (EQ) in Alaska Daylight Time (-8)

Comment Comments about the haul and haul performance Text 250

NetType Lined or unlined net. Hauls 1-15 were with a lined Text 50

net (see field description "Accessories" - code 122 - 

for a liner description; the unlined nets were 

standard 83-112 - see field description "Gear"

DoorUsed Code 15 from AFSC / RACE ADP code book, Long Integer 4

supplementary table, "Gear Accessories"; 6' x 9' 

steel V-doors (standardized to 1800 lbs after 1988), 

double 30 fm 5/8" dandylines, 1.28" mesh codend 

liner, 24" chain extension between lower dandyline 

and footrope.

Skipper Captain of the F/V Ocean Explorer Text 255

HaulType All bottom tows were standard bottom tows as Text 255

those conducted on Eastern Bering Sea surveys

Performance This code corresponds to the table Text 255

"tblBotHaulPerformCode"; see this table for code 

definitions

BottomType Was "qualitatively" estimated by viewing the echo Text 255

sounder and examinging what substrate was found 

in the catch

BottomTypeMethod Was "qualitatively" estimated by viewing the echo Text 255

sounder and examinging what substrate was found 

in the catch

DistanceFished Distance net was on bottom "fishing"; using all Text 255

RACE methods of calculating and estimating 

distance fished

DistanceFishedMethod Lat/Long's are converted to a nautical mile value; a Text 255

21 span running mean smoother is applied to each 

point between begin/end of tow. Distance is 

calculated as Pythagorean distance between each 

pair of smoothed points; then summed for distance 

fished

AreaSweptkm2 Calculated by taking "DistanceFished" * Double 8

"AvgNetSpread" / 1000 (for km2)

AvgNetSpread The average, in meters, of the horizontal net Text 255

opening (based on ping "values" recorded by 

NETMIND during tow operations).

190
NetMensuration The net mensuration gear used was NETMIND Text 255

form Northstar Technical Inc. 

(http://www.northstar-technical.com/)

NetSpreadPings The number of pings recorded in NETMIND from Text 255

the net sensors on the net; the signal is transmitted 

to the hydrophone lowered from the side of the 

vessel into the water during tow operations. Min of 

13 pings, in general for good net spread data

NetSpreadStdDev The standard deviation of the mean values from the Text 255

net spread (recorded from hydrophone during tow)

AvgNetHeight The average, in meters, of the net height (based on Text 255

ping "values" recorded by NETMIND during tow 

operations)

NetHeightPings The number of pings recorded in NETMIND per Text 255

tow (see field description "NetSpreadPings" above)

NetHeightStdDev The standard deviation of the mean values from the Text 255

net height (recorded from hydrophone during tow)

AvgGearDepth Average depth obtained from the SBE 39, Seabird Text 255

Electronics Inc.: 

http://www.seabird.com/products/spec_sheets/39dat

a.htm

GearDepthMethod Obtained from the SBE 39 depth recorder Text 255

(http://www.seabird.com/products/spec_sheets/39da

ta.htm)

AvgBottomDepth Obtained from the SBE 39 depth recorder and the Text 255

net mensuration sensors - NETMIND 

(http://www.seabird.com/products/spec_sheets/39da

ta.htm and http://www.northstar-technical.com/)

BottomDepthMethod Obtained from the SBE 39 depth recorder and the Text 255

net mensuration sensors - NETMIND 

(http://www.seabird.com/products/spec_sheets/39da

ta.htm and http://www.northstar-technical.com/)

WireOut In meters; amount of wire from vessels main wires Text 255

(connected to trawl doors) for net to obtain bottom 

depth; recorded by skipper based on measured wire 

calibration

WireOutMethod Autotrawl readout in wheelhouse that was calibrated Text 255

by cable meter (i.e. wire marking)

Gear Eastern trawl; 112' footrope; 83' headrope; 4" mesh Long Integer 4

#60 thread (#48 prior to approx 1984) wings / 

body; 3.5" mesh (#96) intermediate / codend; 41 

floats on headrope - 8" diameter; mean path width - 

17.0 m, no range, mean vertical - 2.3 m - range 

Accessories Code 122 = tickler chain, hula and 1.5" liner Text 255

covering entire bottom body, wings, complete top 

and bottom of the intermediate and codend (with 30

mesh overlap with standard 1.25" liner extending 

65 meshes up from conded. Code 15 = 6'x9' steel 

doors, double

BottomContactMethod AFSC - RACE bottom contact sensor Text 255

SurfaceTemp Temperature recorded in °C Text 255

SurfaceTempMethod SBE 39 depth recorder Text 255

GearTemp Temperature recorded in °C Text 255

GearTempMethod SBE 39 depth recorder Text 255

WindSpeed In knots; Estimated by the scientist recording haul Text 255

data; QUALITATIVE data (on 2008 Beaufort Sea 

survey it was Libby Logerwell)

WindSpeedMethod Estimated by the scientist recording haul data; Text 255

QUALITATIVE data (on 2008 Beaufort Sea survey

191
it was Libby Logerwell)

WindDirection In degrees; Estimated by the scientist recording Text 255

haul data; QUALITATIVE data (on 2008 Beaufort 

Sea survey it was Libby Logerwell)

WindDirectionMethod From vessels magnetic compass; Estimated by the Text 255

scientist recording haul data; QUALITATIVE data 

(on 2008 Beaufort Sea survey it was Libby 

Logerwell)

WaveHeight In meters; Estimated by the scientist recording haul Text 255

data; QUALITATIVE data (on 2008 Beaufort Sea 

survey it was Libby Logerwell)

WaveHeightMethod Estimated by the scientist recording haul data; Text 255

QUALITATIVE data (on 2008 Beaufort Sea survey

it was Libby Logerwell)

WaveDirection Estimated by the scientist recording haul data; Text 255

QUALITATIVE data (on 2008 Beaufort Sea survey

it was Libby Logerwell)

WaveDirectionMethod From vessels magnetic compass; Estimated by the Text 255

scientist recording haul data; QUALITATIVE data 

(on 2008 Beaufort Sea survey it was Libby 

Logerwell)

SwellHeight In meters; Estimated by the scientist recording haul Text 255

data; QUALITATIVE data (on 2008 Beaufort Sea 

survey it was Libby Logerwell)

SwellHeightMethod Estimated by the scientist recording haul data; Text 255

QUALITATIVE data (on 2008 Beaufort Sea survey

it was Libby Logerwell)

SwellDirection In degrees; Estimated by the scientist recording Text 255

haul data; QUALITATIVE data (on 2008 Beaufort 

Sea survey it was Libby Logerwell)

SwellDirectionMethod From vessels magnetic compass; Estimated by the Text 255

scientist recording haul data; QUALITATIVE data 

(on 2008 Beaufort Sea survey it was Libby 

Logerwell)

RecorderName Libby Logerwell Text 255

TimeZone Alaska daylight time which is -8 hours from GMT Text 255

SpeedMethod from vessel Text 255

 

Data Quality: 

There are no haul locations in this table (see above). All methods of data collection and recording in this table 

followed the Alaska Fisheries Science Center’s RACE Division protocols (Stauffer 2004). 

Note: the field “NetType” and “Accessories” are the only 2 fields in the database that inform the reader which 

hauls used each of the 2 gear types. In the field “Accessories”, code “122” refers to net specifications found in 

the RACE ADP Codebook. In the field “NetType”, states whether that haul used a net that was lined or 

unlined; see the MMS Final Report for differences in catches due to gear type. 

192
Table: tblBotHaulPerformCode 

 

Description: Bottom haul; codes from the AFSC / RACE ADP code book under performance codes. 

Field Name (PK) Primary Key Description Type

Length

(PK) ID Auto Number 4

Performance Performance code from AFSC / RACE ADP Text 50

 codebook. 

Definition Definition of performance codes. Text 50

Data Quality: 

Corresponds to “tblBotHaul”. 

Table: tblBotLength 

Description: Bottom haul; lengths from fish species in the bottom hauls

Field Name (PK) Primary Key Description Type

Length

Cruise 200801, year 2008, 1 leg Long Integer 4

Vessel Ocean Explorer was used for the 2008 Beaufort sea Integer 2

survey (148)

Haul Bottom haul numbers were from 1 - 26 Text 50

SpeciesCode Corresponds to the species in the "tblSpeciesList" Long Integer 4

table

Sex 1=male, 2=female, 3=undetermined; a fish was left Integer 2

"unsexed" if the gonads were small or underdeveloped and there was not 100% confidence in 

determining sex.

Length All fish were measured in centimeters and then Integer 2

converted to millimeters in the database; lengths in 

this table are in mm; LENGTHS FROM THE 

"tblBotSpecimen" ARE INCLUDED IN THIS 

TABLE.

Data Quality: 

Note: Lengths from the “tblBotSpecimen” are also included in this table. 

193
Table: tblBotSpecimen 

 

Description: Bottom haul; specimens collected from bottom hauls that include otoliths, ovaries and stomachs. 

Field Name (PK) Primary Key Description Type

Length

Cruise 200801, year 2008, 1 leg Long Integer 4

Vessel Ocean Explorer was used for the 2008 Beaufort sea Integer 2

survey (148)

 Haul Bottom haul numbers are from 1-26 Text 50

SpeciesCode corresponds to the species in the "tblSpeciesList" Long Integer 4

table.

Sex 1=male, 2=female, 3=undetermined; a fish was left Integer 2

"unsexed" if the gonads were small or underdeveloped and there was not 100% confidence in 

determining sex.

Length LENGTHS RECORDED FOR BOTTOM TOWS Integer 2

IN THIS TABLE ARE ALSO INCLUDED IN 

THE "tblBotLength".

Weight in grams Long Integer 4

(PK) SpecNumber corresponds with the otolith vial for ageing, length Integer 2

and weight

MatCode maturity code. field may be filled in future ovary Integer 2

analysis for a subset of the specimens

SubsampleType 1=random subsample of the species; ~20-30 fish Integer 2

were randomly selected for sexing, length, weight 

and removal of otoliths (for ageing)

AgeStructure 1=yes, otoliths were collected; stored at the Alaska Integer 2

Fisheries Science Center, Seattle, WA

EntryOrder autonumber Auto Number 

Data Quality: 

Note: Lengths from the “tblBotLength” are also included in this table. 

Table: tblBotSpeciesOccur

Description: Bottom haul; a table that shows which hauls fish species occur in; includes those species that were ID'd in the lab but could 

not be updated by species in the tblBotCatch table; this is ONLY for the bottom tows. 

Field Name (PK) Primary Key Description Type

Length

(PK) Haul Pertains only to bottom tows and the fish species that Text 255

occurred in these tows. Some species listed in this 

table are lumped at the genus level in the 

tblBotCatch (i.e. Liparis sp.) but were ID in the lab

and split out in the table. Common names are under 

 “Description”. 

Artediellus scaber hamecon Long Integer 4

Aspidophoroides olriki Arctic alligatorfish Double 8

194
Boreogadus saida Arctic cod Double 8

Careproctus sp cf rastrinus (Orr et al) salmon snailfish Double 8

Eleginus gracilis saffron cod Double 8

Eumesogrammus praecisus fourline snakeblenny Double 8

Eumicrotremus derjugini leatherfin lumpsucker Double 8

Gadus macrocephalus Pacific cod Double 8

Gymnelus viridis fish doctor Double 8

Gymnocanthus tricuspis Arctic staghorn sculpin Double 8

Hippoglossoides robustus Bering flounder Double 8

Icelus spatula spatulate sculpin Double 8

Liparis fabricii gelatinous seasnail Double 8

Liparis gibbus variegated snailfish Double 8

Liparis marmoratus festive snailfish Double 8

Lumpenus fabricii slender eelblenny Double 8

Lumpenus maculates daubed shanny Double 8

Lumpenus medius stout eelblenny Double 8

Lycodes mucosus saddled eelpout Double 8

Lycodes polaris Canadian eelpout Double 8

Lycodes raridens marbled eelpout Double 8

Lycodes rossi threespot eelpout Double 8

Lycodes sp unid. eelpout Double 8

Mallotus villosus capelin Double 8

Myoxocephalus verrucosus warty sculpin Double 8

Nautichthys pribilovius eyeshade sculpin Double 8

Reinhardtius hippoglossoides Greenland turbot Double 8

Theragra chalcogramma walleye pollock Double 8

Table: tblBotSpeciesOccur

Triglops nybelini bigeye sculpin Double 8

Triglops pingeli ribbed sculpin Double 8

Lycodes seminudus longear eelpout Double 8

Liparis tunicatus kelp snailfish Double 8

Enophrys diceraus antlered sculpin Long Integer 4

Cottidae sculpin family Long Integer 4

Data Quality: 

All species of fish that occurred in the 2008 Beaufort Sea bottom trawl survey are found in this table. 

However, 2 species, Lycodes seminudus and Liparis tunicatus are not found in the “tblBotCatch” as they were 

identified in the laboratory but we were not able to assign them to the haul on the species level, but assigned 

them on the genus level (they were incorporated in with Lycodes sp. and Liparis sp.). 

195
Table: tblBSSSpeciesKey 

Description: Bottom haul; list of all species by latin name, common name and whether it is a fish or invertebrate (invert).

Field Name (PK) Primary Key Description Type

Length

SpeciesLatinName Species Latin name; species found during the Beaufort Text

50

sea survey, 2008

SpeciesComName Species common name Text 72

SpeciesCode From RACE ADP 2008 codebook, with changes. Long Integer 4

FishInvert Whether it is a fish or invertebrate species Text 50

Data Quality: 

This is a species list excerpted from the “tblRACESpeciesList”. These are species that occurred on the 

Beaufort Sea survey, 2008. The field “SpeciesCode” corresponds with the same field in the 

“tblRACESpeciesList”. In several cases, no common name exists. It is recommended to use the Latin name. 

Table: tblCTDBonHaul 

Description: CTD and Bongo haul information and data. 

Field Name (PK) Primary Key Description Type

Length

Cruise 200801, year 2008, 1 leg Long Integer 4

Vessel Ocean Explorer was used for the 2008 Beaufort sea Long Integer 4

survey (148)

(PK) Station Station at which a bottom haul and/or bongo and/or Double 8

 CTD cast occurred

(PK) Haul Field that connects to sample identification for Text 255

shipment to Poland for data analysis; HaulID 

consists of Cruise, Station, Haul (obsolete), 

GearAbrv, and Net

GearAbrv Gear used (bongo or CTD); definitions found in the Text 255

 "tblCTDBonGearDict" table

Net Net number from which the bongo sample came Text 255

from (1 or 2) and 20 or 60 cm

Comments Comments about the performance CTD and bongo Text 255

casts

AlternateStation Whether a CTD or Bongo cast plus the consecutive Text 255

 number e.g. CTD002 = 2nd CTD cast of the 

Mesh Whether the bongo net mesh size was 150 or 333 Double 8

microns.

GMTDate GMT date (Alaska time is -8 from this date) Date/Time 8

GMTTime GMT time (Alaska time is -8 from this time) Date/Time 8

BottomDepth Bottom depth in meters, from the ship's depth Double 8

sounder

GeographicArea Ocean basin in which survey was conducted Text 255

LatDD In decimal degrees Double 8

196
HemLat Hemisphere for latitude data (e.g. North or South) Text 255

LongDD In decimal degrees Double 8

HemLong Hemisphere for longitude data (e.g. East or West) Text 255

Performance Performance of the specific gear/net. Things that Text 255

may affect the performance are holes in net, bad flow

 meter readings, missing information, bad wire 

angles, lost sample, etc. See COD 

Manual_KB.doc for definitions

Flowmeter The identification number of the flowmeter used Double 8

FlowmeterRevs Total flowmeter count of revolutions from the Double 8

gear/net

MinGearDepth Minimum depth at which gear/net was deployed Double 8

MaxGearDepth Maximum depth at which gear/net was deployed. Double 8

Determined from wire out for CTD and from wire 

out and wire angle for Bongo. Wire angle 

measured manually with "skillet-shaped" angle 

MinWireOut Minimum wire let out Double 8

Table: tblCTDBonHaul

MaxWireOut Maximum wire let out, only recorded for Bongo Double 8

tows. For CTDs maximum wire out is the same as

 MaxGearDepth.

TowMinutes TowMinutes and TowSeconds together show the Double 8

amount of time that gear was sampling in the water.

 Only recorded for Bongo tows.

TowSeconds TowMinutes and TowSeconds together show the Double 8

amount of time that gear was sampling in the water.

 Only recorded for Bongo tows.

CalibrationFactor Calibration factor of flowmeter used for tow. Double 8

Needed for calculation of volume filtered.

StandardHaulFactorA Haul factor used to calculate catch per 10 m2 Double 8

StandardHaulFactorB Haul factor used to calculate catch per 1000 m3 Double 8

VolumeFiltered The volume filtered by the gear in m3 Double 8

TowTimeInSeconds Total tow time in seconds. Used for calculation of Double 8

volume

RevsPerSecond Average revolutions per second of plow meter Double 8

during tow. Used to calculate volume

Data Quality: 

This is all data associated with a CTD cast or Bongo tow. As of August, 2009 the bongo tow data were not 

available for analysis (e.g. zooplankton species). The principal investigator Tom Weingartner has all 

oceanographic data used in the MMS Final Report from the Beaufort Sea survey 2008. 

197
Table: tblMarineMammalSightings 

Description: Marine mammal sightings from the Alaska Fisheries Science Center’s Platforms of Opportunity Program (POP). 

Field Name (PK) Primary Key Description Type

Length

Cruise 200801, year 2008, 1 leg. Double 8

Vessel Ocean Explorer was used for the 2008 Beaufort Sea Double 8

survey (148).

Date Date the marine mammal was sighted, in ADT Date/Time 8

Time Time the marine mammal was sighted, in ADT Date/Time 8

LatDD Latitude in decimal degrees Double 8

LongDD Longitude in decimal degrees Double 8

Species Common name of marine mammal sighted Text 255

EstNumber Number estimated to be see by the observer, this is Double 8

NOT an absolute number, only an estimate of the 

number of individuals.

