NOAA logo JAS 1999 Quarterly Rpt. sidebar

Auke Bay Laboratory

(Quarterly Report for Jul-Aug-Sep 1999)

Fish Use of Eelgrass and Kelp Habitats

Auke Bay Laboratory (ABL) Habitat Program staff sampled eelgrass (Zostera marina) and kelp (e.g., Laminaria) habitats near Sitka, Alaska, to document  their value as essential fish habitat. High value habitats are designated “Habitat Areas of Particular Concern” and receive special consideration during permit reviews of shoreline development.

Fish were sampled monthly by beach seine from April through September 1999 at two subsites of each habitat at four sites. Vegetation was characterized by determining percent cover and biomass.  Fish species diversity was higher at eelgrass (25-34 species) than at kelp (16-27 species) sites. Eelgrass sites also had greater monthly mean fish abundance (2,877 fishes versus 2,117 fishes), although abundance at kelp sites in May and June was higher than at eelgrass sites, largely due to high abundance of pink (Oncorhynchus gorbuscha) and chum (O. keta) salmon fry.

Abundance and use differed between habitats. Chum and pink salmon fry dominated both types of habitat in April and May and persisted in kelp sites through June. Young-of-the-year Pacific herring (Clupea harengus pallasi) were the most numerous species in eelgrass sites in July and  persisted through August, but were not found in kelp. In August and September, young-of-
the-year shiner perch (Cymatogaster aggregata) and juvenile Pacific cod (Gadus macrocephalus) dominated both habitat types. In general, if a species occurred in both habitats, it was more abundant in eelgrass.  Exceptions were higher numbers of salmon fry and white spotted greenling (Hexagrammos stelleri) in kelp relative to eelgrass communities.

Results from this study help to define the role of eelgrass and kelp habitats as essential fish habitat and enable habitat managers to ensure their conservation during shoreline development.

By Pat Harris.

Residence Time of  Juvenile Rockfish in Eelgrass/ Kelp Habitats

Movement of age-1+ black (Sebastes melanops), copper (S. caurinus), dusky (S. ciliatus), quillback (S. maliger), and yellowtail (S. flavidus) rockfishes was investigated in Sitka Sound to determine residence time in eelgrass and kelp habitats, areas of possible high value as Essential Fish Habitat.  Movement of juvenile rockfish between eelgrass and kelp habitats within four small semi-enclosed bays was investigated by mark-recapture methods. Two soft-bottom eelgrass and two cobble-bottom kelp sites in each bay were sampled monthly with a beach seine from April to September 1999.  Fish were marked with injected elastomer tags to distinguish month and site.  Fish held in the laboratory showed no tag loss or handling mortality.  Because of difficulty distinguishing juveniles, rockfish were pooled into three species groups: copper/quillback, black/yellowtail, and dusky rockfish.

A total of 1,747 age-1+ rockfish were captured, of which 1,189 were tagged, and 161 were recaptured.  The recapture rate was similar for all species groups: copper/quillback (14%), black/yellowtail (12%), and dusky (13%).  Recaptured fish showed little movement from the original tagging site or between habitat types.  Only 6% of recaptures were caught more than 30 m from their tagging location.  Only three recaptures changed habitat types.  Recaptures in later months were composed of fish tagged from several earlier periods, indicating residence of up to 4 months.

Results show that juvenile rockfish move into shallow eelgrass and kelp habitats in May and remain in the same local area throughout late spring and summer.  Because of the extended residence of juvenile rockfish in particular habitat types in summer, research will next focus on linkages between habitat and rockfish growth and survival.  This information will further assess the relative value of eelgrass and kelp as essential habitat for juvenile rockfish.

By Mike Byerly.

Habitat Assessment for Tatitlek Harbor

Habitat Program staff conducted a fish habitat assessment at proposed harbor construction sites at Tatitlek, Prince William Sound, Alaska,  in July 1999.  The proposed site for harbor construction, Tatitlek Cove,  has a lush eelgrass  meadow, which is designated as a Special Aquatic Site under the Clean Water Act.  Principal concerns are the potential impacts including the cumulative effects of harbor construction on eelgrass and fish habitat in the Tatitlek area.

