Alaska Fishery Research Bulletin Issues, Vol.11 No. 2 - Winter 2005

Effects of Inbreeding and Family Origin on Variation of Size of Chinook Salmon Oncorhynchus tshawytscha Fry

Cara J. Rodgveller, William W. Smoker, Andrew K. Gray, John E. Joyce, and Anthony J. Gharrett — Vol. 11(2):73–81. 2005.

We cultured separate lines of Chinook salmon fry Oncorhynchus tshawytscha of Chickamin River, Southeast Alaska ancestry in 7 common garden enclosures. A parentage analysis based on variation of microsatellite alleles showed that within these lines, 7 brother-sister matings ( F satellite F = 0.25) had created 35 inbred fish in 7 = 0.25) had created 35 inbred fish in 7 families [bred from 6 females (dams) and 6 related males (sires)], and other matings of unrelated fish had created 37 outbred fish in 10 familes (bred from 7 females and 6 males.) There was no measurable effect of inbreeding on growth of Chinook salmon fry through 114 days post swim-up. A general linear model showing the effects of dam, sire, and the interaction of dam and sire explained a significant amount of the variation of length and weight, but not of condition factor. However, analysis of a mixed model showed that only the interaction between dam and sire explained a significant amount of the variation of lengths and weights. Because variation among individuals from different families can be large, effects of individuals can potentially be confounded with the effects for which a study is designed. To avoid drawing improper conclusions, studies should estimate the amount of variation that can be attributed to family origin, or be certain that many families are sampled.

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Evaluation of Biological Sampling Protocols for At-Sea Groundfish Observers in Alaska

Steven J. Barbeaux, Sarah Gaichas, James N. Ianelli, and Martin W. Dorn — Vol. 11(2):82–101. 2005.

In 1999 the North Pacific Groundfish Observer Program (NPGOP) changed sampling protocols in order to optimize available observer resources. As the NPGOP modifies their program to meet an increasing number of objectives, it is important to ensure that new protocols continue to meet previously defined objectives. In this study, we evaluate how the changes in sampling protocols have affected data critical to stock assessments. We explore how changes to the length and otolith sampling protocols effect estimates of length distributions, mean length, and catch-at-age distributions in the eastern Bering Sea walleye pollock Theragra chalcogramma fishery. We also investigate the spatial distribution of observer length and otoliths samples in relation to total catch. We found that the modified protocols employed by NPGOP in 1999 did not significantly reduce the precision of estimates based on collected data, but did improve the spatial distribution of length and otolith sampling in this fishery. Given these results, coupled with an overall reduction in the time necessary to complete these sampling tasks, we conclude that the modification to observer sampling protocols in 1999 improved data collection in the NPGOP.

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Distribution of Juvenile Pacific Ocean Perch Sebastes alutus in the Aleutian Islands in Relation to Benthic Habitat

Christopher N. Rooper and Jennifer L. Boldt — Vol. 11(2):102–112. 2005.

The habitat of juvenile Pacific ocean perch (POP) Sebastes alutus was identified using data from trawl surveys conducted by the National Marine Fisheries Service and linear modeling techniques. Analyses were carried out to evaluate the POP catch per unit effort (CPUE) data in relationship to depth, temperature, and sponge and coral CPUE. Sponge and coral CPUE were positively correlated, while depth and temperature were negatively correlated. Over 96% of the juvenile POP catch was from depths of 76 to 225 m and their CPUE increased with depth, and decreased with increasing temperature. The most important finding of this analysis was that juvenile POP CPUE increased significantly with increasing sponge and coral CPUE. Multiple regression analysis predicting juvenile POP CPUE explained 16% -17% of the CPUE variability using sponge and coral CPUE and either bottom temperature or depth. Juvenile POP were most abundant at sites in the western Aleutian Islands (beyond 170° W longitude), on large underwater banks (Stalemate and Petrel banks), and in passes between islands where currents are strong and prey availability may be higher than surrounding areas. These results suggest sponge and coral have an important role in the early life history of juvenile POP.

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Co-occurrence of Pacific Sleeper Sharks Somniosus pacificus and Harbor Seals Phoca vitulina in Glacier Bay

S. James Taggart, Alexander G. Andrews, Jennifer Mondragon, and Elizabeth A. Mathews — Vol. 11(2):113–117. 2005.

We present evidence that Pacific sleeper sharks Somniosus pacificus co-occur with harbor seals Phoca vitulina in Glacier Bay, Alaska, and that these sharks scavenge or prey on marine mammals. In 2002, 415 stations were fished throughout Glacier Bay on a systematic sampling grid. Pacific sleeper sharks were caught at 3 of the 415 stations, and at one station a Pacific halibut Hippoglossus stenolepis was caught with a fresh bite, identified as the bite of a sleeper shark. All 3 sharks and the shark-bitten halibut were caught at stations near the mouth of Johns Hopkins Inlet, a glacial fjord with the highest concentration of seals in Glacier Bay. Using a bootstrap technique, we estimated the probability of sampling the sharks (and the shark-bitten halibut) in the vicinity of Johns Hopkins Inlet. If sharks were randomly distributed in Glacier Bay, the probability of sampling all 4 pots at the mouth of Johns Hopkins Inlet was very low (P = 0.00002). The highly non-random distribution of the sleeper sharks located near the largest harbor seal pupping and breeding colony in Glacier Bay suggests that these 2 species co-occur and may interact ecologically in or near Johns Hopkins Inlet.