Behavior Behavior that the marine mammal was seen doing Text 255

during the observation

Comment General comment about the observation Text 255

 

Data Quality: 

These are marine mammal sightings, with estimated numbers observed in transit to/from the survey grounds in 

the Beaufort Sea, during July/August 2008. The data were not collected formally by transects or time. 

Table: tblRACESpeciesList

Description: Alaska Fisheries Science Center’s RACE Division species list of all fish and invertebrate species from Bering Sea (Beaufort 

included); includes code, latin name and common name when available.

Field Name (PK) Primary Key Description Type

Length

SpeciesCode Species code that relates to the AFSC / RACE Decimal 8

division database

SpeciesLatinName Species current Latin name. Text 72

SpeciesComName Species common name, highly variable. Most often Text 72

based on Mecklenburg 2007, Fishes of Alaska

Data Quality: 

This list is merely provided for future invertebrate voucher analysis or clarification on species name/codes. 

The field “SpeciesCode” corresponds to the same field in “tblBSSSpeciesKey”. 

198
Appendix II – Review of Beaufort Sea Fish Studies 

Several studies have been published on the near shore freshwater and anadromous fishes of the 

Beaufort Sea, especially in the Prudhoe Bay vicinity. This brief review focuses on a few 

specifics; marine fish species that may be encountered in the offshore marine waters of the 

Beaufort Sea, the gear used in past surveys, and a general overview (when available) of 

qualitative observations (e.g. schooling Arctic cod in bays during the summer months). 

Frost, K. J., and L. F. Lowry. 1983. Demersal fishes and invertebrates trawled in the 

 northeastern Chukchi and western Beaufort seas 1976 – 1977. U.S. Dep. Commer., 

 NOAA Tech. Rep. NMFS-SSRF-764, 22 p. 

The only known fish survey specifically targeting the offshore Beaufort Sea was in 1976 and 

1977 by Frost and Lowry (1983). Frost and Lowry (1983) primarily sampled fish within the 

benthic habitat and used semi-balloon otter trawls. The head ropes measured 4.9 and 5.8 m with 

31.75 mm stretch mesh webbing and a 6.5 mm mesh liner in the cod ends. Sampling depths 

primarily ranged from 40 to 150 m, however 1 tow was made at 400 m. Sampling locations 

ranged from 70° to 72°N and from the northeastern Chukchi Sea (164°W) to the eastern US 

portion of the Beaufort Sea (141°W). Towing time when net was on the bottom ranged from 5-

10 minutes. 

A total of 33 tows were conducted of which 14 occurred within the vicinity of the 2008 survey 

area (Figure 1). The survey area, in general, only encompassed offshore marine waters; tows 

were not conducted in the coastal or brackish waters, therefore the majority of species 

encountered were entirely marine. A total of 19 fish species or groups (listed below) and 238 

invertebrate species were identified from the surveys conducted in both 1976 and 1977. Arctic 

cod (Boreogadus saida), Canadian eelpout (Lycodes polaris) and twohorn sculpin (Icelus 

bicornis) accounted for 65% of all the fishes caught in the tows. Combining all species, fish fork 

lengths (FL) ranged from 25 mm to 245 mm. Biological information, such as stomach contents 

and reproductive descriptions are summarized in Frost and Lowry (1983) for the most commonly 

caught species (Arctic cod, Canadian eelpout, twohorn sculpin, hamecon, Arctic alligatorfish, 

snailfish sp., leatherfin lumpsucker, fish doctor and spatulate sculpin). 

The most common invertebrates encountered during the survey were (in order of decreasing 

abundance) gastropods, amphipods, polychaetes, echinoderms, bivalves, ectoprocts and shrimps. 

Two major invertebrate community types were identified; east of 150°W was mostly dominated 

by the scallop Delectopecten groenlandicus and the crinoid Heliometra glacialis (Frost and 

Lowry 1983). Sea cucumbers, sea urchins and several sp. of brittle stars were also found within 

this community and in general, the habitat was rocky (Frost and Lowry 1983). 

 

199
200

Fish species (latin and common) reported in Frost and Lowry (1983). An asterisk indicates 

species of highest abundance by number. The species common names in bold overlap with the 

Beaufort Sea 2008 Survey. 

Boreocogadus saida Arctic cod* 

Lycodes polaris Canadian eelpout* 

Icelus bicornis Twohorn sculpin* 

Artediellus scaber Hamecon 

Aspidophoroides olriki Arctic alligatorfish 

Liparis sp. Snailfish 

Eumicrotremus derjugini Leatherfin lumpsucker 

Gymnelis viridis Fish doctor 

Icelus spatula Spatulate sculpin 

Lumpenus fabricii Slender eelblenny 

Lycodes raridens Eelpout 

Gymnocanthus tricuspis Arctic staghorn sculpin 

Eumesogrammus praecisus Fourline snakeblenny 

Triglops pingeli Ribbed sculpin 

Lycodes mucosus Saddled eelpout 

Lycodes rossi Threespot eelpout 

Arctogadus glacialis Polar cod 

Lumpenus medius Stout eelblenny 

Lumpenus maculates Daubed shanny 
Barber, W. E., R. L. Smith, M. Vallarino, and R. M. Meyer. 1997. Demersal fish 

 assemblages of the northeastern Chukchi Sea, Alaska. Fish., Bull. 95:195-209. 

Barber et al. (1997) conducted a fish survey in the Chukchi Sea in 1990 and 1991. The primary 

focus of this study was to document the distribution and abundance of Arctic fishes in the 

Chukchi as well as relate fish assemblages to oceanographic variables. The survey extended to 

the northeast Chukchi Sea and overlapped, to a small extent, with the Frost and Lowry (1983) 

survey in 1976 and 1977 (Figure 2). For the purposes of this brief review, only stations in the 

northeastern Chukchi by Barber et al. (1997) were examined (Figure 1, stations 25-29 and 91-32 

to 91-35). 

The duration of each tow was 30 minutes using the standard 83-112 otter trawl with a 25.2 meter 

head-rope. The head-rope on the small otter trawl used in Frost and Lowry (1983) measured 4.9 

– 5.8 meters. The mesh liner in the 83-112 codend is 31 mm. A total of 64 tows were made in 

1990 (48) and 1991 (16 that included 8 that were sampled in 1990). 

 

Figure 1 Survey stations were estimated from Figure 1 in Barber et al. (1997). Survey 

station locations are from Table 1 in Frost and Lowry (1983). 

201
202

The most abundant species by number and weight was Boreogadus saida (Arctic cod). Arctic 

cod comprised 76% of the total estimated mean abundance (no. fish/km2

) captured in 1990 and 

61% in 1991 (Table1, Barber et al. 1997). However, the northeast stations were comprised of 

substantially fewer numbers of fish/biomass than all other areas (Figure 2, Barber et al. 1997). 

The number of species observed for the northeastern stations were (stations located in 

assemblages 2, 3 and 6 in Table 3, Barber et al. 1997) were between 6 and 11. The species found 

in these stations (in addition to others within that assemblage) are summarized below. 

Fish length was not reported in Barber et al. (1997) for any of the listed species. 

Species found in the northeastern Chukchi Sea, summarized from Table 3 in Barber et al. 1997 

(assemblages 2, 3 and 6). The species common names in bold overlap with the species found in 

the Frost and Lowry (1983) study, and the Beaufort Sea 2008 Survey. An asterisk indicates 

species of highest abundance by weight.

Boreocogadus saida Arctic cod * 

Eleginus gracilis Saffron cod 

Myoxocephalus sp. Sculpin sp. 

Gymnocanthus tricuspis Arctic staghorn sculpin 

Hippoglossoides robustus Bering flounder 

Myoxocephalus verrucosus Warty sculpin 

Artediellus scaber Hamecon 

Lumpenus fabricii Daubed shanny 

Lycodes polaris Canadian eelpout 

Lycodes raridens Raridens eelpout 

Podothecus acipenserinus Alligator fish 

Gadus macrocephalus Pacific cod 

Liparis gibbus Variegated snailfish 
Jarvela, L. E., and L. K. Thorsteinson. 1999. The Epipelagic Fish Community of Beaufort 

 Sea Coastal Waters, Alaska. Arctic, 52(1):80-94. 

The focus of this research was to identify temporal and spatial patterns in marine fish that inhabit 

open-water zones in the near shore Beaufort Sea. Specifically addressed were marine fish 

community compositions, species distribution and abundance, and age-length relationships. 

The study area extended from the Colville River delta (~151°30’N) to Barter Island (~143°N), 

from shoreline to about 30 km. Their study area was divided into a “West” and “East” sector. 

The study area was sampled in 1988 with a purse seine and in 1990 and 1991 with a surface tow 

net. The purse seine was made to specifically target small fish in shallow water and was made 

with a 19 mm stretch mesh and a 6.3 mm mesh for the bunt (analogous to a codend); the purse 

seine was held open for 10 to 20 minutes. At total of 41 seines were completed in 1988. 

The surface tow net consisted of 50.8 mm mesh from the opening, decreasing to 7.9 mm at the 

bag. The net was towed between 2 vessels for 10 minutes. A total of 28 stations were towed 

with a net in 1990 and 35 stations in 1991. 

Catches included many “zeros” and had large variance-to-mean ratios. “Total catches were 

much larger during the open water year (1990), in which marine conditions prevailed, in 

contrast to heavy ice years where heavy pack ice was present and brackish water prevailed for a 

longer period of time (Jarvela and Thorsteinson, 1999”). 

Arctic cod, capelin and Arctic cisco dominated the catch in all 3 years (Table 3, Jarvela and 

Thorsteinson, 1999). On average, Arctic cod and capelin CPUEs in the west sector were larger 

than those in the east sector in all 3 years. Age-0 capelin, liparids (snailfish) and Arctic cisco 

dominated all the catches and age-0 Arctic cod dominated the catch in 1990 and 1991(fish age-1 

+ comprised 7% and 2% of catches in 1990 and 1991, respectively). Based on this, Jarvela and 

Thorsteinson (1999) concluded that Arctic cod, in general, segregate into discrete size or age 

groups. 

In general, surface waters across the West and East sectors were uniform in species richness and 

composition. It is not common to find Dolly Varden or Arctic cisco in offshore waters. 

Combining all species, the range of fork lengths were 10 mm (Liparid larvae) to 172 mm (Arctic 

cod).

203
Fish species that occurred across the study area for all 3 years are summarized below from 

Table 3 in Jarvela and Thorsteinson (1999). The species common names in bold overlap with the 

species found in the Frost and Lowry (1983) study and the Beaufort Sea 2008 Survey. 

Boreogadus saida Arctic cod 

Mallotus villosus Capelin 

Coregonus autumnalis Arctic cisco 

Liparis sp. larvae Snailfish larvae 

Pungitius pungitius Ninespine stickleback 

Myoxocephalus quadricornis Fourhorn sculpin 

Salvelinus malma Dolly Varden 

Cottid larvae Sculpin larvae 

Lumpenus sp. Eelblennies 

Liparis tunicatus Kelp snailfish 

Liopsetta glacialis Arctic Flounder 

Gymnocanthus tricuspis Arctic staghorn sculpin 

Ammodytes hexapterus Pacific sand lance 

Artediellus uncinatus Arctic hookear sculpin 

Osmerus mordax Rainbow smelt 

Agonus acipenserinus Sturgeon poacher 

204
Moulton, L. L., and K. E. Tarbox. 1987. Analysis of Arctic Cod Movements in the Beaufort 

 Sea Near shore Region, 1978 – 79. Arctic, 40(1):43-49. 

The primary focus of this study was to assess distribution and abundance patterns of Arctic cod 

near Prudhoe Bay using hydroacoustic and trawl net. 

However, in addition to Arctic cod, all fish captured in the net were identified and counted. All 

trawls were made on the bottom and towing duration was 15 minutes. A 3 m semi-balloon otter 

trawl was used with 13 mm square mesh in the body and 3 mm mesh in the codend. A total of 

33 tows were made in 1978, 43 in July 1979 and 32 in August 1979. 

Hydroacoustic data were primarily collected on north-south transects in water depths greater than 

4 m. For specific details on verifying acoustic targets with nets, see Moulton and Tarbox, 1987. 

Arctic cod dominated the trawl catches at 98% of the total with traces of kelp snailfish, fourhorn 

sculpin, Pacific sandlance, capelin, rainbow smelt and least cisco. The length frequency of the 

Arctic cod indicated that more than likely only age-1 fish were represented in the trawls (very 

few older fish were captured). Based on the otter trawl captures there is, in general, an offshore 

movement of Arctic cod between July and August (1979). 

205
Craig, P. C. 1984. Fish use of coastal waters of the Alaskan Beaufort Sea: A review. Trans. 

 Am. Fish. Soc., 113(3):265-282. 

This paper reviews research on near shore fishes of the Beaufort. In this summary, the primary 

focus is on the fish found in brackish near shore habitats which comprises a portion of the review 

within Craig 1984. 

Species are listed from most abundant to least abundant by numbers. The species common 

names in bold overlap with those found in Frost and Lowry (1983) and the Beaufort Sea 2008 

Survey. Species listed below with the † symbol comprises 90% of the total abundance fishes 

caught along the Alaskan and Yukon Territory coastlines (several references cited with in Craig 

(1984) 

Coregonus autumnalis Arctic cisco† 

Coregonus sardinella Least cisco† 

Salvelinus alpinus Arctic char† 

Boreogadus saida Arctic cod†

Myoxocephalus quadricornis Fourhorn sculpin†

Coregonus nasus Broad whitefish 

Coregonus pidschian Humpback whitefish 

Liopsetta glacialis Arcitc flounder 

Osmerus mordax Rainbow smelt 

The author summarizes patterns in species distribution and movement in Simpson Lagoon, 

located within the Barrier Islands west of Prudhoe Bay, between the Colville and Sagavanirktok 

rivers 

It was found that these anadromous fish densities ranged significantly from within Simpson 

Lagoon (brackish) to marine offshore waters, with the greatest abundance occurring in the warm, 

turbid waters of the lagoon and few fish occurring in marine waters on the seaward side of the 

barrier islands. Many fish use this corridor where the highest concentrations of fish occur within 

100 m of shore; however, this is influenced by sea state, oceanographic properties (i.e., 

temperature and salinity), extent of the brackish water, and water depth. Arctic char were the 

most abundant anadromous fish on the seaward side of the barrier islands. 

One note of interest on habitats; there is a documented area of rocky bottom near Prudhoe Bay 

(as opposed to the predominance of sand and mud in the Beaufort Sea) termed the “Boulder 

Patch” near Stefansson Sound. There is a relatively low abundance of fish and diversity; 

however, this habitat is home to marine species that spawn on hard substrate and numerous 

invertebrates. 

206
Welch, H. E., R. E. Crawford, and H. Hop. 1993. Occurrence of Arctic Cod (Boreogadus 

 saida) Schools and Their Vulnerability to Predation in the Canadian High Arctic. 

 Arctic, 46(4):331-339. 

The authors document large schools of Arctic cod near shore during the open water season. On 

occasion these large aggregations are close to shore and visible to people on land. There has 

been some debate as to whether these events are rare or occur on an annual basis. It has also 

been documented (through local knowledge) that large schools of fish have been found stranded 

on beaches, possibly driven by whales. 

Arctic cod schools were documented in Allen, Resolute, and Radstock bays, Barrow straight, in 

Northwest Territories, Canada. Schools sizes were estimated via areal views when schools of 

cod were shallow and could be seen clearly. For deeper schools of fish, subjective estimates 

were made via a boat mounted depth finder. School composition was estimated from small otter 

trawls (5 m wide, 5 cm intermediate mesh and 1.3 cm mesh cod end liner), cast nets (2 cm 

mesh), dip nets and trap nets. 

All large open water schools observed were fish age 2+ with mean ages at 3-4+. Schooling cod 

were present continuously within Allen Bay for 7-8 weeks during July, August and September. 

These large schools of cod draw in a wide variety of marine mammals and seabirds. The authors 

estimate biomass on one day in August, 1989 (Table 3) to be approximately 25, 800 tons 

(combining all the schools of cod determined by the echo sounder in Allen Bay, Cornwallis 

Island). 

These large schools of Arctic cod undergo intense predation by seabirds and marine mammals 

and are therefore important prey items in these ecosystems. 

207
Craig, P., and L. Haldorson. 1986. Pacific Salmon in the North American Arctic. Arctic 

 39(1):2-7. 

All 5 Pacific salmonid species occur in Arctic waters; however, only pink and chum salmon have 

maintained populations north of Point Hope, Alaska (although all 5 have occurred at some time 

or other north of Point Hope). Of these 2 species, 85% of catches are composed of pink salmon. 

The authors estimate that salmon comprise 0-4% of the total sample catch of fishes caught in 

Arctic waters (based on other studies from 1970 to 1984). The authors captured actively 

migrating pink salmon from Simpson lagoon, located ~50 km west of Prudhoe Bay. In 1977 no 

salmon were caught and 118 were captured in 1978, using directional nets, 95% of the salmon 

captured were moving in an eastward direction. 

Little is known about the marine phase of pink or chum salmon in the Arctic (do they migrate to 

the Bering and overwinter or remain offshore in the Beaufort Sea?). There is evidence based on 

few tag recoveries that chum salmon spawned in Arctic rivers can migrate as far south as the 

Gulf of Alaska (Neave 1964, as cited in Craig and Haldorson 1986). 

208
Griffiths, W. B., R. G. Fechhelm, B. J. Gallaway, L. R. Martin, and W. J. Wilson. 1998. 

 Abundance of Selected Fish Species in Relation to Temperature and Salinity 

 Patterns in the Sagavanirktok Delta, Alaska, Following Construction of the Endicott 

 Causeway. Arctic 51(2):94-104. 

The authors estimate abundance of four species of marine fish (Arctic cod, fourhorn sculpin, 

Arctic flounder and saffron cod) and two species of freshwater fish (round whitefish and Arctic 

grayling) in the vicinity of Endicott Causeway near Prudhoe Bay. Fish were collected via 4 Fyke 

nets near the Sagavanirktok river delta (Figure 6) from 1985 to 1993. Abundance calculations 

were based on mean CPUE for each net, totaling 4 estimates for each year and species. 

