• A Walleye Pollock (Theragra Chalcogramma) Depletion Estimator For The Eastern Bering Sea

      Battaile, Brian Charles; Terrance J. Quinn, II; Kelly, Brendan; Sigler, Mike; Adkison, Milo (2005)
      The decline of the Steller Sea lion in the eastern Bering Sea over the last 25 years has resulted in increased management of the pollock fishery due to requirements of the Endangered Species Act, as food competition was hypothesized to contribute to the decline. Our research focused on determining if the pollock fishery was causing significant depletion in the eastern Bering Sea, particularly in Steller sea lion critical habitat. DeLury depletion models were fitted to catch and effort data from 1995 to 1999, from the observer program, which required considerable processing to obtain a database at a temporal and spatial scale that is much finer than that used for stock assessment in the eastern Bering Sea. The catch per unit effort (CPUE) data were standardized in a unique way in that the data were stratified in space and time and standardized using separate general linear models for each stratum. A significant amount of depletion was detected in the pollock fishery from 1995--1999. Depletion estimates of fishery mortality tended to be an order of magnitude smaller than those found in traditional stock assessments. Post hoc analyses indicated that depletion is detected more easily in areas of low abundance due to the hyperstable relationship between CPUE and biomass, possibly exacerbated by a lack of search time in the model. Evidence further suggested that dispersing exploitation pressure decreases local depletion, and pollock may repopulate a depleted area within weeks. Finally, a hierarchical spatial Bayesian analysis with a conditional autoregressive model was constructed to unify the analysis. Because the data were relatively clean of outliers and not over dispersed, significant changes in the results between the frequentist and Bayesian based analyses were not found as was little evidence of spatial autocorrelation in the estimates of catchability.
    • Abundance, Recruitment, And Environmental Forcing Of Kodiak Red King Crab

      Bechtol, William R.; Kruse, Gordon H. (2009)
      Commercial harvests of red king crab Paralithodes camtschaticus around Kodiak Island, Alaska increased rapidly in the 1960s to a peak of 42,800 mt in 1965. Stock abundance declined sharply in the late 1960s, moderated in the 1970s, and crashed in the early 1980s. The stock has not recovered despite a commercial fishery closure since 1983. To better understand the rise, collapse, and continued depleted status of the red king crab stock around Kodiak Island, I conducted a retrospective analysis with three primary objectives: (1) reconstruct spawning stock abundance and recruitment during 1960-2004; (2) explore stock-recruit relationships; and (3) examine ecological influences on crab recruitment. A population dynamics model was used to estimate abundance, recruitment, and fishing and natural mortalities. Three male and four female "stages" were estimated using catch composition data from the fishery (1960-1982) and pot (1972-1986) and trawl (1986-2004) surveys. Male abundance was estimated for 1960-2004, but limited data constrained female estimates to 1972-2004. Strong crab recruitment facilitated increased fishery capitalization during the 1960s, but the high harvest rates were not sustainable, likely due to reproductive failure associated with sex ratios skewed toward females. To examine spawner-recruitment (S-R) relationships for the Kodiak stock, I considered lags of 5-8 years between reproduction and recruitment and, due to limited female data, two currencies of male abundance as a proxy for spawners: (1) all males ?125 mm carapace length (CL); and (2) legal males (?145 mm CL). Model selection involved AICc, the Akaike Information Criterion corrected for small sample size. An autocorrelated Ricker model using all males and a 5-year lag, with the time series separated into three productivity periods corresponding to different ecological regimes, minimized AIC c values. Depensation at low stock sizes was not detected. Potential effects of selected biotic and abiotic factors on early life survival by Kodiak red king crab were examined by extending the S-R relationship. Results suggested a strong negative influence of Pacific cod Gadus macrocephalus on crab recruitment. Thus, increased cod abundance and a nearshore shift in cod distribution likely impeded crab stock rebuilding.
    • Advection And Retention Of Larval Dungeness Crab Cancer Magister In Glacier Bay And Adjacent Areas

