• Environmental cues for Pacific herring (Clupea pallasi) spawning in northern Bristol Bay

      Tojo, Naoki (2006-05)
      Pacific herring, Clupea pallasi, is an important forage fish species, which interfaces with various trophic levels including human beings. There have been many herring studies about reproductive biology and migration dynamics, but not many studies about the underlying mechanisms. For fisheries management, reliable spawning prediction models are necessary. I sought to understand the mechanisms behind the variability in northern Bristol Bay herring spawning variability and migration dynamics in the eastern Bering Sea (EBS). Through a combination of spatio-temporal approaches and statistical methods, I found significant statistical relationships between herring spawning and spring environmental variables. All the best models include air-sea-ice interactions through their effects on gonad maturation and migration. EBS herring undergo a pseudo-clockwise seasonal migration with adjustments in response to changes in oceanographic conditions along the ice edge. Ocean temperature changes near the ice edge, which are controlled by atmospheric gradients over the North Pacific Ocean, explain most of the interannual variability of herring spawning in northern Bristol Bay.
    • Environmental, biological, and genetic factors influencing local adaptation of pink salmon (Oncorhynchus gorbuscha) in Auke Creek, Alaska

      Manhard, Christopher V.; Gharrett, Anthony J.; Smoker, William W.; Joyce, John E.; Hard, Jeffrey J.; Adkison, Milo D. (2016-05)
      Pacific salmon form distinct, locally adapted populations because of the spatial and temporal precision with which they home to their natal streams. Local adaptation is recognized as an important component underlying the productivity and sustainability of salmonid populations, yet there remains uncertainty of the scale at which it occurs. This uncertainty was addressed by analysis of demographic, genetic, and experimental data collected from seasonally structured brood lines of Pink Salmon that spawn in Auke Creek, Alaska. An extensive background of research on this system has indicated that the timing of the adult and juvenile migrations is closely aligned with fitness and productivity in this stream; this background provided a framework for synthesizing the results of the analyses to address these questions: (1) What ecological factors influence productivity of the freshwater and marine life history stages; (2) Do these factors suggest a mechanism for evolution of migration time; (3) What are the consequences of disrupting fine-scale local adaptation of migration time? Freshwater productivity appeared to be influenced primarily by competition for spawning habitat, rather than variability in environmental conditions. Marine productivity, conversely, was associated with physical processes that influence survival of juveniles in the nearshore environment. Consistent with these findings, genetic evolution of earlier migration time, which was observed in both adults and juveniles over two generations, appeared to be driven by earlier vernal warming of the nearshore environment. Despite these environmental changes and resulting selection against late migrating fish, recruitment to Auke Creek has remained stable, thereby indicating that seasonal structure of migration time has supported sustained productivity in a changing climate. Experimental relaxation of natural barriers to gene flow that maintain the seasonal structure resulted in intermediate adult migration times in two generations of hybrid fish. These patterns were consistent with an additive genetic basis for migration time and suggest that ecological outbreeding depression is a post-zygotic mechanism that maintains adaptive variation of migration time in Auke Creek. Collectively, these results provide evidence that fine-scale local adaptation can enhance productivity of salmonid populations while providing resilience to climate change.
    • Environmental, ecological, and fishery effects on growth and size-at-age of Pacific halibut (Hippoglossus stenolepis)

