• First-generation effects on development time of outcrossing between geographically isolated and seasonally isolated populations of pink salmon (Oncorhynchus gorbuscha)

      Echave, Jesse D.; Gharrett, Anthony; Smoker, William; Adkison, Milo (2010-12)
      Bootstrap analyses of hatch data collected during two independent experiments revealed that hybridization between pink salmon (Oncorhynchus gorbuscha) breeding populations separated at either a large geographic scale or a fine temporal scale can influence development time. Restricted maximum likelihood estimators also revealed that sire, dam, cross, and parental interaction can influence genetic variance associated with development time at either scale. Few studies have investigated the extent of local adaptation that results from fine-scale ecological variation, the genetic underpinnings of that adaptation, or the potential impacts outbreeding at that level may have on fitness. We tested whether or not local adaptation contributed to genetic divergence among subpopulations of pink salmon that overlap temporally within the same spawning habitat (early-run fish and late-run fish within Auke Creek, near Juneau, Alaska) by determining whether or not outbreeding influenced development time (a fitness-related trait) in first-generation hybrids. We examined genetic divergence among populations isolated at a much broader scale (Pillar Creek on Kodiak Island, Alaska, and Auke Creek, 1,000 km great circle distance) as a more extreme reference to local adaptation. Results provide evidence that development time is locally adapted and expressed primarily in a locus-by-locus manner.
    • Growth and post-harvest quality of selected Pacific oysters (Crassostrea gigas) cultured in Kachemak Bay, Alaska, and Puget Sound, Washington, in October of 2009 and June of 2010

      Thomas, Stuart Rendell; Oliveira, Alexandra; RaLonde, Ray; Eckert, Ginny; Langdon, Chris (2012-05)
      The primary objective of this project was to evaluate the growth, biochemical and fatty acid composition, physical and shell characteristics, and basic reproductive development of families of Pacific oysters (Crassostrea gigas) from the USDA-funded Molluscan Broodstock Program (MBP) planted in suspended culture in Kachemak Bay (KB), Alaska, and at an intertidal site in Thorndyke Bay (TB), Puget Sound, Washington. The MBP selects oysters to improve yields, growth, and survival, but little is known about the effects of selective breeding on other biological characteristics of selected oysters. Shell and meat characteristics of oysters from each of the seven highest-yielding MBP families were compared with those from non-selected control families at each site, which were sampled in October of 2009 and in June of 2010. Biometric and growth data, proximate compositions, fatty acid compositions, and basic degree of reproductive development were measured and compared by family, site, and sampling time. Selection improved yield, growth, and survival in MBP Cohort 20 oysters over three years of growout at KB. Colder water temperatures at KB relative to TB inhibited reproductive development, altering the biochemical composition of oysters within sites and between sampling times. Oysters grown at KB were slower growing and smaller when compared to TB, but higher in glycogen, Omega-3, and Omega-6 fatty acids (particularly docosahexaenoic acid: 22:6 Omega 3). Different latitudes and culture types were contributing factors for observed differences in growth, physiology, and composition, resulting in characteristically unique oysters from either site.
    • Growth physiology of juvenile red king crab, Paralithodes camtschaticus, in Alaska

      Westphal, Miranda J.; Tamone, Sherry; Eckert, Ginny; Siddon, Christopher (2011-08)
      Lack of recovery, following collapse of the Alaskan red king crab, Paralithodes camtschaticus, fishery, has prompted research directed towards rehabilitating the species. To better inform rehabilitation efforts aimed at increasing survival and growth of P. camtschaticus in their first year of life, I compared individual growth of hatchery-raised and wild-caught juvenile crabs in the laboratory and then compared both sets of laboratory individuals with cohorts from the field. To understand molt cycles, hemolymph was collected from age-0 and age-3 crabs to quantify circulating molting hormones (ecdysteroids) and the duration of premolt. Size, growth increment, molt interval, and cumulative molt interval did not differ significantly between hatchery-raised and wild-caught crabs. No consistent differences existed in CL between hatchery, wild-laboratory and field-surveyed juveniles for most months, although spine lengths of hatchery-raised and wild-caught crabs were significantly longer than field-surveyed crabs most months. Patterns of circulating ecdysteroids resembled published profiles for other crustacean species. Peak ecdysteroid levels occurred regularly (approximately 17 d) prior to ecdysis despite varying molt intervals. Age-0 and age-3 juveniles spent approximately 39 % and 32 % of the molt cycle in premolt, respectively. Overall, hatchery-raised and wild P. camtschaticus were markedly similar with respect to growth.
    • Identification of spawning areas and the influence of environmental variation on freshwater migration timing and in-river movements of adult coho salmon in the Buskin River, Alaska

