• 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.
    • Arrowtooth flounder Atheresthes stomias diet and prey consumption near Kodiak Island, Alaska

      Knoth, Brian Anthony (2006-12)
      The arrowtooth flounder Atheresthes stomias (ATF) population in the Gulf of Alaska has increased dramatically over the past 25 years and the resulting ecosystem impacts are unclear. Arrowtooth flounder diet and prey consumption was studied to more accurately assess the predator-prey relationships of this key predator near Kodiak Island, Alaska. Temporal and ontogenetic diet trends were quantified from the analysis of 742 ATF stomachs sampled from annual bottom trawl surveys conducted in May and August from 2002 to 2004. Several significant dietary trends were found, most notably: 1) euphausiids decreased in dietary importance from May to August whereas the importance of capelin Mallotus villosus increased and 2) smaller ATF consumed more capelin and larger ATF consumed more walleye pollock Theragra chalcogramma and Pacific sand lance Ammodytes hexapterus. A bioenergetics model was used to estimate ATF prey consumption. Within the study area, the ATF population was dominated by large individuals ([great than or equal to] 50 cm total length) that accounted for> 75 % of the population's total prey biomass consumption. Arrowtooth flounder were significant predators and consumed an estimated 339 t of fish prey including Pacific sand lance and walleye pollock and 222 t of invertebrate prey such as euphausiids and shrimps.
    • Assessing a macroalgal foundation species: community variation with shifting algal assemblages

      Metzger, Jacob Ryan; Konar, Brenda; Edwards, Matthew; Beaudreau, Anne (2018-08)
      Foundation species provide critical food and habitat to their associated communities. Consequently, they are disproportionately important in shaping community structure, promoting greater biodiversity and increased species abundance. In the Aleutian archipelago, once extensive kelp forests are now relatively rare and highly fragmented. This is due to unregulated urchin grazing shifting the majority of nearshore rocky-reefs from kelp forests to either urchin barrens or "transition forests" - kelp forests devoid of understory algae. The algal communities within kelp forests, transition forests, and urchin barrens represent a stepwise loss in fleshy algal guilds, a regression from a full algal community, to having only canopy kelp, to areas largely denuded of all fleshy algae. This stepwise loss of algal guilds was used to test the designation of the resident canopy-forming kelp, Eualaria fistulosa, as a foundation species--a species that has strong, positive effects on communities where it occurs. Therefore, I assessed the impact that E. fistulosa's occurrence had on faunal community structure (in terms of species diversity, abundance and biomass, and percent bottom cover)and invertebrate size-structure. This study found that the presence of E. fistulosa does not correspond to strong differences in invertebrate size-structure or faunal community structure. However, in kelp forests where E. fistulosa exists in tandem with a variety of subcanopy macroalgae, faunal communities are more species rich, have significantly different community structures with notably higher abundance, biomass, and percent cover of filter feeding taxa, and support sea urchin populations containing significantly higher proportions of larger individuals. Consequently, this study stresses the context dependent role of foundation species and suggests their strong, positive effects on associated communities may change with perturbations to ecosystems. To that end, this study suggests that we may need to reconsider the designation of E. fistulosa as a foundation species following the extensive fragmentation and range restriction that has occurred throughout much of the Aleutian Archipelago.
    • Assessing juvenile sockeye salmon (Oncorhynchus nerka) energy densities and their habitat quality in the Chignik watershed, Alaska

      Finkle, Heather (2004-05)
      The Chignik watershed, on the southern side of the Alaska Peninsula, supports a large salmon fishery vital to the local economy. Recent morphological changes to the watershed generated concern regarding the sockeye salmon (Oncorhynchus nerka) stock that rears in Black Lake, at the head of the system. Studies of the Chignik watershed to date have not incorporated energy density data to explain the life history strategies of Chignik sockeye salmon. Re-estimated condition factor parameters improved our understanding of the length-weight relationships to fish health that isometric models described in Chignik sockeye salmon. Subsequent comparisons of age, length, weight, location, and temperature data to energy density indicated that Black Lake fish, which were all age 0 fish, were significantly affected by temperature and had energy densities greater than did fish from other areas of the watershed. Sockeye salmon captured in Chignik Lake, Chignik River, and Chignik Lagoon were only energetically different from one another based on age. Observed seasonal trends suggested juvenile sockeye salmon emigrate from Black Lake before the onset of winter due to forage and temperature limitations. A constant downstream migration occurred in the watershed during the summer, which suggested smoltification and osmoregulation processes in Chignik Lagoon fish.
    • Assessment and application of DNA metabarcoding for characterizing Arctic shorebird chick diets

