• 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.
    • Biogeochemical tracers of change in Pacific walruses past and present

      Clark, Casey; Horstmann, Lara; Misarti, Nicole; Konar, Brenda; Severin, Ken; Lemons, Patrick (2019-05)
      Reduced sea ice and projected food web shifts associated with warming of the Arctic have raised concerns about the future of Arctic species. Pacific walruses (Odobenus rosmarus divergens) use sea ice as a platform for molting, giving birth, and resting between foraging bouts. Exactly how sea ice loss will affect walruses is difficult to predict, due to a lack of information about regional ecosystems and their responses to climate change. The objectives of the research in this dissertation were to 1) examine how walrus diet changed in response to shifting sea ice conditions over the last 4,000 years, with the goal of generating predictions about how current and future ice loss may affect the walrus population; 2) make it easier to directly compare the results of retrospective and contemporary stable isotope studies of walruses; and 3) generate new tools to assist wildlife managers in monitoring the walrus population in an uncertain future. Stable carbon and nitrogen isotope ratios of walrus bone collagen indicated that diet was similar during previous intervals of high and low sea ice; however, diet variability among individual walruses was greater when sea ice cover was low, suggesting decreased abundance of preferred mollusk prey. Modern walrus diet was different from both previous high and low ice intervals, meaning that food webs in the Arctic are still in a state of flux, or that recent changes are novel within the last 4,000 years. Tissue-specific stable isotope discrimination factors were generated for walrus muscle, liver, skin, and bone collagen to improve comparisons between retrospective and contemporary studies of walrus diet. Additionally, lipid normalization models were parameterized for walrus skin and muscle, thereby making future walrus stable isotope research more feasible by reducing analytical costs and allowing the use of non-lethal sample collection. Finally, a novel technique for estimating the age at onset of reproductive maturity using concentrations of zinc and lead in the teeth of female walruses was established. This new approach has the potential to become a powerful tool for monitoring the walrus population and may be applicable to other species. Use of this technique on archived specimens may make it possible to examine changes in wildlife population dynamics across thousands of years.
    • Dietary effects on protein turnover in three pinniped species, Eumetopias jubatus, Phoca vitulina, and Leptonychotes weddellii

      Inglis, Susan D.; Castellini, Michael; Atkinson, Shannon; Barboza, Perry; Carpenter, James; Rea, Lorrie (2019-05)
      The role of dietary protein in pinniped (seal and sea lion) nutrition is poorly understood. Although these marine mammals derive the majority of their daily energetic needs from lipid, lipids cannot supply essential amino acids which have to come from protein fractions of the diet. Protein regulation is vital for cellular maintenance, molt, fasting metabolism, exercise and development. Proteins are composed of linked amino acids (AA), and net protein turnover is the balance between protein synthesis from component AA, and degradation back to AA. Protein regulation is influenced by dietary intake and quality, as well as physiological and metabolic requirements. In this work, pinniped diet quality was assessed through comparisons of amino acid profiles between maternal milk, blood serum, and seasonal prey of wild juvenile Steller sea lions (Eumetopias jubatus) in Southcentral Alaska. Both Pacific herring (Clupei pallasi) and walleye pollock (Gadus chalcogramma) showed similar patterns to milk in essential and branched chain amino acid content. Serum amino acid profiles suggest the juvenile sea lions were not in protein deficit at the time of capture. Protein metabolism in the blood and urine was assessed through turnover studies using amino acid tracers. The turnover kinetics of ¹⁵N-labelled glycine in the blood amino acid and protein pool, red blood cells, and urine urea were measured in wild adult female Weddell seals (Leptonychotes weddellii) in the Antarctic. Labelled glycine moved quickly into serum protein and red blood cells (1-2 hours) and urinary urea (2-4 hours). The turnover rates in the blood amino acid and urine urea pools demonstrated a reduced turnover rate associated with molting. Lastly, whole body protein turnover experiments using a single bolus ¹⁵N-labelled glycine tracer method with endproduct collection of blood, feces and urine were conducted on 2 Cohort groups of captive Alaskan harbor seals over 2 years. Season was found to have the greatest effect on whole body protein turnover, which increased during the winter and decreased in the summer molt. Conversely, protein intake decreased during the winter and increased in the summer molt. This pattern corresponded with an increase in mass and protein synthesis in the winter, while mass decreased and protein degradation rates increased in molting seals. Weaning also influenced the patterns with reduced protein turnover in newly weaned animals that had recently transitioned from milk to a fish diet. This project presents results on whole body protein turnover rates in nonfasting pinnipeds and reveals that protein turnover is strongly regulated by developmental and seasonal physiological and metabolic demands.
    • Diets, distribution and population dynamics of Arctic cod (Boreogadus saida) in Arctic shelf ecosystems

