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• #### Effects of elevated sediment levels from placer mining on survival and behavior of immature arctic grayling

The effect of placer mining effluents on Arctic grayling (Thymallus arcticus) fingerling and egg survival was tested in mined and unmined streams in interior Alaska. Also the influence of turbidity on Arctic grayling reactive distance and avoidance behavior was tested in a laboratory choice chamber. Arctic grayling fingerlings suffered less than 1% mortality during a 96-hr toxicity test in both clear (mean NTU = 1.4) and mined (mean NTU = 445) streams. Arctic grayling eggs did not show significantly (p > 0.1) higher mortality in mined streams than in unmined streams. In a laboratory choice chamber test, Arctic grayling avoided water with a turbidity above 20 NTU (nephelometric turbidity units). Arctic grayling reactive distance diminished proportional to the natural logarithm of turbidity.
• #### Effects of jet boats on salmonid reproduction in Alaskan streams

Freshwater angling has increased dramatically in recent years in southwestern Alaska, and jet boat operators serve some of these anglers. Resources agencies are under pressure to regulate use of jet boats in waters that support spawning populations of salmonids, but they need more information regarding these potential effects. This thesis describes the methods and results of experiments to determine the effects of water turbulence from passing boats on embryo mortality and behavior of spawning adults. Field experiments on sockeye salmon were conducted in American Creek (in the Naknek drainage in Katmai National Park and Preserve) in 1992 and 1993. Laboratory experiments on rainbow trout were conducted at Fort Richardson Hatchery. These two species were viewed as surrogates for all species of genus Onorhynchus.
• #### Application of decision analysis in the evaluation of recreational fishery management problems

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.
• #### Dynamics of a migratory fish population with applications to the management of sablefish in the Northeast Pacific Ocean

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.
• #### Effects of oil-laden sediments on behavior and growth of juvenile flatfishes

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.
• #### Assessment of the benthic environment following offshore placer gold mining in Norton Sound, northeastern Bering Sea

The effects of placer gold mining on the benthic environment of Norton Sound in the northeastern Bering Sea were assessed. Research focused on red king crab Paralithodes camtschaticus, a species with commercial and subsistence importance in the Sound and seasonal occurrence in the mining area. The study addressed mining effects on: (1) benthic macroinvertebrates, many serving as food for this crab, (2) crab relative abundance, distribution, and food, and (3) heavy metal concentrations in crabs. Mining on variable substrates in $<$20 m water depths occurred between 1986-90 during ice-free months when crabs were further offshore. Sampling nearly a year subsequent to mining revealed moderate substrate alteration. Benthic community parameters and abundance of numerically predominant families (e.g., owenid, spionid, and capitellid polychaetes and echinarachniid sand dollars) were reduced in mined areas. Many reduced taxa are known crab prey. Although young individuals of opportunistic taxa predominated, taxa were generally smaller at mined areas. Multi-year surveys of a once-mined area showed continued smoothing of bottom relief. Ordination of taxon abundance from mined (1 yr after mining), recolonizing (2-7 yrs after mining), and unmined stations reflected decreasing station disturbance. At least four years were required for benthos to recover from mining. Mining had a negligible effect on crabs. Crab catches, size, sex, and most prey groups in stomachs were similar between mined and unmined areas. Concentrations of eight heavy metals in muscle and hepatopancreas tissues were generally not different in mined areas. Furthermore, these metals were not different in sediments upcurrent and downcurrent of mining. Concentrations of most metals in tissues showed no temporal trend. Elemental concentrations in muscle tissues were below or within the range of concentrations in red king crabs from other North Pacific locations. Most metals from Norton Sound crabs were well below federal guidance levels for human consumption. Effects from mining were apparent for benthic macrofauna with virtually no effects observed for king crabs. Absence of any demonstrable effects of mining on this crab is primarily a result of the high natural dynamics of the Sound and opportunistic feeding behavior and high mobility of the crab.
• #### Estimation of abundance and mortality of emigrating chum salmon and chinook salmon in the Chena River, Alaska

During May-June, 1995 and 1996, the outmigration of juvenile chum salmon (Oncorkynchus keta) and chinook salmon (O. tschazvytscha) was sampled with floating traps in the area of the Chena River Lakes Flood Control Project, Chena River, Alaska. Catch-per-unit-effort (CPUE) was higher at night than day for chinook juveniles, but not for chum juveniles. CPUE of both species decreased as the season progressed, but usually increased during higher-discharge events. CPUE is standardized by time; discharge was monitored as a covariate but was not included in CPUE calculations. The Jolly-Seber family of models was used on recapture data of fin-dipped fish to obtain estimates of abundance and survival in 1996. Abundance estimates were 266,104 chum salmon (95% Cl 128,031 - 404,177) and 171,952 chinook salmon (95% Cl 146,342 - 197,561) during the May-June outmigration period. These abundance estimates are probably underestimates of the entire Chena River population. Survival estimates were 0.135 (95% Cl 0.042 - 0.228) for chum salmon and 0.713 (95% Cl 0.492 - 0.935) for chinook salmon over the same period.
• #### Health and condition of juvenile chinook and chum salmon near the Chena River Dam, Alaska