      Sullivan, Jane Y.; Kruse, Gordon H.; Mueter, Franz J.; Martell, Steven J. D. (2016-08)
      Size-at-age of Pacific Halibut (Hippoglossus stenolepis) has declined significantly since the 1980s. For instance, the average weight of a 20-year-old female declined from 55 kg in 1988 to 20 kg in 2014. The decline in size-at-age corresponds to a period of declining Pacific Halibut recruitment, spawning biomass, and reductions in catch limits for the directed commercial Pacific Halibut longline fishery. The causes of changes in Pacific Halibut size-at-age are poorly understood. Our project investigates several hypotheses related to declines in size-at-age, including the effects of environmental and ecological variability on growth, and the cumulative effects of harvest and size-selective fishing. Specific potential environmental covariates include the Pacific Decadal Oscillation, which is an index of basin-wide sea surface temperatures, and summer sea surface temperatures along the continental shelf of the Gulf of Alaska. Specific ecological variables include annual biomass estimates of Arrowtooth Flounder (Atheresthes stomias) and Pacific Halibut to investigate the potential role of inter- and intraspecific competition, respectively. We used a population modeling approach to simulate the effects of fishing on size-at-age. We found that the large increase in Arrowtooth Flounder biomass since the 1970s corresponds to declines in Pacific Halibut size-at-age. Our results also suggest that periods of high Pacific Halibut biomass relates to poor growth and low size-at-age. Finally, we found that harvest and size-selective fishing explains between 30 and 65% of observed declines since the 1980s in the Gulf of Alaska, and up to 100% of the declines in Southeast Alaska and British Columbia where harvest rates were high in the 1990s and 2000s. Our findings have implications for fisheries management, including balancing tradeoffs associated with size limits, and understanding how changes in environmental and ecological conditions can shift management reference points such as maximum sustainable yield.
    • Estimability of time-varying natural mortality in groundfishes: covariates and hierarchical models

      Ganz, Philip D.; Quinn, Terrance J. II; Hulson, Peter-John F.; Kruse, Gordon H. (2017-08)
      Natural mortality, M, has historically been a difficult parameter to estimate in conjunction with other stock assessment parameters. Time-varying M, while likely to be experienced by a population, is a particularly difficult process to estimate with the data and methods currently available to most stock assessments. Although auxiliary information in the form of a covariate to M has been shown to improve model fit for some stocks, such data are rarely available. Meanwhile, hierarchical models continue to be utilized in capturing processes that vary in time and space. I tested both the covariate and hierarchical methods in their ability to estimate time-varying M. I attempted to fit hierarchical models by two different methods: penalized likelihood and the integrated likelihood approach associated with mixed effects models. Mixed effects models performed poorly in comparison to penalized likelihood. Including a covariate to natural mortality aided the estimability of time-varying M, regardless of the observation error associated with the covariate. Estimating a constant value of M resulted in biased estimates when M was time-varying in the simulated population. I showed that the Akaike information criterion (AIC) is a useful metric for comparing models although it does not necessarily align with the accuracy of estimates that are of most interest to managers, such as terminal year spawning stock biomass. In addition to showing empirically that incorporating a covariate is a robust approach to estimating time-varying M, I conclude that this approach is also advantageous to stock assessment on theoretical grounds, as it is more amenable than hierarchical models to making predictions.
    • Estimates of primary production sources to Arctic bivalves using amino acid stable carbon isotope fingerprinting

      Rowe, Audrey G.; Wooller, Matthew; Iken, Katrin; O'Brien, Diane (2018-12)
      Benthic invertebrates are a crucial trophic link in Arctic marine food webs. However, estimates of the contribution of primary production sources sustaining these organisms are not well characterized. Potential sources could include sinking particulate organic matter from sea ice algae and phytoplankton, terrestrial organic matter eroded from the coastal environment, macroalgal material, or microbial organic matter. Proportions of these sources could also be significantly altered in the future as a result of environmental change. We measured the stable carbon isotope values of essential amino acids in muscle tissue from two common bivalve genera (Macoma spp. and Astarte spp.) collected in Hanna Shoal in the northeastern Chukchi Sea, considered an Arctic benthic hotspot. We used stable isotope mixing models in R (simmr) to compare the stable carbon isotope amino acid fingerprints of the bivalves to a suite of amino acid source endmembers, including marine phytoplankton, brown and red macroalgae, bacteria, and terrestrial plants, to estimate the proportional contributions of primary production sources to the bivalve species from Hanna Shoal. The models revealed relatively high contributions of essential amino acids from phytoplankton and bacteria averaged across both species in the region as a whole. We also examined whether stable carbon isotope fingerprints could be measured from essential amino acids preserved in bivalve shells, which could then allow proportional contributions of food sources to be estimated from ancient bivalve shells, allowing source estimates to be extended back in time. To investigate this, we measured the stable carbon isotope values of essential amino acids in a suite of paired modern bivalve shells and muscle from Macoma calcarea from the Chukchi Sea. These analyses revealed a correspondence between the fingerprints and mixing model estimates of the dominant primary production source of essential amino acids derived from analyses of these two tissue types. Our findings indicate that stable carbon isotope amino acid fingerprinting of marine bivalves can be used to examine dominant organic matter sources in the Arctic marine benthos in recent years as well as in deeper time.
    • Estimating movement with a spatially-explicit stock assessment model of eastern Bering Sea walleye pollock, Theragra chalcogramma