Concentration on the four observed marine species, their abundance and observed relationship to 

temperature and salinity will be the primary focus of this brief summary. The impetus for this 

study was the concern that oceanographic conditions such as temperature and salinity might 

change in favor or a more “marine” type environment, thus favoring marine species. Increased 

abundances of marine species would be indicative that changes enacted by causeway 

construction may play a role. 

Many of the citations that occur within Griffiths et al. 1998 concentrate on near shore surveys 

that took place during open-water seasons; however only one offshore survey of the Beaufort Sea 

marine species mentioned below has occurred (see Frost and Lowry 1983). 

Arctic cod – 

The abundance of Arctic cod increased in the first 3 years after construction of the Endicott 

causeway, however abundance did not increase over time (between 1985 and 1993). Arctic cod 

abundance estimates were widely variable among years and locations along the Beaufort Sea 

coast (as cited by other studies in Griffiths et al. 1998). Arctic cod are can be found inshore, as 

well as offshore during the open water season. It was concluded by the authors that Arctic cod 

habitat use in the vicinity of the Endicott causeway did not change as a result in changing 

temperatures and salinity. 

Fourhorn sculpin – 

Fourhorn sculpin can occur in both near shore and offshore waters of the Beaufort Sea (as cited 

in Griffiths et al. 1998). Griffiths et al. 1998 concluded that fourhorn sculpin abundance was 

positively correlated with salinity levels (Table 1 in Griffiths et al. 1998); however they did not 

see an increase in abundance, due to higher salinity levels caused by the construction of the 

Endicott causeway. 

Arctic flounder – 

The Arctic flounder can be found in shallow coastal waters during the open water season where 

it can reside in low-salinity habitats (as cited in Griffiths et al. 1998). During the first 5 years 

post constructions, abundance of Arctic flounder in the vicinity of the Endicott causeway was 

low. From 1990 to 1993, CPUE increased within the Griffiths et al. 1998 study area. Based on 

length frequency and age data, the authors conclude that this increase in abundance was possibly 

due to a large over-winter survival rate of the 1989 year class rather than changes in 

oceanographic conditions near the causeway that would favor marine species (i.e. increased 

salinity). 

209
Saffron cod – 

The abundance levels of saffron cod within the Griffiths et al. 1998 study area varied, but were 

relatively low over all years compared to the Arctic cod, fourhorn sculpin and Arctic flounder. 

There was no significant relationship detected for saffron cod and temperature/salinity in the 

Endicott causeway study area. 

 

210
211

Mecklenburg, C. W., D. L. Stein, B. A. Shieko, N. V. Chernova, T. A. Mecklengurg, and B. 

 A. Holladay. 2007. Russian-American long term census of the Arctic: benthic fishes 

 trawled in the Chukchi Sea and Bering Strait, August 2004. Northwest. Nat. 88:168-

 187. 

An otter trawl with a 7.1 m headrope and a 37-mm stretch mesh liner was used to capture adult 

and large juvenile fishes. Bottom towing times varied from 10 to 15 minutes. A 3.05 m 

plumbstaff beam trawl with a 7-mm mesh lining in the body and 4-mm mesh codend was used to 

capture small adult and juvenile fishes. Towing time on the bottom varied form 1 to 5 minutes. 

Depths varied from 34 to 101 meters; there were 26 otter trawls and 19 beam trawls at 17 

different stations. Bottom substrate most commonly encountered at stations was sand and mud. 

A total of 3,193 fish specimens were collected that included 33 species. The 4 species: Arctic 

staghorn sculpin (Gymnocanthus tricuspis), shorthorn sculpin (Myoxocephalus scorpius), Bering 

flounder (Hippoglossoides robustus) and Arctic cod (Boreogadus saida) accounted for 79% of 

all fishes caught. Fish length varied from 20 to 403 mm TL. 

All species found on the survey are described in detail (numbers and at what station) that include 

voucher and station number, range extent (previous and current) and substrate association.
Majewski, A.R., J.D. Reist, B.J. Park, J.E. Sareault, and M.K. Lowdon. 2009. Fish catch 

data from offshore sites in the Mackenzie River estuary and Beaufort Sea during 

the open water season, July and August, 2005, aboard the CCGS Nahidik. Canadian 

Data Report Fisheries Aquatic Sciences 1204: vii + 53 p. 

This study took place in the Canadian Beaufort Sea, from the Mackenzie River estuary (~10 m 

isobath) into the marine offshore waters, approximately 50-60 nautical miles offshore (~50 m 

isobath). The gear types employed were a multimesh gill net, a midwater trawl, benthic sled and 

a box core. Stations where gear was deployed occurred along two transects. The report states 

that “fishing activities were exploratory in nature”, therefore no quantitative estimates of species 

biomass were made. The report summarizes species catch, timing, location, depth, gear type and 

a suite of biological parameters (e.g. length, maturity). NO fish were captured in the midwater 

trawls and only 1 fish was captured in the box core sampling. All summaries of fish reported 

below were captured in the benthic trawl. 

A total of 18 species were captured at 17 stations (2 transects), which included 167 adult and late 

juvenile fish and 651 larval and early juvenile fish. Pacific herring made up 37.72% of the total 

adult and late juvenile catch, and they were only caught in the gill nets. Arctic cod were the 

most abundant larval and juvenile fish captured (n=485), making up 74.39% of the total and 

those were only caught in the midwater trawl. 

The species common names in bold overlap with those found in Frost and Lowry (1983) and the 

Beaufort Sea 2008 Survey.

Clupea pallasii Pacific herring 

Myoxocephalus quadricornis Fourhorn sculpin 

Osmerus mordax rainbow smelt 

Coregonus autumnalis Arctic cisco 

Eleginus gracilis saffron cod 

Platichthys stellatus starry flounder 

Boreogadus saida Arctic cod 

Gymnocanthus tricuspis Arctic staghorn sculpin 

Liparis tunicatus kelp snailfish 

Liparis fabricii gelatinous seasnail 

Ulcina olrikii Arctic alligatorfish 

Triglops pingelii Ribbed sculpin 

Lumpenus fabricii slender eelblenny 

sculpin species unid. Icelus sp. 

snailfish species unid. Liparis sp. 

cod/pollock/whitefish etc. Gadidae (genus species not known) 

Anisarchus medius stout eelblenny 

Gymnelus hemifasciatus halfbarred pout 

Icelus spatula spatulate sculpin 

Lycodes rossi threespot eelpout 

juvenile eelpout unid. juvenile Lycodes sp. 

Lycodes polaris Canadian eelpout 

212
Majewski, A.R., J.D. Reist, B.J. Park, J.E. Sareault, and M.K. Lowdon. 2009. Fish catch 

data from offshore sites in the Mackenzie River estuary and Beaufort Sea during 

the open water season, August 2006, aboard the CCGS Nahidik. Canadian Data 

Report Fisheries Aquatic Sciences 1218: vi + 37 p. 

Similar to the 2005 survey by the same authors, this study took place in the Canadian Beaufort 

Sea, from the Mackenzie River estuary (~10 m isobath) into the marine offshore waters, 

approximately 50-60 nautical miles offshore, in water depths that ranged from 11 to 225 m. The 

gear types employed were a benthic trawl and a midwater trawl. Stations where gear was 

deployed occurred along two transects. There appears to be little or no overlap between these 2 

transects in Mackenzie Bay and near Hershel Island, and those transects in the 2005 survey. The 

report states that “fishing activities were exploratory in nature”, therefore no quantitative 

estimates of species biomass were made. The report summarizes species catch, timing, location, 

depth, gear type and a suite of biological parameters (e.g. length, maturity). 

A total of 619 adult and late juveniles from 17 species were collected. Arctic cod were the most 

abundant species captured (by number) and made up 38.18% of the total catch at 13 of the 14 

stations. Stout eelblennies were the second most common species (by number) captured during 

the survey. Stout eelblennies were not found on the Beaufort Sea 2008 Survey. 

The species common names in bold overlap with those found in Frost and Lowry (1983) and the 

Beaufort Sea 2008 Survey.

Boreogadus saida Arctic cod 

Gymnocanthus tricuspis Arctic staghorn sculpin 

Liparis fabricii gelatinous seasnail 

Ulcina olrikii Arctic alligatorfish 

Triglops pingelii Ribbed sculpin 

Lumpenus fabricii slender eelblenny 

Anisarchus medius stout eelblenny 

Lycodes rossi threespot eelpout 

Icelus spatula spatulate sculpin 

Icelus bicornis twohorn sculpin 

Gymnelus viridis fish doctor 

Leptoclinus maculates daubed shanny 

Lycodes reticulatus Arctic eelpout 

Lycodes marisalbi White sea eelpout 

Artediellus scaber hamecon 

Lycodes polaris Canadian eelpout 

213
Appendix III – CTD cast data 

Table III.1. CTD casts and bongo tows, latitude and longitude, date, time, and depth. 

Station CTD # Bongo # Date (GMT) Time (GMT) Bottom Depth (m) Latitude Longitude 

1 CTD001 BON001 8/6/2008 23:49 445 71.89 -154.95 

2 CTD002 BON002 8/7/2008 4:20 300 71.84 -154.96 

3 CTD003 BON003 8/7/2008 5:19 300 71.79 -154.97 

4 CTD004 BON004 8/7/2008 18:21 200 71.74 -154.98 

5 CTD005 BON005 8/8/2008 1:44 357 71.90 -153.89 

7 CTD006 BON006 8/9/2008 2:24 158 71.81 -154.46 

9 CTD008 BON007 8/10/2008 1:00 275 71.97 -154.41 

13 CTD009 BON009 8/10/2008 18:53 190 71.88 -154.45 

15 CTD010 BON010 8/11/2008 3:38 333 71.72 -152.85 

16 CTD011 BON011 8/11/2008 18:41 333 71.66 -152.48 

18 CTD012 BON012 8/12/2008 1:41 187 71.52 -152.21 

19 CTD013 BON013 8/12/2008 21:45 66 71.75 -153.94 

20 CTD014 BON014 8/13/2008 2:10 50 71.69 -154.49 

21 CTD015 8/13/2008 17:50 47 71.59 -153.99 

22 CTD016 BON015 8/13/2008 20:56 47 71.48 -153.94 

24 CTD017 BON016 8/14/2008 3:48 31 71.35 -154.13 

25 CTD018 8/14/2008 17:53 40 71.25 -153.12 

26 CTD019 BON017 8/14/2008 22:50 75 71.37 -153.06 

27 CTD020 BON018 8/15/2008 0:16 72 71.32 -153.09 

28 BON019 8/15/2008 2:22 64 71.45 -153.03 

29 CTD022 8/15/2008 2:54 72 71.41 -153.04 

30 CTD023 8/15/2008 3:44 60 71.50 -153.01 

31 CTD024 8/15/2008 4:11 58 71.55 -153.00 

32 CTD025 8/15/2008 4:42 63 71.60 -152.98 

34 CTD026 BON020 8/15/2008 19:03 49 71.28 -152.30 

35 CTD027 BON021 8/15/2008 22:09 85 71.36 -151.99 

37 CTD028 BON022 8/16/2008 16:22 44 71.58 -155.06 

38 CTD029 BON023 8/16/2008 18:36 20 71.37 -155.08 

39 CTD030 8/16/2008 19:16 21 71.41 -155.08 

40 CTD031 BON024 8/16/2008 19:45 24 71.46 -155.06 

41 CTD032 8/16/2008 20:30 27 71.51 -155.06 

42 CTD033 BON025 8/16/2008 21:33 56 71.62 -155.03 

43 CTD034 8/16/2008 22:07 90 71.66 -156.00 

44 CTD035 8/16/2008 22:42 150 71.71 -154.99 

46 CTD036 8/17/2008 3:14 457 71.89 -154.95 

47 CTD037 8/17/2008 16:40 26 71.51 -155.06 

48 CTD038 8/17/2008 22:21 42 71.63 -154.52 

49 CTD039 BON026 8/18/2008 19:01 25 71.20 -153.60 

51 CTD040 8/18/2008 22:07 57 71.42 -153.53 

52 CTD041 BON027 8/19/2008 0:07 52 71.55 -153.49 

53 CTD042 BON028 8/19/2008 4:05 112 71.65 -152.97 

55 CTD043 BON029 8/19/2008 16:28 63 71.46 -153.04 

57 CTD044 8/19/2008 20:33 32 71.21 -153.12 

58 CTD045 BON030 8/19/2008 21:00 26 71.17 -153.13 

59 CTD046 8/19/2008 21:36 22 71.12 -153.14 

214
Station CTD # Bongo # Date (GMT) Time (GMT) Bottom Depth (m) Latitude Longitude 

60 CTD047 8/19/2008 23:19 25 71.15 -152.68 

61 CTD048 BON031 8/20/2008 5:14 225 71.63 -152.46 

62 CTD049 BON032 8/20/2008 16:35 36 71.20 -152.21 

63 CTD050 BON033 8/20/2008 18:37 63 71.36 -152.13 

64 CTD051 8/20/2008 21:42 267 71.52 -152.07 

66 CTD052 BON034 8/21/2008 3:28 59 71.53 -152.87 

67 CTD053 BON035 8/21/2008 15:33 52 71.55 -153.49 

68 CTD054 BON036 8/21/2008 19:37 26 71.39 -154.58 

69 CTD055 BON037 8/21/2008 21:40 21 71.41 -155.07 

70 CTD056 BON038 8/22/2008 0:39 102 71.67 -154.99 

71 CTD057 8/22/2008 4:30 297 71.78 -154.99 

215
216

Appendix IV – Net mensuration data and trawl design and rigging 

Net spread (m) Net height (m) 

Haul Distance 

fished 

(km) 

Area 

swept 

(km2

) 

Average Standard 

deviation 

Average Standard 

deviation 

Mean 

head rope 

depth (m) 

Wire out 

(m) 

1 3.65 0.052 14.4 2.07 5.1 1.13 423 not 

recorded 

2 1.16 0.019 16.4 0.78 3.1 0.13 467 1052 

3 1.39 0.023 16.3 0.98 3.4 0.84 195 549 

4 1.34 0.021 15.8 0.43 2.6 0.3 344 823 

5 1.30 0.020 15.4 0.29 3.1 0.3 140 411 

6 1.48 0.027 18.2 3.2 0.18 155 457 

7 1.67 0.027 16.1 0.5 3.7 1.05 318 823 

8 1.44 0.023 15.6 0.72 2.7 0.13 315 732 

9 1.57 0.024 15.5 0.45 2.9 0.42 299 777 

10 1.58 0.024 15.4 0.78 2.8 0.49 172 503 

11 1.41 0.020 14.4 1.15 2.5 63 229 

12 1.58 0.022 14.1 1.22 3.4 0.54 47 183 

13 1.41 0.021 14.6 1.66 3.0 0.52 46 183 

14 1.18 0.019 15.8 3.09 2.4 0.85 39 183 

15 1.49 0.023 15.7 2.65 40 183 

16 0.46 0.008 16.7 2.6 40 183 

17 0.51 0.009 18.0 0.92 72 229 

18 0.60 0.010 17.1 61 229 

19 0.50 0.007 13.9 1.9 28 183 

20 0.62 0.009 15.2 2.38 2.8 0.87 47 183 

21 0.69 0.012 16.7 1.69 2.5 80 274 

22 0.78 0.013 16.9 3.2 2.6 1.03 175 503 

23 0.69 0.011 16.5 1.3 0.38 43 183 

24 0.64 0.010 16.1 1.64 3.9 0.84 46 183 

25 0.70 0.011 16.2 2.07 2.5 0.74 57 229 

26 0.55 0.009 16.5 0.72 2.3 0.27 50 183 

Table IV.1. Net mensuration data from all bottom trawls. Area swept was calculated from 

distance fished and average net spread. Net spread for hauls 6, 18 and 23 was calculated from 

a regression on wire out (Lauth and Acuna, 2007), because there was not a sufficient number 

of net spread observations collected due to instrument failure. Missing net height data are due 

to instrument failure. 
Trawl door detail, rigging, footrope plan and frame lines exerted from Stauffer, 2004. 

217 206
218
Appendix V – Sample size and final destination of biological samples 

Table V.1. Sample sizes for biological collections by species and the type of sample collected. 

An * indicates the sample was a subsample of the total number of samples collected. 

Species Sex Length Weight Gonads Stomach Otoliths Genetics Total 

Arctic cod 1,493 1,493 753* ~120* 95 1,210* N/A 1,493 

Bering flounder 27 27 27 N/A 27 N/A N/A 27 

Greenland turbot 10 10 10 N/A 10 N/A N/A 10 

Pacific cod 2 2 2 N/A N/A N/A N/A 2 

walleye pollock 99 99 99 N/A N/A 95 95 99 

All vouchered fish specimens collected on the Beaufort Sea Survey 2008 are located in the 

University of Washington’s Burke Museum Ichthyology Collection. 

http://www.washington.edu/burkemuseum/collections/ichthyology/index.php

Approximately 152 specimens are vouchered at the University of Washington; contact Katherine 

Maslenikov at (206) 543-3816 or email at: pearsonk@u.washington.edu for a complete list of 

catalog numbers for each specimen. 

All vouchered invertebrates collected on the Beaufort Sea Survey 2008 are located at the 

University of Alaska Fairbanks (UAF). The contact person for the collection is Dr. Bodil 

Bluhm, Research Assistant Professor at UAF. http://www.uaf.edu/ 

Two speces of crabs, Chionoecetes opilio and Hyas coarctatus, were collected for a special 

project at NOAA’s Alaska Fisheries Science Center, Seattle, WA (see “Special Projects” in 

Methods). The contact person is Dr. Frank Morado of the RACE division’s Pathobiology 

Laboratory. 

Several species of fish were collected for genetic barcoding, Fish Barcode of Life Initiative, 

FISH-BOL, (see “Special Projects” in Methods). The contact person for this special project is 

Catherine W. Mecklenburg, Research Associate, Department of Ichthyology, Point Stephens 

Research, Auke Bay, AK. 