      Stratton, Michelle Eileen; Westley, Peter; Finkle, Heather; Falke, Jeff (2019-08)
      The timing of freshwater entry by anadromous salmonids varies markedly among species and populations within species and is frequently used as an indicator of local adaptation to sitespecific patterns of selection. Although complex stock structure is most often associated with large watersheds that have extensive habitat diversity, even small drainages can produce multiple co-occurring stocks that differ in migratory timing. In addition, migration timing can be influenced by within-year environmental conditions experienced by migrating individuals en route to spawning sites, staging near the river mouth in the ocean, or within the river itself. Each stage of migration through both freshwater and saltwater could be altered based on climatic drivers and how each individual fish reacts to these stressors. The objective of this thesis was to assess the potential for stock structure in Coho Salmon within a small coastal watershed on Kodiak Island, Alaska by 1) identifying important differences in spawning and holding locations associated with run timing, length, and stream life between main stem and tributary spawners, 2) quantifying the influence of large-, intermediate-, and local-scale climate variables on freshwater entrance timing and in-river movements. To address the first objective, fish were tracked to their spawning locations using acoustic telemetry in three spawning seasons (2015-2017). I detected no statistically or biologically meaningful differences in body size (length, mm) or migration timing into the river between main stem and tributary spawning fish. Unexpectedly, I found that a large portion of fish (80%) utilize the lake during their in-river migration suggesting the lake may represent critical staging habitat for adult Coho Salmon prior to spawning. I also identified holding habitat throughout the river that both spawning groups consistently used across years that also appears to be important to premature migrating Coho Salmon. In Chapter Two, I analyzed 33 years of freshwater entrance timing data and utilized radio tags to track in-river movement to quantify the influence of precipitation and temperature on total distance moved and probability of moving. Despite marked variation among years, I found no evidence of a temporal trend in entrance timing based on escapement counts, which contrasts with other recent examples throughout Alaska reporting changes in run timing. The strongest influence on timing of freshwater entry was ocean sea surface temperature, where cold temperatures delayed entry up to 11 days. Within-river movements were positively related to precipitation and temperature, confirming local traditional knowledge in this system, and consistent with life history patterns of Coho Salmon. The primary messages of this thesis are that i) any within-watershed stock structure is unlikely to be differentially affected by harvest or management given overlapping run timing, body size, and use of main stem holding areas; future population genetics analyses would be an obvious and illuminating next step to assess the extent to which main stem and tributary spawners are reproductively isolated groups; ii) both main stem and tributary spawners use Buskin Lake as holding habitat prior to spawning, and thus assumptions that fish that enter the upper watershed are destined to spawn in headwater tributaries are invalid, which in turn limits the utility of enumerating adult passage into the lake for escapement-based management, iii) adult freshwater entrance timing is highly variable but not changing systematically through time, though the extent to which the variation in timing reflects environmental response vs. uncertainty in the counts at the weir is unknown, and iv) low precipitation and warm temperatures suppress movement and result in protracted use of main stem and lake habitats for holding, which may put some individuals at risk to angler harvest or, in extreme events, potentially low dissolved oxygen environments. Spatial management that restricts fishing in locations of known primary holding habitats may be an option to reduce probability of mortality and stress in years of low adult abundance.
    • Incorporating stakeholder input in research priorities for the Aleutian Islands

      Wadsworth, Rachael Margaret; Criddle, Keith R.; Muse, Ben; Kruse, Gordon H. (2012-12)
      Federal law requires that resource management agencies consider stakeholder input in the selection of preferred alternatives for proposed actions. Not only do stakeholders contribute unique perspectives on the impact of alternative actions and the desirability of various policy objectives, including stakeholders in the decision process adds to the perceived legitimacy of those decisions. Incorporating stakeholder input is legally required and advantageous to sustainable governance of the oceans and implementation of a National Ocean Policy such as ecosystem-based management. Agencies use a variety of formal and informal mechanisms to solicit and incorporate stakeholder input. In this study, we compare expert panel and stakeholder rankings of research and information needs in the Aleutian Islands region to see if stakeholder preferences are consistent with those of resource managers and experts when the analytical hierarchy process is used to prioritize those research and information needs. Normalized individual ratings were averaged across interest groups and compared to ratings averaged across all respondents. Spearman rank-order correlations were used to test the statistical significance of differences between groups and against the overall mean. Sensitivity analyses were used to check the robustness of the rankings across groups. We found a high level of association between rankings by an expert panel and rankings by stakeholders and little sensitivity to the make-up of stakeholders. These results suggest that the analytical hierarchy process can serve as a useful mechanism for organizing stakeholder input for environmental planning and resource management.
    • Inter-decadal change in sablefish, Anoplopoma fimbria, growth and maturity in the Northeast Pacific Ocean