      Marsh, Jennifer M.; Mueter, Franz; Danielson, Seth; Iken, Katrin; Quinn, Terrance J. II (2019-05)
      With climate warming and longer open-water seasons in the Arctic, there is an increased interest in shipping, oil exploration and the expansion or development of commercial fisheries. Anticipated natural and anthropogenic changes are expected to alter the Arctic shelf ecosystems, including their fish communities. As a component of the Arctic Ecosystem Integrated Survey (Arctic Eis), this project presented a unique opportunity to assess the ontogenetic, spatial and temporal variability in the distribution, abundance and trophic roles (trophic level and diet sources) of key fish species in the Chukchi Sea. For my dissertation, I addressed three objectives to advance our understanding of Arctic cod (Boreogadus saida) as a key component of Arctic ecosystems. First, I characterized the current range of variability in trophic roles within the system and explored the role of advection in shaping the fish communities' diet (isotopic signatures) with a focus on Arctic cod. Second, I examined environmental and biological influences on the distribution and abundance of Arctic cod and provided an updated stock assessment for the Chukchi Sea. Finally, I broadened the geographic scope and used available time series of survey data at the southern margin of their range in the Pacific (eastern Bering Sea) and Atlantic (Newfoundland/Labrador shelves) sectors to assess the influence of temperature, predators and competitors on their distribution. Compared to age-1+ Arctic cod, age-0 Arctic cod had a less diverse diet regardless of water mass and were limited to colder temperatures. Together, this suggests that younger Arctic cod are more vulnerable to climate change. Estimates of egg production and early survival suggest that the numbers of mature Arctic cod present in the survey area during summer are unlikely to produce the observed high abundances of age-0 Arctic cod in the Chukchi Sea. Moreover, Arctic cod distributions in their southern ranges were highly influenced by temperature and to a lesser extent by competitors and predators. When temperatures were warmer, Arctic cod occupied a smaller area. These results inform the management of Arctic cod in a rapidly changing environment and provide benchmarks against which to assess future changes.
    • Ecological interactions among important groundfishes in the Gulf of Alaska