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Development of a Long-term Monitoring Project to Estimate Abundance of Chinook Salmon in the Copper River, Alaska, 2001-2004

Jason J. Smith, Michael R. Link, and Bruce D. Cain — Vol. 11(2):118–134. 2005.

We used fishwheels and 2-event mark-recapture methods to estimate the annual drainage-wide abundance of adult Chinook salmon Oncorhynchus tshawytscha returning to the Copper River in Southcentral Alaska. In the first event, fish were captured from May through July using 2 fishwheels operated in Baird Canyon (river km 66) in the lower Copper River. All marked fish received a back-sewn spaghetti tag during each year of study, and up to 500 fish in each of 2002, 2003 and 2004 were also fitted with radio tags. In the second event, marked fish were recaptured in one or 2 additional fishwheels operated on the Copper River near Canyon Creek (river km 157). The Baird Canyon fishwheels were operated from 2001 to 2004, and the Canyon Creek fishwheels were operated from 2002 to 2004. Unbiased system-wide abundance estimates were made in 2003 and 2004. An estimated 44,764 (SE=12,506) Chinook salmon measuring 810 to 1,070 mm fork length (FL) passed through Baird Canyon from 17 May to 1 July 2003. From 22 May to 22 June 2004, an estimated 40,564 (SE= 4,650) Chinook salmon (equal to or greater than 600 mm FL) passed through Baird Canyon. Capture probabilities during both events varied over the season in 2003 and 2004 and appeared to be influenced by flow-related changes in fishwheel catchability. We developed vertical-slot "escape panels" to place in the fishwheel live tanks, which allowed the much more abundant sockeye salmon O. nerka to easily escape from the live tanks back into the river while retaining Chinook salmon. The project has evolved into a successful long-term monitoring program and has demonstrated that Federal, State and Tribal agencies can work cooperatively to collect valuable data on Copper River salmon stocks.

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Estimating Capture Probability of a Survey Bottom Trawl for Bering Sea Skates (Bathyraja spp.) and Other Fish

Stan Kotwicki and Kenneth L. Weinberg — Vol. 11(2):135–145. 2005.

Capture probabilities for skates (Bathyraja spp.), 3 species of flatfish, and 7 other fish species were estimated for the standard survey trawl (83-112 Eastern bottom trawl) used to conduct the National Marine Fisheries Service annual eastern Bering Sea bottom trawl survey. Capture probability data were collected by an experimental trawl consisting of a standard survey trawl with an auxiliary net attached beneath the footrope. Capture probability was estimated for each 1-cm length interval by calculating the ratio of fish caught in the standard survey trawl to the sum of fish caught in both standard survey trawl and auxiliary net. Four competing models describing different capture processes were fitted to the data using a maximum likelihood method, and the best model was chosen by likelihood ratio test. Capture probability for skates increased monotonically with length from approximately 0.65 for 30 cm skates to approximately 0.8 for skates >100 cm. Capture probability for flatfish (arrowtooth flounder, Atheresthes stomias; rex sole, Glyptocephalus zachirus; and Pacific halibut, Hippoglossus stenolepis); sturgeon poacher, Podothecus accipenserinus; wattled eelpout, Lycodes palearis; and great sculpin, Myoxocephalus polyacanthocephalus, was constant across lengths and close to unity (> 0.97). Capture probability was constant, but significantly lower than 1.0 for sawback poacher Leptagonus frenatus (0.89), searcher Bathymaster signatus (0.94), and spinyhead sculpin Dasycottus setiger (0.69). For spectacled sculpin Triglops scepticus capture probability was 1.0 for fish smaller than 15 cm but decreased for larger fish.

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Mortality Rates for Juvenile Pink Oncorhynchus gorbuscha and Chum O. keta Salmon Infested with Sea Lice Lepeophtheirus salmonis in the Broughton Archipelago

Alexandra Morton and Rick Routledge — Vol. 11(2):146–152. 2005.

Wild juvenile pink Oncorhynchus gorbuscha and chum salmon O. keta were captured and sorted by the number of sea lice Lepeophtheirus salmonis infecting each fish. These fish were placed in groups of 60 in flowthrough containers immersed in seawater near the site of capture. There were 3-4 replicates for each infection category and 3 consecutive trials or Series run to assess the impact of sea lice on short-term fish mortality. Control groups of lice-free fish were included to measure handling and containment effects. In each trial or Series, significantly more fish died in the categories with sea lice than in the lice-free category. The majority of fish infected with motile-stage sea lice died. These observations indicate that short-term mortality of wild juvenile pink and chum salmon is increased by infestations of 1-3 sea lice.

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