During May-June, 1995 and 1996, outmigrating chum salmon, Oncorhynchus keta, and chinook salmon, O. tschawytscha, were captured in the Chena River near the Chena River Lakes Flood Control Project. Fish condition was determined through the investigation of physical injury and scale loss. Except for one sample, the proportion of injured fish was never greater than 7% for chum or chinook salmon. Few injuries were severe. The proportion of chinook salmon with scale loss ranged from 1-33%, most of which were only partially descaled. When significant length differences existed, injured, descaled, and partially descaled fish were always larger than non-injured and non-descaled fish. Arctic grayling (Thymallus arcticus) diet by weight consisted of chum salmon (2%), invertebrates (89%), other fish (3%), and miscellaneous material (6%). Plasma cortisol levels were used as an indicator of the primary stress response of chinook salmon and did not indicate any unusual physiological stress level.
• #### Successional changes in the hydrology, water quality, primary production, and growth of juvenile Arctic grayling of blocked Tanana River sloughs, Alaska

A comparative stream study was conducted to assess the influence of development and blockage on the hydrology, water quality, primary production, and Arctic grayling of Badger Slough, Alaska. Data collected showed that Badger Slough exhibited stable, clear flows throughout the summer, and higher total and total dissolved phosphorus, orthophosphate, alkalinity, pH, conductivity, and average temperatures, and lower winter dissolved oxygen concentrations than both Piledriver and 23-Mile Sloughs. Mean algal biomass (3.3 mg m-3) and primary production (6.9 g O2 m-2 d-1) are greater than that recorded for any other interior Alaska streams and percent fines in riffle substrates have increased. However, growth of age-0 grayling remains high. Badger Slough has eutrophied due to increased nutrients and stable flows, and the quality of rearing habitat for age-0 fish remains good. However, an annual flushing flow of 8.0 m3 s-1 is recommended for controlling accumulations of fines and maintenance of grayling habitat.
• #### Effects of sample size and ageing error on estimates of sustained yield

A Monte Carlo simulation model of an exploited age-structured fish population was constructed, to evaluate the effects of sampling and ageing the catch on estimates of population parameters from catch-age analysis with auxiliary information and resultant estimates of sustained yield. A factorial experimental design was used where input parameters were varied among: small (100), medium (300) and large (900) catch sample sizes; high and low levels of ageing precision; and a range of ageing biases. Ageing bias and precision had dramatic effects on estimated sustained yield: positive ageing bias and ageing imprecision generally caused under-estimation of sustained yield, while negative ageing bias caused over-estimation of sustained yield. The multiple reader/reading ageing scenarios designed to mitigate ageing error were able to reduce the affects of ageing imprecision, but were unable to alleviate the problems associated with ageing bias. The simulation model can be modified for a variety of recreational fish populations; a diskette and user manual are available.
• #### Genetic linkage mapping of allozyme loci in even- and odd-year pink salmon (Oncorhynchus gorbuscha)

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.
• #### Heterogeneity And Bias In Abundance Estimates Of Outmigrating Chinook Salmon In The Chena River, Alaska

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>
• #### Heterogeneity and bias in abundance estimates of outmigrating chinook salmon in the Chena River, Alaska

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, α=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.
• #### Interrelationships of Pacific herring, Clupea pallasi, populations and their relation to large-scale environmental and oceanographic variables

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.
• #### Reproductive cycle of the dungeness crab, Cancer magister, in Southeastern Alaska

This study examined if female Dungeness crabs in Alaska reproduce annually. Crabs (287) were reared in flow-through tanks for one year and gonadosomatic indexes (GSI) and oocyte areas were calculated for seven months. Non-reproducing females had higher GSI and oocyte areas than reproducing females (<0.0001); resorption of gonads was observed. Male GSI varied significantly over the year. Crabs (27,506) were sampled with commercial pots and scuba in April and September in Glacier Bay, Alaska from 1992 to 1998. A large percentage (86%) of non-ovigerous females were observed in the spring when females should be brooding eggs. Molting probability is reduced as females become larger and they rely on stored sperm to fertilize eggs. A tagging study confirmed some females skip at least one mating season and extrude eggs in another season without ecdysis. This study demonstrated not all mature female Dungeness crabs in Alaska, especially larger females, reproduce annually.
• #### Studies on the ecological physiology of Porphyra abbottae and Porphyra torta (Rhodophyta): development of new species for mariculture in Alaska

Environmental factors affecting the distribution and growth of Porphyra abbottae and Porphyra torta were studied in a research project on the feasibility of nori mariculture in southeast Alaska. In situ abundance of Porphyra abbottae was compared at sites in Sitka Sound, Cross Sound and Chatham Strait. Growth of laboratory cultured Porphyra torta gametophytes was studied in response to nutrients, salinity, crowding and substrate. The seasonal progression of abundance in Porphyra abbottae varied between study sites, with associated differences in water motion and temperature. Double sampling techniques improved accuracy of in situ abundance estimates. Germination and initial growth of cultured Porphyra torta gametophytes were dependent on plant density, and substrate texture affected recruitment. Nitrate positively affected growth and pigment concentration at environmental levels; negative effects of low nitrate were reversible. Porphyra torta gametophytes tolerated low salinity and inorganic carbon at least to half of normal levels.