      Park, Wongyu; Shirley, Thomas C. (2007)
      Spatial and temporal variations of larval abundance of Dungeness crabs were investigated as indications of larval advection and retention in southeastern Alaska. Larvae were collected in five transects: upper Chatham, Icy Strait, Cross Sound, and Icy Point, May to September 1997-2004 and Cape Edward in June 1998-1999. Larval densities were higher in inland water transect and lowest in offshore transects. In all transects, larval densities were highest in June. Zoeae I (ZI) were predominant with a small portion of later larval stages (ZII to ZV) in May. In May and June, late stages (ZIV and ZV) co-occurred with ZI. Later larval hatching in 1997 and 2002 and earlier larval hatching in 1998 may have been related to water temperature during the egg incubation period. Late larval stages that co-occurred with early larval stages can be transported from southern parts of their range where hatching occurs earlier. Mixing, loss, and distribution of larval Dungeness crabs were investigated inside and outside of Glacier Bay, southeastern Alaska, biweekly from late May to mid-September and monthly in Icy Strait from late May to late August in 2004. Larvae were collected from two different portions of the water column: above and below the thermocline and at four stations in Icy Strait. Larval loss was markedly high for ZI, ZIV, and ZV, and relatively low for ZII and ZIII. ZI occurred from late May to late July. Larval stages progressed seasonally from ZI to ZV and density decreased from ZI through ZV. The larval densities at the inner and outer bay stations and at the shallow and deep depths were similar. Co-occurrence of late and early larval stages and larvae with different rostrum lengths may be evidence of mixing of larvae incubated in different thermal regimes. The pattern of larval stages in Alaskan sites was markedly different from other parts of the species range: many of the early and intermediate stages occurred within inland waters, as opposed to increasing abundance of later stages with distance offshore.
    • Application of decision analysis in the evaluation of recreational fishery management problems

      Merritt, Margaret Faye; Reynolds, James B.; Criddle, Keith R. (1995)
      Fisheries management is a decision-making process, yet typically formal decision analysis techniques are not used in structuring problems, quantifying interactions, or arriving at a prioritized solution. Decision analysis tools are applied in the decision-making process for Alaska's recreational fisheries management as a means to reduce risk in management at the policy (Chapter 2) and field (Chapter 3) levels. In Chapter 2 the analytic hierarchy process is applied to the recreational fishery for chinook salmon (Oncorhynchus tshawytscha) in the Kenai River. Model structure is developed through an iterative interview process involving individuals asked to represent the perspectives of 15 different stakeholders. Individual stakeholder judgments are combined using a geometric mean, and maximax and maximin criteria. The sensitivity of the results to under-representation is explored through various models. Despise the contentious differences of perspective represented among stakeholders, the analytic hierarchy process identifies management options that enjoy broad support and limited opposition. In Chapter 3 decision analysis is applied to the recreational spear fishery for humpback whitefish (Coregonus pidschian) in the Chatanika River. A modified form of catch-age analysis is used to combine information derived from creel surveys and run age composition with auxiliary information in the form of mark-recapture estimates of abundance. Four systems are used in weighting annual observations: prior beliefs regarding their reliability, by the inverses of their variances, through a combination of these two weighting schemes, and equal (no) weights. The perception-weighted model generates the most reasonable estimates of abundance, which are relatively precise and associated with small bias. Forecasts of mature exploitable abundance are calculated based on various recruitment scenarios, maturity schedules, and exploitation rates. From these outcomes, the odds of stock abundance occurring below a threshold level are presented. By applying decision analysis methodologies which incorporate judgments and perceptions into decision-making affecting fisheries, sensitivity to uncertain information is made explicit, components of the problem are structured, interactions among components of the problem are quantified, and options are prioritized, thus increasing the chances of finding an optimal solution.
    • Blasting Bridges And Culverts: Water Overpressure And Vibration Effects On Fish And Habitat

      Dunlap, Kristen N.; Smoker, William; Timothy, Jackie; Kelley, John; Quinn, Terrance II (2009)
      Water overpressures and ground vibrations from blasting may injure or kill salmonid fish in streams and embryos in streambeds. Explosives are used to remove failing structures in remote areas of the Tongass National Forest that impair watershed function. The State of Alaska Department of Fish and Game standards limit blast induced water overpressures to 2.7 lb/in 2 (18.6 kPa) and streambed vibrations to 0.5 in/s (13 mm/s) when embryos are present. Researchers, however, have reported salmonid mortality from pressures only as low as 12.3 and 19.3 lbs/in2 (85 and 133 kPa) and embryo mortality from vibrations as low as 5.75 in/s (146 mm/s). I recorded in-stream overpressures and streambed vibrations with hydrophones and geophones at various distances from log bridge, log culvert, and metal culvert blasts. Peak water pressures (lb/in2) were directly related to cube-root scaled distances with an attenuation rate of -1.51. Peak particle velocities in gravel were directly related to square-root scaled distances (SRSD, ft/lb 1/2) with an attenuation rate of -0.75. Water pressures were less than 7.1 lb/in2 (49.0 kPa) in all but one blast, and streambed vibrations did not exceed 5.5 in/s in gravel streambeds. State standards should be revised to reflect reported mortality and these observations of blasts in streams.
    • Competition And Recruitment In Southeast Alaskan Subtidal Kelp Communities