The objective of the habitat assessment study was to characterize fish and habitat in the project area in order to provide perspective on the relative value as fish habitat of alternative construction sites. Six beaches in the Tatitlek area were sampled with a seine to determine use by fish and crab species.  Submerged aquatic vegetation along the shoreline in the Tatitlek area was surveyed by skiff and with a remotely operated vehicle (ROV).

Beach seining showed that eelgrass beds had higher species diversity (9-15 species) than non-eelgrass sites (5-9 species) and also had greater fish abundance (mean, 277 fishes and crabs) than non-eelgrass sites (mean, 77 fishes and crabs).  Eelgrass assemblages were dominated by juvenile Pacific cod (53-196 cod per seine haul), with lesser catches of  lingcod (Ophiodon elongatus) and other species.  Non-eelgrass sites were dominated by tubesnouts (Aulorhynchus flavidus) and juvenile Pacific cod. Skiff and ROV surveys found eelgrass along an estimated 80% of the shoreline in the Tatitlek area.  Eelgrass occurred in all suitable enclosed areas, as well as in some marginal areas that were exposed to wind and waves.  Relatively few locations had bare substrate or non-eelgrass (e.g., Laminaria) vegetation.

The site of proposed harbor construction in Tatitlek Cove was typical of other eelgrass habitats in the area, with high species diversity and fish abundance.  An alternative construction site south of Tatitlek Cove (South Point) had predominantly filamentous algae and Laminaria, and fish assemblages there were less diverse and less abundant than in Tatitlek Cove.  South Point, however, was one of the few sites in the study area that contained Laminaria, which may be important for biodiversity. Because eelgrass was ubiquitous in the study area, the cumulative effects of harbor construction in Tatitlek Cove are not a major concern.

By Mike Murphy.

Habitat Areas of Particular Concern

ABL  staff assisted the North Pacific Fishery Management Council in analyses for the Draft Environmental Assessment/ Regulatory Impact Review for Habitat Areas of Particular Concern (HAPC). Specifically, they reported on the description and distribution of coral in the Gulf of Alaska and Bering Sea and on the impacts of fishing on coral. Corals had previously been identified as HAPC. In the draft report, the Council proposed options for management measures to reduce adverse impacts on HAPC.  The options are:

  1. Status quo. No additional fishery management actions to protect HAPC from fishing impacts would be taken.

  2. Reclassify some living substrate HAPC as a prohibited species.  This would specifically prohibit retention of all coral, sponges, kelp, rockweed and mussels.

  3. Establish no fishing zones in areas of Gorgonian coral abundance.

Note that both options 2 and 3 can be adopted.

ROV Observations of Essential Fish Habitat in Southeast Alaska

boulderye.JPG (25661 bytes)
Figure 1. Rockfish observed via a video-equipped ROV inhabited areas with complex habitat such as bedroock walls and boulder piles.

Information is limited on the nearshore habitat of many commercially important groundfish species in Alaska, especially during their larval and juvenile stages. Many groundfish species utilize shallow (<70 m deep), nearshore areas during their early life.  Information is needed by managers to protect and conserve those habitats that are essential to maintain healthy fisheries.


In 1999, the ABL used a remotely operated vehicle (ROV) equipped with a video camera to study the association between habitat and fish assemblages in nearshore waters of Southeast Alaska. Approximately 100 ROV dives were conducted in a variety of habitat types from southern Southeast Alaska near Craig to northern Southeast Alaska near Sitka and in inside waters near Juneau.  Important commercial species observed included 6 species of rockfishes (Sebastes spp.), Pacific cod, longcod, and walleye pollock (Theragra chalcogramma).   Most rockfish were in areas with complex habitat, such as bedrock walls and boulder piles, with numerous cracks and overhangs for cover (Figure 1 above), whereas areas with not much relief, such as basin bottoms, were void of rockfish.  Juvenile rockfish were often seen in shallower water than adults were, particularly in areas with vegetation, such as eelgrass meadows, Laminaria beds, and Nereocystis forests.

Distribution of rockfish differed between outside and inside waters and between southern and northern Southeast Alaska.  For example, juvenile yelloweye rockfish (Sebastes ruberrimus) were seen in outside waters between Craig and Sitka but not in inside waters near Juneau.  Similarly, most lingcod were seen in outside waters near Sitka, whereas few were observed in inside waters. Quillback rockfish were ubiquitous, occurring in both inside and outside waters between Craig, Sitka, and Juneau.