      Barnes, Cheryl L.; Beaudrea, Anne H.; Dorn, Martin W.; Holsman, Kirstin K.; Hunsicker, Mary E.; Mueter, Franz J. (2019-12)
      Complex ecological interactions such as predation and competition play an important role in shaping the structure and function of marine communities. In fact, these processes can have greater impacts than those related to fishing. We assessed ecological interactions among economically important fishes in the Gulf of Alaska - a large marine ecosystem that has recently undergone considerable shifts in community composition. Specifically, we developed an index of predation for Walleye Pollock (Gadus chalcogrammus) to examine spatiotemporal changes in consumption, quantify portfolio effects, and better understand diversity-stability relationships within the demersal food web. We also evaluated the potential for competition between two important pollock predators, Arrowtooth Flounder (Atheresthes stomias) and Pacific Halibut (Hippoglossus stenolepis). We found highly variable predation intensity on Gulf of Alaska pollock. The combination of a single dominant predator and synchronous consumption dynamics indicated strong top-down control in the region. Spatial heterogeneity, however, may offset trophic instability at the basin scale. Assessments of resource partitioning provided little indication for competition between Arrowtooth Flounder and Pacific Halibut of similar lengths. Morphological differences between the two flatfish predators prompted an exploration into whether our conclusions about resource partitioning were dependent upon the size metric used. From this study, we found a relatively early onset of piscivory for Arrowtooth Flounder. Relationships between predator size and prey size also suggested gape limitation among Pacific Halibut sampled. Trophic niche separation was more pronounced for fishes with larger gapes, indicating greater potential for competition among smaller Arrowtooth Flounder and Pacific Halibut in Southeast Alaska. Reexamining basin-scale relationships between spatial and dietary overlap according to gape size would further elucidate the effects an increasing Arrowtooth Flounder population has had on changes in Pacific Halibut size-at-age. Results from this dissertation improve our understanding about the impacts of complex ecological interactions on population and community dynamics, and how those interactions may change in time, space, and under different environmental conditions.
    • Foraging tactics of humpback whales feeding near salmon hatchery-release sites in Southeast Alaska

      Kosma, Madison M.; McPhee, Megan V.; Straley, Janice M.; Szabo, Andrew R.; Wooller, Matthew J. (2019-12)
      Increases in the humpback whale (Megaptera novaeangliae) population have generated considerable interest in understanding the foraging habits of these large marine predators in the Gulf of Alaska. Globally, humpback whales are classified as generalist predators but are known to exhibit localized differences in diet. Intensified predation pressure is of particular concern to resource managers, who have observed whales feeding at juvenile hatchery salmon release sites in Southeast Alaska. We assessed the diets and behavioral tactics of humpback whales foraging near Hidden Falls Hatchery release sites (in Chatham Strait, 2016 to 2018) to better understand their predatory effects on juvenile hatchery-reared salmon. We used skin biopsies, prey sampling, and stable isotope analysis to estimate whales' diet composition. Aerial footage and photographic sequences were used to assess the foraging tactics used on this prey source. We observed three individual whales repeatedly feeding on juvenile hatchery-reared salmon, and we were able to sample them multiple times over a period spanning shifts in diet. Overall, the diets of these whales were higher trophically than other humpback whales foraging in the area, even before feeding on juvenile hatchery salmon started. These hatchery-feeding whales may be generally more piscivorous than other whales, which focused on planktivorous prey. Our repeat sampling, in conjunction with scheduled introductions of a novel prey source, provided a semi-controlled feeding experiment that allowed for incorporation and turnover rate estimates from humpback whale tissue in a way that was not previously possible for large, free-ranging cetaceans. Finally, during the course of this study we discovered an undescribed feeding tactic employed by hatchery-associated whales. We observed the use of solo bubble-nets to initially corral prey, followed by calculated movements to establish a secondary boundary with the pectoral fins that further condensed prey and increased foraging efficiency. Our study provided the first empirical evidence for what we describe as "pectoral herding". This work deepens our knowledge about humpback whale foraging ecology, how this innovative species is able to exploit newly available prey, and to what extent they feed on commercially valuable hatchery salmon.
    • Mercury concentrations and feeding ecology of fishes in Alaska

