• A Multiple Stable Isotope Study Of Steller Sea Lions And Bowhead Whales: Signals Of A Changing Northern Environment

      Dehart, Pieter Andrew Philip; Wooller, Matthew J. (2006)
      The North Pacific and Arctic marine realm is currently experiencing dramatic environmental changes as a result of global climate change. Stable isotope analysis of western arctic bowhead whales (WABW, Balaena mysticetus ) and Steller sea lions (SSL, Eumetopias jubatus) were conducted to examine the influence of these changes on life history characteristics (migration and foraging) of these marine mammals. WABW baleen plates were analyzed for their stable oxygen and hydrogen isotope composition (delta 18O and deltaD) and were compared to the delta18O and deltaD in water and zooplankton prey along their seasonal migratory route. The delta18O and deltaD varied along the baleen (8 to 18�; -180 to -80�, respectively) and corresponded to stable isotopic differences in zooplankton from the winter (Bering Sea) and summer (eastern Beaufort Sea) habitats of WABW. Baleen delta18O and deltaD confirmed the seasonal annual migration of WABW and were subsequently compared to historical sea ice concentrations (SIC). This illustrated that WABW migration patterns appeared to have altered concomitant with changes in SIC. Years with a higher SIC (colder climate regimes) correlated with the largest difference in deltaD between winter and summer in WABW baleen during the period from 1972 to 1988. For a similar time period (1955 to 2000), the feeding ecology of SSL was also examined by analyzing the stable carbon and nitrogen isotope compositions (delta13C and delta 15N, respectively) of archived SSL bone and tooth collagen. Both delta 15N and delta13C varied greatly with location and sample year (14.6 to 20.5�; - 16.7 to -11.8�, respectively), with a significant change in delta13C observed around the 1976 regime shift. Bottom-up processes may have limited growth of SSL populations throughout this region over time, with animals focusing their foraging on offshore regions to mitigate this environmental change. Stable isotope analyses of historical samples of WABW (baleen) and SSL (bone and tooth collagen) both illustrated that recent environmental changes influenced the ecology (migration and feeding) of these marine mammals in the recent past.
    • 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 and feeding ecology of humpback whales (Megaptera novaengliae) in Kodiak, Alaska

      Witteveen, Briana Harmony (2003-08)
      A feeding aggregation of humpback whales (Megaptera novaeangliae) in the Kodiak Island region has received little previous study. A mark-recapture experiment was conducted in 2001 and 2002 to estimate its abundance. Historical abundance was back-calculated from this estimate, whaling records, and suspected survival and productivity values within a population model. The current population was estimated at 157 whales and the pre-whaling population at 343 whales. Prey consumption by humpback whales was modeled using three methods for two hypothetical diets based on prey availability surveys conducted within the study area and stomach contents of commercially caught whales. By assuming current consumption is proportional to prey availability, the current population removes an estimated 9,600 tons of prey annually. Historical populations may have removed over 19,000 tons of prey annually.
    • 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.
    • Acute exposures of salmonid embryos to total dissolved solids

      Failor-Rounds, Barbi Jean (2003-08)
      Two exposure methodologies are described here utilizing embryonic and juvenile life stages of several species of salmonids. Specific life stages of the fish were exposed to solutions of varying total dissolved solids (TDS) modeled after the measured produced water from the Red Dog Mine in Kotzebue, Alaska. Embryonic and juvenile coho salmon (0. kisutch) were exposed for 96 hours to determine acute response to TDS. Following exposure, fish were grown out to button up to assess delayed effects. Results from the 96-hour study suggest fertilization is the most sensitive developmental stage of salmon exposed to TDS. Six fish species were then used to assess a new 24-hour embryo toxicity study during fertilization. We examined short- and long-term mortality, number of unfertilized eggs, and the overall percent affected. The endpoint for the assay is the success of egg fertilization. Based on the results of these experiments, it is reasonable to conclude that the fertilization assay can be generalized across these species and may be useful in setting site-specific criteria for discharging wastes.
    • Adaptations Of The Bacterial Flywheel For Optimal Mineral Cycling In Oligotrophic Surface Waters