      Okamoto, Daniel Kenji (2009)
      Shallow subtidal rocky reefs in the Northeast Pacific host frequent physical and biological disturbances as well as multiple competing algal species, including kelps and algal crusts. Kelps serve a critical role in local ecosystems by generating primary productivity and essential fish habitat. While kelp forests rank among the best understood ecosystems in the marine environment, protected and subarctic systems remain largely ignored. Because of the importance of kelp habitat in Southeast Alaska, and the susceptibility of kelps to both disturbance and competition, I estimated the variability in kelp community structure of subtidal, kelp dominated reefs in the Lynn Canal and quantified kelp recruitment in response to both competing algae and bare space which included clearings, artificial reefs, and settlement tiles installed at different periods. Surveyed communities varied most within rather than among reefs. Kelps exhibited strong, rapid, variable and apparent taxa specific colonization potential to clearings, artificial reefs and settlement tiles installed from summer to late fall. Algal crusts imposed a near 100% inhibition of kelp recruits in the field and lab; however the strong colonization potential of kelps facilitated recruitment in the face of strong inhibition by algal crusts.
    • Dynamics of a migratory fish population with applications to the management of sablefish in the Northeast Pacific Ocean

      Heifetz, Jonathan; Quinn, Terrance J. II (1996)
      Quantitative models are developed to describe the dynamics of an age-structured migratory fish population subject to exploitation. Migration rates are quantified, alternative ways of apportioning harvest among areas are examined, and the dynamics of a migratory population is described within the general theoretical framework of a projection matrix model. Application of these modeling efforts is within the context of the sablefish (Anoplopoma fimbria) fishery in the North Pacific Ocean. A Markov model that includes natural and fishing mortality, tag reporting and shedding rates, and migration is used to quantify migration rates of tagged sablefish among fishery regulatory areas. Estimates of annual migration rates out of an area are in the range 19-69% for small (<57 cm fork length (FL)), 25-72% for medium (57-66 cm FL), and 27-71% for large (>66 cm FL) sablefish. The predominant direction of migration along the continental slope is eastward for large sablefish and westward for small sablefish. Most estimates of migration are precise, unconfounded, and robust to perturbations of input constants. An age-structured model that includes migration is constructed to examine harvest policies for sablefish. Areal estimates of yield-per-recruit depends on the geographic distribution of recruitment. In general, when evaluated under the current annual exploitation rate of 10%, apportioning harvest among areas based on areal estimates of biomass and apportionment based on the steady-state distribution of biomass give similar results. A policy of apportionment based on a weighted moving average of areal estimates of available biomass is preferred to others. This policy adapts to current information about geographic distribution of biomass, reduces the effects of measurement error, and does not require estimates of migration probabilities for implementation. The reproduction, mortality and migration of an age-structured fish population are incorporated into a projection matrix model. The model is parameterized to include areal specificity in the stock-recruitment relationship and events such as larval dispersion that is decoupled from local reproduction. For the sablefish fishery where direction of movement is age dependent, fishing at a common rate among areas may be detrimental to the population in a given area. Area-specific fishing strategies can be devised to meet management objectives such as maintenance of areal spawning potential.
    • Early Life History Dynamics Of Lake Sturgeon

      Caroffino, David C. (2009)
      Populations of lake sturgeon Acipenser fulvescens in the Laurentian Great Lakes have not recovered after dramatic declines in the late 1800s despite the implementation of numerous recovery plans. Although extensive lake sturgeon research has and continues to occur, critical knowledge gaps remain. Recruitment of lake sturgeon is variable, but the extent of that variation, its limiting factors, and mortality rates experienced by early life stages are unclear. The purpose of this study was to increase our understanding of lake sturgeon early life stages by examining characteristics of a remnant population in the Peshtigo River, Wisconsin. Specifically, this research sought to empirically estimate rates of early life stage mortality, describe the vertical distribution of drifting larvae, evaluate the impacts of predation on recruitment, and describe patterns in movement and abundance of age-0 juveniles. Extensive sampling of lake sturgeon eggs, larvae, age-0 juveniles, and potential predators occurred during 2006 and 2007. Although drifting lake sturgeon larvae were captured in all parts of the water column, more were found near the surface than the substrate. After drifting to nursery areas, individuals exhibited variable movement patterns. Some fish were never recaptured more than 10 m from the initial capture site, while other individuals moved more than 9 km. Even though absolute abundance of juveniles differed by an order of magnitude between 2006 and 2007, a pattern of steady decline during the summer months was similar during both years. This downstream movement may have resulted in emigration from the Peshtigo River, as there was no evidence of predation on this life stage. Overall mortality from the egg to age-0 juvenile life stage exceeded 99.9% in both study years. Predation on eggs was extensive by both crayfish and fish (white sucker Catostomus commersonii ), but was minimal on other life stages. These results suggest that recruitment can vary significantly, and predation is likely only limiting at the egg life stage. These results will allow more effective monitoring and management of lake sturgeon early life stages, thereby promoting population recovery.
    • Ecology Of Juvenile Pink Salmon In The North Gulf Of Alaska And Prince William Sound