We observed some distinct associations between fish assemblages and habitat in nearshore waters of Southeast Alaska.  For example,  juvenile rockfish, lingcod, and Pacific cod were often in shallow water areas with vegetation (e.g., eelgrass, Laminaria), whereas juvenile yelloweye rockfish were only in high-relief, vertical wall-habitat.  Distribution of fish between northern and southern and inside and outside waters of Southeast Alaska was patchy, especially with few fish observed in inside waters near Juneau.  Differences in physical and biological factors, such as salinity, temperature, food, and cover likely account for the presence or absence of some species among our study sites. Information on fish assemblages and habitat will help managers identify and protect those habitats in nearshore areas susceptible to impacts from shoreline development.

By Scott Johnson

Juvenile Salmon Surveys In Eastern Bering Sea

The Ocean Carrying Capacity program conducted a survey of juvenile salmon in the eastern Bering Sea  from 2 to 12 September 1999.  The survey began 30  nmi east of Cape Seniavin, near Port Moller, and extended southwestward to Cape Mordvinof, east of Unimak Pass.  Surface trawls were made along eight transects spaced 30 nmi apart; each transect began near the coast and extended to 60 nmi offshore or farther if large numbers of juvenile salmon were encountered at offshore stations.  Co-investigators in the study included scientists from the University of Alaska.

Our results indicate a much broader offshore distribution of  juvenile sockeye salmon (O. nerka)  than that  from our previous survey in July 1999.  During July 1999, juvenile sockeye salmon were encountered  nearshore (less than 10 nmi offshore) and were distributed northeastward of Port Moller. During September 1999, most of the juvenile sockeye salmon were encountered southwestward of Port Moller to 60 nmi east of Unimak Pass and were distributed from nearshore environment to 60 nmi offshore and further (80 nmi offshore) along the 50 fathom shelf break.

The expanded distribution of juvenile sockeye salmon encountered during September 1999 may have been the result of increased sea surface temperatures.  During July 1999, juvenile sockeye salmon were only encountered when sea surface temperatures were 6EC or more; sea surface temperatures in offshore waters during July were 4E-5EC.   During September 1999, sea surface temperatures had warmed considerably; nearshore sea surface temperatures were 10E-10.5EC, while offshore surface water temperatures were 8.5E-9.5E C.

Increased sea surface temperatures may also have lead to rapid increase in growth.  During July 1999, juvenile sockeye salmon were generally small in size, ranging in length from 80-105 mm near the coast to 105-115 mm off Port Moller.  During September 1999, juvenile sockeye salmon lengths near the coast ranged from 105 to 140 mm, while lengths of juvenile sockeye salmon encountered at offshore locations ranged from 190 to 240 mm. Analyses of plankton, stomach contents, freshwater age, and scale growth data collected during both surveys will be done to shed additional light on the growth and migration characteristics of juvenile sockeye salmon emigrating from Bristol Bay.

By Steve Ignell.

SASPop Up and Running

Biologists from the ABL’s Marine Salmon Interactions Program accepted the completion report for development of the Statewide Escapement Survey Database by the Alaska Department of Fish and Game (ADF&G).  The project, initiated in FY95 though a grant developed by the ABL and funded by NOAA’s Enviromental Services Data and Information Management Program (ESDIM),  has been funded with $370,000 in ESDIM grants over the last four fiscal years, as well as an equivalent amount of in-kind funding from the ADF&G.  The project has created a geo-referenced salmon and escapement data system, the Status of Alaska Salmon Populations Geographic Information System (SASPop GIS), incorporating over 1.5 million escapement observations from almost 4,000 streams throughout  Alaska.  The system includes digitized, statistical area maps defining fishing districts and escapement locations and identification of several hundred streams statewide for which survey data exists, but which have not been previously identified in the Alaska Anadromous Water Catalog.  This information will allow the inclusion of these anadromous streams in the catalog, so that they will be afforded the regulatory protection of the Anadromous Stream Act.  The data system will be an invaluable tool for both research and management, providing new capabilities for assessing the trends and status of Alaska salmon populations and examining salmon production in relation to landscape and watershed scale habitat alterations.  Now that the system is operational, the ADF&G will maintain it with annual updates from regional escapement surveys.