      Cyr, Andrew Philip; López, Juan Andres; O'Hara, Todd; Wooller, Matthew; Seitz, Andrew (2019-05)
      Mercury (Hg) is a ubiquitous contaminant found in nearly every fish species analyzed. Certain forms of Hg accumulate efficiently in fish tissues, sometimes reaching concentrations of concern for human and wildlife health when consumed. This has motivated considerable research and interventions surrounding fish consumption with Hg concentrations as the underlying cause of over 80% of fish consumption advisories in the United States and Canada. The ecological and physiological drivers that influence the concentrations of Hg in fishes are complex and vary among taxa spatially and temporally. Studying these drivers and their respective influences on Hg concentrations can help elucidate observed differences in Hg concentrations across space and time, which can then be used to improve management and consumption strategies. Here I present a series of studies focused on the chemical feeding ecology of Hg by measuring total Hg (THg) concentrations and ratios of nitrogen and carbon stable isotopes in multiple fish species from three regions in Alaska. In Chapter 2 I described foundational field collection efforts to characterize the fish communities from West Creek and the Taiya River in Klondike Gold Rush National Historical Park, and the Indian River in Sitka Historical National Park, Alaska. This chapter and agency report presents a survey of the fish species assemblage of the rivers and laid the framework for the regional analyses I conducted in the study presented in Chapter 3. In Chapter 3 I report inter- and intra-river comparisons of THg concentrations and associated feeding ecology of riparian Dolly Varden, separated by anadromous barriers in each system. I concluded that resident Dolly Varden that co-habit riverine locations with spawning salmon consume more salmon eggs than resident Dolly Varden from other locations of the same river that do not co-habit with spawning salmon. This is reflected in the isotopic composition of their tissues, and subsequently the THg concentrations of these fish are lower relative to Dolly Varden from parts of the same river above anadromous barriers. In Chapter 4, I describe regional patterns of THg concentrations and stable isotope values of carbon and nitrogen in nine species of fish and invertebrates from the Bering Sea and North Pacific Ocean along the Aleutian Islands, using Steller sea lion management zones as a spatial framework. I determine that most species from the Western Aleutian Islands have greater THg concentrations, and more negative δ¹³C values than those from the Central Aleutian Islands, indicating ecosystem-wide differences in THg concentrations and fish feeding ecology. I also determined that Amchitka Pass, a well-documented oceanographic and ecological divide along the Aleutian Island chain, aligns better with differences in THg concentrations than the boundary between Steller sea lion management zones. In Chapter 5, I report THg and methylmercury concentrations in fishes of Kotzebue Sound, including seven species that are important for subsistence users. I determined that fork length influences Hg concentrations within individual species, and that trophic relationships within a food web, a factor associated with biomagnification, influences Hg concentrations across the entire food web. I also observed that muscle tissues from virtually every individual fish had Hg loads below the State of Alaska's criteria for unlimited consumption. Taken together, the work conducted in this dissertation helps us better understand the ecological dynamics of Hg in aquatic food webs and has contributed to Hg monitoring of fish resources across parts of Alaska.
    • 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).
    • Tracing sea ice algae into various benthic feeding types on the Chukchi Sea shelf

      Schollmeier, Tanja; Iken, Katrin; Wooller, Matthew; Hardy, Sarah (2018-12)
      Climate change in the Arctic is expected to have drastic effects on marine primary production sources by shifting ice-associated primary production to an overall greater contribution from pelagic primary production. This shift could influence the timing, amount, and quality of algal material reaching the benthos. We determined the contribution of sea ice particulate organic matter (iPOM) to benthic-feeding invertebrates by examining concentrations and stable carbon isotope values (expressed as δ¹³C values) of three FAs prominent in diatoms: 16:4(n-1), 16:1(n-7) and 20:5(n-3). Our underlying assumption was that diatoms make up the majority in sea ice algal communities compared with phytoplankton communities. According to the FA concentrations, subsurface deposit feeders consumed the most iPOM and suspension feeders the least. Conversely, there were little differences in δ¹³C values of FAs between deposit and suspension feeders, but the higher δ¹³C values of 16:1(n-7) in omnivores indicated greater consumption of iPOM. We suggest that omnivores accumulate the ice algal FA biomarker from their benthic prey, which in turn may feed on ice algae from a deposited sediment pool. The dissimilar results between FA concentrations and isotope values suggest that the FAs used here may not be sufficiently source-specific and that other unaccounted for production sources, such as bacteria, may also contribute to the FA pool. We propose that FA isotope values are a more indicative biomarker than FA concentrations, but there is a further need for more specific ice algal biomarkers to resolve the question of ice algal contributions to the Arctic benthic food web.