      Boldt, Jennifer Lynn; Haldorson, Lewis J. (2001)
      Increased production of salmon in Alaska has been accompanied by a decrease in average body size and decreased wild stocks, indicating a possible density-dependent response to increases in salmon populations and hatchery releases. Pink salmon have a short two-year life cycle and most post-hatch mortality is thought to occur during their first months at sea; therefore, processes in the early marine residence period may determine abundance. Geographic and seasonal patterns in distribution, growth, and condition of juvenile pink salmon during their first months at sea were examined in Chapter 1. The migration of pink salmon from Prince William Sound (PWS) occurred over several months. Fish lengths, weights, and energy contents varied geographically and seasonally. Pink salmon energy content was highest on the Gulf of Alaska (GOA) shelf in July and August and lowest in PWS in July, indicating that growth conditions were better on the GOA shelf. Spatial and temporal variation in growth and condition is indicative of disparate feeding opportunities for juvenile pink salmon. An unusual aspect of this study was the concurrent collection of zooplankton and fish in PWS and on the GOA shelf. Geographic and seasonal changes in juvenile pink salmon diets were examined during their first six months at sea in Chapter 2. Pink salmon diets varied geographically and seasonally, and prey size increased as fish grew. A unique opportunity existed to compare the energy content of thermally marked hatchery pink salmon to their wild counterparts in PWS (Chapter 3). Fish condition varied geographically, however, there were no differences among hatchery groups and/or wild pink salmon at any one location. This indicates that fish were staying together as a group. In Chapter 4, pink salmon consumption was estimated to represent a small fraction of the production but potentially a large proportion of the available standing stock of zooplankton in PWS. Geographic variations in fish condition, diet, and zooplankton densities were observed in this study. This supports the hypothesis that local processes, including food depletion and/or zooplankton availability are important to juvenile pink salmon.
    • Effects Of Adult Salmon Carcasses On The Energy Allocation Strategies Of Juvenile Salmonids

      Heintz, Ron A. (2009)
      When adult salmon return to their natal streams to spawn they deliver energy in the form of carcass tissues and eggs. Currently, the effect of this marine-derived energy on the growth and energy allocation strategies of juvenile salmonids is unknown. This thesis examined the effects of marine-derived energy on the growth and energy allocation strategies of juvenile coho salmon and resident Dolly Varden. Fatty acid analysis was developed as a tool for monitoring the flow of marine-derived lipids and hence energy from carcass tissues to consumers in laboratory and field settings. Fish in these settings were examined before and after the arrival of adult salmon carcasses in their respective habitats. The allocation of protein and lipid was monitored in concert with the fatty acid analysis. In addition, the effect of different diets on fasting of wild coho salmon was studied to determine how marine-derived diets might influence over winter survival. Marine-derived energy was acquired by juvenile salmonids through both direct and indirect processes. Direct acquisition entailed consumption of marine-derived lipids or short trophic linkages between carcass tissues and consumers. Indirect acquisition was typified by long trophic linkages between consumers and carcass tissues in which marine lipids were incorporated by consumers after marine-derived lipids permeated food webs. The benefits of consuming marine-derived lipids depended on the method of acquisition. Fish that directly acquired marine-derived lipids altered their energy allocation strategies by storing greater amounts of lipid; allowing them to maintain elevated metabolic rates over winter and start spring in a high nutritional state. In contrast, indirect acquisition of marine-derived lipids afforded fish few benefits. These fish survive winter by down regulating metabolic rates and start spring in a low nutritional state. The ubiquity of direct acquisition by coho salmon and variable routes of acquisition in Dolly Varden suggest that the presence of carcass tissues may serve to reinforce anadromy among juvenile salmonids rearing in streams.
    • Effects Of Glacial Discharge On Kelp Bed Organisms In An Alaskan Subarctic Estuary