      Gustafson, Elizabeth S.; Button, Don K. (2008)
      Nutrient cycling in a subarctic oligotrophic lake was explored using current kinetic theory for organisms adapted to low nutrient environments with emphasis on bacterial contributions to system function. Techniques were refined which minimize sample disturbance and contamination for the purpose of accurately measuring bacterioplankton activity. Seasonal variations in DNA content, cell mass, species composition, specific affinity for amino acids and cell yield were observed. Quasi-steady state formulae describe bacteria as a flywheel in nutrient cycling; energy is conserved within a relatively constant biomass by varying bacterial activity with nutrient availability. The bacterial flywheel paradigm provides a bacteriocentric view of mineral cycling, linking kinetics to specific cytoarchitectural properties while maintaining links to substrate and grazing pressures. As an extention of the microbial loop paradigm, the flywheel becomes essential at high latitudes. In winter, low solar input interrupts the microbial loop so that the dissolved organic carbon (DOC) pool is cycled through bacteria only. This activity allows bacterioplankton to persist through winter and respond rapidly to springtime warming and nutrients. Microbial adaptations to seasonal variations in nutrient availability and temperatures were examined within the bacterial flywheel framework. Organisms are well-adapted to a narrow (17°C) in situ temperature range. Activation energies for small warming were low at the temperature extremes (20.6 kJ mol -1 at 0.5°C; -32 kJ mol-1 at 17°C) and high in spring (110 kJ mol-1 at 1.2°C). Nutrition varies by season, supplied in large part by amino acids in spring and summer. Winter growth rates are at least 0.013 day-1 whereas partial growth rate on amino acids for that season is only 2.8 x 10-5 day -1. It is proposed that winter organisms rely on diffusion transport and/or shift toward concurrent use of a large suite of substrate types for growth and maintenance.
    • Adaptive cluster sampling of Gulf of Alaska rockfish

      Hanselman, Dana Henry (2000-08)
      National Marine Fisheries Service trawl surveys result in more variable biomass estimates for long-lived Gulf of Alaska rockfish than researchers expect. Adaptive cluster sampling (ACS) was investigated to improve these surveys. In August 1998 east of Kodiak, AK, a sampling cruise tested ACS for Pacific ocean perch (POP), and shortraker and rougheye rockfish (SR/RE). In each of six strata, simple random sampling was conducted, then ACS was performed on top stations. Stopping rules prevented sampling from continuing indefinitely. Results did not resolve whether ACS alone was better than simple random sampling. ACS, combined with stratification, increased precision of POP estimates by 30% over random sampling, suggesting that the spatial distribution has both fine-scale and habitat-scale patterns. Variograms indicated that the expected aggregation was not encountered for POP, but that POP are more aggregated than SR/RE. Some diel movement of POP was evident. Both species were concentrated at specific depths.
    • Adrenal responsiveness of black-legged kittiwake chicks (Rissa tridactyla): interannual variation and the effects of nestling status, brood size and investigator disturbance

      Brewer, John H. (2007-08)
      The adrenal response to stress in birds is characterized by the release of the hormone corticosterone. Measurement of corticosterone of individuals is increasingly being promoted as a means to gauge the effects of environmental change or human disturbance on populations. However, species respond differently to stressors based upon their natural history, individual life history stage and the context of the stressor; thus, the collection of baseline data from individuals in their natural environment has been advocated. We measured baseline and stress-induced corticosterone levels of 12-15 day-old black-legged kittiwake (BLKI) chicks from 2002-2005 in Chiniak Bay, Alaska. The goals of the study were to explore the relationships between the adrenal responsiveness of BLKI chicks and 1) BLKI colony productivity; 2) brood size and nestling status; and 3) investigator disturbance. Adrenal responsiveness of chicks negatively correlated with colony productivity, implicating corticosterone concentration as an accurate indicator of colony productivity in poor years. Neither brood size nor nestling status affected the adrenal responsiveness of chicks in both natural broods and broods manipulated to control for maternal hormone deposition. Lastly, two levels of investigator disturbance analogous to that of a growth rate study on chicks did not significantly affect the adrenal responsiveness of chicks.
    • 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.
    • An age structured model for assessment and management of Copper River chinook salmon