All Arctic cod otoliths (age structures) collected on the Beaufort Sea Survey 2008 were aged and 

are currently stored at NOAA’s Alaska Fisheries Science Center, Seattle, WA. The contact 

person is Dr. Thomas Helser, Manager of the Age and Growth Program. 

Walleye pollock otoliths collected on the Beaufort Sea Survey 2008 were aged and are currently 

stored at NOAA’s Alaska Fisheries Science Center, Seattle, WA. The contact person is Dr. 

Thomas Helser, Manager of the Age and Growth Program. 

Walleye pollock genetic fin clips collected on the Beaufort Sea Survey 2008 are currently stored 

at NOAA’s Alaska Fisheries Science Center, Seattle, WA. The contact person is Dr. Mike 

Canino, of the RACE division’s Genetic Laboratory. 

219
Approximately 20 Arctic cod fin clips were sent to the University of Victoria BC, Victoria, 

British Columbia. The contact person is Dr. John Nelson, Institute of Ocean Sciences, 

Department of Biology. 

Stomachs of three fish species were collected during the Beaufort Sea Survey 2008 and are 

currently stored at NOAA’s Alaska Fisheries Science Center, Seattle, WA. The fish species are 

Arctic cod, Bering flounder, and Greenland turbot. The contact person is Dr. Kerim Aydin, 

Manager of AFSC Resource Ecology and Ecosystem Modeling Program. 

Stable isotope samples from fish species and bongo tows collected during the Beaufort Sea 

Survey 2008 are currently stored at the NOAA’s Alaska Fisheries Science Center, Seattle, WA. 

The contact person is Dr. Kerim Aydin, Manager of AFSC Resource Ecology and Ecosystem 

Modeling Program. 

Arctic cod ovaries collected during the Beaufort Sea Survey 2008 are currently stored at the 

NOAA’s Alaska Fisheries Science Center, Seattle, WA. The contact person is Dr. Elizabeth 

Logerwell of AFSC Status of Stocks and Multispecies Assessment Program. 

Fish species were collected for acoustics (target strength) during the Beaufort Sea Survey 2008 

and are currently stored at the University of Washington’s, School of Aquatic and Fishery 

Sciences. The contact person is Dr. Sandra Parker-Stetter of the Fisheries Acoustics Research 

Laboratory. 

Approximately 20 juvenile Arctic cod collected during the Beaufort Sea Survey 2008 are 

currently stored at the Mineral Management Service (MMS), Anchorage, AK. The contact 

person is Kate Wedemeyer of MMS, Anchorage, AK. 

220
Appendix VI – Auxiliary studies 

Bitter crab syndrome in Beaufort Sea snow (Chionoecetes opilio) and Arctic lyre (Hyas 

coarctacus) crabs. 

J. Frank Morado, Pamela C. Jensen, and Amelia Whitcomb 

Background 

Bitter crab syndrome is a fatal disease of North Pacific Tanner crabs that is caused by a parasitic 

dinoflagellate of the genus Hematodinium Chatton and Poisson 1931. The disease was 

diagnosed in the North Pacific after lots of southeast Alaska Tanner crabs, Chionoecetes bairdi, 

were rejected by processors for possessing a bitter flavor and “chalky” appearance (Meyers et al. 

1987). The estimated economic loss to fishers as a result of the initial disease episode was 

$175,758 (US). Since the southeast Alaska epizootic, the disease has been reported throughout 

the Northern Hemisphere with increased frequency and severity. For example, in the North 

Pacific and in addition to southeast Alaska, the disease has been documented in Gulf of Alaska 

Tanner crabs, eastern Bering Sea, Norton Sound and Chukchi Sea snow crabs, C. opilio, eastern 

Bering Sea Arctic lyre crabs, Hyas coarctacus, and in red, Paralithodes camtschaticus, and blue, 

P. platypus, king crabs from the Sea of Okhotsk (Meyers et al. 1996, Ryazanova 2008). 

Currently, over 40 species of crustaceans are known to be infected of which several species are 

of economic importance. 

In an effort to continue monitoring the prevalence and distribution of the disease, we requested 

opportunistic samples of Beaufort Sea snow and Arctic lyre crabs. Presence of the disease would 

extend the known distribution of the disease east of the Chukchi Sea. 

Methods 

Intact specimens were placed in plastic bags with species and station identification data. All or 

several specimens of the same species were placed in common bags to conserve freezer space. 

Frozen samples were shipped to Seattle upon completion of the survey. 

Upon arrival, crabs were partially thawed and their sex, size (carapace width for C. opilio, 

carapace length for H. coarctacus) and shell condition was noted. Skeletal muscle of the 

approximate size of a rice grain was removed from a periopod of each crab and placed in 100% 

ethanol. DNA extraction and conventional polymerase chain reaction (cPCR) sample processing 

was performed as previously described (Jensen et al. in press). Crabs are identified as positive 

when two bands, one of 187 bp and the other of approximately 1682 bp in length were amplified 

and visualized on 2% agarose gels stained with SYBR® Green. 

Results 

A total of 85 snow and 50 Arctic lyre crabs were collected during the survey. Of these, 4 (5%) 

snow crabs and 1 (2%) Arctic lyre crab met our criteria for infection by the parasitic 

dinoflagellate. Amplification of only the short band occurred in another 13 snow and 12 Arctic 

lyre crabs, but because the long band was not evident, these are not considered to be infected. 

221
Discussion 

The results of this study extend the range of the disease east of the Chukchi Sea, the area 

previously known to harbor Hematodinium infected snow crabs. We were also able to confirm 

the presence of the disease in Beaufort Sea Arctic lyre crabs. The data do not otherwise permit 

an examination of host/disease relationships, but do emphasize the need for further collections. 

At the present time, the Beaufort Sea prevalences are similar to disease prevalences in eastern 

Bering Sea snow and Arctic lyre crabs, but the prevalence in Beaufort Sea snow crab is 

considerably lower than that reported in Chukchi Sea snow crabs from the 1990's. 

Literature Cited 

Jensen, P.C., K. Califf, V. Lowe, L Hauser, and J.F. Morado. 2009. Molecular detection of 

Hematodinium sp. in Northeast Pacific Chionoecetes spp. and evidence of two northern 

hemisphere Hematodinium species. Dis. Aquat. Org. (in press). 

Meyers TR, Koeneman TM, Botelho C, Short S (1987) Bitter crab disease: A fatal dinoflagellate 

infection and marketing problem for Alaskan Tanner crabs Chionoecetes bairdi. Dis. Aquat. Org. 

3:195-216. 

Meyers TR, Morado JF, Sparks AK, Bishop GH, Pearson T, Urban D, Jackson D (1996) 

Distribution of Bitter Crab Syndrome in Tanner crabs (Chionoecetes bairdi, C. opilio) from the 

Gulf of Alaska and the Bering Sea. Dis. Aquat. Org. 26:221-227. 

Ryazanova, T.V. 2008. Bitter Crab Syndrome in Two Species of King Crabs from the Sea of 

Okhotsk. Russian J. Mar. Biol. 34:411–414. 

222
223

Platforms of Opportunity Program – Marine Mammals 

Marine mammals were observed while en route to/from the survey grounds and during the 

survey. Data were collected for the Platform of Opportunity Program (POP) in the AFSCs 

National Marine Mammal Laboratory (NMML). 

In the case of the gray whale sightings, individuals were too numerous to accurately count, 

therefore were estimated. Sightings include one Steller Sea lion, gray whale (~93), bearded seal 

(10), polar bear (4), and ice seal (~25). Figure VI.1 summarizes the location of marine mammal 

sightings (the one Steller sea lion sighting is not shown) and Table IV.1 summarizes all of the 

marine mammal sightings and behaviors observed. 

Figure VI.1. Marine mammal sightings during the Beaufort Sea survey, 2008. 
Date 

(ADT) 

Time 

(ADT

) 

Latitude 

(N) 

Longitude 

(W) 

Species Numb

er 

Behavior Comments 

7/31/2

008 

21:12 57.9 167.467 steller sea 

lion 

2 Jug handle; porpoising 

8/1/20

08 

13:13 63.6 168.467 gray 

whale 

1 Blow visible from distance 

8/1/20

08 

13:19 63.6166

7 

168.45 gray 

whale 

4 Blow visible from distance 

8/2/20

08 

18:11 64.3833

3 

168.433 gray 

whale 

2 Blow visible from distance; 

tail fluke 

8/2/20

08 

18:45 64.4666

7 

168.417 gray 

whale 

12 Blow visible form distance 

8/2/20

08 

19:22 64.5833

3 

168.4 gray 

whale 

6 Blow visible form distance; 

tail fluke 

8/2/20

08 

20:07 64.7 168.383 gray 

whale 

18 Blow visible form distance; 

tail fluke 

8/4/20

08 

16:41 70.8 161.183 gray 

whale 

18 Blow visible form distance; 

tail fluke 

8/4/20

08 

17:25 70.85 160.883 gray 

whale 

4 Blow visible form distance; 

tail fluke 

8/5/20

08 

8:52 71.3333

3 

157.033 bearded 

seal 

1 Mature adult? 

8/5/20

08 

12:27 71.4666

7 

156.583 polar bear 3 Walking on ice Female? and 2 cubs 

(large) 

8/6/20

08 

5:20 71.8 153.9 polar bear 1 Swimming towards ice 

edge 

14:38 71.8 154.9 bearded 

seal 

3 2 adults and 1 

juvenile 

8/10/2

008 

7:34 71.8666

7 

154.433 ice seal 5 

8/11/2

008 

7:43 71.6833

3 

152.567 ice seal 2 

8/11/2

008 

8:00 71.6333

3 

152.467 ice seal 14 

8/11/2

008 

6:00 71.5833

3 

155 ice seal 4 Swimming and bobbing 

8/22/2

008 

13:00 70.9166

7 

160.417 gray 

whale 

5 Blow visible; breaching; 

tail fluke 

8/22/2

008 

14:20 70.8333

3 

160.867 bearded 

seal 

6 

8/22/2

008 

15:12 70.7666

7 

161.15 gray 

whale 

7 Diving; leaving mud 

plumes 

8/24/2

008 

12:11 65.1666

7 

168.717 gray 

whale 

6 

8/24/2

008 

11:46 65.3833

3 

168.767 gray 

whale 

11 

Table VI.1. Marine mammal observations collected opportunistically on route to and from the survey 

grounds and during the survey. Data were collected for the Platform of Opportunity Program (POP) 

in the AFSCs National Marine Mammal Laboratory (NMML). Gray whale individuals were often 

too numerous to count precisely, therefore the numbers presented are estimates. 

224
Marine bird and mammal surveys conducted during AFSC marine fish surveys in the Beaufort 

Sea and transit routes, August 2008 

Kathy Kuletz1

, Elizabeth Labunski1, Elizabeth Logerwell2, and Martin Renner3

1

 U.S. Fish and Wildlife Service, 1011 E. Tudor Rd., Anchorage AK 99503. kathy_kuletz@fws.gov

2

 Alaska Fisheries Science Center, NOAA-Fisheries, Sand Point Way, Seattle, WA 

3

 Alaska Biological Services, USGS, Homer, AK

Background 

It is the long-term goal of the U.S. Fish and Wildlife Service (USFWS) to update and expand 

data in the North Pacific Pelagic Seabird Database (NPPSD) for all waters of Alaska. The 

USFWS collects data on seabird distribution and abundance for the NPPSD by using vessels of 

opportunity to conduct pelagic surveys. Marine bird and mammal surveys were conducted 

during the Alaska Fisheries Science Center’s (AFSC) July 27 – August 30, 2008 marine fish 

survey of offshore waters of the Beaufort Sea (E. Logerwell, Principal Investigator). The AFSC 

project was part of the Status of Stocks and Multispecies Assessment (SSMA) Program and was 

funded by the Mineral Management Service (MMS). Surveys were conducted onboard the F/V

Ocean Explorer, under charter with AFSC. The 155 ft vessel transited from Dutch Harbor, 

Alaska to the Beaufort Sea study area and returned to Dutch Harbor. Data on the distribution 

and abundance of seabirds were collected during the transit to and from Dutch Harbor and during 

the acoustic transects, when conditions allowed (Figure VI.2). 

This project was a collaboration between the AFSC and USFWS; AFSC personnel conducted the 

surveys using the protocol and data entry program provided by USFWS. Data were summarized 

for this report by Kathy Kuletz (USFWS), and raw and processed data were submitted to MMS. 

These data will also be archived in the NPPSD, and will be available under NPPSD version 2.1 

(USFWS and USGS, Anchorage, Alaska). This report summarizes seabird and marine mammal 

data for the 2008 Beaufort Sea cruise, with a focus on the Beaufort Sea study area. 

Methods 

Data collection

Surveys were conducted on 14 days between August 1-25, 2008, with the Beaufort Sea surveys 

occurring on August 6 and 16-20. We surveyed marine birds and mammals from the starboard 

side of the bridge using standard survey protocol (USFWS 2008) during daylight hours while the 

vessel was underway. One observer scanned the water ahead of the ship using hand-held 

binoculars and recorded all birds and mammals within a 300-m arc, extending 900

 from the bow 

to the beam. We used strip transect methodology with three distance bins extending from the 

center line: 0-100 m, 101- 200 m, 201-300 m. Unusual sightings beyond the 300 m transect (‘off 

transect’) were also recorded for rare birds, large bird flocks, and mammals. We noted the 

animal’s behavior (flying, on water, foraging, on ice). Birds on the water were counted 

continuously, whereas flying birds were recorded during quick ‘Scans’ of the transect window at 

approximately 1-min intervals. Foraging birds were considered the functional equivalent of 

225
birds on the water and thus were counted continuously, even if the birds were hovering or 

surface plunging. 

We entered observations directly into a laptop computer using the DLOG2 program (Ford 

Ecological Consultants, Inc.) with a GPS interface from the ship’s system. Location data from 

the GPS were automatically written to the program in 20 second intervals (Figure VI.2), as well 

as our entries on weather conditions, Beaufort Sea State, ice type and coverage, and glare 

conditions. At the beginning of each transect we recorded wind speed and direction, air 

temperature, and sea surface temperature. Data were exported into an Excel spreadsheet for 

editing and minor corrections. 

Opportunistic marine mammal sightings were also recorded in collaboration with the Platforms 

of Opportunity program at the National Marine Mammal Laboratory (NMML). The date, time, 

location, species and number of animals observed were recorded by all personnel whenever 

possible. These opportunistic sightings were not included in this report, but are archived with 

the NMML. 

Data processing

 

Survey transect width and track lines from the GPS entries were used to measure km2

 of survey 

effort, and this was used to calculate overall bird densities (birds or mammals • km-2). For the 

Beaufort study area, which had more intensive coverage (Figure VI.3) we processed the raw data 

with a program developed by MR written in ‘R’ (R Development Core Team 2008). This 

program divided the transects into 3km bins and calculated bird density per bin; bin densities 

were then used to calculate mean density. For a small portion of the data, transect widths were 

reduced to 200 m or 100 m because of fog or poor visibility; for these segments we used the 

recorded transect width to calculate densities. Due to segmentation of original transects, not all 

segments were exactly 3-km in length. 

To determine water depths associated with bird observations in the Beaufort study area we used 

ArcGIS to overlay bathymetric coverage with bird locations. Seabird-ice association was based 

on the DLOG record of ice coverage recorded along the transect during the survey. 

226
227

Figure VI.2. Seabird transects during transit and in the Beaufort Sea study area. 
228

Figure VI.3. Seabird transects in the Beaufort Sea. Depth contours labeled in meters. 
229

Results 

Marine Birds

We surveyed a total of 1,245 km, including 428 km in the Bering Sea, 361 km in the Chukchi 

Sea, and 456 km in the Beaufort Sea study area (Figure VI.2). On transect we recorded 2,921 

birds of 23 identified species (Table IV.1). We encountered the highest densities and greatest 

species diversity (19 identified species, plus unidentified phalaropes [Phalaropus spp]) in the 

Bering Sea. The Bering Sea avifauna was dominated by least auklets (Aethia pusilla; 28 %), 

murres (Uria spp; 23 %), shearwaters (short-tailed shearwater [Puffinus tenuirostris] identified; 

13 %) and lower numbers of northern fulmars (Fulmarus glacialis), black-legged kittiwakes 

(Rissa tridactyla), and tufted puffins (Fratercula cirrhata) (Table IV.1). Murres, particularly 

thick-billed murres (U. lomvia) were found in all three regions, particularly near Nunivak Island 

in the Bering Sea and Cape Lisburne in the Chukchi Sea (Figure VI.4). 

In the Chukchi Sea we identified 13 species plus unidentified loons (Gavia spp), phalaropes, and 

guillemots (Cepphus spp). Predominate birds in the Chukchi were murres (33 %), Aethia auklets 

(primarily crested auklets [A. cristatella] identified; 27 %) and phalaropes (red phalaropes 

[Phalaropus fulicaria] identified; 14 %). The Beaufort Sea study area had the lowest overall 

bird density and fewer species (7 identified, plus unidentified loons and phalaropes), and 

predominate species were terns (arctic terns [Sterna paradisaea] identified; 41%), black-legged 

kittiwakes (26 %) and phalaropes (16 %). 
230

Common Name Scientific Name Bering Sea Chukchi Sea Beaufort Sea Total Bering Sea Chukc

Unidentified Loon Gavia spp. 1 2 3 0.

Northern Fulmar Fulmarus glacialis 127 30 157 9.30 3.Short-tailed Shearwater Puffinus tenuirostris 32 50 82 2.34 5.

Unidentified Shearwater Procellariidae spp. 156 32 188 11.42 3.

Fork-tailed Storm-petrel Oceanodroma furcata 1 1 0.07

Pelagic Cormorant Phalacrocorax pelagicus 3 3 0.22

Unidentified Duck Anatidae spp. 22 0.Surf Scoter Melanitta perspicillata 2 2 

Red Phalarope Phalaropus fulicaria 88 0.Unidentified Phalarope Phalaropus spp. 8 110 113 231 0.59 12

Unidentified Shorebird Charadrii (suborder) 1 35 36 0.07 

Pomarine Jaeger Stercorarius pomarinus 5 9 14 0.37 1.

