• 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.
    • 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.
    • 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.
    • Insight into the diet history of ice seals using isotopic signatures of muscle tissue and claws

      Carroll, Sara Shanae; Norcross, Brenda; Horstmann-Dehn, Larissa; Quakenbush, Lori; Wooller, Matthew (2012-05)
      Climate change and sea ice reduction in the Arctic may impact foraging of ice-associated predators. The goal of my thesis work was to examine interannual differences in the diet of ringed, bearded, spotted, and ribbon seals as described by stable nitrogen and carbon isotope ratios of muscle tissue and claws to assess foraging plasticity. Isotopic mixing models from muscle data were used to describe the proportional contribution of prey groups during 2003, 2008-2010. Results showed a higher proportional contribution of smelt (Osmeridae) and benthic prey to ringed and bearded seal diets in 2003 compared to 2008-2010. Seasonal keratin layers deposited in claws can document trophic history up to about 10 years. During 2007 (record ice minimum), proportionally more ringed seals fed at a lower trophic level, while spotted seal adults and young-of-the-year fed at a lower trophic level during 2006. Bearded seals may have been foraging more pelagically from 2008 to 2010. Ice seals may be taking advantage of more abundant pelagic crustaceans as the Arctic ecosystem changes to a pelagic-dominated food web. Interannual variations and high variability among species and individual diets illustrate the opportunistic nature and flexibility of ice seals to changes in prey composition.
    • Lake trout (Salvelinus namaycush) otoliths as indicators of past climate patterns and growth in Arctic lakes

      Torvinen, Eric S.; Falke, Jeffrey; Arp, Christopher; Zimmerman, Christian; Sutton, Trent (2017-05)
    • Regional distribution, life history, and morphometry of spawning stage Capelin Mallotus villosus

      Ressel, Kirsten N.; Sutton, Trent M.; Bell, Jenefer L.; Seitz, Andrew C. (2019-12)
      Capelin Mallotus villosus is a forage fish that is integral to many Arctic and subarctic marine food webs, but is less thoroughly studied outside the Atlantic Ocean. The goal of this research was to study spawning Capelin in data-poor areas, particularly in waters off the coast of Alaska and the western Canadian Arctic, to enrich baseline data and allude to intraspecies diversity. Chapter one examined the distribution and life history of spawning Capelin in Norton Sound, Alaska, by conducting aerial surveys, collecting sediment samples to characterize beach spawning habitats, and identifying biological attributes of spawners (e.g., body size, age, fecundity, etc.). Chapter two used a geometric morphometric approach (i.e., relative warps) and multiple statistical techniques (i.e., relative warp analysis, Procrustes analysis of variance, estimates of morphological disparity, and canonical variates analysis) to differentiate among and within putative populations of spawning Capelin in the western Canadian Arctic, Newfoundland, Canada, and Alaska. Spawning Capelin in Norton Sound portrayed similar behaviors, occupied similar beach habitats, and encompassed a similar range in biological attributes as fish observed in other regions throughout this species' geographic distribution. However, average spawner body size, age, fecundity, and morphometry differed among regions. These results suggest that Capelin exhibit some similarities in spawning behavior and habitat use across their geographic distribution, but may exhibit population-specific differences in biological attributes among and within regions.
    • Sensitivity to hydrocarbons and cytochrome P4501A enzyme activity in Arctic marine birds and waterfowl