      Savereide, James W. (2001-08)
      Chinook salmon in Alaska support human uses through a variety of fisheries. Age-structured assessment models are rarely used for estimating the abundance of exploited stocks. This thesis develops a model for the Copper River chinook salmon population to show its advantages over typical assessment models. Information consists of catch-age data from three fisheries (commercial, recreational, subsistence), and two sources of auxiliary data (escapement index, spawner-recruit relationship). Four approaches utilizing different information sources are explored. Results suggest that an approach utilizing pooled catch-age data with time-varying brood-year proportions produces the best estimates, although retrospective and sensitivity analyses suggest that all four approaches explored are robust. The model should assist managers when making management decisions, because it integrates all sources of information, accounts for uncertainty, and provides estimates of optimal escapement. The model shows promise as a method for assessing and forecasting chinook salmon populations.
    • Agonistic behavior, social dominance, and predator evasion of Oncorhynchus mykiss from lake and stream parents: an evaluation of lacustrine refuges as a conservation strategy for threatened or endangered salmonids

      Ammann, Erika R. (2004-08)
      The possibility of lakes providing temporary natural refugia for endangered salmonid populations, creating an alternative to hatchery propagation, is the context for this research. To investigate this possibility resident trout (Oncorhynchus mykiss) derived from a population that had been sequestered in a lake for seventy years were compared to fish from their founding anadromous steelhead trout population as well as to hybrid crosses of the two populations. Comparisons were made in the areas of aggression, dominance and predator evasion. In aggression trials the lake-derived population chased more than stream-derived O. mykiss at two life stages, age-0 and age-1. Lake-derived fry and the lake x stream hybrid fry also chased more than the stream x lake hybrid fry. Fin conditions (dorsal and pectoral fin lengths, an index of aggression) did not differ significantly. In dominance acquisition the stream x lake hybrid were least frequently dominant of all the crosstypes, and stream-derived parr were less dominant than lake-derived parr. Avoidance of a Dolly Varden predator by fry showed that the stream x lake hybrids achieved the highest survival rates. Seventy years of sequestration in a lake may be adequate time for divergence in aggressive behavior, social dominance and predator evasion between lake-resident and stream, O. mykiss populations.
    • Alaskan Arctic epibenthic communities: distribution patterns, links to the environment, and brittle star population dynamics

      Ravelo, Alexandra Mariela; Konar, Brenda; Bluhm, Bodil; Mahoney, Andrew; Winsor, Peter; Zimmerman, Christian (2016-08)
      The Arctic marine shelves are characterized by areas of high and low invertebrate standing stock and communities that vary spatially in patches. Large-scale environmental characteristics, such as the distribution of water masses, the fenology of sea ice cover, and variability of water depth define changes in epibenthic community structure throughout the Arctic shelves. The longevity and relatively low mobility of epibenthic invertebrates make them especially relevant as indicators of long-term environmental patterns. In terms of standing stock and biomass, the most representative group among Arctic epibenthic taxa are brittle stars. Large areas of the Arctic shelves have dense assemblages of brittle stars; however, despite their ecological importance for Arctic shelf systems, little is known of their age, growth and turnover rates. The research developed through this dissertation examined how environmental drivers influence epibenthic invertebrate communities of the Alaska Arctic shelves and the population parameters of the dominant brittle star species. The first chapter of my dissertation focused on the northeastern Chukchi Sea and the second one focused on the Alaskan Beaufort Sea. The overarching questions addressed in chapters 1 and 2 focused on characterizing the epibenthic communities of the Alaskan Chukchi and Beaufort seas and defining environmental characteristics that influence the community structure. To answer this question, biological and environmental data were collected and analyzed in 2009 and 2010 in the Chukchi Sea, and in 2011 in the Beaufort Sea. For my third chapter, the overarching question was: what is the predictive power of the seasonality of sea ice for epibenthic community structure in the Alaskan Arctic, and how does it compare to more commonly used environmental descriptors. To test this relationship, six variables depicting the patterns of the seasonality of sea ice were computed from passive microwave sea ice concentration data. For the fourth chapter, the overarching question was, what are the population parameters of the two dominant brittle star species of the Alaskan Arctic. For this analysis, individuals of Ophiura sarsii and Ophiocten sericeum were collected in 2013 for age and organic mass determination. Findings of this research indicate that epibenthic communities have a patchy distribution with one or a few taxa dominating the community over large spatial extents. In both the Chukchi and Beaufort seas, communities were dominated by either crustaceans or echinoderms. Only in the mid-depth stations of the Beaufort Sea were both groups equally abundant. The environmental measure that best correlated to epibenthic commuity structure in both regions was longitude. Biologically relevant variables, such as sediment grain size, sediment phaeopigments, bottom water temperature and salinity, though region specific, were also important drivers of commuity structure. As predictors of epibenthic community structure, sea ice variables resulted in moderate to high correlation values. In the Beaufort Sea, sea ice variables performed better than traditionally used environmental descriptors; however, this was not the case for the Chukchi Sea. This study is the first to report on the age, growth and turnover of Arctic brittle stars. The asymptotic age was higher for O. sarsii than for O. sericeum; however, both species had significantly higher maximum ages than temperate region congeners. The individual production of O. sarsii surpassed that of O. sericeum by an order of magnitude throughout the size spectra. As a whole, this research highlights the complexity of the biological-environmental interactions that create the large spatial variability in community structure, benthic biomass and diversity throughout the Alaska Arctic. The variability in community structure throughout the Chukchi and Beaufort seas was linked qualitatively to large-scale environmental patterns. Quantitatively, these environmental forces were represented by the date of sea ice return and date of sea ice retreat in the Beaufort Sea. The predictive power of sea ice variables was reduced in the Chukchi Sea by the large inter-annual variability in wind direction and intensity that in turn affect the pattern of seasonality of sea ice. As integrators of large-scale environmental patterns, sea ice variables proved useful as additional predictors of epibenthic community structure. The dominant shelf brittle star species do not experience short-term fluctuations in population size. Top-down and bottom-up controls on these populations, such as predation and food supply, may be governing their growth strategy and total annual growth. Considering the longevity and slow growth of many Arctic epibenthic species such as brittle stars, the recovery after disturbance could require decades to restore high biomass in some areas. Environmental changes associated with climate change and resource development in the Arctic shelves have the potential to create large changes in the benthic system, such as local changes epibenthic community composition, dominant taxa, community diversity and benthic biomass hotspots. Future research focusing on the biological interactions that influence epibenthic communities, the supply and success of new recruits to the benthos and the temporal stability of epibenthic communities would help complete our understanding of the spatial and temporal variability of Arctic epibenthic communities and make solid predictions of future scenarios.
    • Alaskan king crab: Bering Sea distributions and a parasitic castrator