Parasitic Jaeger Stercorarius parasiticus 1 5 6 0.07 

Unidentified Jaeger Stercorarius spp. 1 1 4 6 0.07 0.

Glaucous Gull Larus hyperboreus 2 3 35 40 0.15 0.

Glaucous-winged Gull Larus glaucescens 1 1 0.07

Black-legged Kittiwake Rissa tridactyla 60 60 181 301 4.39 6.

Unidentified Kittiwake Rissa spp. 15 5 20 1.10 0.

Sabine's Gull Xema sabini 1 3 4 8 0.07 0.

Unidentified Gull Larinae spp. 25 5 7 37 1.83 0.

Arctic Tern Sterna paradisaea 261 261 

Unidentified Tern Sterninae spp. 24 24 

Common Murre Uria aalge 11 6 17 0.81 0.

Thick-billed Murre Uria lomvia 30 116 2 148 2.20 13

Unidentified Murre Uria spp. 292 164 15 471 21.38 18Pigeon Guillemot Cepphus columba 2 2 0.15

Unidentified Guillemot Cepphus spp. 22 0.Cassin's Auklet Ptychoramphus aleuticus 1 1 0.07

Parakeet Auklet Aethia psittacula 20 20 1.46Crested Auklet Aethia cristatella 7 37 44 0.51 4.

Least Auklet Aethia pusilla 386 386 28.26

Whiskered Auklet Aethia pygmaea 22 0.Horned Puffin Fratercula corniculata 25 7 32 1.83 0.

Tufted Puffin Fratercula cirrhata 60 2 62 4.39 0.

Unid.small dark alcid Aethia spp. 56 193 249 4.10 22Unidentified Alcid Family Alcidae 35 15 50 2.56 1.Unidentified Bird Aves 2 2 4 0.15 0.

Grand Total 1366 865 690 2921

Number on transect Percent of tot

Table VI.1. Marine birds recorded on transect during surveys from July 27 to August 30, 2008. 
231

Figure VI.4. The distribution of murres (# birds/km2) during transit and in the Beaufort 

Sea study area. 
232

In the Beaufort study area, we recorded 690 birds on transect. Using the binned transect 

segments (N = 159), densities (birds • km-2) ranged from means of 0.01 for unidentified loons to 

3.05 for arctic terns (Table IV.2). The remaining two abundant species had densities of 2.23 for 

black-legged kittiwakes and 1.20 for unidentified phalaropes. The majority of birds (53 %) were 

recorded in the mid-shelf domain (50 -100 m depth), followed by offshore (100-500 m deep) and 

lowest numbers in inner-shelf waters (20 – 50 m deep) (Table IV.2). Among the three most 

abundant species, terns were primarily distributed in the offshore (59%) and mid-shelf regions 

(38 %), with the largest aggregations near the shelf breaks of 300 m and 50 m contours (Figure 

VI.5). Black-legged kittiwakes were most abundant in the inner (44 %) and mid-shelf (50 %) 

regions, and were more widely distributed throughout these two domains (Figure VI.6). 

Phalaropes were very patchy (Figure VI.7), being observed in high abundances at just two 

locations in the mid-shelf domain, with 94 % of observations in water ~50 m deep (Table IV.2). 

The percentage of ice coverage we encountered was generally low, with the majority of water 

ice-free on or near the transects. The Beaufort study area had surface water ice coverages of 10-

20 %, primarily of new and small floe categories (based on the NOAA ice guide). The species 

most frequently associated with ice was the arctic tern, with 40 % of their observations occurring 

near ice, primarily ice coverage of 20 % small floes. The phalaropes were also associated with 

the ice, with 18 % of their observations occurring in ice coverage of 10 % medium floes. Other 

birds occasionally recorded near ice included glaucous gull (Larus hyperboreus) and Sabine’s 

gull (Xema sabini). 

Marine Mammals (Note: data does overlap with Platforms of Opportunity Program)

We recorded a total of 23 marine mammals of 3 identified species on transect during the entire 

cruise, with gray whales (Eschrichtius robustus) the most frequent observation (Table IV.3). 

Gray whales were observed (apparently feeding) during the transit to and from the study area, 

with the highest numbers in the Chirikov Basin of the North Bering Sea (11 on transect and 15 

off transect). No confirmed bowhead whale sightings were made during the transit or in the 

study area. Off transect observations also included an adult polar bear (presumably female) and 

two cubs on the ice near Pt. Barrow. A swimming polar bear was also observed in the same area. 

Three of the gray whales and the bearded seals (Erignathus barbatus) were also recorded near or 

on ice, respectively. 

In the Beaufort Sea study area the only marine mammal observations on transect were one 

unidentified pinniped and two unidentified whales. The pinniped was in the offshore domain 

(100 m depth) and the whales were in the inner-domain (40 m depth) (Table IV.2). 
Table VI.2. Marine birds and mammals recorded on transect in the western Beaufort Sea, August 6-25, 2008 

Marine Birds

-400 -300 -200 -100 -90 -80 -70 -60 -50 -40 -30 -20 Total

Unidentified Loon 1 1 2 

Surf Scoter 2 2 Unidentified Phalarope 1 5 2 105 113 

Unidentified Shorebird 15 20 35 Parasitic Jaeger 5 5 

Unidentified Jaeger 1 3 4 

Glaucous Gull 2 3 1 4 1 4 4 3 7 6 35 Black-legged Kittiwake 3 4 5 12 26 23 29 24 38 17 181 Sabine's Gull 1 3 4 

Unidentified Gull 1 2 4 7 

Arctic Tern 104 7 43 10 89 8 261 Unidentified Tern 6 1 1 16 24 

Thick-billed Murre 2 2 Unidentified Murre 11 3 1 15 Total Birds 3 120 18 67 23 21 44 32 247 39 47 29 690Percent of Total by Depth 0.43 17.39 2.61 9.71 3.33 3.04 6.38 4.64 35.80 5.65 6.81 4.20Percent of Total by StrataMarine MammalsUnidentified Whale 2 2Unidentified Pinniped 1 1

30.14 53.19 16.67

Off shelf Outer shelf Inner shelf 

233
Bering Sea Chukchi Sea Beaufort Sea Grand Tot

Unidentified Porpoise Phocoenidae spp. 1 1

Gray Whale Eschrichtius robustus 11 3 14Unidentified Whale Cetacea spp. 1 2 3

Steller Sea Lion Eumetopias jubatus 1 1

Bearded Seal Erignathus barbatus 1 1

Unidentified Pinniped Pinnipedia spp. 21 3

Total marine mammals 14 6 3 23

Table VI.3. Marine mammals recorded during transit to and surveys in the Beaufort Sea, July 27 - August 30, 20

234
235

Figure VI.5. Distribution of Arctic terns (# birds/km2

) in the Beaufort Sea study area. 
Figure VI.6. Distribution of black-legged kittwakes (# birds/km2

) in the Beaufort Sea study area. 

236
Figure VI.7. Distribution of phalaropes (# birds/km2

) in the Beaufort Sea study area. 

237
Discussion 

The late July through August period of this study coincided with post breeding dispersal and 

migration for the more abundant species groups we observed in the Beaufort Sea – phalaropes, 

arctic terns, and black-legged kittiwakes. Red phalaropes (identified in our surveys) and rednecked phalaropes (P. lobatus) nest in the tundra throughout western Alaska and the arctic 

coastal plain, but the red phalarope nests farther north and migrates in more pelagic waters than 

other phalaropes (Tracy et al. 2002). Little is known about red phalarope migratory routes 

because of their remote, offshore habits, but they arrive in the arctic coast nesting grounds by 

early June. In the late summer, females leave nesting areas prior to males, but during our August 

surveys, adults of both sexes and juveniles were likely starting their westward offshore staging 

and migration (Johnson and Herter 1989). By mid-August, large groups of phalaropes have been 

documented moving west past Pt. Barrow (Watson and Divoky 1974) and pelagic surveys 

between 2006 and 2008 recorded them offshore in the same region (Kuletz et al. 2008). 

Together these data improve our knowledge of the northern migratory patterns and habitat use of 

this species. Red phalaropes are known to forage in association with ice and at ocean 

convergences or fronts, where food is abundant near the surface. At sea they consume primarily 

copepods, larval fish, and amphipods, and are known to take advantage of the plumes of 

crustacea brought to the surface by foraging gray whales (Tracy et al. 2002). 

Arctic terns also nest throughout the arctic coastal plain, with documented colonies along the 

Beaufort coast, particularly along the Plover Islands east of Pt Barrow. However, birds raising 

chicks typically forage < 20 km from their colonies (Hatch 2002), and we observed terns much 

farther than that from the nearest coast. Their post breeding migration is westward from the 

Beaufort Sea to the Chukchi Sea, occurring from late July to early September, with a peak in 

mid-August (Hatch 2002), thus our surveys corresponded to peak migration in this region. Terns 

feed at the water’s surface, plunging for small fish to 150 mm long, euphausiids and amphipods 

caught in currents near the surface, and during this early migratory period are known to feed at 

euphausiid swarms near Pt. Barrow (Hatch 2002). We observed terns primarily near shelf 

breaks, which may create fronts that concentrate prey near the surface. 

Black-legged kittiwakes have a few small breeding colonies along the Chukchi and Beaufort 

coasts, but the large colonies are at Cape Lisburne and farther south (USFWS 2006). The 

kittiwakes we observed were likely post-breeding or non-breeding birds. During the ice-free 

months, black-legged kittiwakes are common in pelagic waters of the western Beaufort Sea 

(Divoky 1983). In the Chukchi and Beaufort seas, black-legged kittiwakes feed heavily on arctic 

cod (Bradstreet 1980), although during the summer adults may consume more amphipods and 

euphausiids (Hobson 1993). Black-legged kittiwakes feed at the surface, primarily on a variety 

of small fish, although they will also feed on euphausiids and other macrozoolankton (Baird 

1994). 

Our data indicate that in the western Beaufort, phalaropes, terns, and kittiwakes forage in 

offshore waters during this migratory or post-breeding period. At this time they appear to be the 

most abundant birds in Beaufort waters with depths greater than 20 m, but highest densities are 

found in deeper waters, particularly at shelf breaks. During USFWS aerial surveys of the 

Beaufort coastal areas, Fischer and Larned (2004) found few kittiwakes or shorebirds (< 1 % of 

238
total birds), rather the nearshore areas supported large numbers of benthic-feeding eiders, scoters 

and long-tailed ducks (Clangula hyemalis). In more pelagic waters we found a very different 

avifauna predominated by surface feeders, with two of those three species being primarily 

piscivorous, but also opportunistic foragers on macrozooplankton. 

The offshore waters of the Beaufort Sea may be an important pre-migratory staging and foraging 

area for phalaropes and arctic terns, both of which must prepare for extreme migrations to distant 

southern hemisphere wintering areas. Another long-distance migrant is the gray whale, which 

we only identified in the Chukchi and Bering Seas. Our surveys substantiate the importance of 

the Chirikov Basin, in the north Bering Sea, and to a lesser extent the Chukchi Sea, as feeding 

grounds for gray whales in late summer. 

Climate change could affect timing of migration, and there is little information on seabird 

distribution during the migration and over-winter phases. At sea surveys that capture these 

critical phases, especially in areas with little data, allow managers to identify seasonally 

important habitats. Seabirds and many shorebirds are typically monitored at breeding colonies or 

nesting grounds, yet they spend most of the year dispersed offshore. At-sea surveys can be used 

to identify relative abundances of marine birds and their distribution with respect to pelagic 

habitats. Even during the breeding season, seabirds may feed 20-100 km from their colonies 

(Coulson 2002), and they are most susceptible when foraging on the water (King and Sanger 

1979). Pelagic surveys provide current information on the spatial and temporal distribution of 

birds at sea to address conservation issues related to fisheries, vessel traffic, oil exploration, and 

catastrophic spills. 

Literature Cited 

Baird, P. H. 1994. Black-legged Kittiwake (Rissa tridactyla). In The Birds of North America, no. 

92 (A. Poole and F. Gill, Eds.). Academy of Natural Sciences, Philadelphia, and American 

Ornithologists’ Union, Washington, D.C. 

Bradstreet. M. S. W. 1980. Thick-billed murres and black guillemots in the Barrow Strait area, 

N.W.T., during spring: diets and food availability along ice edges. Can. J. 2001.58: 2120-2140. 

Coulson, J.C. 2002. Colonial breeding in seabirds. Pages 87-113 in Schreiber and Burger 

(editors), Biology of Marine Birds, CRC Press, New York. 

Divoky, G.J. 1983. The pelagic and nearshore birds of the Alaskan Beaufort Sea. Pages 397-513 

In: Envir. Assess. Alaskan Cont. Shelf, Final Rep., Princ. Invest., Vol 23. BLM/NOAA, 

OCSEAP, Juneau, Alaska. 

Fischer, J. B., and W. W. Larned. 2004. Summer Distribution of Marine Birds in the Western 

Beaufort Sea. Arctic, Vol. 57(2): 143– 159. 

Hatch, J. J. 2002. Arctic Tern (Sterna paradisaea). In The Birds of North America, no. 707 (A. 

Poole and F. Gill, Eds.). The Birds of North America, Inc., Philadelphia, PA. 

239
Hobson, Keith A. 1993. Trophic relationships among high Arctic seabirds: insights from tissuedependent stable-isotope models. Mar. Ecol. Progr. Ser. 95:7-18. 

Johnson, S.R. and D.R. Herter. 1989. The Birds of the Beaufort Sea. BP Exploration (Alaska) 

Inc. Anchorage, Alaska. 

King, J.G., and G.A. Sanger. 1979. Oil vulnerability index for marine oriented birds. Pages 227-

239 in J.C. Bartonek and D.N. Nettleship (eds.), Conservation of marine birds of North America. 

U.S. Fish and Wildlife Service, Wildlife Research Report 11:1-319. 

Kuletz, Kathy J., Elizabeth A. Labunski, Martin Renner, and David B. Irons. 2008. The North 

Pacific Pelagic Seabird Observer Program. North Pacific Research Board Final Report, Project 

No. 637. 

R Development Core Team: 2007, R: A Language and Environment for Statistical Computing, R 

Foundation for Statistical Computing, Vienna, Austria. 

Tracy, D.M., D. Schamel, and J. Dale. 2002. Red Phalarope (Phalaropus fulicarius). In the Birds 

of North America, No. 698 (A. Poole and F. Gill, eds.). The Birds of North America, Inc., 

Philadelphia, PA. 

USFWS-MBM 2008. Migratory Bird Management (Region 7) Methods Manual for Seabird and 

Marine Mammal Surveys. Unpublished manual, U.S. Fish and Wildlife Service, Anchorage, 

Alaska. 

U.S. Fish and Wildlife Service. 2006. Beringian Seabird Colony Catalog- computer database and 

Colony Status Record archives. U.S. Fish and Wildl. Serv., Migr. Bird Manage., Anchorage, AK. 

Watson, G.E. and G.J. Divoky. 1974. Marine birds of the western Beaufort Sea. Pages 681-695 

In: J.C. Reed and J.E. Sater (eds.), The coast and shelf of the Beaufort Sea. Arctic Inst. of North 

America, Washington, D.C. 

240
Appendix VII – Under-ice sampling workshop 

WORKSHOP SYNTHESIS 

After the workshop, the report authors (Rand and Logerwell) constructed the following two 

scenarios for surveys of fish distributions in the Beaufort Sea during the winter ice-covered 

season. The scenarios are based on informal discussions conducted throughout the workshop 

and the report authors’ synthesis of the material presented by the participants. These scenarios 

do not represent all possible methods for conducting winter fish surveys, and details such as 

sample size, sampling gear (i.e., AUV vs. ROV), survey costs, etc. should be regarded as 

preliminary. The goal of the scenarios is to provide a very broad and general overview of the 

resources required to conduct a winter survey in the Beaufort Sea and the kind of data that could 

reasonably be obtained, in other words, a starting point. The first scenario is of a survey of fish 

distributions on the shelf, involving a team of scientists occupying temporary ice camps 

(SCENARIO A). It is the more expensive of the two scenarios. The second scenario is of a 

survey in nearshore waters involving periodic sampling by local fishers (SCENARIO B). This 

scenario is expected to be less expensive than the first. 

SCENARIO A 

Study design 

This scenario represents the most comprehensive sampling of the OCS Planning Area in the icecovered season and consequently is the most expensive. The under-ice marine survey will occur 

in three stages. Initially, local residents in Beaufort Sea villages will be interviewed on their 

knowledge of marine fish species types and distribution to identify species seasonality and 

habitats. Local residents will also be recruited to conduct passive fishing (pots, traps) under the 

ice through the ice-covered season. Time lapse cameras will also be installed on existing 

stationary Beaufort Sea moorings. The second component will use the results of the initial 

sampling to design a pilot survey using both passive gear and active surveys by divers and 

underwater vehicles to estimate spatial and temporal patterns of fish abundance. The third 

component, an active under-ice survey will evaluate Arctic cod abundance in three types of 

habitats on the under surface of the ice (smooth, rough, and creviced). These surveys will be 

performed by DIDSON sonar, a remotely operated vehicle (ROV) and scuba diver transects. 

Once the under-ice habitat has been evaluated, estimates of Arctic cod abundance will be 

calculated. Each survey component will collect physical, chemical, biological and other 

environmental data necessary to evaluate and test the significance of independent variables that 

potentially affect fish presence and distribution. The pilot study will provide statistical 

hypothesis testing between the open water, ROV and dive surveys, providing a baseline for 

subsequent surveys and provide sampling statistics, including variance estimators, for future 

time-series analysis. 

Logistics 

First stage – local knowledge, passive sampling and time-lapse cameras 

For the initial passive fishing under the ice, ice augers would be needed, but depending on the 

sampling gear, the holes would only need to be 12-24 inches in diameter. Fish sampling gear 

(pots and traps) would be lightweight, portable and relatively inexpensive. The majority of the 

241
project costs for this stage would be for fishers’ transit to the sampling sites (e.g. fuel for snow 

machines) and compensation for their time and effort. In addition, project scientists would need 

to make several trips to North Slope communities for interviewing, training, project monitoring 

and outreach. Costs for this component would be expected to be on the order of 100,000’s of 

dollars. 