      Sparkland, Tania Marie; Iken, Katrin; Braddock, Joan; Gradinger, Rolf; Himelbloom, Brian; Konar, Brenda; Whitledge, Terry (2011)
      Global climate warming is having large-scale, pronounced effects on the physical environment of Arctic and subarctic nearshore marine ecosystems, such as the widespread melting of glaciers. The purpose of this study was to determine how changing environmental conditions due to glacial melting affect subarctic kelp bed community structure and organism fitness. This study compared kelp bed community structure under disparate environmental conditions on a glacially-influenced and an oceanic shore in the same subarctic Alaskan estuary. Laboratory tests assessed the effects of varying salinity and irradiance on growth and physiological competence (as maximum quantum yield ( Fv/Fm)) of the dominant kelp, Saccharina latissima. Reciprocal in situ shore transplant studies examined seasonal growth, Fv/Fm, morphology and storage product levels (mannitol) in S. latissima. This study showed that kelp communities were distinctly different in these two nearshore regions within the same subarctic estuary. In addition, the kelp S. latissima from these two environments, exhibited phenotypic plasticity in terms of growth to varying levels of salinity and light availability, while both populations maintained high physiological competence year-round. However, this phenotypic plasticity was constrained within different seasonal growth patterns in the populations from the two shores, which likely are genetically fixed. This is the first time that phenotypic plasticity within a genetically fixed seasonal growth cycle has been described for macroalgae and especially for two populations in such close proximity. However, the ability to elicit plastic responses and seasonal adaptations in S. latissima may be limited and concerns remain about the long-term persistence of this and other important foundation species and nearshore habitats with continued climate change.
    • Effects of oil-laden sediments on behavior and growth of juvenile flatfishes

      Moles, Adam D.; Norcross, Brenda L. (1996)
      Three species of juvenile Pacific flatfishes: yellowfin sole (Pleuronectes asper), rock sole (P. bilineatus), and Pacific halibut (Hippoglossus stenolepis) were exposed to sediments contaminated with Alaska North Slope crude oil to determine the behavior and growth of juveniles in polluted nursery grounds. Responses were correlated with known biomarkers of toxicant exposure. In the behavior experiments, fish exhibited a strong preference for fine grained sediments ($<$500 microns) when presented with eight different sediment types ranging from mud to pebble. Juvenile yellowfin sole showed a preference for mud and mixed mud substrate, rock sole preferred sand substrates and halibut chose both mud and sand sediments. Flatfishes were able to detect and avoid heavily oiled (1400 $\mu$g/g total petroleum hydrocarbons-TPH) sediments but did not avoid sediments at oil concentrations of 400 $\mu$g/g TPH. Among yellowfin sole and rock sole, sediment preference altered behavioral response to oil whereas halibut did or did not avoid oil irrespective of sediment type. If flatfish do not avoid oil concentrations of 1600 $\mu$g/g and higher on preferred sediment, growth reductions occur. Fish reared on oiled sediment grew slower than controls on non-oiled sediments. Growth reductions in all three species were significant following 30 days of exposure to 1600-1800 $\mu$g/g TPH and became more pronounced over time. As the toxicant concentration or the length of exposure increased, growth per day decreased. By 90 days of exposure, fish exposed to 1600-1800 $\mu$g/g TPH grew 38-57% slower than controls. Halibut had the greatest change in growth rate following oil exposure. Exposure of halibut to sand laden with 4700 $\mu$g/g total hydrocarbons resulted in an 93% reduction in growth in 30 days. Condition factor was also most reduced in halibut. Changes in tissues and parasites indicated a reduction in fish health for all three species. There was an increase in fin erosion, liver lipidosis, gill hyperplasia and hypertrophy, and gill ciliate infestation combined with a decline in macrophage aggregates and gut parasites. Chronic marine oil pollution that results in hydrocarbon concentrations of 1600 $\mu$g/g in nursery sediments has the potential to reduce growth and health of juvenile flatfishes. Recruitment of juveniles to the fishery would be reduced due to increased susceptibility to predation and slower growth to maturity.
    • Genetic And Environmental Effects On Developmental Timing, Otolith Formation, And Gill Raker Development In Pink Salmon From Auke Creek, Alaska

      Oxman, Dion; Gharrett, Anthony; Milo, Adkison,; Cailliet, Gregor; Hagen, Peter; Smoker, William (2012)
      To determine how inheritance, environment, and hybridization influenced developmental timing, otolith formation, and gill raker development in pink salmon (Oncorhynchus gorbuscha), full and half-sibling families from Auke Creek, Alaska and third generation outbred hybrids between Auke Creek females and Pillar Creek males from Kodiak Island, Alaska (1,000 km distant) were incubated in ambient, chilled, and warmed water. Variation in development time of embryos from the odd-year broodline was primarily influenced by additive genetic factors, whereas no genetic effect was detected in the even-year run. No genotype-by environment (GxE) effects were associated with sires or families in either broodline, indicating that the observed variation in development time was likely the result of phenotypic plasticity. Hybridization (outbreeding) significantly prolonged development time in both broodlines, indicating that the phenotypic effects of outbreeding can last at least three generations. Early otolith development was genetically conserved and canalized, but the phenotypic expression of these genes is plastic and strongly influenced by environmental factors. There was no evidence that local adaptation or outbreeding influenced otolith morphology or shape. Otoliths from fish exposed to thermal stress were bilaterally asymmetrical, whereas the bilateral symmetry of otoliths from outbred fish exhibited evidence of heterosis because they were more symmetrical than their native counterparts. Unlike development time and otoliths, gill raker development was linear and consistently stable in the face of both hybridization and environmental stress. These results make it clear that different biological attributes respond to genetic control and stress in different ways.
    • Genetic linkage mapping of allozyme loci in even- and odd-year pink salmon (Oncorhynchus gorbuscha)

