• Migration patterns and energetics of adult chinook salmon Oncorhynchus tshawystcha in Alaska rivers

      Neuneker, Kristin R.; Falke, Jeffrey; Seitz, Andrew; Nichols, Jeff; Cox, M. Keith (2017-12)
      Adult Chinook Salmon Oncorhynchus tshawytscha undertake extensive and energetically costly migrations between food resources in the ocean and their freshwater spawning habitats, requiring them to adapt behavioral and physiological traits that allow them to successfully reach their spawning streams and reproduce. Such adaptations may be shaped by physical factors in the environment and individual- and population-specific biological characteristics. Chinook Salmon in North America are important resources for both United States and Canadian stakeholders, but relatively little is known about their freshwater migration patterns and energetic status in many rivers across their range. This research explored variation in migration timing and migration rates of Chinook Salmon in two Southeast Alaska transboundary rivers (Taku River, Stikine River), examined energetic status at multiple sampling locations in Alaska, and created and tested a predictive model for energetic status using bioelectrical impedance analysis (BIA). Migration timing was earlier for fish that spawned in more distant tributaries in both transboundary systems and the Taku River was earlier compared to the Stikine River. Migration rates decreased during periods of high flows, were slower for fish in the Taku River, and were slower in both systems in 2016 compared to 2015. Migration rates were faster for fish with spawning sites farther upstream when compared to those that spawned closer to the river mouth, but these rates decreased over time as fish swam farther upriver. Chinook Salmon (N = 129) sampled for energetic status at the beginning of their freshwater spawning migration had higher total percent lipid than those near the spawning grounds (ANOVA: F = 202.1, df = 3, P < 0.001), and total percent lipid and water were precisely predicted based on BIA measurements (R² = 0.82, RMSE = 5.33; R² = 0.78, RMSE = 2.43 respectively). The BIA model was tested to determine if it could be generalized between similar species, but this was found to be less precise than species-specific models. The BIA measurement technique was also easily implemented into an existing study on a remote Chinook Salmon population. Given threats from climate change and mining activities, this information will be useful for fisheries researchers as a benchmark for understanding migration behaviors in these Chinook Salmon populations, and indicates that integration of BIA into population monitoring may be a useful tool for creating management practices targeted at facilitating successful migration behaviors and increasing or maintaining energetic status for these fish.
    • Migratory patterns of Yukon River inconnu as determined with otolith microchemistry and radio telemetry

      Brown, Randy J. (2000-05)
      Migratory patterns of Yukon River inconnu Stenodus leucichthys were evaluated using otolith aging and microchemical techniques and radio telemetry. Research was conducted each fall between 1997 and 1999, on inconnu captured at a study site 1,200 river km from the Bering Sea. Biological data were collected to establish maturity and spawning condition. Sagital otoliths were analyzed optically to determine age distribution, and microchemically to determine amphidromy. Inconnu were tagged with radio transmitters and located in upstream spawning destinations. Inconnu captured at the study site were uniformly large, mature fish preparing to spawn. Age estimates ranged from 7 to 28 years. Microchemical analyses suggested that the population was amphidromous rather than freshwater only. Preliminary testing of radio transmitter attachment methods showed that the internal method (pushed through the esophagus into the stomach) was superior to the external method (attached behind the dorsal fin) for use with migrating inconnu. Most radio-tagged inconnu were located during their spawning time in a common region of the Yukon River. Inconnu captured at the study site each fall were mature fish engaged in a spawning migration that originated in the lower Yukon River or associated estuary regions, and continued towards a common spawning destination in the Yukon River, approximately 1,700 river km from the sea.
    • Milk fatty acid composition of perinatal and foraging Steller sea lions: examination from pup stomachs