Two sets of cameras with IR lights and measuring lasers would need to be purchased for 

deployment on moorings. Additional requirements would be underwater housing and data feed 

cables designed for extreme cold temperatures. The total cost would be approximately $50,000. 

Second stage – pilot survey

Depending on the success of the first stage of the project, local fishermen could implement the 

passive sampling component of the pilot survey. The costs would thus be similar to the first 

stage, on the order of 100,000’s of dollars. 

A dive team of three people (minimum) would be required for the active sampling during the 

pilot survey. Ice-approved equipment including communication equipment would be needed. A 

shelter would need to be constructed at the dive site. A chartered helicopter would need to be 

available for evacuation to a hyperbaric chamber, at a cost of about $6,000/day plus $1,500/hour 

of flight time. 

A medium-sized ROV could be leased for the project, along with an operator. Other 

requirements include a shelter for launch and retrieval of the ROV. Two sets of video cameras 

with IR lights and measuring lasers would need to be purchased, along with underwater housing 

and data feed cables designed for extreme cold temperatures. The total cost would be 

approximately $50,000. 

An Ice Camp would be required to support the active sampling. In addition to basic camping 

equipment, a gas-powered generator for living and science activities would be needed. However, 

it is the logistic costs of setting up and maintaining an ice camp that are most important to 

address. Helicopter support would cost on the order of $6,000/day plus $1,500/hour of flight 

time. For purposes of cost estimation we assume that each site requires 4 days occupation 

(including camp setup and removal), with a daily average crew size of 6 people on the ice and 6 

people onshore (housed in Prudhoe Bay, for example). We also consider 6 helicopter trips/day 

for camp setup and take down (2 days) and 4 trips/day for the two days of sampling effort for a 

total of 20 helicopter flights/station. The helicopter operations alone amount to about $900,000 

with the science costs (field staffing, sample collection, data processing, and reporting) being the 

same order of magnitude if 30 stations are occupied. 

Third stage – active Arctic cod survey

The first step in the Arctic cod survey would be an aerial survey of ice habitat types. In addition 

to a survey airplane, still (digital) cameras and photographers would be needed. The price of the 

aerial survey will depend on the number of days it takes to survey the OCS. A generous 

allocation for bad weather days should be provided. The cost of an aerial survey can be expected 

to be on the order of $80,000 or more. 

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In addition to leasing the ROV, two sets of DIDSON cameras would need to be purchased, along 

with underwater housing and data feed cables designed for extreme cold temperatures. The total 

cost would be approximately $160,000. 

As in the pilot survey, a dive team of three people would be required for the active sampling 

during this stage (with helicopter support). Also required would be a shelter for deploying the 

ROV and an Ice Camp to support the entire field party. 

Based on the preliminary cost estimates described above, the annual cost of Scenario A would be 

over $2,000,000. 

SCENARIO B 

Survey design 

This scenario does not replicate the 2008 summer survey effort in the OCS, but it is less costly 

than the scenario described above. 

This fish survey would be accomplished by periodic (e.g. bi-weekly) sampling through the ice by 

local fishers. Stations inshore of the 20m isobath, which defines the stamukhi zone (or the edge 

of the landfast ice) could be reached by snow machine, Rologon, or sled dog teams. The survey 

design would be a collaborative effort by local fishers and project scientists, and thus would take 

advantage of the traditional ecological knowledge afforded by the fishers’ experience. The 

fishers would design the sampling gear (e.g., gill nets, hook and line, etc.) and the scientists 

would train the fishers on methods of catch processing and data recording (counting, weighing, 

measuring and preserving specimens). The relatively high frequency of sampling would help to 

compensate for the expected low catch rates. 

This survey design would provide information on fish species presence/absence and habitat 

association. Although an abundance estimate analogous to the summer survey would not be 

possible, this survey could provide an index of relative abundance within the 20 m isobath. In 

addition, temporal changes in fish presence or abundance at the scale of weeks-months could be 

documented. 

Logistics 

The logistic complexity and costs for this scenario would be much lower than for the first 

scenario. Ice camps would not be required, because the stations would be close enough to shore 

to be sampled over the course of several day-long trips. Ice augers would be needed, but 

depending on the sampling gear, the holes would only need to be 12-24 inches in diameter. Fish 

sampling gear (e.g. nets, hook and line, etc.) would likely be lightweight, portable and relatively 

inexpensive. The majority of the project costs would be for fishers’ transit to the sampling sites 

(e.g. fuel for snow machines) and compensation for their time and effort. In addition, project 

scientists would need to make several trips to North Slope communities for training, project 

monitoring and outreach. 

Total project costs for this scenario would be expected to be on the order of 100,000’s of dollars. 

243
244

Appendix VIII -- Recommendations for future monitoring methods 

“Based on results of the survey, recommend methods for future monitoring that could provide 

time-series and data trend information necessary to support offshore development decisions and 

serve as a proto-type fisheries component of future MMS or other ocean observing systems.” 

(from the Memorandum of Understanding). 

Recommendations are to use the same methods as used in this pilot. As stated in the earlier 

discussion, additional effort is also needed to examine the potential importance of offshore nearsurface regions for YOY fish and to quantify the relative contribution of offshore regions to 

YOY recruitment. 

Vessel

The survey was conducted from a 155-foot commercial trawler. This type of vessel proved to be 

a good platform for a survey of this kind as it had the berthing, fuel and water-making and 

storage capacity to support 6 scientists and 6 vessel crew for 35 days without re-fueling or reprovisioning. This vessel was limited in its ability to go ashore (if re-supply or fueling were 

needed) due to the vessel draft (4 to 6 m). It would also be difficult if not impossible to sample 

in water less than 20 meters depth due to vessel draft and maneuverability. The vessel had two 

net reels, allowing us to deploy bottom and midwater trawls without re-rigging nets. It should be 

noted that due to U.S. Coast Guard regulations, no more than 6 science crew can participate in a 

research cruise on board a chartered fishing vessel. This is not the case on a NOAA vessel such 

as the Miller Freeman or Oscar Dyson, where more than 6 scientists can participate. There was 

ample storage for scientific supplies and equipment. The vessel had good sea-worthiness, 

although winds were mild during the 2008 survey. However, this was a fishing vessel and not 

designed for breaking through large amounts of ice, as were encountered on the way to the 

survey grounds. Moving the survey to a later time period (1-2 weeks after our survey began) 

may lessen the chance of heavy ice encounters. There was sufficient deck space for sorting and 

weighing the catch and space was available to mount the AFSC portable winch that was used to 

deploy the CTD and plankton nets. 

Table 60 illustrates the characteristics of a variety of vessels that might be employed for a future 

Beaufort Sea fish and oceanographic survey. A commercial trawler is more limited than a 

NOAA research vessel or an ice-breaker in terms of the number of scientists it can support and 

the oceanographic and acoustic equipment likely to be available. A trawler has an advantage 

over an ice-breaker in that the latter generally cannot tow medium to large benthic or midwater 

trawls. It is often true that commercial trawlers, operating under a charter or contract, have more 

flexibility in the scheduling of days at sea than do NOAA vessels and ice-breakers. Commercial 

trawlers and NOAA vessels have a disadvantage over ice-breakers in that they cannot operate in 

ice-covered waters. All three of these types of vessels have similar seaworthiness and depth 

ranges. The launch is much reduced in seaworthiness, range, and scientific personnel 

accomodation. The advantage of a launch is its relatively low cost of operation and the ability to 

conduct operations at more frequent intervals (e.g., short multiple day trips conducted throughout 

the ice-free season). 
Vessel Season Seaworthiness Range/ 

duration 

Personnel accomodations 

Depth Trawling Acoustics 

Commercial trawler (~100 ft.) 

ice-free only 

winds to ~ 35 knts 

21-35 days 

6 scientists > 20m Commercial and 

research bottom and pelagic trawls 

Limited or no scientific acoustics 

NOAA research vessel (~200 ft.) 

ice-free only 

winds to ~ 35 knts 

40 days 15 scientists > 20m Research bottom and 

pelagic trawls 

Scientific acoustics 

Ice-breaker ice-free 

and icecovered 

winds to ~ 35 knts 

40 days 35 scientists > 20m Limited or no fish 

trawling 

Scientific acoustics 

Launch (~ 35 ft.) ice-free 

only 

winds to ~20 knts 

7 days 3 scientists < 20m Small bottom and 

pelagic trawls 

No scientific acoustics 

Table 60. Comparison of characteristics of different research vessels with regard to conducting fish and oceanogra

Beaufort Sea. 

Vessel = Examples of types of vessels Season = Seasons in which surveys could be done Seaworthiness = Winds speeds in which scientific operations could be conducted 

Range/duration = Number of days vessel could operate without re-fueling or re-provisioning Personnel accomodations = Number of scientists that could live and work on vessel Depth = Bottom depths over which vessel could operate Trawling = Types of bottom and/or pelagic fish trawls that could be deployed Acoustics = Types of acoustic system that could be employed Oceanography = Types of oceanographic sampling (physics and zooplankton) that can be conducted Scientific accomodations = Whether dedicated scientific laboratory space would be available (e.g. wet labs, com

labs, specimen freezers, etc.) 

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Survey design and methods

Station and transect spacing 

This survey plan was for seven acoustic transects spaced 10 nmi (18.52 km) apart and 25 bottom 

trawl stations dispersed along the transects among three depth strata (20-40 m, 40-100 m, and 

100-500 m). The starting point for the acoustic transects and the bottom trawl station grid was 

randomly selected. The number of bottom trawl stations was selected based on coefficients of 

variation (CVs) observed during AFSC Eastern Bering Sea (EBS) bottom trawl surveys 

(approximately 0.22). CVs (both net types combined) observed during the 2008 Beaufort Sea 

survey exceeded those from EBS surveys. Ideal bottom trawl sample sizes for the Beaufort Sea 

survey would range from 55 to an unrealistically large 14,253 (Table 10), depending on the 

required CV and the delta values specified (percent difference between the estimated and true 

mean). The unusually high CVs are attributed to the fact that a codend liner was not used in 

bottom trawl sampling net during the latter half of the survey. The lack of a codend liner 

resulted in systematically lower catches during the latter half of the survey. Future monitoring 

studies will require additional analysis of catch variability and target sample size to determine 

the ideal number of bottom trawls in a given area. During the acoustic survey, the midwater 

trawl was used to verify the species and length distributions of observed targets (i.e. fish). No 

CV calculations were made for the midwater trawl as net samples were not used in acousticbased density estimates. In this survey, twenty-eight midwater trawl collections were made. 

Additional midwater trawling effort is recommended for future surveys if an objective is to 

classify and separate young-of-the-year (YOY) species and for target strength evaluation (see 

below). Additional midwater trawl effort would also allow the presence of other pelagic species 

(e.g. capelin) to be examined. 

Acoustic observations of YOY fish and yearling-and-older (year-plus) Arctic cod density 

distributions indicated that survey transects (bounded in the south by the 20 m contour and in the 

north by the 500 m contour) did not capture the full extent of YOY or year-plus distributions. 

The highest densities of YOY fish and year-plus Arctic cod were observed at the ends of 

transects and along cross-transects. A complete survey of Arctic cod would necessitate 

extending transects into deeper water for year-plus fish and to shallower water for YOY fish. A 

dedicated nearshore (20 m and less) acoustic-trawling survey of YOY is warranted. Such a 

dedicated nearshore survey would also facilitate the development of acoustic techniques to 

separate YOY fish and year-plus Arctic cod that vertically overlap (i.e. not vertically separated in 

the water column) in the 20-40 m depth depth. 

A cursory geostatistical analysis of the YOY fish and year-plus Arctic cod density distribution 

data suggested that the 18.52 km (10 nmi) transect spacing used in this study did not detect 

spatial patterns in the data. Directional empirical variograms for both YOY and year-plus are 

relatively flat, indicating that there was little autocorrelation in density values. The lack of 

autocorrelation suggests that density distributions of YOY fish and year-plus Arctic cod was 

uniform within the study area or that the 18.52 km (10 nmi) transect spacing was too coarse to 

detect spatial patterns. 

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Bottom trawl field methods and data analyses (demersal fish sampling) 

Comparing the bottom trawl results of the present survey to the previous survey of offshore 

marine fish in the Beaufort Sea (Frost and Lowry 1983) was hampered by the lack of catch-perunit-effort (CPUE) data from the previous survey and by differences in gear type. Net 

mensuration and gear standardization (i.e. maintaining consistent trawl net and hardware design 

among surveys) are recommended for an on-going monitoring study. Net mensuration would 

provide data on area swept by the net and thus CPUE. Gear standardization would allow for 

comparisons between survey years without bias due to changes in gear type. A research survey 

conducted without standardized gear and net mensuration would only be able to document fish 

species presence and would not be comparable to other survey results. 

The distribution and abundance of adult and juvenile demersal fish was assessed with a 83-112 

eastern otter trawl with a 25.3 m headrope and a 34.1 m footrope (a.k.a. “bottom trawl”). This 

net is the standard for Alaska Fisheries Science Center (AFSC) bottom trawl surveys of the 

Bering Sea shelf (Acuna and Kotwicki 2004), and Chukchi Sea (Barber et al. 1997). The 

primary bottom trawl nets were lined throughout with 1.5-inch mesh to insure catches of smaller 

fish typical of the Arctic. 

The otter trawl is the most widely used type of bottom trawl in commercial fisheries, and their 

success is due to the herding action of the trawl doors and sweeplines. The trawl doors, 

sweeplines and the mud and sand clouds they produce upon contact with the bottom have been 

shown to produce strong visual and auditory stimuli that result in herding fish and invertebrates 

into the net (Main and Sangster 1981, Wardle 1986). Experimental work has shown that the 

effectiveness of the herding action of the sweeplines depends on the size of the fish (Engås and 

Godø 1989). In addition, some fish are able to escape beneath the footrope of the trawl. This is 

particularly true for flatfish species such as plaice (Hippoglossoides platessoides), although 

escapement has been shown to be reduced at night (Walsh 1991). In general, the sampling 

effectiveness of the otter trawl varies with depth, season, time of day, ambient light and response 

to noise produced by the survey vessel and gear. 

The other bottom trawl gear that was considered before the field survey was a beam trawl. Beam 

trawls are designed to catch small fish (<20 cm) and do not require net mensuration because the 

beam holds the horizontal opening constant. The beam trawl is a smaller net, with smaller 

meshes and it fishes very close to the bottom, potentially “scooping up” benthic invertebrates. 

The decision to conduct the survey with the 83-112 eastern otter trawl was so that results could 

be comparable to previous, contemporary and/or future AFSC trawl surveys of the Bering and 

Chukchi Seas. 

Before committing a monitoring study of the Beaufort Sea to a particular gear type, some gear 

development work will be required. The intention of the present bottom trawl survey design was 

to sample all stations with a lined 83-112 bottom trawl net. The presumption was that the lined 

net would catch small arctic fishes more effectively than an unlined 83-112. While the lined net 

did appear to catch small fish effectively, the nets were highly susceptible to damage caused by 

large catches, heavy mud and boulders. One helpful modification that was employed during the 

present survey was to shorten tow times from 30 minutes (the standard for AFSC Bering Sea 

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surveys) to 15 minutes or less. However, even at these shorter tow times all lined nets were 

eventually damaged. Recommendations for strengthening the lined 83-112 for future surveys 

are: 1) heavier riblines to cope with weight of rocks and large catches, 2) stronger attachment of 

the net to the footrope and headrope, and 3) guard mesh in the bosom and belly panel with a 

light-weight mesh inside that can break away in case of rocks or mud in the belly of the net 

(Darin Vanderpol, pers. com., captain of the F/V Ocean Explorer). Strengthening the lined 83-

112 will be particularly important if future surveys intend to sample in waters shallower than 40 

m. The bottom at these depths appeared to be excessively hard and rocky, such that even a 

strengthened 82-112 might nonetheless be inappropriate gear to use. 

See “Station and transect spacing” above for discussion of demersal fish survey design. 

The original data analysis plan was designed to estimate demersal fish and dominant benthic 

invertebrate biomass from bottom trawl data using the area-swept method (Alverson and Pereyra 

1969). For each species, catch-per-unit-effort (CPUE) was calculated for each tow by dividing 

catch numbers and weight (kg) by the area swept by the tow (km2

). A mean CPUE for each 

depth was calculated as the mean of the individual tow CPUE (including zero catches) within 

that depth. Biomass and abundance estimates were calculated by multiplying each depth mean 

CPUE by the depth area (Britt and Martin 2001). 

The original data analysis plan also called for statistical tests for differences in demersal fish 

abundance (numbers and biomass) among strata (e.g. ANOVA or non-parametric rank-sums 

tests). This would have allowed us to evaluate the null hypothesis that the abundance of species 

does not vary across habitat. Data on depth, water temperature, salinity, etc. would have been 

used to characterize the three habitats (strata). Statistical analyses of the environmental and fish 

data, such as ANOVA, would have allowed us to test the significance of the independent 

variables that may affect demersal fish abundance. However, it was not possible to conduct the 

hypothesis testing as originally proposed because gear type (lined vs. unlined trawls) and tow 

time (15 vs. 5 minutes) were thoroughly confounded with each other and with survey strata 

(shelf, slope and rise). With the exception of one station, all the rise stations (bottom depths 101-

500 m) were sampled with the lined net and tows were 15 minutes long. Nearly all the 

shelf/slope stations (9 out of 12 stations in bottom depths 40-100 m) were sampled with the 

unlined net and were 5 minutes long. This confounding was not intentional but was the result of 

the fact that only the rise stations were free of ice early in the survey and so we sampled them 

first with the lined net. When the ice cleared out of the shelf/slope area we had damaged all the 

lined nets and were forced to complete the survey with the unlined net. Tow time was reduced to 

5 minutes when we switched to the unlined net to minimize the chance of damaging our last 

remaining bottom trawl net. In summary, the sample collection order imposed by practical 

constraints during the cruise (ice cover and availability of nets) prevented collection of the data 

as originally planned. The data as collected had a confounding of gear type, tow time and survey 

strata that made it impossible to statistically examine or control for the effects of gear type and 

tow time on catch density. Thus we could not test for differences in benthic fish and invertebrate 

density among survey strata or for the effects of habitat characteristics as originally proposed. 