      Gerik, Danielle Elizabeth; López, J. Andrés; Lanctot, Richard; Gurney, Kirsty; Wipfli, Mark (2018-12)
      Climate change in the Arctic is affecting the emergence timing of arthropods used as food by nesting shorebirds and their young. Characterizing the diets of shorebird young is a prerequisite to evaluate the potential for asynchrony to occur between the timing of arthropod emergence and when shorebird young hatch, an example of trophic mismatch. In this study, DNA metabarcoding was used to identify arthropod remains in feces collected from wild-caught Red Phalarope (Phalaropus fulicarius), Pectoral Sandpiper (Calidris melanotos), and Dunlin (Calidris alpina), young in Utqiaġvik, Alaska between 2014 and 2016. Arthropod specimens were collected at the field site to generate DNA reference sequences from potential prey items. The newly generated sequences in combination with publicly available sequences served as a reference set for species determinations. I assessed the ability of two mitochondrial markers (CO1 and 16s) to detect arthropods in the feces of captive pre-fledged young in controlled feeding experiments. After combining information from both markers, experimental prey taxa were detected in chick feces 82-100% of the time, except for Trichoptera which was never detected. I used the same strategy to characterize the diets of wild-caught shorebird young. The technique detected nearly all prey families documented in historical gut content analyses, as well as 17 novel families. Some of the novel prey diversity may be the result of detecting the prey of prey, known as secondary consumption. We observed that the diets of shorebird young shifted over the course of a summer. Changes in diet generally reflected arthropod composition in the environment estimated from collection of arthropods in pitfall traps. Evidence of diet flexibility by shorebird young suggests that chicks can shift their diets to take advantage of intra-seasonal changes in prey availability. Here, I provide an evaluation and application of DNA metabarcoding to characterize prey resource use by shorebird young for assessing the presence and impacts of trophic mismatch.
    • Assessment and prediction of electroshocked-induced injury in North American fishes

      Holliman, Farland Michael (2003-05)
      Electrofishing has served as an efficient method for scientific sampling of freshwater fishes since the mid-1900s, but it has become apparent since the 1990's that electroshock can cause fish injury. Electroshock-induced fish injury (damage to hard or soft tissues), which is primarily manifested as vertebral fracture or hemorrhage (broken blood vessels) along the backbone, can be a critical determinant of fish survival. The ability to predict factors influencing fish injury rate (the proportion of. injured fish in a sample) would be very useful to biologists. To test the null hypothesis of no effect of electrical waveform (W), voltage gradient (E), and fish size (S) on injury rate, I conducted controlled electroshock experiments on chinook salmon Oncorhynchus tshawytscha, rainbow trout O. mykiss, channel catfish Ictalurus punctatus, largemouth bass Micropterus salmoides, bluegill Lepomis macrochirus, and hybrid striped bass Morone saxatalis x M. chrysops. Data collected included electrical stimulus, fish behavioral response (R), length (L) and weight (W), and injury status (present/absent). Vertebral injury was determined using radiography, and hemorrhage by bilateral filleting. My model selection criteria, which was based on Akaike's Information Criterion (AIC), indicated that risks for both types of injury in chinook salmon and channel catfish were best represented by the (W, E, S) model, the (W, S) model for both types of injury in rainbow trout, the (W, E) model for hemorrhage and the (W, E, S) model for vertebral injury in largemouth bass, the (W) model for both injury types in hybrid striped bass, and, that risk for injury in bluegill injury was best described by the null model (no effect of W, E, S). A mechanistic model relating electrical stimulus, the force of contraction, and the resistance to contraction to electroshock-induced injury, using (R) as a surrogate for electrical stimulus, (L) as a surrogate for force of contraction, and vertebral count (V) as a surrogate of resistance to injury, was explored. Application of the mechanistic model (R, L, V) to the pooled data set demonstrated a strong predictive relationship. This model offers guidance for the reduction and prevention of electroshock-induced injury for all species in all situations.
    • Assessment of the benthic environment following offshore placer gold mining in Norton Sound, northeastern Bering Sea