      Miller, Carlene Nicole; Polasek, Lori K.; Oliveira, Alexandra C. M.; Horstmann-Dehn, Larissa A. (2014-08)
      To investigate the relationship of milk fatty acid composition between perinatal and foraging Steller sea lions and within each maternal state (i.e., perinatal or foraging), milk samples were collected in 2010 and 2011 via gastric intubation from Steller sea lion pups on a small rookery in the central Gulf of Alaska. Subsamples of initial milk samples were taken over four hours post-collection to examine changes of fatty acids within milk over time. Maternal states of lactating females of sampled pups were determined via remotely operated video cameras on the rookery. Fatty acid composition within milk, collected from Steller sea lion pup stomachs, did not change over the four hour post-collection period, and thus milk fatty acids were not modified within milk over time. Milk fatty acid composition between Steller sea lion maternal states was different, and thus can be utilized to distinguish between perinatal and foraging Steller sea lions of the same geographic region. In the absence of direct observations, this study demonstrated the use of a viable method to determine maternal state. Milk fatty acid composition remained relatively constant within perinatal Steller sea lions, suggesting steady mobilization of fatty acids from blubber to milk, and within foraging Steller sea lions, implying females forage in the vicinity of the rookery and on similar prey species. Differences in milk fatty acid composition between maternal states, including differences in the relative percentages of polyunsaturated fatty acids, may have implications for growth and development of offspring. For lactating Steller sea lions, foraging after the perinatal period is important for continued delivery of fatty acids needed by young pups.
    • Mitochondrial DNA haplotype genealogies and population histories in the late Pleistocene: contrasts of pink salmon broodyears

      Churikov, Dmitri Yurievich (2000-12)
      Seven segments of mtDNA, comprising 97% of the mitochondrial genome, were PCR-amplified and examined for restriction site variation using 13 restriction endonucleases in three Oncorhynchus species: pink (O. gorbuscha), chum (O. keta), and sockeye (O. nerka) salmon. Multiple haplotypes, but shallow mtDNA trees were observed for each species. 'Star-like' structures indicating historical population explosions were observed in haplotype genealogies. Given reasonable rates of mtDNA sequence evolution, this may reflect recolonization of vast areas in Alaska after the last (Wisconsinian) or preceding (Illinoian) glacier retreats. The phylogeographic survey of 18 Alaskan and Eastern Asian pink salmon populations revealed a distinct phylogeographic break between Alaska and Asia in even-year, but continuous distributions of the mtDNA lineages throughout the same range in the odd-year broodline. A nested cladistic analysis of geographical distances indicates that spatial distribution of mtDNA lineages in both broodlines resulted from interplay between historical range expansions and isolation by distance.
    • Molecules to marinescapes: the characterization of microbial life in the Arctic Ocean

      Hassett, Brandon T.; Gradinger, Rolf; Collins, R. Eric; Leigh, Mary Beth; McBeath, Jenifer; Lopez, J. Andres (2016-05)
      Microbes are the base of all marine food webs and comprise >90% of all living biomass in the world’s oceans. Microbial life and functioning in high-latitude seas is characterized by the predominance of unknown species that encode uncharacterized genes, replenish nutrients, and modulate ecosystem health by interfacing with disease processes. This research elucidates eukaryotic microbial diversity and functionality in Arctic and sub-Arctic marine environments by describing the culturable and genetic diversity of eukaryotic microbes and the life histories of marine fungi belonging to the Chytridiomycota. This work includes the description of two new mesomycetozoean species, the assembled and annotated genome of Sphaeroforma sirkka, the first description of a cryptic carbon cycle (the mycoloop) mediated by fungi from any marine environment, and the description of large-scale eukaryotic microbial diversity patterns driven by temperature and latitude in the eastern Bering Sea. These results help establish a valuable baseline of microbial diversity in high latitude seas.
    • Monitoring stress hormones in rehabilitated and captive otariids

      Petrauskas, Lisa (2005-08)
      Cortisol and corticosterone are the primary mammalian stress hormones released in response to a perceived stressor. Cortisol is rapidly metabolized in the blood, while corticosterone is the dominant product in fecal material. Radioimmunoassay procedures to measure fecal corticosterone and serum cortisol in California sea lions were validated, and adrenal response to surgical and non-surgical procedures was assessed. Other objectives included seasonal and behavioral variability in fecal corticosterone concentrations in captive Steller sea lions, as well as adrenal response to various stressors of a rehabilitated Steller sea lion. There was a significant (P ... 0.05) adrenal response for rehabilitated California sea lions that underwent minor invasive surgical procedures. The small sample size in this study allowed the identification of a correlation of season and behavior in three captive Steller sea lions. This study found that peak fecal corticosterone values reflected responses to acute stressors during rehabilitation for a Steller sea lion pup. Overall, fecal corticosterone was an adequate tool for monitoring stress non-invasive1y in California and Steller sea lions. In turn, the results indicate that California sea lions may be a suitable surrogate species to study the adrenal response to more invasive procedures that may be used in Steller sea lions.
    • Movement and habitat utilization by golden king crab Lithodes aequispinus benedict 1895 in southeastern Alaska