      Zacher, Leah Sloan; Hardy, Sarah; Eckert, Ginny; Kruse, Gordon; Horstmann, Lara; Morado, Frank (2018-05)
      King crab play an integral role in both marine ecosystems and fisheries; they influence benthic community structure through predation, help regulate trophic cascades, and are an important food source for large fishes, marine mammals, and humans. To sustainably manage king crab fisheries in a changing climate, it is essential to have a thorough understanding of king crab biology and behavior, as well as knowledge on how they utilize and interact with other components of the ecosystem. I investigated factors important to king crab sustainability and management, including distribution patterns and a parasitic castrator. Rhizocephalan barnacles in the genus Briarosaccus parasitize and castrate king crab hosts, thereby preventing host reproduction and potentially altering host abundance. In Alaska, prevalence is generally low (< 1% infection rate), yet higher prevalence has occurred in localized bays and fjords. I studied the larval biology of Briarosaccus regalis infecting Paralithodes camtschaticus (red king crab) to better understand how environmental factors in Alaska may influence prevalence. Maximum larval B. regalis survival occurred from 4 to 12°C and at salinities between 25 and 34. Given these parameters, current conditions in the Gulf of Alaska and Bering Sea appear favorable for high survival of B. regalis larvae. Rhizocephalans not only castrate their hosts, but they cause changes in host morphology, physiology, and behavior. I used an untargeted metabolomics (liquid chromatography mass spectrometry) approach to compare the metabolite profiles (e.g., signaling molecules, hormones) of P. camtschaticus and Lithodes aequispinus (golden king crab) with and without rhizocephalan infections. Hundreds of putative metabolites were identified, yet few differed with crab sex and no metabolites could differentiate infected from healthy crab (regardless of crab sex). There were large variations in the crab metabolome with collection year and location, perhaps associated with environmental variability, which likely masked differences between sex and infection status. Summer distributions of Bristol Bay red king crab are well documented from surveys, but their distribution patterns at other times of year are poorly understood. Daily fishing logs, kept by vessel skippers in the red king crab fleet since 2005, contain detailed information on the spatial distribution of fishery effort and catch of legal sized male crab during the autumn crab fishery. However, data contained in these hand-written logbooks have not been readily accessible. I digitized daily fishing logs from 2005 to 2016 and used spatial information to infer geographic distributions. These distributions were compared across temperature regimes. In warm years (2005, 2014 - 2016) crab aggregated in the center of Bristol Bay, while in cold years (2007 - 2013) they were closer to the Alaska Peninsula. There are regions in Bristol Bay that are closed to the bottom trawl fisheries to protect red king crab; these results have management implications because they show the extent to which crab use these closure areas in the autumn, shortly before the winter trawl fisheries begin. As temperatures continue to shift in the Bering Sea, it will be important to continue monitoring crab distributions outside the summer survey period. Overall, these studies should help guide the placement of trawl closure areas, predict crab movement with temperature changes, understand the larval biology of B. regalis and what that could mean with climate change, and lead to a better understanding of the physiology of Briarosaccus infection.
    • Alternative sampling and estimation methods for multispecies trawl surveys