      Jewett, Stephen Carl; Smith, Ronald L. (1997)
      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.
    • Assessment of the reproductive ecology of harbor seals (Phoca vitulina) and northern sea otters (Enhydra lutris kenyoni) in Alaska using subsistence biosampling programs

      Hutchinson, Emily A.; Atkinson, Shannon; Hoover-Miller, Anne; Kruse, Gordon; Wynne, Kate (2014-08)
      Harbor seals (Phoca vitulina) and northern sea otters (Enhydra lutris kenyoni) in Alaska have experienced extreme fluctuations in abundance in recent decades. The purpose of this study was to examine growth and determine the age and size at sexual maturity in populations of these two species, as spatial and temporal variations in environmental conditions and changes in ecological constraints as a result of population fluctuations can influence growth and reproductive characteristics of individuals. All samples for this research were collected via biosampling, the collection of measurements and biological tissue samples, as a component of subsistence harvesting by Alaska Natives. In Chapter 1, morphometric measurements and reproductive tracts were collected by the Alaska Native Harbor Seal Commission's Biosampling Program from female harbor seals harvested throughout the Gulf of Alaska from 1998 through 2005. Seals attained an asymptotic standard length (SE) of 147.7 ± 2.6 cm and body mass of 82.2 ± 4.8 kg. Female harbor seals did not mature until a minimum age of 3 yr, a standard length of 122 cm, and a weight of 48 kg. The average age of sexual maturity was 4.2 ± 0.7 yr (95% CI). Fetal growth was measured by standard length, curvilinear length, axillary girth, the cube root of fetal mass, skull length, condylobasal length, zygomatic width, and skull width against the day of the year the mother was harvested. The x-intercept of the linear regression of each fetal growth measurement against the day of the year produced estimates of the implantation date that ranged from September 22nd to October 17th, with a mean date of September 30th ± 8 d (SD). Harbor seals from this study are smaller in length, have a later implantation date, and are larger at sexual maturity compared to harbor seals in the Gulf of Alaska from the 1960s. In Chapter 2, morphometric measurements and reproductive tracts were collected by a Native Alaskan subsistence hunter from 40 male sea otters near Gustavus, in Southeast Alaska. The maximum recorded standard length and axillary girth were 160 cm and 78.7 cm, respectively. Sexual maturity was assessed by the histological examination of the testes and epididymides and the subsequent measurement and characterization of the seminiferous tubules. Male sea otters in the region reached sexual maturity at 3 to 4 yr of age, after attaining a standard body length of 130 cm., a mean seminiferous tubule diameter of 140 µm, and a baculum length of 14 cm. Sea otters outside Gustavus, Alaska exhibit increased body size and lower ages of sexual maturity compared to sea otters in other regions of Alaska, suggesting that resources are abundant and are not limiting maturation rates of male sea otters near Glacier Bay. In the future, as anthropogenic influences continue to increase and environmental conditions fluctuate, biosampling programs will be an invaluable tool for continued monitoring of marine mammals in Alaska.
    • An assessment of trap efficiency to estimate coho salmon smolt abundance in a small Alaskan stream

      Eskelin, Anthony Alexander (2004-08)
      Smolt abundance is commonly estimated using trap efficiency-based methods; however, few studies have investigated the accuracy of trap efficiency estimates. The objectives of this study were to: (1) test the hypotheses that (i) trap efficiency is not affected by release timing nor release distance, (ii) trap efficiency-based estimates of smolt abundance are concordant with smolt-adult mark-recapture estimates, and (2) evaluate if water level and turbidity influence trap efficiency. In Deep Creek, Alaska, during 2001 and 2002, coho salmon Oncorhynchus kisutch smolt abundance was estimated using trap efficiency-based methods and compared to independent smolt-adult mark-recapture estimates. Marked smolts were released at two times of day (1200 hours and 0000 hours) and two release distances upstream of the trap (400 m and 1500 m) every 2 to 4 d throughout each year. Trap efficiency estimates were highly variable (range 0%-55%) and trap efficiency-based estimates of abundance were not concordant with smolt-adult mark-recapture estimates. Release timing and turbidity significantly influenced trap efficiency, whereas release distance did not. Several assumptions of the trap efficiency approach were not met, which produced biased estimates and conflicting results among years when comparing estimation techniques. These results suggest that assumptions of the trap efficiency-based methods be fully assessed to accurately estimate smolt abundance.