      Hoyt, Zachary N. (2003-12)
      Movements and habitat use of golden king crabs (GKC), Lithodes aequispinus, were investigated with a manned submersible and ultrasonic telemetry in Frederick Sound, Alaska. Crabs were collected with commercial crab pots and ultrasonic transmitters were attached to the carapaces of 26 crabs; movements and depth distribution of male and female crabs were monitored bi- monthly from May 11, 2000 to April 12, 2001. Crabs preferred steep, complex habitat with hard substrate; few were on flat, soft substrate. Male and female GKC were not segregated by depth in mid-May. Seventeen pairs of courting crabs were observed during dives; 14 of these pairs were associated with either intermittent or continuous boulder fields and 3 with wall substrates. Crabs did not have seasonal site fidelity. Crabs had seasonal changes in depth distribution, moving to deeper water during late fall and winter and returning to shallower depths during spring. Crabs moved as far as 39 km over one year. No evidence of spatial fidelity was observed; golden king crabs may be moving greater distances or site fidelity maybe on a longer temporal scale than our study, or golden king crabs may be nomadic in nature.
    • Movement of the giant red sea cucumber Parastichopus californicus in Southeastern Alaska

      Cieciel, Kristin (2004-08)
      This thesis provides information on sea cucumber movement that could inform management of the growing fishery for the sea cucumber, Parastichopus californicus, in Southeast Alaska. Daily movement of individual P. californicus was quantified at six sites to assess spatial variation in movement, at three-month intervals over one year at one site to assess seasonal changes in movement, and densities were measured monthly at three depths over one year. Movements varied among seasons and sites ranging from 0 to 34.5 m·24 h⁻¹, and were highest in summer (mean ± SE = 4.6 ± 0.5 m) and lowest in fall (mean ± SE = 1.9 ± 0.3 m). Densities were highest in spring and summer and lowest in fall and winter. Recently tagged animals move, on average, 2 m more than animals tagged 72 h earlier, indicating that movement is best assessed 48 h after tagging. Stock assessments should be conducted in spring and summer to coincide with increased animal densities, with the fishery occurring in fall and winter to provide a possible refuge for a portion of the population. Overall, P. californicus demonstrate limited adult movement, indicating that populations are geographically limited with little possibility of animal migration or repopulation of adults in harvested areas.
    • A multi-proxy approach to determine paleoecological change of mangroves, during the holocene, in Belize, Central America

      Monacci, Natalie Marie (2007-12)
      This thesis presents multiple analyses of mangrove peat cores from Spanish Lookout Cay (BT - 79) and from along the banks of the Sibun River (SR-63), Belize to examine ecosystem responses to environmental change during the Holocene. Radiocarbon measurements showed these sites were colonized by mangroves ~8,000 cal. yrs BP and have decreased sedimentation rates from ~6,000 to ~1,000 cal. yrs BP, which is attributed to a decrease in sea-level inundation. Core SR-63 has a change in lithology from primarily mangrove peat to fluvial material at 2,500 cal. yrs BP, which is attributed to erosion inputs of the drainage basin. Changes in the pollen assemblage, such greater input from non-mangrove pollen, are coeval with changes in sedimentation rates at both sites. Subfossil mangrove leaves, from core BT-79, are used for stable isotope ([delta]¹⁵N, [delta]¹³C, and [delta]¹⁸O) analyses to illustrate past physiology and seawater inundation. The composition of organic material in core SR-63 changes from autochthonous to allochthonous sources, which is coeval with the change in lithology. A decrease in the rate of sea-level rise is assumed to be the cause of the significant changes seen in these mangroves, which counters existing sea-level curves.
    • Multi-scale movement of demersal fishes in Alaska