By Alex Wertheimer.

 Stock Identification of Salmon Samples from the Vessel Ying Fa

Samples of chum and sockeye salmon seized from the stateless fishing vessel Ying Fa were analyzed to determine their region of origin using genetic stock identification (GSI), otolith marks, parasite analysis, and scale data.  Based on GSI, the chum salmon samples originated in Russia, 86%; Japan, 2%; western Alaska, 2%; Alaska Peninsula and Kodiak Island, 8%; and British Columbia, 2%.  Origins of the sockeye salmon sample were not so clear because there was some disagreement between the parasite data and the GSI and scale data.  Results of parasite analysis suggested the sample was nearly all of Alaskan origin, with at least 15% coming from Bristol Bay.  The GSI analysis indicated that 30% of the sockeye salmon originated in Russia and 70% in North America.  The scale analysis showed that 97% of the sockeye salmon sample were ocean age 3, whereas the return to Bristol Bay in 1999 was approximately 70% ocean age 2 fish.

By Richard Wilmot.

Migration of Yukon River Chum Salmon

A total of 892 Yukon River fall chum salmon were tagged with radio transmitters during the 1999 field season.  Locations and migration rates are being determined through radio-telemetry monitoring.  As of the end of September 1999, 508 fish (57%) were in the U. S. portion of the main-stem Yukon River, and 44 fish (5%) had crossed the border into Canada.  In the Porcupine River system, 115 fish (13%) had crossed the border into Canada, and 22 fish (2%) were in the U. S. portion of the river. The Chandalar River in the U.S. portion of the drainage continues to be one of the major spawning destinations, with 203 tagged fish (23%) currently located.

By Richard Wilmot.

Forage Fish Diet Study

The role of forage fish—abundant, schooling fishes that transfer energy from primary or secondary producers to higher trophic levels—is being examined in coastal Alaska and ecosystems worldwide. In Prince William Sound (PWS), the Exxon Valdez (EVOS) Oil Spill Trustee Council, between 1994 and 1997, sponsored the Alaska Predator Ecosystem Experiment (APEX), a multi-disciplinary ecological research program undertaken by a consortium of natural resource agencies and academic institutions to assess forage fish populations and their trophic interactions with one another and with jellyfish, seabirds, and marine mammals.

One component of APEX is the Forage Fish Diet Study, conducted as a cooperative project of the ABL’s Marine Salmon Interactions and Habitat Investigations Programs.  Stomachs were examined from 14 forage species (> 5,100 specimens) caught mainly in midwater trawls, purse seines, and beach seines, and representing nine sampling periods during 1994-96.  Food habits data were used in conjunction with prey field samples to examine diet, prey partitioning and preference, diet overlap, and potential competition between forage species.   A final report  of the Forage Fish Diet Study, published in 1999 by the EVOS Trustee Council, describes monthly and interannual diet composition and overlap between 14 forage fish species; compares young-of-the-year Pacific herring and pollock feeding in allopatric and sympatric aggregations in summer and autumn 1995; and compares feeding of juvenile herring, sand lance, and pink salmon in allopatric and sympatric aggregations in summer 1996.  These data were also used with another APEX component to examine the potential competition between four zooplanktivorous jellyfish species (Aurelia, Cyanea, Aequorea, and Pleurobrachia) and the four forage species and have been an important data component in the development of bioenergetic models and energy flows between trophic levels in the PWS marine ecosystem.

By Molly Sturdevant.

Sablefish Longline  Survey Completed

The AFSC has conducted an annual longline survey of sablefish and other groundfish off Alaska from 1987 to 1999.  The survey is a joint effort involving the ABL and the Resource Assessment Conservation Engineering (RACE) Division. Beginning in 1996, biennial sampling of the Aleutian Islands region and eastern Bering Sea was added.