      Matsuoka, Makoto P.; Smoker, W. W. (1998)
      Genetic linkage maps of allozyme loci were constructed in even- and odd-year pink salmon (Oncorhynchus gorbuscha). The loci were mapped based on the results of gene-centromere (G-C) mapping and joint segregation analysis. For G-C mapping, 160 gynogenetic progeny families were produced, and 8,080 progeny from 74 families were analyzed using starch gel electrophoresis and histochemical stain techniques. G-C distances of 37 loci ranged from 0.5 cM at sMDH-A1* to 50 cM at sMDH-B2*. Eleven loci showed high G-C distances (>45 cM), indicating that one crossover on one chromosome arm is usual in pink salmon. Variation observed at sMDH-B1,2* in even-year families suggests that both of this loci is polymorphic and that there is possible inter-broodline chromosomal variation. Large variation was observed among families in G-C distance at several loci. Whether the variation was a reflection of difference in physical position, recombination rate, or some other factors needs clarification using a technique such as physical mapping with FISH, because this variation affects results of gene mapping based on recombination frequency. For joint segregation analysis, 320 biparental families were produced, and 13,068 progeny from 164 families were electrophoretically analyzed. Joint segregation was analyzed at over 200 locus pairs. Combined this with data from G-C mapping, 14 linkage groups involving 26 loci were constructed. The linkage maps contain eight classical linkage groups and four pseudolinkage groups. Two linkage groups found in pink salmon were conserved in widely divergent vertebrate species. Recombination frequency between linked loci were different between sexes, and it tends to be reduced in males in pink salmon. The order of loci, which probably duplicated in the recent tetraploidization event, in linkage groups I (sAAT-3 * &rarr; mAH-4*) and III (mAH-3* &rarr; sAAT-4*) was reversed. This is evidence of paracentric inversion during salmonid evolution after the duplication. Development of additional markers that are common (homologous) to many species will be necessary to examine syntenic stability and rearrangement over the evolutionary period.
    • Growth Of Western Alaska And Asian Chum Salmon (Oncorhynchus Keta) In Relationship To Climatic Factors And Inter- And Intraspecific Competition

      Agler, Beverly Ann; Smoker, William; Hagen, Peter T.; Kruse, Gordon H.; Mueter, Franz J. (2012)
      Ocean climate shifts and interspecific interactions with Russian pink salmon and Asian chum salmon are all believed to influence the growth of chum salmon in the North Pacific Ocean. Stepwise generalized least squares regression and Mantel's tests were used to examine factors influencing mean annual growth from adult scales collected during 1962-2008. First-year scale growth was affected by warmer regional temperatures, the North Pacific Index (NH), and reduced ice cover. Significant negative effects of Asian chum salmon abundance were found on third-year growth of five of six age 0.3 populations and three of four age 0.4 populations examined, indicating intraspecific competition. I found a negative correlation with third-year growth, North Pacific annual sea surface temperature (SST), and NM. Effects of interspecific interactions on third-year growth due to Russian pink salmon abundance were smaller than effects of Asian chum salmon abundance and SST. Warmer large-scale SSTs associated with reduced third-year growth contradicted the original hypothesis and suggested that the abundance of Asian chum salmon created a masking effect overwhelming other factors promoting growth. Strong correlations among third-year growth suggested that chum salmon experienced similar environmental conditions in the North Pacific and had overlapping distributions. More synchronous growth was observed among populations from close rivers than distant ones, indicating the importance of regional scale versus oceanwide studies. In the first year, intercircular distance declined then rapidly increased at circuli 5-9, Intercircular distance was similar by gender until the third year when male growth exceeded female growth for all populations except Japan. Back-calculated lengths indicated that fish reach ~494 mm fork length by the third year before returning as age 0.3 adults. Smolts entering the ocean during odd years had greater distances between adjacent circuli the next year, indicating reduced growth in the first year and compensatory growth during the second and third years. Overall, these results suggested possible effects on chum salmon growth due to abundance of Asian chum salmon, and this effect led to a reduction in length of approximately 42 mm, potentially affecting fecundity by 3%. These results contribute to growing evidence of competition among conspecific salmon.
    • Gulf Of Alaska Pacific Ocean Perch: Stock Assessment, Survey Design And Sampling