      Miller, Sara Elizabeth (2007-05)
      The standard Eastern Bering Sea (EBS) walleye pollock (Theragra chalcogramma) stock assessment model has no spatial dimension. To advance the understanding of EBS walleye pollock movements and spatial structure on finer temporal and spatial scales, a spatially explicit migration model of EBS walleye pollock was developed. However, there are no estimates of movement rates for this population. Using standard sample size formulae in a Petersen-type experiment, we showed that only a moderate mark-recapture program [minimum number of tags for ages-1 + was 9,475 (all sectors included) and 20,924 (only catcher-vessel shoreside sector included)] is needed to estimate abundance. Given these sample size requirements determined for abundance estimation, the Darroch method was used to estimate movement parameters between two regions, the northwest (NW) and southeast (SE) EBS in a simple compartment model. Directed movement could be reasonably estimated with Monte Carlo simulation. To develop the EBS walleye pollock age-structured movement model, the standard stock assessment model was extended into a two-region (NW and SE EBS), two-season, age-specific movement model. Movement could be estimated from disaggregated data without mark-recapture information, but with low precision. However, the uncertainty indicates that a mark-recapture study is needed before such a model could be applied for management applications.
    • Estimating sizes of fish consumed by ice seals using otolith length-fish length relationships

      Walker, Kelly; Norcross, Brenda L.; Brown, Randy; Lopez, Andres; Quakenbush, Lori (2017-12)
      Arctic fishes and ice seals are key components of the Alaskan Arctic ecosystem. Bearded (Erignathus barbatus), spotted (Phoca largha) and ringed (Pusa hispida) seals are consumers of Arctic marine fishes. Little is known about the sizes of fish that ice seals consume because prey items are digested quickly once exposed to stomach acids. Otoliths, fish ear bones, are often the only parts of a fish that remain in a seal stomach. Otolith length relates directly to fish length, making size estimations of consumed fish possible for piscivore diet studies. Otoliths were measured from fishes collected from cruises in the Beaufort and Chukchi seas during 2009 - 2014. Otolith length - fish length and fish length - fish weight relationships were developed for 11 Arctic marine fish species that are commonly consumed by ice seals in Alaska. Otoliths from seal stomachs provided by subsistence hunters to the Alaska Department of Fish and Game were identified to species level and measured for total length. A mixed effects model was used to determine how the variables of seal species, harvest location, seal age class and sex influenced the sizes of fish consumed. Harvest location and seal age class were the primary factors that affected fish size in ice seal stomachs. Estimating length and weights of fishes consumed by ice seals will help further diet and energetics studies that have not previously been possible in the Alaskan Arctic.
    • Estimating ¹³C and ¹⁵N turnover rates in the Arctic amphipod Onisimus litoralis: implications for analysing the transfer of sea ice production to under-ice fauna

      Nielson, Mette R. (2006-12)
      The Arctic amphipod Onisimus litoralis migrates from the seafloor to the sea ice to graze on ice algae, a rich food source during the Arctic spring, resulting in complex trophic dynamics. I assessed the effect of temperature and season on the rate of change in stable isotopic composition of amphipods by simulating a diet switch in the laboratory using amphipods collected near Barrow, Alaska in spring and autumn 2004. Additionally, the proportional contributions of food sources to the amphipods' diet in the field were estimated. Isotopic change occurred faster in spring with half-lives of 13.9 (1°C) and 18.7 (4°C) days for carbon and 22.4 days for nitrogen compared to autumn rates of 77 (carbon) and 115 days (nitrogen). Temperature did not have a significant effect on turnover. Change occurred primarily through metabolic turnover (versus growth-related dilution) and was responsible for 84-89% of the change in carbon and 67-77% of the change in nitrogen in both seasons. A two-source mixing model estimated that ice-derived biota contributed 59 (±17)% to the amphipods' diet in May. These data show that the rate of isotopic change can vary temporally for a single species, highlighting the importance of experimental work for interpreting stable isotope field-data.
    • Estimation of abundance and mortality of emigrating chum salmon and chinook salmon in the Chena River, Alaska