      Nielsen, Julie K.; Seitz, Andrew C.; Loher, Timothy; McDermott, Susanne F.; Mueter, Franz J.; Adkison, Milo D. (2019-05)
      Information on the movement of migratory demersal fishes such as Pacific halibut, Pacific cod, and sablefish is needed for management of these valuable fisheries in Alaska, yet available methods such as conventional tagging are too coarse to provide detailed information on migration characteristics. In this dissertation, I present methods for characterizing seasonal and annual demersal fish movement at multiple scales in space and time using electronic archival and acoustic tags. In Chapter 1, acoustic telemetry and the Net Squared Displacement statistic were used to identify and characterize small-scale movement of adult female Pacific halibut during summer foraging in a Marine Protected Area (MPA). The dominant movement pattern was home range behavior at spatial scales of less than 1 km, but a more dispersive behavioral state was also observed. In Chapter 2, Pop-up Satellite Archival Tags (PSATs) and acoustic tags were deployed on adult female Pacific halibut to determine annual movement patterns relative to MPA boundaries. Based on observations of summer home range behavior, high rates of year-round MPA residency, migration timing that largely coincided with winter commercial fisheries closures, and the demonstrated ability of migratory fish to return to previously occupied summer foraging areas, the MPA is likely to be effective for protecting both resident and migrant Pacific halibut brood stock year-round. In Chapter 3, I adapted a Hidden Markov Model (HMM) originally developed for geolocation of Atlantic cod in the North Sea for use on demersal fishes in Alaska, where maximum daily depth is the most informative and reliable geolocation variable. Because depth is considerably more heterogeneous in many regions of Alaska compared to the North Sea, I used simulated trajectories to determine that the degree of bathymetry heterogeneity affected model performance for different combinations of likelihood specification methods and model grid sizes. In Chapter 4, I added a new geolocation variable, geomagnetic data, to the HMM in a small-scale case study. The results suggest that the addition of geomagnetic data could increase model performance over depth alone, but more research is needed to continue validation of the method over larger areas in Alaska. In general, the HMM is a flexible tool for characterizing movement at multiple spatial scales and its use is likely to enrich our knowledge about migratory demersal fish movement in Alaska. The methods developed in this dissertation can provide valuable insights into demersal fish spatial dynamics that will benefit fisheries management activities such as stock delineation, stock assessment, and design of space-time closures.
    • Multiple stable isotopic analyses ([delta]¹³C, [delta]¹⁵N, [delta]¹⁸O, and [delta]D) of the Boulder Patch, a high arctic kelp community: trophic and temporal perspectives

      Debenham, Casey William Jones (2005-12)
      The Boulder Patch, a high Arctic kelp community, is a rarity in the Alaskan Beaufort Sea. Considered a biodiversity oasis, this area provides habitat for many organisms. Trophic relationships, spatial patterns, and isotopic changes over time were examined within the Boulder Patch using stable carbon and nitrogen isotopes. 394 samples, representing over 55 species were analyzed. Isotope values showed considerable variability in the food web base, particularly for the kelp Laminaria solidungula. Isotopic values for most animals fit their known feeding strategies. Little spatial variation was observed in isotope values, however temporal differences were found in L. solidungula isotope values between 2002 and 2004, and between archived samples collected during the 1980's. To better understand patterns in stable oxygen and hydrogen isotopes, values were assessed and applied in an ecological context. Sixty-four samples were analyzed, encompassing 29 species. Results indicated distinct differences between primary producers and animals, offering insights into a possible application of [delta]¹⁸O and [delta]D in ecological studies. By defining trophic structure and elucidating feeding strategies of organisms, this study enhanced the biological knowledge in the Boulder Patch, providing ecological information on a high arctic kelp community.
    • Multispecies Age-Structured Assessment Modeling As A Tool Of Fisheries Management In The Gulf Of Alaska