      Dressel, Sherri Christine (2004-05)
      Multispecies demersal trawl surveys are used in the United States and internationally to estimate the relative abundance of commercial and non-commercial fish species. Their usefulness for estimating species' abundance is often limited by the variance associated with estimates. This study implemented and evaluated alternative sampling and estimation methods, with the goal to incorporate additional sources of information for increased precision of individual species' estimates from multispecies trawl surveys. First, habitat characteristics and past spatial distributions of four flatfish species' density were incorporated into a multispecies trawl survey design conducted in Kalsin and Middle Bays, Kodiak Island, Alaska. Stratification by depth and percent sand produced estimates of relative abundance with lower CV s than those from unstratified sampling. Additional decreases in relative precision were generally not achieved by estimating the relative abundance of multiple species from regions of species-specific suboptimal habitat. Second, a poststratification technique was used to incorporate species-specific habitat characteristics and previous distributions of species' density into the estimation of species' abundance from the Kalsin and Middle Bays' trawl survey. Poststratification by habitat gave estimates with lower variance and/or less design-bias than an unstratified estimator for all species in all years. Poststratification by habitat and fish density produced estimates with the least design-bias for all species in all years and the lowest variance when stratum sample sizes were sufficient. Third, mixed model linear regression (MMLR), empirical Bayes (EB) and hierarchical Bayes (HB) estimation methods were used to incorporate historical trends of yellowfin sole, Limanda aspera biomass from the eastern Bering Sea trawl survey into annual biomass estimates. Using MMLR, EB, and HB methods resulted in biomass estimates that were less anomalous than survey estimates with respect to a linear regression trend. Estimates for all three methods had lower CV s than surveys in most years. The results of this thesis suggest that incorporating additional information into survey design and estimation can decrease the variability of survey estimates and/or correct for possible bias. Methods that can incorporate additional information, therefore, have the potential to improve survey assessments for management use.
    • Analysis and comparison of age-structured assessment models for two Pacific herring populations

      Hulson, Peter-John F.; Quinn, Terrance J. II; Norcross, Brenda L.; Marty, Gary D. (2007-12)
      Substantial research has been devoted to identify causes for decline the of Prince William Sound (PWS) Pacific herring in the early 1990's because of the proximity to the 1989 Exxon Valdez oil spill (EVOS). A potential source for decline has been identified with the isolation of disease in the PWS population. There have been limited investigations of PWS Pacific herring population dynamics related to other stocks in the Gulf of Alaska. The objective of this thesis was to compare observations and age-structured assessment (ASA) model results between PWS and Sitka Sound Pacific herring. Data conflicts were evaluated in the PWS ASA model and indicate that hypotheses about natural mortality in the four years subsequent to EVOS depend on the type and weighting of population indices. In Sitka, the ASA model was used to show that time-dependent natural mortality can be estimated. Comparison between PWS and Sitka indicated that age structure and recruitment have been comparable, but abundance indices and weight-at-age data have not been similar after 1993. The differences identified in this thesis between PWS and Sitka imply uniqueness in natural mortality and condition within each Pacific herring population.
    • 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.
    • Application of molecular markers to mixed-stock analysis of Yukon River fall chum salmon