      Howard, Katy B.; Adkison, Milo D.; Hillgruber, Nicola; Sigler, Michael F. (2008-08)
      Errors in growth and maturity estimates can drastically affect the spawner-per-recruit threshold used to recommend commercial fish catch quotas. Growth and maturity parameters for Alaskan sablefish, Anoplopoma fimbria, have not been updated for stock assessment purposes for 20 years, even though sablefish aging has continued. In this study, the old length-stratified data set (1981-1993) was updated and corrected for bias. In addition, newer, randomly collected samples (1996-2004) were analyzed, and new length-at-age, weight-at-age, and maturity-at-age and length parameters were estimated. A comparison of the two datasets showed that in recent years, sablefish are growing larger and maturing later and that growth and maturity differ somewhat among regions. The updated growth information improves data fits in the sablefish stock assessment model. It also provides results that are biologically reasonable. These updated and improved estimates of sablefish growth and maturity help ensure the continued proper management of this commercially important species in Alaskan waters.
    • Interannual and spatial variation in the population genetic composition of young-of-the-year Pacific Ocean Perch (Sebastes alutus) in Alaskan waters

      Kamin, Lisa M.; Gharrett, Anthony J.; Heifetz, Jonathan; Tallmon, David (2010-05)
      We know little about the population structure of Gulf of Alaska (GOA) and Bering Sea rockfish, including Pacific ocean perch (POP, Sebastes alutus), and early life history information is sparse for many rockfish species. Young-of-the-year (YOY) POP were collected with surface trawls during surveys of juvenile salmon in the GOA and Bering Sea. These samples presented a unique opportunity to study POP genetics and life history. Fourteen microsatellite loci were used to characterize the genetic variation in POP collected in a total of 45 hauls over five years. The coincidence in timing and location of several collections between years allowed examination of both fine- and broad-scale geographic variation (within cohorts) as well as interannual (between cohorts) genetic variation. The geographic genetic structure of these collections was also compared to geographic structure of adult POP described in a previous study (Palof, 2008). As in the adult study, significant broad-scale geographic divergence was observed in YOY POP in the GOA. Fine-scale geographic divergence was also observed and may be the result of variable current regimes and oceanographic features at several locations. The limited amount of temporal variation observed seems to be the result of variable oceanography and fine-scale population structure rather than the influence of a sweepstakes effect. The relationship between genetic divergence and geographic separation is virtually identical in YOY and adult POP, which confirms that dispersal of POP is limited in all life stages and also demonstrates that most YOY are produced by adults that are located nearby.
    • Interdisciplinary assessment of the skate fishery in the Gulf of Alaska

      Farrugia, Thomas J.; Seitz, Andrew C.; Kruse, Gordon H.; Criddle, Keith R.; Goldman, Kenneth J.; Tribuzio, Cindy A. (2017-12)
      Skates are common bottom-dwelling fishes and valuable non-target species in Gulf of Alaska fisheries. Although there is little demand for skates in the United States, markets in Europe and Asia are fueling desires for additional fishing opportunities on skates in Alaska. Management agencies, however, have been hesitant to allow increased harvests due to the lack of information on the ecology and population dynamics of skates, and the bioeconomics of skate fisheries. Specifically focusing on the two most commonly landedskate species in the Gulf of Alaska (GOA), the big skate (Beringraja binoculata) and the longnose skate (Raja rhina), I conducted an interdisciplinary project to address these knowledge gaps. First, I advanced our understanding of the movement patterns and habitat use of skates by satellite tagging big skates in the GOA. The results show that big skates can, and likely frequently do, travel long distances, cross management boundaries within the GOA, and spend more time in deeper waters than previously thought. Second, I used the insights from the movement study to develop the first stock assessment models for skates in the GOA. This represents an important improvement in modeling, laying the groundwork for the North Pacific Fishery Management Council to move from Tier 5 (more data limited) to Tier 3 (less data limited) harvest control rules, which should lead to increased confidence with which the total allowable catch (TAC) for skates is set. Finally, I used the sustainable harvest estimates from the stock assessment models to develop a model that examined the impacts of management decisions on the profitability of skate fishing. My research provides essential information about these understudied fishes, helping to improve the sustainability and profitability of skate harvests. Incorporation of best available science regarding skate ecology, population dynamics, and bioeconomics into fishery management fosters more responsible development of skate fisheries, sustainable fishery revenues, and employment, and reduces the risk of overfishing, stock collapse, and prolonged fishery closures. It is my hope that fishery management agencies and the fishing industry make use of the new information and insights presented in this dissertation to work collaboratively towards the responsible development of skate fisheries.
    • Kelp forests and barren grounds: phlorotannin production and holdfast community structure in the Aleutian dragon kelp, Eualaria fistulosa