In 1999, 73 stations were sampled in the Gulf of Alaska and 16 stations were sampled in the eastern Bering Sea from 28 May to 5 September.  Sixteen kilometers of groundline were set each day, containing 7,200 hooks baited with squid.  The survey vessel was the chartered fishing vessel Ocean Prowler.  Catch rates on the survey are critical for the determination of the annual Allowable Biological Catch of sablefish.  The survey’s sablefish abundance index for all regions combined increased 9.8% in numbers and 4.7% in weight from 1998 to 1999, following decreases of 5.7% in numbers and 5.8% in weight from 1997 to 1998. Approximately 4,633 sablefish, 603 shortspine thornyhead (Sebastolobus alascanus), and 188 Greenland turbot (Reinhardtius hippoglossoides) were tagged and released during the survey.  Length-weight data and otoliths were collected from approximately 2,451 sablefish.  During the survey a surface gill net was deployed to sample juvenile sablefish (ages 0 and 1).  The net was set at  35 different stations and caught juvenile sablefish as well as other fish species, especially juvenile and adult salmon. Sperm (Physeter macrocephalus) and killer (Orcinus orca) whales took fish from the longline at several stations as in previous  years.

By Michael Sigler.

Sablefish Longline Hook Spacing Experiment

The effect of hook spacing has been measured for sablefish in two experiments.  The purpose of  both experiments was to test an assumption of how to interpret longline fishery catch rates.  The fishery catch-per-skate is assumed to be an index of relative abundance. For example, a 10% difference in catch rate reflects a 10% difference in relative abundance.  This assumption would be wrong if increasing the hook spacing increased the fishing power of each hook.  Most (about 70%) sablefish longline fishermen currently use 1-m  hook spacing, but the spacing differs between vessels and may change with time.

The first experiment was conducted in Chatham Strait near Tenakee Inlet during 4-13 July 1986 from the NOAA ship John N. Cobb.  Circle hooks (size equivalent to 13/0) baited with herring were used.  Three hook spacings were tested: 1, 2, and 4 m; all three hook spacings were tested in each set.  The second experiment was conducted 25-26 July 1999 in the Gulf of Alaska off Icy Bay aboard the chartered fishing vessel Ocean Prowler. Circle hooks (size 13/0) baited with squid were used.  Four hook spacings were tested:  0.5, 1, 2, and 4 m.  For both experiments, catch-rate-per-hook increased as hook spacing increased.

For both the 1986 and 1999 experiment, catch-rate-per-hook increased as hook spacing increased to an asymptote at 4-m spacing.   Catch-per-hook for 1-m spacing, the most common spacing currently in the fishery, was about half that for the 4-m spacing.  These results imply that fishery catch rates should be standardized by longline set to account for differences in hook spacing.

By Michael Sigler.

Stock Assessment of Slope Rockfish and Pelagic Shelf Rockfish in  Gulf of Alaska

Updated stock assessments of slope rockfish and pelagic shelf rockfish in the Gulf of Alaska will be completed during the first quarter of FY 2000. The results of the recently completed triennial trawl survey will be included in the updated stock assessments. The most recently completed assessment of  Pacific ocean perch (Sebastes alutus), a member of the slope rockfish assemblage, used an age-structured model and estimated exploitable biomass at 228,190 metric tons (t) and determined the stock is increasing. The assessments of most other species of slope rockfish and pelagic shelf rockfish in the Gulf of Alaska rely on biomass estimates provided by trawl surveys.  The most recently completed assessments indicate the following stock levels and stock trends; Shortraker (S. borealis) and rougheye (S. aleutianus) rockfish exploitable biomass 65,380 t, trend unknown; northern rockfish (S. polyspinis) exploitable biomass 65,380 t, trend unknown; other slope rockfish, exploitable biomass 103,710 t, trend unknown; pelagic shelf rockfish exploitable biomass 54,220 t, trend unknown.

Age-structured Model of Northern Rockfish in  Gulf of Alaska

The northern rockfish, S. polyspinis, is one of the most abundant and commercially valuable members of its genus in Alaska waters, second only to Pacific ocean perch, S. alutus. The stock assessment of northern rockfish in the Gulf of Alaska used to recommend catch levels has relied almost entirely on biomass estimates provided by trawl surveys.  An age-structured analysis of northern rockfish population dynamics has been suggested as a way to improve the stock assessment.  Preliminary results were presented at the Gulf of Alaska Groundfish Plan Team meeting held in September 1999, and a report will be included in the NPFMC Stock Assessment and Fishery Evaluation Report.  The model will be updated with additional data and further evaluated prior to application and determination of the status of the northern rockfish stock. The value of the model at this stage is the feature of incorporating several disparate fisheries and survey data sources in the analysis.  In particular, the model provided a subjective framework for evaluating the effect of the different data components on the estimated population and suggested a rationale for determining an appropriate level of confidence in apparently inconsistent data components.