      Flannery, Blair G. (2004-05)
      Country of origin provides the basis for allocating harvests of Yukon River chum salmon. The genetic divergence among Yukon River chum salmon populations adjacent to the international border as revealed by allozyme and micro satellite variation is insufficient to determine the country of origin of returning fish using mixed-stock analysis (MSA). Consequently, we investigated the resolution provided by alternative genetic markers in an attempt to detect levels of divergence that would be sufficient for MSA. We analyzed 10 Yukon River chum salmon populations for variation at 30 variable amplified fragment length polymorphism (AFLP) loci and for mitochondrial DNA (mtDNA) restriction site variation. We assessed these markers for their utility in MSA and, for mtDNA, phylogeographic analysis. The AFLP results show that MSA was most successful when mixtures were allocated to regions. The AFLP data were able to provide improved country of origin MSA estimates for the border populations with a 6.5% improvement for the Canadian populations over micro satellite analysis. No divergence in mtDNA haplotype frequency distributions was detected (P>0.05) within the Yukon River. Lack of mtDNA divergence likely resulted from a Pleistocene bottleneck that led to panmixia of the mtDNA genome.
    • Aquatic community responses to stream restoration: effects of wood and salmon analog additions

      Martin, Aaron Eugene (2007-08)
      Many aquatic ecosystems in the Pacific Northwest have been impacted by land use activities. Often these impacts have resulted in deleterious effects that directly or indirectly limited the capacity of habitat to produce fish. Habitat restoration potentially increases the quantity and quality of resources available to the aquatic communities within these impaired systems, thus increasing biotic integrity and fish production. In this study, responses of aquatic communities exposed to woody debris bundle and salmon analog additions were measured in the year following creation of off-channel, fish habitat in southcentral Alaska. Biofilm, invertebrates and juvenile coho salmon, Oncorhynchus kisutch, were sampled in four treatment types (control, wood, analog, and analog+wood). Biofilm significantly increased in analog enriched treatments. No treatment effects were detected in benthic invertebrate responses, however, treatment differences were detected in coho diets. Coho density and standing stock were significantly higher in the wood treatment, and coho in the control treatment showed signs of density-dependent limitations. Condition for fish was highest in the analog enriched treatments after treatment additions. These results suggest salmon analog and woody debris bundle additions may be viable short-term restoration tools, providing a boost in food and shelter for aquatic communities in habitats undergoing restoration.
    • Arctic circulation pathways, heat and freshwater fluxes: results from numerical model integrations

      Whitefield, Jonathan David; Winsor, Peter; Hoperoft, Russ; Weingartner, Thomas (2016-05)
      With increasing attention on Arctic warming and consequent reductions of sea ice, many studies are focusing on the “gateways” to the Arctic Ocean - the regions where water enters and exits the Arctic Basin. The Chukchi Sea is the only pathway for Pacific water to enter the Arctic Ocean. While the Chukchi naturally undergoes large seasonal and interannual variability, currently it is also undergoing larger and rapid changes, which include transition to a longer icefree season. Numerical models are often used to explore this region, due to observational restrictions associated with sea-ice. Most past and current models tend to represent riverine inputs in a non-realistic manner; adding freshwater on or past the shelf break, not accounting for seasonality of the river discharge, and omitting riverine heat content. In addition, in many of these models, buoyant coastal currents are not well resolved. Here, I present a new river discharge and river temperature data set (at 1/6° resolution). Employing this new data set within a high-resolution pan-Arctic model, freshwater content on the Arctic shelves increased by ~3600 km3 and summer heat fluxes increased by 8 TW (compared to previous models), resulting in a reduction of the Arctic-wide September sea ice extent by up to ~10%. With both the improved riverine forcing included in the model calculations, and the model’s ability to resolve the Alaskan Coastal Current, the model suggests an additional 0.25 Sv of flow to the long-term Bering Strait volume transport. This translates to a 64% increase in the heat transport and a 32% increase in freshwater transport (including 4% from sea ice). The model also resolves individual transport pathways in the Chukchi Sea, including that of Bering Sea Water, which could influence species composition and distribution in the eastern Chukchi Sea. Increased computing power and improved observational tools lead to more accurate reproductions of coastal currents and riverine influences in these numerical models. Greater understanding of this near-shore region and its influences is vital to further interpret larger connections between terrestrial and marine ecosystems, as well as Arctic-wide and global oceanic changes.