      Peterson, Brent David (1997-05)
      During May-June, 1995 and 1996, the outmigration of juvenile chum salmon (Oncorkynchus keta) and chinook salmon (O. tschazvytscha) was sampled with floating traps in the area of the Chena River Lakes Flood Control Project, Chena River, Alaska. Catch-per-unit-effort (CPUE) was higher at night than day for chinook juveniles, but not for chum juveniles. CPUE of both species decreased as the season progressed, but usually increased during higher-discharge events. CPUE is standardized by time; discharge was monitored as a covariate but was not included in CPUE calculations. The Jolly-Seber family of models was used on recapture data of fin-dipped fish to obtain estimates of abundance and survival in 1996. Abundance estimates were 266,104 chum salmon (95% Cl 128,031 - 404,177) and 171,952 chinook salmon (95% Cl 146,342 - 197,561) during the May-June outmigration period. These abundance estimates are probably underestimates of the entire Chena River population. Survival estimates were 0.135 (95% Cl 0.042 - 0.228) for chum salmon and 0.713 (95% Cl 0.492 - 0.935) for chinook salmon over the same period.
    • Evaluating potential age structures for three Alaska crustacean species

      Rebert, April L.; Kruse, Gordon; Webb, Joel; Tamone, Sherry (2019-05)
      Banding patterns are observed in calcified structures of red king crab (Paralithodes camtschaticus), snowcrab (Chionoecetes opilio), and spot shrimp (Pandalus platyceros). Recent research supports an age determination method based on these banding patterns; however, processing methodologies for these structures have not been established. Further, species-specific evidence is needed to determine whether these patterns indicate actual age or growth. The objectives of this thesis are to: (1) describe optimal species-specific methods for producing and evaluating band counts for red king crab, snow crab, and spot shrimp; and (2) use differences in shell condition to test whether band counts indicate age for snow crab. For each species, we comprehensively thin-sectioned structures, evaluated each section for banding pattern presence (readability), and developed band count criteria. To address objective 1, we used generalized additive models to describe readability across structures to find the location that optimizes the production of readable sections. For objective 2, we used a one-way ANOVA to compare band count and endocuticle measurements among shell conditions in snow crab. Results indicated preferred structures, locations, section orientation, and thickness. Results also indicated that there is no relationship between band count and shell condition for terminally molted snow crab. These results describe optimal methods for processing crustacean structures and suggest that the potential age structures may not continue to produce bands after terminal molt in the case of snow crab. Further evaluation is needed to validate potential age relationships and the use of this technique for age estimation.
    • Evaluating the Accuracy of Unmanned Aerial Systems to Quantify Glacial Ice Habitats of Harbor Seals in Alaska

      Pegus, Courtney; Atkinson, Shannon; Quinn, Terry; Pyare, Sanjay (Wiley-Blackwell, 2021-11-17)
      Long-term monitoring programs to evaluate climate-driven changes to tidewater glaciers, an important habitat for harbor seals (Phoca vitulina) in Alaska, are primarily carried out by costly, weather-dependent aerial surveys from fixed-winged aircraft. Unmanned aerial systems (UAS) can be an alternative cost-effective solution for gathering image data to quantify, monitor, and manage these habitats. However, there is a paucity of information related to the accuracy of using imagery collected by UAS for purposes of measuring floating icebergs. We evaluated the accuracy of using a UAS with a built-in 20 megapixel (MP) camera as well as a consumer-grade digital 16 MP camera to capture images of floating and stationary icebergs for the purpose of collecting vertical height measurements. Images (n=869) were captured of simulated icebergs (Cuboidal foam boxes) “Cb” (n=5) and real icebergs (n=5) that were either grounded or floating. The mean error ratios obtained were less than 10% and derived by comparing the mean calculated measurements of heights of Cb obtained from images captured by UAS with the physical measured heights of these Cb. The mean error ratio for height measurements of grounded icebergs (n=4) and one floating iceberg was also less than 10%. Within an object-image distance range of 6-25 m, the cameras captured images that were suitable to accurately calculate the heights of floating and grounded objects, and drift or uncontrolled movement of the UAS caused by wind or temporary loss of GPS did not appear to have any significant effects on measurement error. Our study provides substantial evidence of the high accuracy associated with using images captured by UAS for measuring dimensions of structures positioned on water and land surfaces. Ultimately, accurate surveys of glacial ice used by harbor seals will improve our understanding about the role of decreasing habitat in explaining population variability between different tidewater glaciers.
    • Evaluating the hooking injury and immediate physiological response of wild rainbow trout to capture by catch-and-release angling