      Hanselman, Dana Henry; Terrance J. Quinn, II (2004)
      Pacific ocean perch (Sebastes alutus) stock size in the Gulf of Alaska has been difficult to assess because of an imprecise survey biomass index. This imprecision has been attributed to low sampling effort on a species with an aggregated distribution. In this thesis, I examined the importance of estimated survey biomass in the stock assessment and ways to improve them. First, I presented the complete stock assessment for 2003, with an analysis of uncertainty. Uncertain parameters included natural mortality, recruitment, and biomass estimates. Second, I examined adaptive cluster sampling (ACS) as a method to reduce survey uncertainty. ACS results provided lower estimates of mean abundance and lower standard errors than did simple random sampling (SRS). Bootstrapping suggested that the ACS mean may be a superior measure of central tendency. ACS results were better than SRS, but not as dramatically as suggested by previous literature. I used simulations to explore why ACS did not perform optimally. These simulations showed that it would be necessary to sample over 10% of the population to obtain large gains in precision. This is impractical for a large marine population. I explored the use of hydroacoustic data recorded on survey vessels to gain precision in biomass estimation. I used the data to (1) develop a catch prediction model based on near-bottom backscatter, (2) simulate an adaptive design, (3) apply ratio estimation in double sampling using hydroacoustic data, and (4) post-stratify survey data. Using hydroacoustic data in these designs showed gains in precision over SRS and may be useful. Finally, I used the S. alutus age structured model presented above to simulate effects of five factors: survey measurement error, catchability trends, a second biomass index, data source weighting, and sensitivity of prior distributions. Simulations showed that the stock assessment model was ineffective at high measurement error and was unable to detect trends in the data. A second biomass index yielded gains in model precision. The weight given lengths measured in the fishery was most important because of its long time series, and the prior distribution on natural mortality was most influential because it was difficult to estimate.
    • Heterogeneity And Bias In Abundance Estimates Of Outmigrating Chinook Salmon In The Chena River, Alaska

      Lambert, Ted Martelle (1998)
      The objective was to examine bias due to heterogeneity in capture probability (p) in an abundance estimate for chinook salmon (Oncorhynchus tschawytscha) outmigrants in the Chena River, Alaska. A higher proportion of day-marked fish (21/636 = 0.0330) compared to night-marked fish (17/1724 = 0.0098; p $<$ 0.0001, $\alpha$ = 0.05) was recaptured at the lower site in a Cormack-Jolly-Seber experiment with upper, middle and lower sites. Heterogeneity was also likely at the middle site between upper site-marked and unmarked fish. Simulations with heterogeneity confined to the middle and lower sites (i.e., due to inadequate mixing) caused small bias ($<$2.5%) in the upper site abundance estimate. With heterogeneity at all three sites (a subpopulation effect), the upper site estimate had 22.9% to 29.3% negative bias. Because heterogeneity observed in the Chena was probably due to inadequate mixing (related to daytime trap evasion), bias in the upper site estimate was probably small. <p>
    • Interrelationships of Pacific herring, Clupea pallasi, populations and their relation to large-scale environmental and oceanographic variables

      Williams, Erik Hamilton; Quinn, T. II (1999)
      Recruitment estimates for Pacific herring, Clupea pallasi, populations in the Bering Sea and Northeast Pacific Ocean are highly variable, difficult to forecast, and crucial for determining optimum harvest levels. Age-structured population models for annual stock assessments of the sac-roe fisheries rely on fishery and survey age composition data tuned to an auxiliary survey of total biomass. In Chapter 1, the first age-structured model for Norton Sound herring was developed similarly to existing models. Estimates of variability from age-structured stock assessment models for Pacific herring are often not calculated. In Chapter 2, a parametric bootstrap procedure using a fit of the Dirichlet distribution to observed age composition data was developed as a quick and easy method for computing error estimates of model estimates. This bootstrap technique was able to capture variability beyond that of the multinomial distribution. This technique can provide estimates of variability for existing population models with age composition data requiring little change to the original model structure. Recruitment time series from Pacific herring stock assessment models for 14 populations in the Bering Sea and Northeast Pacific Ocean were analyzed for links to the environment. For some populations, recruitment series were extended backward in time using cohort analysis. In chapter 3, correlation and multivariate cluster analyses were applied to determine herring population associations. There appear to be four major herring groups: Bering Sea, outer Gulf of Alaska, coastal SE Alaska, and British Columbia. These associations were combined with an exploratory correlation analysis of environmental data in chapter 4. Appropriate time periods for environmental variables were determined for use in Ricker type environmentally dependent spawner-recruit forecasting models. Global and local scale environmental variables were examined in forecasting models, resulting in improvements in recruitment forecasts compared to models without environmental data. The exploratory correlation analysis and best fit models, determined by jackknife error prediction, indicated temperature data corresponding to the year of spawning resulted in the best forecasting models. The Norton Sound age-structured model, parametric bootstrap procedure, and recruitment forecasting models serve as enhancements to the decision process of managing Pacific herring fisheries.
    • Juvenile Bristol Bay Sockeye Salmon Ecology