By Jon Heifetz.

Rockfish Adaptive Sampling Experiment

A cooperative study between the ABL and the Juneau Center for Fisheries and Ocean Science, University of Alaska Fairbanks was conducted 13-29 June 1999 aboard the chartered factory trawler Unimak in the Gulf of Alaska.  This was the second year of a 2-year study to improve survey techniques for assessing abundance of slope rockfish using adaptive sampling. Partial funding for both years was provided by the Sea Grant - NOAA Partnership Program.  The study focused on three commercially important species of slope rockfish, Pacific ocean perch, shortraker rockfish, and rougheye rockfish.  For 1998, contrary to expectations, adaptive sampling results showed only modest gains in the precision of abundance estimates when compared with random sampling. These results appeared highly dependent on the stratification pattern used. For 1999, the number of strata were reduced. Although final analyses have not been completed, the larger sample size (165 hauls) and lack of stratification of the 1999 study area appeared to improve the precision of adaptive sampling abundance estimates for Pacific ocean perch. However, for abundance estimates of shortraker/rougheye rockfish the 1999 results did not appear to show a marked advantage for adaptive sampling over random sampling.

By Jon Heifetz.

Sablefish Assessment

A preliminary revision of the sablefish assessment was presented to the Plan Teams in September 1999.  The revision consisted mainly of the addition of about 20 years of historical data and the addition of contemporary fishery catch rates.  Also included in the model were 1) a Bayesian analysis that incorporated prior probabilities for natural mortality and survey catchability into parameter estimation, 2) a decision analysis using the posterior probability from the Bayesian analysis to determine what catch levels likely will reduce abundance, and 3) an alternate method of apportioning Allowable Biological Catch (ABC) that adds fishery catch rate data to the survey data currently used to apportion the ABC. The final assessment will be completed in November after further external review. The abundance of sablefish is considered low but stable.

By Mike Sigler.

Effects of Trawling on  Soft-bottomed Marine Ecosystem

ABL staff completed a research cruise on 24 August to study the effects of bottom trawling on the seafloor near Kodiak Island.  This was the final cruise of the 2-year study to make observations of the seafloor in areas open to bottom trawling and adjacent areas which have been closed to bottom trawling since 1986. Cruises during both years were supported by the ADF&G vessel Medeia, and the research submersible Delta was used to make in situ observations of the seafloor.  Study objectives were to compare nontrawled zones and trawled zones to determine if changes have occurred to 1) infaunal species abundance and diversity; 2) abundance of fish and invertebrate populations, and 3) substrate characteristics, including grain-size composition and total organic carbon content.

During the August 1999 cruise, one of two sites investigated in 1998 was revisited, and a third site 25 km south of the Trinity Islands was investigated.  Ten 3,000-m long transects were completed at each site, and 60-70 sediment samples were collected per site.  Experimental trawl sampling was  also conducted at each site to collect animals observed from the submersible for definitive identification and to estimate relative species composition.  An epibenthic camera sled designed by Ken Krieger (ABL) and Brad Stevens of the AFSC’s Kodiak Laboratory was successfully tested as a potential tool for collecting benthic video data in future studies on soft-bottomed marine habitat. Digital camera capabilities are being developed for the sled used in studies concerning fishing impacts and essential fish  habitat.  Several submersible dives were also made in shallow areas of Albatross Bank to investigate the uniqueness of that area as a potential Habitat Area of Particular Concern.

Video footage is currently being analyzed for counts of fish and invertebrates in the trawled and nontrawled zones and should be completed by October 2000.  Infaunal composition, grain size composition, and organic carbon content analyses from the 1998 sediment samples are completed and analysis of the 1999 samples will be completed by January 2000.

By Robert Stone.