      Van Kirk, Kray F.; Quinn, Terrance J. II; Collie, Jeremy; Criddle, Keith; Kruse, Gordon; Mueter, Franz (2012)
      A multispecies age-structured assessment model (MSASA) for the Gulf of Alaska (GOA) is developed to examine the effects of integrating predation mortality into stock assessment efforts. Age-specific predation mortality is modeled as a flexible function of predator and prey abundances, constructed from species-preference and size-preference parameters and fitted to stomach-content data. Modeled species include arrowtooth flounder ( Atheresthes stomias), Pacific cod (Gadus macrocephalus), walleye pollock (Theragra chalcogramma), Pacific halibut (Hippoglossus stenolepis) and Steller sea lion ( Eumatopias jubatus). Recruitment, residual natural mortality, full-recruitment fishing mortality, and fishery/survey selectivities are estimated for pollock, cod, and flounder; abundances for apex predators sea lions and halibut are input. Estimated trophic structures and predation links show significant changes as a result of the inclusion of higher trophic level predators, and model results are highly sensitive to assumptions regarding sea lion diet. Simulation exercises suggest that model performance degrades more due to model misspecification and data scarcity than assumptions regarding data weighting and variance. Estimates of predation mortality work in tandem with survey data, constraining predation estimates in the face of incomplete diet data and potentially improving estimates of cohort structure. Exploration of predator functional responses (PFR) shows the default GOA MSASA Holling Type II PFR to be more flexible than initially thought, and that explicitly modeling predator competition for the same prey can improve model fit to stomach-content data. Median parameter estimates and their respective variances from the fitted MSASA model are used to construct management strategy simulations. Reducing fishing pressure on pollock during periods of high predator biomass is less effective at preserving pollock stocks than raising fishing pressure on flounder, and multispecies harvest control rules and biological reference points are shown to be more conservative and more efficient at preserving stock abundance while maintaining catch levels than their single-species counterparts.
    • Natural abundance of nitrogen(15) in a subarctic lake and biogeochemical implications to nitrogen cycling

      Gu, Binhe (1993)
      Stable isotope ratios of nitrogen ($\delta\sp{15}$N) were employed to track the origin and fate of nitrogen in a subarctic lake, Alaska. The annual planktonic nitrogen cycle was dominated by N$\sb2$ fixation in spring and NH$\sb4\sp+$ assimilation in summer. In winter, microbial nitrification was the major sink for NH$\sb4\sp+$ and denitrification was accounted for most of the loss of NO$\sb3\sp-.$ The small isotope fractionation in nitrification is proposed as a result of substrate (NH$\sb4\sp+)$ limitation. The temporal and spatial homogeneity of the $\delta\sp{15}$N of dissolved organic nitrogen may be related to its large pool size and refractory nature. A stable isotope mass balance suggests that the winter phytoplankton was only composed of 10 to 20% of the suspended organic matter in water column due to low primary productivity during the ice cover period. A close correlation between $\delta\sp{15}$N of phytoplankton and $\delta\sp{15}$N of dissolved pools indicates that NH$\sb4\sp+$ was the predominant nitrogen source for non-N$\sb2$-fixing algae. The similarity of $\delta\sp{15}$N between a spring blue-green bloom and N$\sb2$ suggests an atmospheric origin for nitrogen. A mixing model estimated that the blue-green algal bloom derived approximately 70% of its nitrogen from molecular nitrogen. This fixed nitrogen was further transferred to higher trophic levels via the food chain and to other primary producers following mineralization. The $\delta\sp{15}$N of aquatic macrophytes indicates that non-rooted species obtained their nitrogen from the water column while rooted species obtained their nitrogen largely from the sediment. Evidence from dual isotope tracers ($\delta\sp{15}$N and $\delta\sp{13}$C) suggests that the zooplankton were supported by phytoplankton throughout the growing season despite an apparent abundance of detritus in the water column. Benthic fauna relied on either phytoplankton detritus or other organic matter in the sediment. The $\delta\sp{15}$N data exhibit only two to three trophic levels in both planktonic and the benthic communities in Smith Lake.
    • Navigating the predator gauntlet: consumption of hatchery- and wild-born juvenile chum salmon (Oncorhynchus keta) by common nearshore marine fishes in Southeast Alaska