      Meka, Julie M. (2003-08)
      Rainbow trout from the Alagnak River watershed, Alaska, were captured by angling to determine the types of terminal gear contributing to hooking injury and the physiological response to angling based on concerns over high incidences of hooking injuries and the physiological impact of multiple recaptures on individual fish. Landing and hook removal times were recorded for a portion of fish captured, and plasma cortisol, glucose, ions (sodium, chloride, potassium), and lactate were evaluated in fish following capture to document physiological changes in relation to capture duration. The majority of new injuries resulted when fish were captured using barbed J hooks, and barbed J hooks took longer to remove than barbless hooks. Fish were hooked internally more frequently when captured with J hooks compared to circle hooks, but similar overall hooking injury rates were observed for both hook types. Novice anglers injured proportionally more fish than experienced anglers, and experienced anglers took longer to land fish than novice anglers. Plasma cortisol and lactate increased significantly with increasing landing and handling times. Fish captured at cooler water temperatures had significantly lower cortisol and lactate concentrations than fish caught at warmer temperatures indicating that water temperature influenced the magnitude of the physiological response.
    • Evaluation of growth and migration trends on the survival and recruitment of chinook salmon in Southeastern Alaska rivers

      Berkman, Stephanie; Sutton, Trent; Adkison, Milo; Mueter, Franz (2017-12)
      Highly variable recruitment and declines in productivity and abundance of Chinook Salmon Oncorhynchus tshawytscha have created economic and cultural hardships for communities throughout Alaska. Although pre- and post-smolt growth are important for determining brood-year (BY) survival and productivity for Pacific salmon through size-mediated mortality, these relationships remain unclear for Chinook Salmon. As a result, it is necessary to better understand the relationships between environmental and biological factors that influence freshwater and marine growth, smolt outmigrations, and recruitment success. This study used retrospective growth to identify the importance of annual growth in determining BY survival and recruitment, determine if growth dependency between growth zones was present, and examine growth differences among age classes for Chinook Salmon in the Chilkat (BYs 1985 - 2007) and Stikine (BYs 1991 - 1998 and 2000 - 2007) rivers. Biological and environmental factors were also assessed to determine their influence on freshwater smolt production, smolt outmigration, and marine survival. Greater first-year marine growth was correlated with higher BY total return and productivity for Chinook Salmon from the Chilkat River and higher BY marine survival for Chinook Salmon from the Stikine River. Daily smolt outmigration of Chilkat River Chinook Salmon was positively correlated to water temperature and negatively correlated to discharge (Deviance explained = 68.5%), while timing of the start of outmigration was influenced by nearshore sea surface temperatures (R² = 0.57) and timing of the mid and end points were positively related to smolt length (R² = 0.72 and 0.34, respectively). Freshwater smolt production was negatively correlated to parr length and fall discharge and positively correlated to spring temperature and discharge (R²adj= 0.52). Marine survival of Stikine River Chinook Salmon was significantly related to smolt size (R² = 0.26), while Chilkat River Chinook Salmon were positively related to migration timing and smolt length and negatively related to discharge (R² = 0.5). These results support the importance of the early marine period in determining year-class strength and highlight the variation in mechanisms that influence recruitment success of Chinook Salmon stocks.
    • Evaluation of growth, survival, and recruitment of chinook salmon in Southeast Alaska rivers