      Schuster, Martin D.; Konar, Brenda; Iken, Katrin; Coyle, Kenneth (2012-12)
      The canopy forming kelp Eualaria fistulosa inhabits two organizational states throughout the Aleutian archipelago, kelp forests and barren grounds. Urchin abundance and behavior determines which state dominates in any given area. Sporophyll phlorotannin content and holdfast epibiont fauna were investigated at multiple islands along the Aleutian archipelago to determine how the organizational state affects the production of secondary metabolites and the taxon richness, abundance and biomass of holdfast communities. Barren ground sporophylls had higher phlorotannin content than kelp forest sporophylls, although grazing rates on sporophylls from each state did not differ during in situ grazing experiments. The taxon richness, abundance and biomass of holdfast communities were similar between kelp forests and barren grounds at all islands, although these communities varied among islands and were mostly driven by holdfast volume. These results suggest that physical differences such as light and nutrient availability in the kelp forest structure between organizational states may be responsible for differences in phlorotannin content, but that these differences are not reflected in the holdfast community structure. It appears that barren ground holdfast communities are remnants of a once forested area.
    • Linking freshwater growth to size-dependent marine survival of sockeye salmon: interactions between processes of climate, density, and natural selection

      Ree, Marta Elizabeth; Westley, Peter; Finkle, Heather; Beaudreau, Anne (2019-05)
      Due to the mediating role of body size in determining fitness, the 'bigger is better' hypothesis still pervades evolutionary ecology despite evidence that natural selection on phenotypic traits varies in time and space. For Pacific salmon (genus Oncorhynchus), the size at which juveniles migrate to sea (i.e., smolts) has been linked to survival during the early marine period, where larger smolts typically survive at a higher rate than their smaller counterparts. However, the relationship of smolt size and survival becomes more ambiguous when considering confounding factors of age, ocean entry timing, and environmental variability. Despite equivocal results, smolt size appears to be a key trait and therefore changes in freshwater conditions may have consequences for population productivity. Furthermore, due to differences in site-specific habitats, trophic dynamics, and population traits the response of specific populations to these changes is likely to be context specific. The objective of this thesis was to 1) quantify the direction and magnitude of natural selection on smolt size for three age classes of sockeye salmon in a small watershed on Kodiak Island, AK and 2) explore stock-specific effects of temperature and conspecific density on smolt size over a multi-decade time-series to understand historic and possible future trends. To address our first objective, we calculated standardized selection differentials by comparing observed size distributions of out-migrating juvenile salmon to back-calculated smolt length from the scales of surviving, returning adults. Results reveal the magnitude of selection on size was very strong and consistent among years. However, the direction of selection on size consistently varied among age classes. The absolute magnitude of selection was negatively correlated to apparent marine survival and positively correlated to late mean ocean entry timing. To address our second objective, we back-calculated smolt size from returning adult scales to reconstruct a time-series of smolt length of two stocks within a small Alaska watershed on Kodiak Island. Using a dynamic linear model framework, we detected evidence that for one stock, temperature was important in explaining smolt length, and density effects influenced both stocks utilizing the same lakes. Furthermore, forecasts of smolt length showed highly variable responses under scenarios of increasing temperature and high and low densities. Collectively, these results demonstrate that interactions between processes of climate, density, and natural selection are highly context-specific in terms of both inter- and intra- population variability.
    • 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.
    • Otters, sea stars, and glacial melt: top-down and bottom-up factors that influence kelp communities

      Traiger, Sarah B.; Konar, Brenda; Hardy, Sarah; Okkonen, Stephen; Edwards, Matthew; Litaker, Wayne (2017-08)
      Kelp beds are important features of the Alaska coastline and provide habitat, protect coastlines, and support commercial and subsistence harvests. Kelp beds are affected by top-down and bottom-up factors, which are changing due to human and climate-related impacts. The influences of these top-down and bottom-up factors on kelp beds are investigated in three chapters. My first chapter investigated the influence of glacial discharge on recruitment and early community development in subtidal kelp communities by monitoring benthic sessile algae and invertebrates on cleared rocks across a glacial gradient along with various physical and biological parameters in the summers of 2013-2014. It has been predicted that Alaska's glaciers will lose 30-60% of their volume by 2100. The melt from glaciers increases sedimentation and lowers salinity, impacting important habitat-providing kelp. I found that sites upstream from glacial discharge had higher kelp recruitment than downstream sites, and that up to 72% of the variation in community development was related to mobile invertebrates and kelp in the surrounding community. Glacially-influenced environmental factors did not explain any variation that was not already explained by biological factors. My second chapter explored whether patterns in the recruitment of the dominant canopy kelp, Nereocystis luetkeana and the subcanopy kelp, Saccharina latissima were a result of dispersal limitation or failure to grow to macroscopic size. My goals were to determine 1) whether glacial melt conditions affect adult fecundity (spore production) of either species, 2) how sedimentation affects early gametophyte growth and survival in each species, and 3) whether competitive interaction between species at the gametophyte stage is altered by sediments. I found that glacial melt conditions did not affect the fecundity of either species, but sedimentation affected survival and competition. Saccharina latissima was the superior competitor under high sediment conditions. Because glacially-influenced coastal areas often have little exposed hard substrate and predation by sea otters and sea stars on clams can provide hard substrate for kelp colonization, my third chapter examined methods for determining predation on clams by these predators without direct observation. I found that foraging pits of sea otters and sea stars could not be distinguished using quantitative measurements. In contrast, shell litter proved useful in quantifying relative foraging rates. Clam consumption by sea otters and sea stars was equal at all but one site. Collectively, my thesis chapters provide information on the effects of glacial discharge on microscopic and early kelp life stages in Alaska which can be incorporated into management practices.
    • Pacific herring juvenile winter survival and recruitment in Prince William Sound