      Duncan, Douglas H.; Beaudreau, Anne H.; McPhee, Megan V.; Westley, Peter A. H. (2018-12)
      Juvenile chum salmon (Oncorhynchus keta) undergo extensive mortality at marine entry, a period which is believed to be a potential population bottleneck. Although this early mortality has been consistently observed, our understanding of the mechanisms responsible is limited. Furthermore, the implications of large-scale salmon hatchery releases for the ecology of juvenile chum salmon and their consumers is another important knowledge gap. To better understand the predation responses of abundant consumers to hatchery- and wild-born juvenile chum salmon, we examined the diets of Pacific staghorn sculpin (Leptocottus armatus) and Dolly Varden (Salvelinus malma) near Juneau, Alaska, in 2016 and 2017. Chum salmon composed 4.5% and 19.6% of the diets of staghorn sculpin and Dolly Varden by weight, respectively, and 88% of chum salmon individuals consumed were of hatchery origin. Chum salmon prey were shorter than average when compared to chum salmon concurrently collected by beach seine and hatchery releases of chum salmon. Regression analyses indicated that occurrence of juvenile chum salmon in diets varied primarily by date and site. Predation generally occurred more frequently at sites closer to hatchery release areas. The quantity of chum salmon in staghorn sculpin stomachs was related to predator length, chum salmon catch-per-unit-effort (CPUE), and the proportion of hatchery fish present; however, date was the only important predictor explaining quantity of chum salmon in Dolly Varden stomachs. To translate diet data into consumption rate, we experimentally determined gastric evacuation rate for staghorn sculpin and implemented a field-based consumption model. Average daily consumption of chum salmon was low relative to all other prey groups. Estimates of average seasonal consumption of juvenile chum salmon by staghorn sculpins suggest that predator populations would have to be implausibly large to consume even 1% of local hatchery chum salmon production. Together, these results yield new insights into the interactions between the predators of wild-born and hatchery-born salmon during the critical stage of marine entry.
    • Nitrogen utilization during spring phytoplankton bloom development in the southeast Bering Sea

      Sambrotto, Raymond Nicholas (1983-12)
      Interactions between a high latitude, continental shelf, spring phytoplankton bloom and water column physics and chemistry were studied using measured rates of nitrogen uptake. Peak bloom conditions commenced when the mixed layer shallowed and minimized respirational losses. Integrative light-mixing growth models were accurate during early bloom stages. An advection-diffusion model associated peak bloom nitrate uptake with pycnocline mixing rates of 2.1 m d * in an 18 m mixed layer. The accumulation of surface buoyancy was a reliable index of peak bloom temporal and spatial "patchiness" since mixing rates influenced both respirational losses and nutrient supply. Maximum nitrogen specific uptake rates (h r .- 1 ), unlike those of carbon, coincided with peak bloom conditions. Although species com positions among peak bloom periods were similar, particulate C/N ratios were not. Apparently, both intercellular factors and prevailing mixing conditions influence specific uptake rates and cell composition. A large proportion of new (nitrate) to total productivity was associated with the dominance of the early bloom forming diatoms in the mixed layer. In the absence of these net plankton the residual nanoplankton dominated community exhibited a greater dependence on regenerated nitrogen. Nitrate uptake averaged 700 mg-at m during the spring bloom and 1 g-at m-2 year-1 The yearly f factor was 0.40. Nitrogen uptake based carbon productivity was 188 g C m -2 year -1 A mass balance of the inorganic carbon system indicates that nitrate uptake alone cannot account for all the carbon leaving the surface layer. The correspondence between 1SN0~ uptake measurements and nitrate decreases suggests the diffusion of slope water into the middle shelf is slow. Large scale meteorological patterns may be responsible for the inter annual variability observed in production. Frequent May storm activity prolonged peak bloom periods, while calm conditions promoted extensive Chijl layers. The passage of atmospheric low pressure system s was also associated with the cross shelf "pumping" of water masses.
    • Non-linear dynamics of marine ecosystem models