      Graham, Cory J.; Sutton, Trent; Adkison, Milo; McPhee, Megan (2016-12)
      Recent reductions in the run sizes of Chinook Salmon Oncorhynchus tshawytscha in Southeast Alaska have resulted in social and economic hardships within the region. Pacific salmon yearclass strength may be determined by size-selective processes during the early marine phase of their life cycle; however, the relative importance of growth during freshwater and marine residence in determining recruitment success is unknown. A scale-based retrospective analysis was conducted to examine the effects of freshwater and annual marine growth and early marine conditions on survival to reproductive maturity for female Chinook Salmon by brood year (BY) in the Taku (BYs 1979 -- 1985, 1990 -- 1999, 2002 -- 2004) and Unuk (BYs 1981 -- 1983, 1986 -- 1988, 1994 -- 2003, 2005 -- 2006) rivers. First-year marine growth was positively related to survival and total return for Chinook Salmon stocks from both systems. Growth during freshwater residence (i.e., size-at-ocean entry) was not related to survival or total return of either stock. In addition, there was a positive relationship between marine survival of Unuk River Chinook Salmon and sea-surface temperatures in Upper Chatham Strait, Icy Strait, and Auke Bay Monitor (P = 0.04) during early marine residence. The results of my research highlight the importance of growth and marine conditions during the first year at sea in determining the survival of Chinook Salmon in Southeast Alaska and suggest that current declines in run sizes and survival of stocks within this region may be the attributed to poor growth conditions or growth during early marine residence.
    • Evaluation of marine and freshwater growth and survival of Auke Creek coho salmon

      Russell, Joshua R.; Tallmon, David; McPhee, Megan; Adkison, Milo; Vulstek, Scott (2019-08)
      Coho Salmon (Oncorhynchus kisutch) are a species of great social and economic importance for commercial, sport, personal-use, and traditional harvest. We explored factors influencing Auke Creek Coho Salmon smolt production, growth, and marine survival. We analyzed 35 years (1980-2014) of data collected at the Auke Creek Research Station weir in Juneau, Alaska. This extensive data series allowed for an analysis of Auke Creek Coho Salmon growth and survival that is not possible elsewhere. Creek flow best explained variation in smolt-per-adult production. Analysis of freshwater and saltwater scale growth zones failed to identify a specific growth zone with a significant influence on marine survival. Marine survival had a positive relationship with the magnitude of regional hatchery releases and the Pacific Decadal Oscillation. Changes in climate and hatchery production could have negative effects on survival of Auke Creek Coho Salmon, as evidenced by low returns in recent years associated with anomalously high temperatures in the Gulf of Alaska. The impact of climate change and increased hatchery production should be considered in future management decisions.
    • Evaluation of prey composition and nutritional value of diets of free-ranging harbor seals (Phoca vitulina) from Tugidak Island

      Geiger, Gretchen L.; Atkinson, Shannon; Carpenter, James; Horstmann-Dehn, Larissa; Wynne, Kate (2012-12)
      Changes in climate can cause shifts in ecosystem structure that can affect quantity or quality of prey available to predator populations. Due to sex or age-specific behaviors of predators, certain classes within a population may be more severely impacted by changes in their diet. This study evaluated prey composition and nutritional value of summer diets of harbor seals (Phoca vitulina richardii) from Tugidak Island, Alaska from 2001-2009. The MIXIT-WIN program was used to estimate the nutritional value of average harbor seal diets. Changes in relative abundance of certain prey species were correlated to sea surface temperature anomalies. Despite changes in prey composition, the nutritional value of the average harbor seal diet did not change. Fecal corticosteroid metabolite profiles were analyzed to identify age and sex of individual harbor seals from scats. Profiles obtained from a known adult male harbor seal could be differentiated from those of known adult female and juvenile male seals. Similar profiles were observed in unknown age and sex samples. Even though diet diversity differed between these groups, the nutritional quality of consumed diets was not significantly different. Tugidak Island harbor seals have flexible diets allowing them to capitalize on available prey to maintain their nutritional intake.
    • An examination of hydrography and sea level variability in the Gulf of Alaska