      Sewall, Fletcher; Norcross, Brenda; Mueter, Franz; Kruse, Gordon; Heintz, Ron; Hopcroft, Russ (2020-05)
      Small pelagic fish abundances can vary widely over space and time making them difficult to forecast, partially due to large changes in the number of individuals that annually recruit to the spawning population. Recruitment fluctuations are largely driven by variable early life stage survival, particularly through the first winter for cold temperate fishes. Winter survival may be influenced by juvenile fish size, energy stores, and other factors that are often poorly documented, which may hamper understanding recruitment processes for economically and ecologically important marine species. The goal of this research was to improve understanding of recruitment of Pacific herring (Clupea pallasii) within Prince William Sound (PWS) through recruitment modeling and by identifying factors influencing winter survival of young-of-the-year (YOY) herring. Towards this end, my dissertation addresses three specific objectives: 1) incorporate oceanographic and biological variables into a herring recruitment model, 2) describe patterns in growth and condition of PWS YOY herring and their relationship to winter mortality risks, and 3) compare the growth, condition, swimming performance, and mortality of YOY herring that experience different winter feeding levels. In the recruitment modeling study, annual mean numbers of PWS herring recruits-per-spawner were positively correlated with YOY walleye pollock (Gadus chalcogrammus) abundance in the Gulf of Alaska, hence including a YOY pollock index within a standard Ricker model improved herring recruitment estimates. Synchrony of juvenile herring and pollock survival persisted through the three-decade study period, including the herring stock collapse in the early 1990s. While the specific mechanism determining survival is speculative, size-based tradeoffs in growth and energy storage in PWS YOY herring indicated herring must reach a critical size before winter, presumably to reduce size-dependent predation. Large herring switched from growth to storing energy, and ate more high-quality euphausiid prey, which would delay the depletion of lipid stores that compelled lean herring to forage. Lipid stores were highest in the coldest year of the seven-year field study, rather than the year with the best diets. With diets controlled in a laboratory setting, spring re-feeding following restricted winter diets promoted maintenance of size and swimming ability, but had little effect on mortality rates compared to fish continued on restricted rations. Declines in gut mass, even among fully fed herring, and low growth potential suggest limited benefits to winter feeding. Mortalities due to food restriction compounded by disease were highest among herring that fasted through winter months, and among small herring regardless of feeding level. Taken together, these findings illustrate the importance of achieving a critical size and high lipid stores in the critical period before winter to promote YOY herring winter survival and ultimately recruitment.
    • Population genetic structure of Alaskan Pacific ocean perch (Sebastes alutus)

      Palof, Katie J.; Gharrett, Anthony J.; Heifetz, Jonathan; Hillgruber, Nicola (2008-05)
      Knowledge of the population structure of a species is essential for its effective management and sustained production. Although Pacific ocean perch (Sebastes alutus, POP) is an important species both economically and ecologically, little is known about its population structure and life history in Alaskan waters. The objectives of this study were to describe the population structure of POP in terms of the numbers and geographic scale oflocal populations, their connectivity, and the compatibility of that structure with current management. Fourteen micro satellite loci were used to characterize the population structure genetically in eleven geographically distinct collections from sites along the continental shelf from the Queen Charlotte Islands to the Bering Sea. In spite of the many opportunities for most life stages to disperse, there was strong geographically related genetic structure (Fst =0.0123, p <10⁻⁵). Adults appear to belong to neighborhoods that exchange genetic information at relatively small spatial scales (14 to 90 km). Although this suggests limited movement, connectivity is evidenced by the isolation-by-distance relationship, the apparent northwestward movement of gene flow in the Gulf of Alaska (GOA), and the break in geneflow in the central GOA. The observed population structure has a finer geographic scale than management areas, which suggests that current fisheries management should be revisited.
    • Quantity and quality of freshwater rearing habitat in relation to juvenile Pacific salmon abundance in the Kulukak River, Alaska