This is the case for both parametric tests such as ANOVA or non-parametric tests such as a ranksum test. 

248
We thus revised the data analysis plan, and proposed to attempt a test of the effects of habitat on 

benthic fish and invertebrate density using General Additive Models (GAM). We analysed data 

from stations sampled with the lined net (all of which were towed for 15 minutes), separately 

from those sampled with the unlined net. This analysis was designed to test the null hypothesis 

that habitat characteristics do not effect benthic fish and invertebrate density without the 

problems associated with variable net type and tow duration. The dependent variable was fish or 

invertebrate density (#/ha or kg/ha). Independent habitat variables included depth, bottom 

temperature, salinity, stratification and longitude. Which variables were included in the final 

model depended on whether they are correlated with each other and how many degrees of 

freedom the appropriate GAM smoother allowed. “Patchiness” in the fish and invertebrate catch 

data (low sample size and increasing variance with increasing means) was managed by logtransforming the data. In cases where there was a zero observation, 0.5 was added to all data 

observation points in that group, and then the values were log transformed. For some species the 

number of zero observations was so exceptionally high that it was not appropriate to use GAM 

techniques on transformed data. In these instances, it was more appropriate to examine the 

presence/absence of the species rather than density with a generalized linear model (GLM), 

assuming a poisson distribution with a log link. 

Acoustic field methods and data analysis (pelagic fish survey) 

Pelagic fish distributions were assessed using acoustic methods. Adult and juvenile fish were 

surveyed with a calibrated Simrad ES60 echosounder with a 38kHz split beam transducer, the 

frequency typically used for fish surveys. Acoustics is ideal for assessing pelagic fish 

distributions, but due to the acoustic “dead zone” near the bottom (0.5 m), this method is limited 

in its use for assessing bottom fish. For many fish targets, the gas in the swim bladder is 

responsible for most of the acoustic signal, such that fish that lack a swim bladder are poor 

candidates for acoustic surveys. The data are collected continuously such that patchiness along 

transects can be measured (this is difficult with bottom trawl data). The physics of sound are well 

understood and can be used to quantify the level of acoustic energy in the returning echoes. 

However, acoustic systems used in surveys are not capable of discriminating among different 

species of fish, so target identification with trawls is an integral part of an acoustic survey. Noise 

can cause bias in the acoustic data, so noise levels in the system should be reduced through 

proper system engineering. Sources of noise include ship noise, internal noise introduced by the 

echosounder’s amplifier and processing circuitry, ocean noise such as breaking waves and 

intermittent biological noise caused by fish and marine mammals. While many of the noise 

sources can be minimized by ship and electronic design, noise can never be eliminated entirely. 

In addition, acoustic energy can be lost due to attenuation by air bubbles entrained along the hull 

of the ships. This source of error can be avoided with careful location and mounting of the 

transducer. For more details regarding sources of acoustic survey bias and methods of 

minimizing them, see Gunderson 1993. 

Midwater trawling is the method most commonly used for acoustic target identification. The 

ability of fish avoid midwater trawls can be remedied with the use of trawls with large openings, 

towed at high speeds. However, large mesh sizes used in the wings of some midwater trawls 

means small fish can escape the net. Nakashima (1990) evaluated the selectivity of a large 

midwater net by attaching sampling bags outside the net and comparing the catches with those in 

249
the cod end. Fish that were smaller than the meshes escaped from the trawl in significant 

numbers. As a consequence, acoustic surveys are best suited for situations where the fish 

aggregations are dominated by species with a narrow size range. In situations where multiple 

species are present, a relatively large number of trawls will be required to achieve species 

identification. 

The preferred make and model echosounder for future studies is a Simrad splitbeam EK60 

echosounder, but an ES60 transceiver is also acceptable. In either case, the transceiver box must 

be physically accessible to allow the inspection of grounding and to potentially create a second 

output display. Because of depth penetration requirements, 38 kHz is the optimal acoustic 

frequency. If a second frequency is available, 120 kHz provides a reasonable contrast but will be 

limited to depths shallower than 300 m. In addition to an updated Simrad transceiver, it is also 

imperative to know the model and location of the acoustic transducer. During the current survey, 

the vessel had an updated Simrad ES60 transceiver but had an old 38 kHz transducer mounted in 

the hull. As this was not known until the time of the survey, additional time was required to 

process the acoustic data after the survey. Known location(s) of the transducer in the vessel hull 

will reduce the amount of time required to set up calibration equipment. 

As most AC vessel generators produce electrical noise that can be detected by the echosounder, 

it is recommended that a vessel noise profile be generated under all operating conditions (e.g. 

running at various speeds, trawling, etc.). This procedure will assist in the identification of noise 

sources and can be used to determine an optimal, acoustically-quiet, survey speed. Since noise 

characteristics of any vessel are rarely known, both AC and DC power sources and a separate 

ground should be available for the echosounder. Availability of an AC power conditioner is 

optimal and recommended. A separate ground and an electrical line conditioner will improve 

performance of the ship’s echosounder after the survey. 

The vessel’s acoustic system must be calibrated using the final equipment configuration, 

including grounding location, power source, and cables used between the transceiver and the 

operating computer. Ideally, this calibration will occur before the survey, with sufficient time to 

process the data and make necessary adjustments to equipment settings. If time permits, a 

second calibration is recommended following the survey to detect any changes in equipment 

performance that occurred. 

To increase the ability to measure target strengths of individual fish, future acoustic surveys 

should incorporate stationary daytime sounding to observe single targets and possibly use a droptransducer (acoustic transducer using a shorter pulse duration lowered to depth) to obtain target 

strength measurements. High Arctic cod densities within aggregations and layers limited our 

ability to collect single target data. If Arctic cod target strength values must be obtained from the 

edges of schools or layers, future surveys should dedicate midwater trawl sampling the edges and 

middle of aggregations to verify that the length distribution of Arctic cod is consistent 

throughout the aggregation. Ideally a closing cod-end net combined with net depth-monitoring is 

recommended to provide definitive length samples through the water column. 

Future midwater trawl sampling to support acoustic-based density and abundance estimates 

should collect length and weight information from young-of-the-year (YOY) Arctic cod to 

250
establish a length to weight regression for Arctic cod. A relationship between yearling-and-lder 

(year-plus) Arctic cod length and weight was developed from bottom trawl samples, but this 

analysis did not include YOY-sized individuals. Development of a length to weight relationship 

specifically for YOY Arctic cod, or extending the range of values in the year-plus relationship, 

would make the calculation YOY Arctic cod biomass within the survey area consistent with the 

year-plus calculations. 

A larger midwater trawl is recommended for future pelagic surveys of year-plus Arctic cod. 

Midwater nets such as an Aleutian wing trawl (AWT), Polish rope trawl, or Cantrawl are 

recommended alternatives. The AWT was considered before the field survey, but the decision 

was made not to use it because doors different from the ones used to fish the 83-112 bottom 

trawl net would be required. This would necessitate changing doors between bottom and pelagic 

net deployments, which would consume valuable survey time. Because the research vessel had 

two net reels there was no need to change nets themselves between bottom and pelagic net tows. 

Due to its size and the need to fish the net slowly because of the large trawl doors, catches in the 

Marinovich midwater trawl used in the current study were small and year-plus Arctic cod were 

observed on the vessel’s third wire display to be avoiding the net. On the positive side, the small 

size of the Marinovich allowed it to be fished in a tow-yo fashion and near bottom, which 

permitted sampling of near-bottom year-plus Arctic cod layers. 

Even though YOY fish and euphausiids were caught in the midwater trawl, selectivity and 

escapement through the Marinovich meshes was unknown. For that reason, a smaller Methotstyle net is also recommended for future studies that target YOY fish or large invertebrates. 

However, an advantage of the Marinovich trawl used in the current study was that the use of 

trawl doors made near-surface deployments very stable. 

It is recommended that all nets be equipped with net mensuration equipment. Depth and 

dimensions of the Marinovich trawl used in this study were monitored using the vessel’s third 

wire system. In future studies, other instruments, such as the Netmind system used for the 

bottom trawl, would allow for more careful real-time monitoring of net dimensions and the 

ability to record these dimensions while the net fished. 

See “Station and transect spacing” above for discussion of pelagic fish survey design. 

Densities of pelagic fish (predominantly Arctic cod) were calculated scaling the exported 

acoustic backscatter values with estimates of Arctic cod target strengths. When scaling to 

density, mean target strengths for Arctic cod within the 20-40, 40-100, and 100-500 m depth 

strata were calculated by converting the mean fork length (within the depth) to target strength 

using a target strength to length relationship. Different from the bottom trawl sampling, there 

were no limitations to acoustic sampling in the rocky/muddy 20-40 m depth depth. Density 

estimates were made for 1-kilometer analytic bins along the north-south transects and the 

connecting east-west cross-transects. We used a Pearson’s Chi-Squared test to statistically 

evaluate differences in mean fish densities among depth strata (<40, 40-100, 100-500 m). 

We used linear models and General Additive Models (GAM) to evaluate relationships between 

pelagic Arctic cod densities with oceanographic characterizations of the habitat. Due to spatial 

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correlation in both the acoustic and oceanographic data, this analysis used individual CTD casts 

paired with collocated acoustic data. A 3 km radius around each CTD location was considered a 

“point” observation. Independent variables included longitude, bottom depth, salinity, density, 

temperature and mixed layer depth. The response variables, fish densities, were log transformed 

to reduce issues of heteroscedasticity in the regression models. Some environmental variables 

were also log transformed to help stabilize model variance. The young-of-the-year (YOY) fish 

models (comparing density to biological and standard predictors) were run using a simple linear 

model (with normal error structure) and a GAM. The two model types were run for comparison. 

For the linear model, the optimal model was selected using AIC criteria. This procedure 

produces a global model that includes all possible combinations of variables as a starting point, 

but variable deletions are used to find the model with the lowest AIC score. The GAM was run 

on the same dataset, but the number of knots in the smoother was limited due to the small sample 

size. For the yearling-and-older (year-plus) Arctic cod density models, the presence of zero 

values in the nearshore where year-plus densities were not estimated complicated the analysis. 

When zero values were included in the model run, general linear models were used but when 

zero values were excluded from the model run, linear models were chosen. Models comparing 

year-plus density to environmental predictors were performed using linear models (simple or 

general) and GAMs (for comparison) both including and excluding the nearshore zero values. 

We consider the models with zero values excluded to be the most appropriate given that zero 

values are artificial (i.e., analytic not biological). 

Fish habitat (phycial oceanography) 

The best oceanographic data were collected within the same day along a given transect. This 

type of near synoptic sampling is ideal for resolving oceanographic patterns and for relating 

water properties to fish distributions. More survey time dedicated to oceanographic sampling 

would thus be recommended. In addition, it would have been advantageous to have an Acoustic 

Doppler Current Profiler (ADCP) on board to measure the flow field at the time of fish catch. 

An important consideration when designing future studies and when interpreting the data 

collected here is that the Beaufort Sea changes rapidly and that there are many different water 

masses with widely varying properties. These different water masses represent different fish 

habitats. In particular there is no reason to think that the water mass distributions in the western 

Beaufort Sea are similar to the central and eastern Beaufort Sea. For example, there likely will 

be less influence of the Bering-Chukchi water and more influence from the Mackenzie shelf 

further east. 

Quality control and disposition of samples and/or data 

We prepared a detailed Cruise Plan and submitted it for review by AFSC Division Directors and 

NOAA Marine and Aviation Operations (NMAO) before the field season. 

All field data (including inventory of samples taken) were entered and error-checked daily at sea. 

Additonal details regarding entry of field data at sea are found in the Methods section of this 

report (under “Fish and habitat methods”, “Demersal fish and pelagic trawl data entry”).

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All field data (including inventory of samples taken) were entered and error-checked daily at sea. 

Additonal details regarding entry of field data at sea are found in the Methods section of this 

report (under “Fish, invertebrate and habitat data collection methods, Demersal fish and pelagic 

trawl data entry”). The field data and inventory of samples taken was entered into databases upon 

return to Alaska Fisheries Science Center (AFSC) and University of Washington and errorchecked again. The taxonomic identification of all voucher specimens was confirmed or revised 

(if necessary) in the laboratory at AFSC. Details of sample collection methods are found in the 

Methods section of this report (under “Fish, invertebrate and habitat data collection methods). 

The eventual disposition of all specimens is detailed in Appendix V. 

NOAA conforms to the guidelines set forth in the Federal Data Quality Act. The following link 

contains the explicit NOAA guidelines for data quality and dispersion: 

http://www.noaanews.noaa.gov/stories/iq.htm

A Cruise Report was completed immediately after the end of the cruise. The Cruise Report 

contained an overview of the study and objectives, a description of sampling methods, scientific 

personnel, a detailed cruise schedule, and preliminary results. The Cruise Plan was posted on the 

Alaska Fisheries Science Center website. Results from the survey were presented to MMS in 

quarterly Progress Reports, to the scientific community at professional conferences and to 

Beaufort Sea communities at local meetings. 

Survey Planning

Scientific staffing 

An unexpected result of the survey was the high invertebrate catch biomass and diversity. Our 

science team was comprised predominantly of fish biologists, with only one scientist dedicated 

to sampling the invertebrate catch. This scientist was required to spend more time on deck than 

the rest of the science party to identify and quantify the species composition of the invertebrate 

catch. Future surveys should consider including more invertebrate species biologists if that 

component of the catch is to be properly sampled. It proved to be essential to have a fish 

biologist on board who was well experienced in fish taxonomy. It was important to identify as 

many species correctly as possible in the field, even though all species were verified in the 

laboratory from examination of voucher specimens. In the few instances were species were not 

identified in the field but were identified in the laboratory, it impossible to assign weights and 

numbers to the catch of those species. 

Logistics 

The 35-day vessel charter included one day at the start and end of the charter to un-pack/pack the 

gear. Three days were required for acoustic set-up and calibration, two at the start of the survey 

and one at the end. Two days were required at the beginning of the survey to diagnose and fix 

noise issues on the acoustic system that occurred because of the vessel’s acoustic and electrical 

configuration. There were seven transit days from Dutch Harbor to the survey grounds and six 

transit days in return, for a total of 13 transit days. There was an additional day of transit to the 

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survey area because of heavy ice around Pt. Barrow that slowed vessel progress substantially. 

The survey itself took 16 days to complete. No survey days were lost to weather. 

One challenge for the 2008 survey was the presence of substantial amounts of sea ice on the 

survey grounds when we arrived on August 6. All stations with water depths <100 m were 

inaccessible until the ice cleared out on August 13. The start date of the survey was based 

loosely on the long-term summer ice conditions, and on external scheduling conflicts. In 

retrospect it would have been better to determine the start date based on the seasonal forecast of 

ice break up that is available from the National Ice Center (http://www.natice.noaa.gov/). 

Supporting vessel operations in the arctic is challenging. Barrow has no facilities for large 

vessels and shallow alongside depths at the causeway make Prudhoe Bay unfavorable. While 

Nome should not be completely ruled out for a future “jumping off” port, Dutch Harbor, because 

of the fishing industry presence, has the best infrastructure for vessel/equipment staging, 

provisioning and fueling. Early in the planning of this project we considered staging out of 

either Barrow or Deadhorse/Prudhoe. A site visit to Barrow quickly eliminated Barrow because 

there are neither port facilities nor good small boat landing/launching areas that could be 

considered “all weather”. Barrow is the North Slope Borough headquarters, and, as such, is 

home for north slope search and rescue, medical facilities and other government functions. Any 

north coast at-sea emergencies that require assistance must be coordinated through the Barrow 

Police Department and the search and rescue unit, so it is important to keep these two 

organizations apprised of planned offshore activities. Coast Guard presence in Barrow is 

extremely limited, although the Coast Guard is exploring ways to increase their presence there. 

Re-fueling a vessel anywhere on the north coast is weather dependent and must be done by barge 

service. Crowley Maritime currently provides fuel barge service to north slope communities 

during the ice-free months, so re-fueling would have to be coordinated through Crowley. 

The Deadhorse/Prudhoe Bay area was not visited. Examination of area nautical charts and 

several phone conversations with on-site personnel quickly eliminated Deadhorse/Prudhoe Bay 

as a staging port. While it would not be impossible to stage people and equipment out of 

Deadhorse/Prudhoe, the shallow water depths at the causeway in Prudhoe Bay dictate extensive 

use of small boats for personnel and equipment transfers. Adverse weather conditions or the 

presence of ice could easily halt any small boat operations. 

Nome was briefly considered as a potential personnel staging port in order to decrease the 

amount of time the science party was required to spend transiting from Dutch Harbor to the 

project area. However, due to the limited amount of vessel time available and the additional time 

required for transit and a port call in Nome, we decided that Nome was not a viable option. 

Nome has made considerable improvements to their port facility over the last several years, so it 

may be possibile to use Nome as a staging port. However, it must be pointed out that Nome’s 

fuel supply is barged from Dutch Harbor, so fuel will be more expensive. Alongside depths at 

the causeway are approximately 22 feet. For the foreseeable future, Dutch Harbor is the 

recommended port of departure for arctic at-sea operations. 