      Gibson, Georgina Anne (2004-12)
      Despite a rapid trend towards more realistic Nutrient-Phytoplankton-Zooplankton (NPZ) models, in which zooplankton are presented with multiple nutritional resources, investigations into the fundamental dynamics of these newer models have been limited. The objective of this dissertation was to explore the dynamical behavior of such NPZ models parameterized for the coastal Gulf of Alaska. With alternative stationary forcing regimes and zooplankton grazing functions, the dynamics of one-dimensional NPZ models were investigated for a range of specific predation rates (h) and predation exponents (q), which together define the form of the predation (model closure) function. Oscillations in state variables are shown to be an intrinsic property of the NPZ models, not dependent on variable seasonal forcing for their existence. Increasing mixed layer diffusivity or reducing mixed layer depth increased model excitability; it is hypothesized that this is due to the resultant increase in flux of utilizable nutrient. Model behavior was also strongly influenced by the form of both the grazing and predation functions. For all of the grazing functions implemented, Hopf bifurcations, where the form of the solution transitioned between steady equilibrium and periodic limit cycles, persisted across the q-h parameter space. Regardless of the values of h and q, with some forms of the grazing function steady equilibrium solutions that simultaneously comprised non-zero concentrations for all model components could not be found. The inclusion of sinking detritus in the model had important implications for the composition and excitability of model solutions, generally increasing the region of q-h space for which oscillatory solutions were found. Therefore, in order to correctly simulate the depth-explicit concentrations of model components, or to have an accurate understanding of the potential excitability of the system, inclusion of this component is valuable. This dissertation highlights the importance of understanding the potential impact that choice of functional response may have on the intrinsic oscillatory nature of a model prior to interpreting results from coupled bio-physical simulations. As we come to rely more on ecosystem models as a tool to interpret marine ecosystem functionality it will be important to improve our understanding of the non-linear behavior inherent in these models.
    • Nucleic Acid Ratios As An Index Of Growth And Nutritional Ecology In Pacific Cod (Gadus Macrocephalus), Walleye Pollock (Theragra Chalcogramma), And Pacific Herring (Clupea Pallasii )

      Sreenivasan, Ashwin; Smoker, William (2011)
      Pacific cod (Gadus macrocephalus), walleye pollock (Theragra chalcogramma), and Pacific herring (Clupea pallasii) are among the most ecologically and commercially important species in the North Pacific Ocean. In spite of their importance, little is known about larval and juvenile growth strategies in these fish. Since larval and juvenile fish growth may determine future growth, possibly affecting recruitment success, assessments of growth strategies might improve predictive growth models. Nucleic acid ratios (RNA/DNA) can have applications as a sensitive growth index in larval and juvenile Pacific cod, walleye pollock, and Pacific herring, and can potentially be used to determine growth responses and energetic assessments at the cellular level. Determining physiological growth responses in these fish after exposure to different temperatures and nutritional states can help in understanding growth strategies and condition. Nucleic acid ratios from white muscle of juvenile Pacific herring and whole-body Pacific cod and walleye pollock larvae were used as a cellular growth index to provide energetic assessments in these species. Growth responses were studied in these fish across a range of temperatures and nutritional states. Growth was compared between fed, starved/fed and terminally starved Pacific herring cultured at 6.5�C, 8.5�C, and 12.5�C. Relative to fed controls, starved/fed fish showed similar RNA/DNA ratios and soluble protein concentration, but reduced mass. Nucleic acid ratios in starved/fed fish during the starvation phase, and in terminally starved fish, indicated incipient terminal starvation. Also, a seasonal variation of RNA/DNA, protein concentrations and total body lipid concentrations was seen in fed fish, reflecting changes in resource allocation. Early growth was compared in yolk-sac Pacific cod and walleye pollock larvae cultured at 5�C and 8�C, and in yolk-sac Pacific cod larvae cultured in two nutritional states (fed and starved). Growth responses in Pacific cod and walleye pollock larvae were affected by small differences in temperature. Exposure to the lower temperature resulted in higher RNA/DNA in both Pacific cod and walleye pollock larvae. Based on nucleic acid patterns with larval development, it was possible to identify distinct growth stanzas in Pacific cod larvae.
    • Numerical investigations of the hydrography, dynamics, and ice distributions of Chukchi Sea shelf