      Coleman, Jesse M.; Sutton, Trent; Zimmerman, Christian; Adkison, Milo (2012-12)
      Monitoring of freshwater habitat and its influence on stream-rearing fish is essential for recognizing and mitigating the impacts of human- and climate-induced changes. For the purposes of developing a monitoring program in the U.S. Fish and Wildlife Service Togiak National Wildlife Refuge, densities and habitat relationships of juvenile coho salmon Oncorhynchus kisutch and sockeye salmon O. nerka were estimated in two tributaries of the Kulukak River, Alaska, in July 2010. Multiple-pass depletion electrofishing was used to estimate density in a random sample of habitat units belonging to one of four categorical habitat classes. Regression methods were also used to quantify the physical habitat associations of juvenile coho and sockeye salmon density in the study areas. Densities of juvenile coho and sockeye salmon ranged from 0.22 fish-m⁻² in West Fork riffles and 0.05 fish·m⁻² East Fork riffles to 2.22 fish M⁻² and 1.32 fish-m⁻² in East Fork eddy drop zones (EDZ), respectively. The largest proportions of freshwater habitat were comprised of run (71 %) and EDZ habitats (44%) in the East Fork and West Fork, respectively. Regression coefficients for coho and sockeye salmon densities were positive with respect to proportional areas of in-stream overhanging vegetation (0.78 and 0.74, respectively), large wood (0.99 and 0.97, respectively), and undercut banks (0.99 and 0.02, respectively). Conversely, coho and sockeye salmon density was negatively related to depth ( -1.45 and -0.52, respectively) and velocity ( -2.45 and -1.67, respectively). Although substrate size was negatively related to sockeye salmon density ( -0.40), this variable had a weak positive relationship with coho salmon density (0.08). These findings suggest that EDZ habitats are important for juvenile coho and sockeye salmon during summer rearing and in-stream cover is an essential component of these rearing habitats.
    • The reproductive biology and management of walleye pollock (Gadus chalcogrammus) in the Gulf of Alaska

      Williams, Benjamin C.; Kruse, Gordon; Criddle, Keith; Dorn, Martin; Quinn, Terrance II (2018-08)
      Ecosystem-based fishery management (EBFM) entails treating resource allocation and management as elements of a comprehensive framework that accounts for ecological linkages. The goal of EBFM is to maintain ecosystem resiliency in a manner that provides for the services desired e.g., fishery catch, species abundance, economic viability. Historically fisheries have been managed on a per species basis with a general focus on increasing or decreasing harvest rates. This management strategy often excludes meaningful processes such as interactions with other species, environmental changes, and economic effects of management changes. One feasible path for implementation of EBFM is through enhancement of existing single-species fishery management models. Contemporary age-structured stock assessment models generally use an estimate of spawning stock biomass (SSB), i.e., the biomass of female spawning fish, to approximate stock reproductive potential (RP). This approximation inherently assumes a proportional relationship between SSB and RP. Maturity at age or at length is a key aspect of reproductive biology that is central to estimating both RP and SSB. As a sequential augmentation to a single species management model the relationships among body condition, population abundance, the probability of being mature, relative fecundity, and environmental correlates were examined for female walleye pollock Gadus chalcogrammus in the Gulf of Alaska. Maturity data were corrected for spatial sampling bias using a mixed-effects generalized additive model. Once corrected for spatial bias, relationships between maturity, ocean temperature, body condition, ocean productivity (in the form of chlrophyll-a), and population abundance were explored. Estimates of fecundity were updated through the processing of archived samples and were also examined with mixed-effects generalized additive models to explore relationships between the previously listed covariates. Multiple measures of RP were examined to explore differences between methods currently incorporated into the stock assessment and updated measures of total egg production and time varying maturity. Walleye pollock body condition is density-dependent, declining with population abundance. However, after accounting for the effects of length, age, location, year, chlorophyll-a concentrations, summer ocean temperature and sample haul, condition has a positive effect on the probability of a fish being mature. Similarly, condition has a positive effect on relative fecundity, after accounting for length, age, egg diameter, chlorophyll-a concentrations, winter ocean temperature and sample haul. A positive relationship is observed between depth-integrated summer ocean temperature and maturity and depth-integrated winter ocean temperature and fecundity. Chlorophyll-a concentrations have a dome shaped relationship with maturity, peaking at 2.3 mg/m⁻³, and a negative relationship with fecundity. Variations in body condition have a direct influence on the estimated RP of the fish stock through both differences in the maturation schedule and total egg production. Over some periods these updated estimates of RP differ from estimates of female SSB from the annual stock assessment. Alternative estimates of annual RP, particularly total egg production, may provide better estimates of annual reproductive output than spawning stock biomass. In addition, relationships to density-dependent and density-independent factors provide informative predictions that can be incorporated into stock assessment analyses. Inclusion of spatially explicit information for walleye pollock maturity has implications for understanding stock reproductive biology and thus the setting of sustainable harvest rates used to manage this valuable fishery. Additionally, because management decisions have economic as well as biological consequences a suite of management strategies were simulated to examine the economic viability of a proposed small-vessel walleye pollock fishery in Alaska state waters in the Gulf of Alaska. As a case-study for straddling stocks, an agent-based model was developed to examine a suite of available federal and state management strategies as they relate to the economic viability of a nascent Alaska state-waters trawl fishery for walleye pollock that may develop after a long history of parallel state and federal waters management. Results of alternative strategies were compared in terms of indicators, such as variance of catch and quasi-rent value. Given the input characteristics of these simulations, the management strategy that produces the best overall improvements relative to status quo involved a federal-waters management strategy that allows for community-based cooperatives and an open access strategy in state-waters. Agent-based models may be used to inform managers of the underlying dynamics of catches and revenues in order to avoid unintended consequences of management decisions and to improve the likelihood of attaining fishery management objectives. This dissertation provides incremental additions to our knowledge of walleye pollock reproductive biology its spatial and temporal dynamics, and environmental correlates that may serve as ecological indices. These indices, coupled with an improved understanding of the socio-economic examinations of fishery management changes through agent-based modeling, may assist in producing more holistic management strategies, such as EBFM.
    • The response of juvenile coho and chinook salmon stocks to salmon spawner abundance: marine nutrients as drivers of productivity