Safety 

Emergency contact phone numbers (as of August 2008): 

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 North Slope Borough (Barrow)......Police......................907-852-6111 

 Search and Rescue.......907-852-2822 

 or 800-830-2822 

 Hospital....................907-852-4611 

 Prudhoe Bay (BP)......................Security Dispatch.........907-659-5631 

 Duty Officer...............907-659-4437 

 Emergency.................907-659-5300 

 Alaska Clean Seas........907-659-2405 

 U.S. Coast Guard, Juneau, D17 Command Center..............907-463-2001 

The U.S. Coast Guard currently does not have a regular presence in the Beaufort Sea. So, for the 

2008 survey the emergency plan was to contact the North Slope Borough (NSB) Search and 

Rescue (SAR) unit directly in case of serious injury/illness which requires medevac. After hours 

contact would be initiated with NSB Police, who would contact the SAR duty pilot. Consult 

would be made with medical personnel at the hospital. If a helicopter evacuation from the vessel 

was required, a chartered aircraft would have to be arranged through British Petroleum (BP) in 

Prudhoe Bay. The oil companies typically have hoist-equipped helicopters under contract. The 

full range of BP assets, including helicopters, small boats, and coordination team, can be 

accessed by calling the BP emergency number, and this would include both medical and nonmedical emergencies, such as fire, flooding and other emergencies that can occur at sea. 

Ultimately, all medical emergencies would be coordinated through the SAR unit at Barrow 

because they have the air ambulance and medical assets. 

Should the U.S. Coast Guard have helos in Barrow and/or a vessel (such as the USCGC 

HEALY) in the area, requests for emergency assistance from USCG would be coordinated 

through the District 17 Command Center, phone number above. 

There is no routinely available water taxi or helo evac service at Prudhoe Bay. It is possible to 

use the causeway (west dock) at Prudhoe Bay to conduct personnel transfers if necessary, but 

this should not be a routine occurrence. The survey vessel’s small boat would have to be used. 

Security requests that a courtesy call be made to advise them if personnel are coming ashore. If 

the survey is a federal activity and personnel are government employees, no other actions are 

needed (per Mr. Ramoth). 

Contigency planning 

A total of 35 days was scheduled for the survey. This total includes three days for set-up and 

breakdown of the survey vessel (two days before the survey and one day after), one day to mark 

trawl wires and test gear, two days for acoustic calibration, one day for bad weather and 12 days 

for round-trip transit. The weather did not cause any delays during the 2008 survey, although 

heavy ice pack around Pt. Barrow on the transit to the study area increased our total round-trip 

transit time to 13 days. Ice coverage also hindered our ability to sample nearshore stations 

during the first week of the survey. The details are described below: 

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6 Aug. Encountered fairly dense ice around Pt. Barrow. Floes appeared to be multi-year 

ice (not flat pancakes). Spent the entire night and day picking our way through. Sighted 

a female Polar bear with two cubs midday (1227 local time). Ice resulted in about a oneday delay in transit. 

7-11 Aug. Much of the survey area was still covered with ice. Bottom tows conducted in 

deepest depth (100-500 m), at times as close as 0.25 nmi from the ice or even in low 

density (~3/10) ice. Some midwater tows also conducted in the offshore depth when ice 

prevented access to new bottom trawl stations. 

12 Aug. Were finally able to conduct some bottom trawls at stations less than 100 m 

depth (in the middle depth). We were required to navigate through the ice to reach open 

water on the mid-shelf and were fishing within 0.5 to 3 nmi of ice. 

13 Aug. Mid-shelf region at Line 3 was clear of ice. Ice not encountered in densities 

requiring a change in survey plans for the duration of the cruise. 

Ice coverage maps were examined whenever they were updated (generally, every two days). 

Maps were faxed to the vessel from Seattle. It was important to monitor ice coverage to insure 

that the vessel had clear passage out of the Beaufort Sea after the survey. 

Multiple trawls, net sensors and zooplankton nets were on board in case of damage to nets during 

the survey. Similarly, a spare CTD was on board in case of damage to any of the components of 

that instrument. The only gear that suffered damage during the survey were the 83-112 bottom 

nets. In short, all three lined bottom trawls were damaged sufficiently to become unusable after 

nine days of survey (6-14 August). The remainder of the survey was conducted with the two unlined bottom nets, one of which was damaged on 15 August. The cause of the damage to the 

bottom nets was either heavy rocks, mud or a mixture of both. The details are described below: 

6 Aug. First trawl, in 350-400 m of water, using lined 83-112 (net # LL16), 30 minute 

tow. Cod-end ripped out. Replaced with another lined net (#1) and trawled again for 30 

minutes. Caught a large net of opilio crabs. 

7 Aug. Trawl 3 was deployed in 200 m water, net hung up briefly 15 minutes into the 

tow and was hauled back immediately. There were large rocks in the cod-end. There 

was a 10-12 foot tear in the belly of the net, behind the bosom. Net was repaired. 

Reduced tow time to 15 minutes. Bottom looks hard and flat, perhaps with some rock 

piles (hard to tell for sure). 

8 Aug. Trawl 6 was in 160 m of water. Cod-end so full of mud that it was too heavy to 

lift without damaging net. Weight estimated volumetrically. No net damage. 

13 Aug. Trawl 13 was along Line 3 (middle of survey grounds). It was difficult to find 

good bottom (very rocky and/or muddy). We had to drop two stations offshore of this one 

due to bad bottom. Catch was comprised of seastars and mud. 

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During Trawl 14 we lost the net. The captain felt it grab 13 minutes into the tow and 

hauled it back immediately. The net had torn off at the poly line holding the net to the 

head and foot ropes. The doors were covered with mud. The captain grappled for the net 

and recovered all of it, including the cod-end. No sensors were lost. The recovered net 

was also covered in mud. Bottom looks soft and somewhat “lumpy”, although the 

skipper was targeting a relatively flat spot. We likely hit a lump of mud right at the end 

of the tow. 

14 Aug. Trawl 15 was set in 40 m water depth. The captain said that the net was 

extremely heavy during haulback. The cod-end ripped out before we could get it on 

deck. This was our third and last lined 83-112. The bottom was level (no major changes 

in overall depth), but was not uniformly flat. 

Trawl 16 was made with an un-lined 83-112 (net #10), and tow duration was cut to 5 

minutes. The cod-end was full of rocks. 

We scouted the inshore end of the transect, Line 5, (<50 m) for a tow. Bottom looked 

similar to the rocky bottom at Trawl 16 and we decided not to trawl in that area. 

All tows were 5 minutes long for the remainder of the survey. 

15 Aug. Trawl 19 was set in 30 m depth. We thought the bottom appeared flat and hard, 

but it turned out to be heavy mud. The net hung up briefly at haulback and tore from the 

bosom to the footrope. We replaced the net with an un-lined 83-112 (our second and 

final un-lined net). The bottom looks soft and “lumpy”. 

Trawl 20 was conducted in 50 m of water. The bottom appeared hard and flat. The codend came on deck full of rocks and the net tore when we were lifting it. The net was 

mended. 

Last six bottom trawls conducted without incident. 

Necessary permits-Federal 

Scientific Research Permits (SRP) 

A SRP is required for any scientific research activity occurring in the Exclusive Economic Zone 

(EEZ) that is conducted or controlled by NMFS and that would otherwise meet the definition of 

fishing under the Magnuson-Stevens Act (MSA). “Conducted or controlled by NMFS” means 

NMFS research conducted from NOAA vessels and NMFS chartered vessels operating under 

contracts or other approved agreements, or vessels whoe research activity is otherwise directed 

by NMFS. The definition of “scientific research activity” is lengthy and defined in 50 CFR 

600.745 (a) but there are elements of this definition that one should be aware of. Those elements 

are: 1) scientific research activity does not include the collection and retention of fish outside the 

scope of the applicable research plan, or testing of fishing gear; 2) data collection designed to 

capture and land quantities of fish or invertebrates for product development, market research, 

257
and/or public display are not scientific research activities and must be permitted under exempted 

fishing procedures; and 3) it has been determined that the sale of fish taken and retained during a 

scientific research activity is not fishing, however, fishing independent of actual scientific 

research activity, such as compensation for the use of the vessel, is not scientific research activity 

and must be permitted under expemted fishing procedures. 

To obtain an SRP for a research activity, one must submit a scientific research plan with the 

request for the SRP to the appropriate Regional Administrator. Submission of the request to the 

Regional Administrator acknowledges that the proposed research is approved and sanctioned by 

the NMFS Center’s Science and Research Director. The Regional Administrator will then 

review the scientific research plan to ensure the scientific research activity is adequately 

described, and to make necessary determinations (including any determinations dealing with 

marine mammals and Section 7 of the Endangered Species Act) to insure the scientific research 

plan is consistent with the applicable regulation, national policy, and other applicable law. The 

determinations shall include the appropriate NEPA document, generally a categorical exclusion, 

if supported by the facts. For research conducted in Alaska, the request should be submitted to 

the Regional Administrator for the Alaska Region. 

At a minimum scientific research plans should include: 

1. a description of the nature and objectives of the project, including the hypothesis or 

hypotheses to be tested; 

2. the experimental design of the project, including a description of the methods to be used, 

the type and class of any vessel(s) to be used, and description of the sampling gear; 

3. the geographical area(s) in which the project is to be conducted; 

4. the expected date of first appearance and final departure of the research vessel(s) to be 

used, and deployment and removal of equipment; 

5. the expected quantity and species of fish to be taken and their intended disposition, and, 

if significan amount of a managed species of species otherwise restricted by size or sex 

are needed, an explanation of such need; 

6. the name, address, telephone and FAX numbers of the sponsoring organization and its 

director 

7. the name, address, telephone and FAX number, and curriculum vitae of the person in 

charge of the research project on board the vessel; and 

8. the identity of any vessel(s) to be used, including the vessel’s name, official 

documentation number and IRCS, home port, and name, address, and telephone number 

of the owner and master. 

Once the SRP is issued, a copy should be provided to the chief scientist(s) or field party chief(s) 

who will be on board the vessel(s) conducting the research. They should make sure a copy is 

available on the vessel at all times. The responsible Division/Lab or program should also 

forward a copy of the permit and research plan to appropriate regional NMFS Enforcement, US 

Coast Guard, and state offices. If there is a change in vessels or dates of operation, a request 

shall be sent to the Regional Office to amend the SRP and then make sure Enforcement, USCG, 

etc. are also provided the amended SRP. 

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The 2008 Beaufort Sea survey was conducted under a Scientific Research Permit (SRP). 

Information on other types of permits is supplied below for the use of future survey planning. 

Letters of Acknowledgement of Scientific Research (LOA) 

An LOA is issued for non-NMFS controlled research activities conducted under the MSA. A 

“non-NMFS controlled” activity is one when neither the vessel nor the research activity on board 

is controlled by either NMFS or NMFS contracted personnel. Examples would be foreign, state, 

academic, or private organization research vessels. Since scientific research is not “fishing” and 

it is outside the control of the MSA, NMFS can only request that non-NMFS parties submit a 

scientific research plan and request an LOA for their scientific activity. The request and research 

plan should be submitted to the appropriate Regional Science and Research Director. The 

research plan is reviewed at the Center and an LOA issued if it is determined that the activity is 

scientific research and there are no likely adverse impacts upon marine mammals or other 

protected species. Copies of the LOA are provided to NMFS Enforcement, the USCG, NMFS 

Region, and state agencies. If there are concerns that the activity is not research or that there 

may be adverse impacts on marine mammals or protected resources, the Center Director can 

suggest that the research plan be modified but the sponsoring organization is not obligated to 

make any changes nor are they required to have an LOA to proceed with their research activity. 

The value of the LOA is to indicate to the enforcement agencies that the Regional Science and 

Research Director believes the activity is scientific research and not a guise of fishing. 

Exempted Fishing Permits (EFP) 

An EFP is required for any fishing that would otherwise be in violation of the MSA or other 

fisheries laws of their implementing regulations and is not considered and exempted educational 

activity. An EFP is also required when otherwise prohibited fishing is authorized for a vessel as 

compensation for conducting a NMFS contracted resource survey (this does not apply to or 

include fish taken during the resource survey or research activity). There is a lengthy process for 

issuance of an EFP which includes publishing of a Federal Register Notice, review by the 

appropriate fishery management council, review by the appropriate NMFS Regional 

Administrator, and NMFS headquarters. There a quite a number of special circumstances and 

thus procedures listed under the guidelines for EFPs. These include: non-controversial EFPs, 

controversial EFPs, emergency EFPs, EFPs for compensation fishing, observer programs, and 

vessel-of-opportunity programs. 

Exempted Educational Activity (EEA) 

An EEA is required for fishing that would otherwise be in violation of the MSA or other 

fisheries laws that is part of an activity conducted by an educational institution for educational 

purposes. 

Public Display 

Collecting fish for public display requires an EFP unless they are collected under an SRP or EEA 

for study and then subsequent display. In considering whether an EEA or EFP is needed for the 

collection of fish for public display, the guideline is that if the collector will be retaining the fish 

and placing them on display for a fee, the activity is considered fishing and would thus require an 

EFP. An EEA could not be issued under those circumstances. 

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Necessary permits-State 

A State permit is required for either federal or non-federal operations: 1) within the territorial (3-

mile) waters, or 2) landing fish or other organisms in the state of Alaska, even if taken outside 

territorial waters. A Fish Resource Permit is issued by the State of Alaska Department of Fish 

and Game. A Study Plan or Research Proposal explaining the purpose and need, the objective, 

and the procedures to be used must be included with the permit application. The application also 

requires the following specific information: 

1. the species, number and disposition of the fish to be captured; 

2. period of time the permit is requested (valid only for dates within a calendar year) 

3. means by which the fish will be obtained 

4. location of study 

5. a brief purpose statement 

6. final disposition of collected specimens (specimens may not be consumed, sold, traded, 

bartered, or used in any commercial manner) 

7. names of people who will participate in field collections under terms of the permit (if 

applicant is representing a corporation or institution, a certification of affiliation may be 

required) 

Completed applications for marine environment collections (and permits involving propagation) 

are submitted to: 

Alaska Department of Fish and Game 

Division of Commercial Fisheries 

Attn: Sara Conrad 

P.O. Box 115526 

Juneau, AK 99811-5526 

sara.conrad@alaska.gov 

Applications for freshwater and estuarine environment collections are submitted to: 

Alaska Department of Fish and Game 

Attn: Bob Piorkowski 

Division of Sport Fish-RTS/FR Permits 

P.O. Box 115526 

Juneau, AK 99811-5526 

robert.piorkowski@alaska.gov 

For the 2008 Beaufort Sea survey, the Chief Scientist (Logerwell) was included on the Alaska 

Fisheries Science Center (AFSC) State Fish Resource Permit for 2008. 

Necessary permits-Local 

No local permits were required for the survey. However, the coastal communities adjacent to the 

survey area were notified well in advance of the survey and provided the opportunity to 

comment on any potential conflicts between the survey and community use of coastal waters. 

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Subsistence activities 

The Alaska Eskimo Whaling Commission was contacted to establish that the survey would not 

interfere with subsistance whaling activities. Whaling typically takes place in September in the 

area near Cross Island (longitude 148° W). Our survey was conducted between August 6 and 22 

between longitudes 152° W and 155° W, so conflicting with the whaling activities was not an 

issue. In addition, the coastal communities adjacent to the survey area were notified well in 

advance of the survey and provided the opportunity to comment on any potential conflicts 

between the survey and other uses of coastal waters, such as fishing. No concerns were voiced. 

Coordination with related projects 

Oceanographic and hydrophone moorings 

Robert Pickart (Woods Hole Oceanographic Institution) and Kate Stafford (Applied Physics 

Laboratory, University of Washington) deployed oceanographic and hydrophone moorings 

between 156 °W and 150 °W across the shelf as part of two National Ocean Partnership Program 

(NOPP) field studies. All but three of the moorings were deployed from the USCG Cutter Healy 

from 7-13 August 2008. The three remaining nearshore moorings were deployed from the R/V 

Annika Marine from 8-11 August. Dr. Pickart contacted us on behalf of himself and Dr. Stafford 

in late July 2008 and we shared with him our transect locations, trawl station locations, dates of 

the survey, survey vessel name and our at-sea contact information. We plotted the mooring 

locations on our charts and avoided trawling within several miles of the moorings. After the 

field season Dr. Pickart sent us a short cruise report describing what they had accomplished and 

showing CTD sections. We likewise sent him a cruise report and a data file with the locations of 

the CTD stations that we occupied. Tom Weingartner is also a P.I. on the Pickart NOPP project 

so the two data sets will be available for a combined analysis of physical oceanographic 

conditions on the Beaufort Sea shelf. 

Bowhead whale survey 

David Rugh (AFSC National Marine Mammal Laboratory) contacted us to discuss possible 

conflicts between their Bowhead whale aerial surveys, part of the “Bowhead Whale Feeding 

Ecology Study, BOWFEST”, funded by MMS. We provided him with our survey plan (dates, 

objectives, location, etc.) and he provided us with the 2008 field schedule. Fortunately, although 

the areas of our Beaufort fish survey and the BOWFEST aerial surveys overlapped, the timing 

did not. The aerial surveys took place 26 August to 19 September 2008, after we had left the 

survey grounds (on 22 August). In an effort to assure information exchange, project P.I. 

Logerwell presented the results of the fish survey at a BOWFEST workshop held in Anchorage 

on 20 January 2009. 

 

Funding 

The funded portion of this survey does not reflect the substantial personnel and equipment assets 

provided by NOAA-NMFS-AFSC at no cost to MMS. For example, all survey nets, rigging, net 

mensuration and associated equipment and electronics were provided by the Resource 

Assessment and Conservation Engineering Division (RACE), AFSC, at no cost to MMS. The 

portable winch that made the oceanographic and zooplankton collections possible was also 

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262

provided by RACE. RACE personnel participated in survey preparation, equipment assembly 

and post-survey data management. The expertise and experience of the RACE personnel was 

invaluable and was key to the success of this project. Additional matching personnel salaries 

included that of the AFSC project P.I. The table below details the matching costs provided by 

AFSC (Table 61). 

Item Value 

Salaries 

AFSC P.I. $105,191

Equipment and supplies 

Bottom trawl nets $100,000

Net mensuration instruments $72,250

Midwater trawl net $14,000

Trawl doors $50,000

Field computers $3,178

Survey supplies $1,000

CTDs $20,000

Portable plankton winch $45,000

Bongo nets $1,000

TOTAL $411,619

Table 61. Estimates of AFSC matching costs for 

the 2008 Beaufort Sea Survey.