      Riddle-Berntsen, Ann E.; Hollmén, Tuula; Buck, C. Loren; Aguilar-Islas, Ana (2017-12)
      The Arctic is host to a taxonomically diverse group of birds, including species of conservation and subsistence importance that spend many months of their annual cycle in the region. With prospects for oil and gas resource development and increases in vessel traffic in the Beaufort and Chukchi Seas, arctic birds could be valuable bioindicators to monitor contaminants and specifically hydrocarbons from crude oil. Using liver cytochrome P4501A (CYP1A) activity, I measured levels of hydrocarbon exposure in three bird species of subsistence importance: king eiders (Somateria spectabilis), common eiders (Somateria mollissima), and greater white-fronted geese (Anser albifrons). Over the course of three years, I collected liver samples during spring and fall hunts near Utqiaġvik (formally Barrow) and validated methods for both direct-take and opportunistic liver sampling. Enzyme activity results show significant differences in CYP1A activity levels among species, seasons, and years. Except birds collected during fall 2014, when significantly high enzyme activity was observed in all sampled species, all other collections resulted in median activity levels similar to those reported in other sea duck species in Alaska from un-oiled or non-industrialized habitats. I also used species-specific hepatocyte culture in a broader selection of arctic marine birds and waterfowl candidate bioindicators to assess and compare species CYP1A activity responses as a measure of sensitivity to hydrocarbons. Cytochrome P4501A results from hepatocyte cultures dosed with positive control reference reagents and Alaska North Slope crude oil showed differences in species responses. Based on sensitivity results, I recommend the common eider and common murre (Uria aalge) as bioindicators for use in CYP1A monitoring due to their consistent and measureable responses in our experiments. However, additional species are promising candidates (e.g., tufted puffin; Fratercula cirrhata) but further testing is needed. This is the first study of reference hydrocarbon exposure and comparative laboratory assessment of CYP1A inducing compounds for arctic marine birds and waterfowl and these results form the basis for hydrocarbon monitoring programs and risk assessments.
    • Using remote sensing, occupancy estimation, and fine-scale habitat characterization to evaluate fall chum salmon (Oncorhynchus keta) spawning habitat usage in Arctic Alaska

      Clawson, Chelsea M.; Falke, Jeffrey; Westley, Peter; Prakash, Anupma; Martin, Aaron (2017-08)
      Groundwater upwellings provide stable temperatures for overwinter salmon embryo development and this process may be particularly important in cold, braided, gravel-bed Arctic rivers where rivers may freeze solid in the absence of upwellings. Aerial counts and remote sensing were used during 2013-2015 to estimate fall chum salmon (Oncorhynchus keta) spawner abundance states (e.g., low or high), classify river segments by geomorphic channel type (primary, flood, and spring), and map thermal variability along a 25.4 km stretch of the Chandalar River in interior Alaska. Additionally, I used on-the-ground examination of fine scale variation in physical habitat characteristics at 11 representative sites to characterize habitat variability, placed temperature loggers to assess overwinter thermal conditions in redds, and used a developmental model to predict hatching and emergence timing given known spawning dates and incubation temperatures. I delineated 330 unique river segments (mean length = 536 m) and used a multi-season multistate occupancy model to estimate detectability, occupancy, and local colonization and extinction rates. Triplicate surveys performed in 2014 allowed me to estimate detectability and the influence of observer bias. I found that detectability did not vary by observer, channel type, or segment length, but was better for high abundance (0.717 ± 0.06 SE) relative to low abundance (0.367 ± 0.07 SE) aggregations. After correcting for imperfect detection, the proportion of segments occupied by spawning fall chum salmon was highest in 2014 (0.41 ± 0.04 SE), relative to 2013 (0.23 ± 0.04) and 2015 (0.23 ± 0.04). Transition probabilities indicated unoccupied segments were likely to remain so from year to year (2013→2014 = 0.67; 2014→2015 = 0.90), but low abundance spawning segments were dynamic and rarely remained in that state. One-third of high abundance sites remained so, indicating the presence of high quality spawning habitat. Mean segment temperatures ranged from -0.5 to 4.4°C, and occupancy varied positively with temperature. I predicted a 50% probability of occupancy in segments with temperatures of 3°C. With my on-the-ground work, I found that habitat characteristics varied among the three channel types, with most significant differences between main channel and off-channel habitats. Dissolved oxygen and pH decreased with increasing temperature, and conductivity increased with temperature. Predicted hatching and emergence timing ranged from 78 and 176 days (December 11th and March 18th) to 288 and 317 days (July 8th and August 6th), respectively, post-spawning, and were highly variable within sites and among channel types owing to high habitat thermal heterogeneity. Because the Chandalar River supports 30% of the fall chum salmon run in the Yukon River Basin, information such as provided by this study will be critical to allow resource managers to better understand the effects of future climate and anthropogenic change in the region.