      Joy, Philip J.; Wipfli, Mark S.; Adkison, Milo D.; McPhee, Megan V.; Stricker, Craig A.; Rinella, Danial J. (2019-08)
      Resource subsidies from spawning Pacific salmon (Oncorhynchus spp.) in the form of marine-derived nutrients (MDN) benefit juvenile salmonids while they rear in fresh water, but it remains unclear if the abundance of spawners in a watershed affects the productivity of salmon stocks that rear in those riverine systems. This dissertation aimed to provide a better understanding of these dynamics by evaluating whether the response of juvenile salmon to MDN is sufficient to enhance overall stock productivity. In Chapter 1, I examined correlative relationships in the abundance of Pink (O. gorbuscha) and Coho (O. kisutch) salmon and simulated spawner-recruit dynamics to determine if those correlations were produced by a Coho Salmon response to marine subsidies from Pink Salmon, a shared response to marine conditions, and/or autocorrelations in the returns of both species. Results demonstrated that observed correlative patterns most closely resembled simulated freshwater effects, providing evidence that marine subsidies from Pink Salmon influence Coho Salmon productivity. In Chapter 2, I examined the relationship between spawner abundance and MDN assimilation by juvenile Coho and Chinook (O. tshawytscha) salmon in the Unalakleet River watershed. Stable isotope analysis demonstrated that after salmon spawned, MDN assimilation by juvenile salmon in the fall was a function of adult Pink and Chinook salmon spawner abundance, regardless of the habitat occupied by rearing juveniles. However, by the following summer, high retention of MDN in complex habitat masked seasonality of MDN assimilation in sloughs and river sections with abundant lentic-lotic exchanges. As such, MDN assimilation in the summer (prior to arrival of spawners) bore only a faint relationship to spawner abundance and distribution from the previous year. In chapter 3 I examined the relationship between MDN assimilation (Chapter 2) and juvenile salmon growth, size, body condition, and abundance. Prior to salmon spawning, residual MDN from past years offered little advantage to juvenile salmon. However, after the arrival of spawning salmon, MDN enhanced juvenile salmon size, growth, and condition in fall and winter. The collective results from this dissertation thus provides compelling evidence that MDN from spawning Pink Salmon may enhance the productivity of Coho and Chinook salmon. Management agencies should explore modified spawner-recruit models that incorporate MDN relationships to determine if they more accurately describe population dynamics. Where they do, such models may be used to forecast salmon returns and possibly adjust escapement goals (the number of spawners desired on the spawing grounds) to improve maximum-sustained yields (MSY).
    • Spatial trends and environmental drivers of epibenthic shelf community structure across the Aleutian Islands

      Bland, Aaron; Konar, Brenda; Iken, Katrin; Johnson, Mark; Zimmermann, Mark (2018-12)
      The continental shelf around the Aleutian Islands supports important commercial and subsistence fisheries as well as multiple seabird and marine mammal populations. To sustainably manage these populations, more information is needed on the distribution of the benthic communities that support some of the top level consumers. Given the vast size and highly variable physical environment of the Aleutian Islands, it is likely that epibenthic community structure on the continental shelf will vary by geographic area and physical and oceanographic conditions. This project examined spatial patterns in Aleutian epibenthic shelf communities among oceanographic regions (island groups separated by major oceanographic passes) and islands within these regions and identified environmental drivers responsible for important community divisions. Benthic trawls were conducted at 12 Aleutian islands across four oceanographic regions to characterize epibenthic shelf community structure along the island chain. It was tested whether the spatial variability in shelf community structure among regions and islands was correlated to multiple environmental variables including bottom water temperature, water depth, distance from shore, exposure, bottom rugosity, sediment grain size, sediment chlorophyll content, and drift algal food subsidies. Overall, communities differed both among regions and among islands within regions. Communities in the Far Western region (Near Strait to Buldir Strait) differed from communities in other regions, largely due to a high density of sand dollars in the Far West. However, none of the measured environmental characteristics explained this difference. Additionally, there was no evidence for a break in epibenthic shelf community structure across Samalga Pass between the East and the Central regions, even though Samalga represents a biogeographic break for many other Aleutian community types, including zooplankton, fish, and kelp forest communities. Within the Central region, a characteristic soft-sediment community (including the flatfish Atheresthes spp. and the crabs Labidochirus splendescens and Chionoecetes bairdi) distinguished Adak Island from other Central islands. Compared with groundfish trawl surveys conducted by the Alaska Fisheries Science Center (AFSC), this study captured less fish but more invertebrates by biomass, which is likely related to different gear selectivity used by the two studies. These findings provide information on the distribution of Aleutian shelf communities that complement existing information from AFSC surveys. In particular, it is shown that there is potentially an important division in epibenthic shelf communities across Buldir Strait, in agreement with the literature identifying this pass as an important biogeographic break. Furthermore, it is suggested that future assessments of Aleutian epibenthic communities should employ a combination of sampling gear types to better represent various epibenthic taxa.
    • Steller sea lion (Eumetopias jubatus) strandings and the role of pathogens in reproductive failure