      Farley, Edward V., Jr.; Adkison, Milo (2008)
      Predicting annual returns of Bristol Bay sockeye salmon (Oncorhynchus nerka) has been difficult due to large, unexplained variations in return strength. Ocean conditions, particularly during the first few months after salmon leave freshwater, are believed to have a strong influence on their early marine growth and survival. Limited historical and present research suggests that sea temperature can affect juvenile Bristol Bay distribution. During years with cool spring sea temperatures, juvenile sockeye salmon are distributed nearshore along the Alaska Peninsula, whereas they are found further offshore during years with warm spring sea temperatures. Juvenile sockeye salmon are larger, in better condition, and have higher marine stage survival after the first year at sea when they are distributed further offshore than when they are distributed nearshore along the Alaska Peninsula. Juvenile sockeye salmon stomach contents also shift from primarily Pacific sand lance ( Ammodytes hexapterus) and euphausiids to age 0 walleye pollock ( Theragra chalcogramma) when their distribution changes from nearshore to further offshore. Annual averages of juvenile sockeye salmon growth rate potential (GRP) were generally lower among years and regions with cool spring sea temperatures. In addition, juvenile sockeye salmon GRP was generally higher in offshore regions than nearshore regions of the eastern Bering Sea shelf. A sensitivity analysis indicated that juvenile sockeye salmon GRP was more sensitive to changes in observed (August to September) sea surface temperatures during years when prey densities were lower. The results of the dissertation suggest that variability in early marine survival is primarily due to bottom-up control of the trophic structure of the eastern Bering Sea ecosystem.
    • Life History, Demography, And Ecology Of The Spiny Dogfish "Squalus Acanthias" In The Gulf Of Alaska

      Tribuzio, Cindy A.; Kruse, Gordon; Fujioka, Jeff; Gallucci, Vince; Hillgruber, Nicola; Lowe, Chris; Woodby, Doug (2010)
      The spiny dogfish (Squalus acanthias) is a small, cosmopolitan shark species, common in sub-tropical and sub-arctic waters. The species is often targeted commercially in most areas of the world throughout its range, and in some cases it is overfished or the subject of conservation concern. In the Gulf of Alaska, spiny dogfish are not targeted and not generally retained, but incidental catches can be high for this schooling species. Previously, biological parameters for spiny dogfish in the Gulf of Alaska were assumed from estimates for this specie's neighboring areas, including British Columbia and Washington State. The purpose of this study was to examine spiny dogfish in the Gulf of Alaska and estimate important parameters for stock assessment in four stages: (1) general biology, distribution, and life history; (2) modeling age and growth; (3) population demographic modeling; and (4) ecological interactions revealed by diet analysis. Spiny dogfish are similar in length in the Gulf of Alaska to neighboring regions, but mature at larger sizes and have a greater fecundity than reported elsewhere. There is high natural variability in estimated ages for the species, which is reflected in the poor fit of the growth models, possibly owing to measurement error from using the dorsal fin spine as the aging structure. A two-phase growth model provided the statistical best fit. However, questions were raised about the biological interpretation of the model and whether more traditional models (e.g., von Bertalanffy and Gompertz) may be more appropriate. Using the life-history and growth data, Leslie matrix type age- and stage-based demographic models were created to estimate sustainable fishing mortality rates and to examine the risk of harvest scenarios. Female Gulf of Alaska spiny dogfish can support up to a 3% annual harvest rate; fisheries that target juveniles have the greatest risk of population decline below threshold levels. Spiny dogfish are generalist opportunistic feeders that feed on whichever prey is available, however shrimp are the most important prey type, followed by cephalopods. Results of this study will be used in future ecosystem modeling and stock assessments for this species. Taking into account the history of targeted fisheries for the species on the U.S. east coast and in British Columbia and Washington, as well as the susceptibility of the species to overfishing, fishery managers will need to take a cautious approach should a target fishery develop in the Gulf of Alaska.