      Kelly, James Bruce; Weingartner, Thomas; Simmons, Harper; Kowalik, Zygmunt (2015-05)
      This thesis summarizes a detailed analysis of Seward sea level (SSL) in the Gulf of Alaska (GOA) and hydrography at oceanographic station GAK1 along the oceanographic monitoring line outside of Resurrection Bay, Alaska. SSL variability was examined with respect to forcing by tides, sea level pressure (SLP), wind, the steric contribution due to water column variations in temperature and salinity, and several climatic indices. In addition, multi-decadal trends in sea level and hydrography were also examined. The period of analysis spans 1970 -2010. Tidal motion (periods < 1day), account for ~97% of the total sea level (SL) variance while SLP variations, induced by the inverted barometer effect, account for ~2% of the total variance. After removing these influences, along-shore wind stress and sea level are highly coherent for the 2 - 60 day subtidal period range and account for ~40 - 50% of the SSL variance over these timescales. The steric contribution, based on the geopotential height referenced to 200 m (GH200), is also coherent with SSL, but it only accounts for ~10% of the SSL variance at these timescales. The along-shore wind stress-SSL coherence varies seasonally and is greatest in winter when winds are strongest and smaller in summer when wind variability is reduced. The annual cycle in SSL is coherent and in-phase with GH200. The latter is primarily controlled by the annual cycle in GOA coastal freshwater discharge and its effect on coastal salinities. SSL variations are also significantly correlated with the Pacific Decadal Oscillation (PDO) and the Southern Oscillation Index (SOI). Over the 40-year record examined here SSL shows a decreasing trend due to continental rebound. There are also statistically significant linear long-term trends in temperature and salinity as measured at GAK1. These trends indicate that the upper 100 m is warming at ~0.20 oC decade-1 and at 0.15 oC decade-1 between 100 - 200 m. Surface salinities are decreasing at 0.15 decade-1, while salinities between 100 and 200 m are increasing by 0.025 decade-1. The surface salinity trends are consistent with an increase in coastal freshwater discharge due to increased glacial ablation and increased precipitation. In aggregate, these trends indicate that the GOA shelf has become more stratified over the past 40 years.
    • Examination of saffron cod (Eleginus gracilis) population genetic structure

      Smé, Noël A.; Gharrett, Anthony; Mueter, Franz; Heifetz, Jonathan (2019-05)
      The Saffron Cod (Eleginus gracilis) is an abundant forage fish that inhabits the coastlines of the north Pacific and Arctic oceans. We examined Saffron Cod population genetic structure to provide a reference baseline in anticipation of human and climate-change alterations of the Arctic environment. Nine microsatellites were designed to describe the genetic compositions of and variation among 40 collections of Saffron Cod from four regions (northwestern Alaska, Gulf of Alaska, Sea of Okhotsk, and Gulf of Anadyr). The northwestern Alaska collections (Bering Sea, Norton Sound, and Chukchi Sea) exhibited little genetic divergence. The Gulf of Anadyr collection differed from other regions but was most similar to those of the northwestern Alaska region. The two collections within the Sea of Okhotsk (Sakhalin Island and Hokkaido Island) differed genetically, but not to the extent they did from other regions. The collections from the Gulf of Alaska (Kodiak Island and Prince William Sound) comprised a lineage that was distinct from all of the other collections, including the geographically adjacent northwestern Alaska collections. The absence of genetic structure among northwestern Alaska collections probably reflects their recent expansion into previously unavailable habitat that became available after the Last Glacial Maximum (~16,000 years ago). The divergence of the Gulf of Alaska lineage may have resulted from recurrent episodes of isolation from previous glaciations.
    • Examining sources of primary production and bottom-up limitations in nearshore ecosystems of the northeast Pacific Ocean using fish based indicators