      Esquible, Janessa A.; Atkinson, Shannon; Burek-Huntington, Kathy; Cox, Keith; Tamone, Sherry (2018-08)
      Steller sea lions (SSL, Eumetopias jubatus) have faced severe population fluctuations over the last five decades with a myriad of possibilities affecting their SSL population including disease, malnutrition, predation, climate change, entanglement in marine debris, and other factors. This thesis examined the effects that anthropogenic factors and disease may play in SSL strandings and reproductive failure. The goal of this study was to characterize long-term seasonality and spatial trends in SSL strandings and to investigate the role Brucella spp., Coxiella burnetti. Chlamydophila spp. and morbilliviruses may play in reproductive failure including spontaneous abortion and premature parturition. In Chapter 1, we utilized stranding data (n=1507) collected in Alaska, Oregon, and Washington from 1990-2015. We assessed temporal trends by identifying seasonality patterns across all years, analyzing sex, age class, body length, and characterizing signs of human interaction including factors contributing to mortality. Clear seasonality trends were evident, with the greatest number of reported strandings occurring during the spring and summer. Gunshot wounds and fishery interactions accounted for a large proportion (46%) of human interaction cases in strandings. Adult males were the most frequently stranded sex and age class in the Alaska and West Coast Regions. This study attempted to quantify efforts to monitor strandings and determined that the apparent increase in strandings following 2000 was likely due to increased stranding response effort resulting from increased federal grant awards. We encourage conducting further spatial analyses of strandings in addition to continued stranding surveillance monitoring with attempts to improve stranding response time. In Chapter 2 of my thesis, we analyzed archived lung, skin lesion and placenta tissues for the pathogens of interest in SSL fetuses (n=18) and neonatal pups (n=2) collected from 1998 2015 in Alaska. Associated pathological findings and morphometric data were examined to identify signs of pathology or abnormalities in all cases. Marine mammal Brucella was detected in the lung tissue of three cases. This is the first documented detection of Brucella in SSL by PCR methods. Phocine distemper virus was also detected in the skin lesion of two cases and in the placenta of one case, in which the cases with skin lesions exhibited abnormal pathology that included vesiculoulcerative dermatitis. Currently, there is very little available information on the significance of Brucella spp. and morbilliviruses in marine mammal populations inhabiting Alaskan waters. Therefore, this study demonstrates the clear need to continue disease surveillance programs and further investigate the role disease may play in SSL reproductive health, and more generally on cohort population stability.
    • Subsistence salmon fishing in Beaufort Sea communities

      Cotton, Shelley S.D.; Carothers, Courtney; Craighead George, John (2012-12)
      Environmental change, combined with observations of increasing numbers of salmon in subsistence fisheries, has generated a need for more information about salmon use, abundance, and distribution in the Arctic. Ethnographic research was conducted in Barrow and Nuiqsut, Alaska, in 2010 and 2011 with 41 active fishermen and elders. Salmon catches were perceived to be increasing; however, perceptions about changing salmon abundance were mixed. While pink salmon (Oncorhynchus gorbuscha) and chum salmon (O. keta) have been observed in subsistence fisheries in the central North Slope region for over 50 years, only within the last 10 to 20 years has local use of these resources begun to increase. In this region, salmon are less important as a subsistence resource compared to whitefish species (Coregonus spp.). However, many fishermen participating in the Elson Lagoon gill net fishery near Barrow have begun to target salmon. Harvest estimates for this fishery in 2011 indicated that chum salmon and pink salmon catches comprise the majority of all fish caught (42% and 23%, respectively). Chinook salmon (O. tshawytscha) have been increasingly targeted, but catches are generally low. While sockeye salmon (O. nerka) numbers were perceived to have increased on the North Slope, catches of this species are rare. Only a few stray coho salmon (O. kisutch) have been captured in this region. Informants identified new stream systems where salmon are present and spawning, suggesting possible distribution shifts. Fishermen in both communities reported developing knowledge of salmon and are increasing their use of salmon as a subsistence resource.