      Lu, Kofan; Danielson, Seth; Weingartner, Thomas; Hedstrom, Kate; Shimada, Koji; Winsor, Peter (2019-08)
      Warm, moderately salty Bering Sea Water (BSW) carried into the Chukchi Sea through Bering Strait provides an oceanic heat flux for melting sea ice comparable to that of the solar heat flux. Intrusions of BSW transport heat and nutrients via intrapycnocline eddies vertically beneath the sea ice and laterally across structural fronts near the ice edge, setting up hydrographic features important to ice edge communities and the seasonal evolution of the ice melt-back. However, the intrapycnocline eddy dynamics and associated hydrography near the fronts have not previously been well described or characterized. Three numerical models using the Regional Ocean Model System (ROMS) are integrated to systematically investigate the importance of the intrapycnocline eddy field and the factors that affect its dynamics. The models suggest that the heat transported by eddies depends on frontal stratification, which is influenced primarily by the Bering Strait inflow discharge and salinity. The eddy field is also indirectly modified by the sea surface height, which varies with strong winds. Two frontal zones near the ice edge are identified according to the model-derived hydrographic structures and eddy dynamics: the Shelf Water Transition Zone (SWTZ) and the Melt Water Transition Zone (MWTZ). Improved understanding of these frontal zones will benefit future research of the ice edge ecosystem. Our models show a noticeable effect of strong wind events on ice edge displacement and vertical transports, both of which may be important to primary production in the frontal zones. Changing winds associated with increasing sea surface temperatures could alter the manifestation of the processes highlighted in this study.
    • Numerical Method For Tsunami Calculation Using Full Navier -Stokes Equations And The Volume Of Fluid Method

      Horrillo, Juan J.; Kowalik, Zygmunt (2006)
      A two-dimensional numerical model was developed to study tsunami wave generation, propagation and runup. The model is based on solving the Navier-Stokes (NS) equations. The free-surface motion is tracked using the Volume of Fluid technique. The finite difference two-step projection method is used to solve NS equations and the forward time difference method to discretize the time derivative. A structured mesh is used to discretize the spatial domain. The model has been conceived as a versatile, efficient and practical numerical tool for tsunami computation, which could address a comprehensive understanding of tsunami physics with the ultimate aim of mitigating tsunami hazards. The prediction capability of tsunami generation, propagation and runup is improved by including more accurately the effects of vertical velocity/acceleration, dispersion and wave breaking. The model has the capability to represent complex curved boundaries within a Cartesian grid system and to deal with arbitrary transient-deformed moving boundaries. The numerical model was validated using laboratory experiments and analytical solutions. The model was used as a tool to determine the adequacy of the shallow water (SW) approximation in the application of tsunami simulations. Numerical results were compared with experimental data, analytical solutions and SW results in terms of the time-history free surface elevations and velocity. Reasonable agreements were observed based on the spatial and temporal distributions of the free surface and velocity.
    • Nutrient Dynamics In The Northern Gulf Of Alaska And Prince William Sound: 1998--2001

      Childers, Amy Ruehs; Whitledge, Terry (2005)
      The northern Gulf of Alaska (GOA) shelf is a productive coastal region that supports several commercially important fisheries. The mechanisms supporting such high levels of productivity over this shelf are not understood, however, since it is a downwelling-dominated shelf. In an effort to understand the mechanisms underlying such high biological productivity, nutrient distributions were determined 25 times throughout 1998, 1999, 2000, and 2001 from over the northern GOA shelf and in Prince William Sound (PWS). Deep water (>75 m) nitrate, silicate and phosphate concentrations were positively correlated with salinity indicating an offshore nutrient source. The average annual cycle was established, in which nitrate, silicate and phosphate responded seasonally to physical and biological processes. Ammonium concentrations were generally low and uniform (<1.2 muM) with occasional patches of higher concentrations. During each summer, an onshore flux of dense nutrient-rich bottom water onto the shelf was evident when the downwelling relaxed. This seasonal flux created nutrient reservoirs over the deeper shelf regions that were eventually mixed throughout the water column during the winter months. This annual evolution may be vital to the productivity of this shelf. A large degree of interannual variability was found during the study, which included El Nino (1998) and La Nina (1999) years. Spring phytoplankton biomass over the shelf was highest in 2000 when the upper waters were nutrient enriched and strongly stratified. The highest phytoplankton biomass was measured in May 1999 during the passage of a slope eddy, which demonstrated the potential of these phenomena to greatly enhance primary productivity. A large degree of spatial variability was also found, both cross-shelf and along-shelf. Hinchinbrook Canyon was found to consistently have high salinity, nutrient-enriched bottom waters suggesting it plays an important role in the transport of slope waters onto the shelf and probably into PWS. Along-shelf trends were found in the upper coastal waters in the winter and spring, with higher salinities, temperatures, and nutrient concentrations upstream of PWS. The nutrient dynamics were similar in PWS and over the shelf/slope in 2001; however, nutrient drawdown, followed by depletion, and the spring bloom appeared earlier and stronger in PWS.