      Biela, Vanessa Rebeca von; Kruse, Gordon H.; Zimmerman, Christian E.; Okkonen, Stephen R.; Mueter, Franz J.; Black, Bryan A. (2015-05)
      Our ability to forecast the fate of ecosystems and species hinges on an understanding of how biological systems respond to their environment. In this dissertation, natural indicators of diet (stable isotopes) and production (otolith growth increment width) in two common fishes were used to investigate energy pathways and biophysical relationships in nearshore kelp forests spanning two large marine ecosystems with contrasting oceanography, the upwelling system of the California Current and the downwelling system of the Alaska Coastal Current. Stable isotope analysis indicated high proportions of kelp-derived carbon in two common predatory fish, pelagic-feeding Black Rockfish and benthic-feeding Kelp Greenling. Routinely using both kelp and phytoplankton energy channels reflects strong benthic-pelagic coupling in nearshore marine food webs and may confer food web resilience to perturbations in either energy channel. A network of annual otolith growth chronologies were used to test bottom-up limits of production for nearshore systems and later explore other possible correlates of production. Results of hypothesis tests were consistent with bottom-up forcing of nearshore marine ecosystems, with light and nutrients constraining primary production in pelagic food webs and temperature constraining benthic food webs. A separate exploratory analysis indicated that biophysical relationships were common with (1-2 years) and without time lags and suggested that differences in the abundance and quality of prey influenced the growth of fish through bottom-up processes. The findings from the separate exploratory analysis were generally consistent with findings from hypothesis testing. Lagged relationships were consistent with increasing higher nearshore prey abundance during warm conditions in the Alaska Coastal Current and during cool conditions in the California Current in both pelagic and benthic food webs. Relationships without time lags indicated that benthic prey quality increased during warm conditions in both current systems, while the quality of pelagic nearshore prey increased during cool conditions in the California Current and warm conditions in the Alaska Current. Overall, results of this dissertation demonstrate that kelp provides a source of energy to higher trophic level predators and that continued warming will likely have a negative influence at lower latitudes first (e.g., California Current), while production in higher latitudes (e.g., Gulf of Alaska) may initially increase.
    • Exploring the potential role of late stage predation and Chinook salmon age structure

      Manishin, Kaitlyn A.; Seitz, Andrew C.; Westley, Peter A. H.; Cunningham, Curry J.; Goldman, Kenneth J. (2018-12)
      Chinook salmon (Oncorhynchus tshawytscha) populations across the North Pacific have displayed a decrease in body size-at-return resulting from declines both in age- and body size-at-maturity. These changes have precipitated the loss of the oldest age classes in some populations and have occurred throughout the range of this species, suggesting a shared - yet currently unknown - driver in the common marine environment. A hypothesis for the cause of these changes is intense and/or selective predation marine mortality after the first winter in the ocean, potentially from predators selectively removing relatively large sub-adult Chinook salmon. Here I consider the question: under what circumstances could predation on large sub-adult individuals by salmon sharks (Lamna ditropis) change the age structure of a Chinook salmon population? To address this question, I first estimated total per capita prey consumption by salmon sharks - an increasingly acknowledged predator of salmon on the high seas - using three methods: 1) daily ration requirement, 2) bioenergetic mass balance, 3) and a von Bertalanffy growth model. Second, I examined the effects of additional predation on an indicator Chinook salmon population from the Yukon River by simulating alternative predation scenarios with a stage-structured life cycle model. Scenarios described the strength and selectivity of predation, and the resulting simulated age structure was then compared to observed demography. The selectivity and intensity of removals required to produce this change in age structure were considered in the context of top predators, focusing on salmon sharks. The daily ration method yielded individual salmon shark consumption estimates of 1461 and 2202 kg·yr-1, the mass-balance method produced estimates of 1870 kg·yr-1, 2070 kg·yr-1, 1610 kg·yr-1, and 1762 kg·yr-1, depending on assumed diet, and the growth model output estimates of 16,900 kg·yr-1 or 20,800 kg·yr-1, depending on assumed assimilation efficiency. The per capita prey consumption estimates from the mass-balance method may be the most realistic because they incorporated life history data specific to salmon sharks and did not produce extreme values. Taken as a whole, these estimates suggest salmon sharks have energetic requirements similar to those of piscivourous marine mammals and corroborates conclusions of previous research suggesting that endothermic fishes exhibit metabolic rates similar to marine mammals. The simulated mortality scenarios that most closely mimicked observed shifts in age structure of the indicator Chinook salmon population focused intense and selective predation on the third year of Chinook salmon residence in the ocean. This simulated predation is corroborated by emerging results from an independent electronic tagging study in which tagged Chinook salmon experienced high predation rates, and research suggesting that killer whales (Orcinus orca) selectively prey upon Chinook salmon in their third year at sea. In summary, salmon sharks likely have high energetic requirements that could result in a large biomass of prey consumed, Chinook salmon populations are sensitive to predation during the third ocean year, and salmon sharks and other predators appear to frequently consume fish at that ocean stage. Taken together, these lines of evidence point to a potentially important mechanism for top down pressure on Chinook salmon populations that may explain observed changes in age-at-return, which in turn can affect population productivity. Future work and more robust data on predator distributions and abundances are needed to explore this finding further.