• Bioenergetic and economic impacts of humpback whale depredation at salmon hatchery release sites

      Chenoweth, Ellen M.; Atkinson, Shannon; McPhee, Megan; Criddle, Keith; Friedlaender, Ari; Heintz, Ron; Straley, Janice (2018-08)
      Since 2008, humpback whales have been documented depredating hatchery-produced juvenile salmon, a novel prey, at points of their release in Southeast Alaska. The objectives of this dissertation are to determine the spatial distribution, seasonal distribution, and frequency of humpback whale foraging at release sites, determine whether whale presence is affecting the economic productivity of hatchery operations, and compare the bioenergetic benefits for whales feeding on juvenile salmon at hatchery release sites relative to typical prey. Five hatchery release sites were monitored over six years during the spring release season for whale presence/absence, numbers, and behaviors. Linear models were used to determine that for coho salmon, cohorts with frequent humpback whale presence had lower marine survival than cohorts with less or no humpback whale presence, but this was not seen for chum or Chinook salmon. Over six years, these sites lost an estimated 23% of revenue from coho salmon totaling almost a million dollars per year in addition to increased rearing costs to mitigate whale predation. A process model was developed to compare the net energy gain for humpback whales foraging on krill, herring and juvenile salmon. Whales were found to feed profitably on krill and chum salmon where they occurred in dense enough distributions and on herring when large coordinated groups impeded the escape of prey. Coho salmon typically distributed too diffusely for humpback whales to recuperate the full energetic costs of engulfment, indicating that behaviors such as bubble net feeding may be essential for increasing prey aggregation to an energetically profitable level, or humpback whales may be feeding to mitigate energetic losses. As intraspecific competition increases due to recovery and or changes to prey resources, generalist humpback whales may expand feeding to exploit new and less profitable prey resources.
    • Marine-derived nutrients in riverine ecosystems: developing tools for tracking movement and assessing effects in food webs on the Kenai Peninsula, Alaska

      Rinella, Daniel J. (2010-05)
      Marine-derived nutrients (MDN) delivered by spawning Pacific salmon (Oncorhynchus spp.) contribute to the productivity of riverine ecosystems. Optimizing methods for measuring MDN assimilation in food webs will foster the development of ecologically based resource management approaches. This dissertation aims to better understand relationships among spawning salmon abundance, biochemical measures of MDN assimilation, and the fitness of stream-dwelling fishes. The goals of my first research chapter were (1) to understand the factors that influence stable isotope ([delta]¹³C, [delta]¹⁵N, and [delta]³⁴S) and fatty acid measures of MDN assimilation in stream and riparian biota, and (2) to examine the ability of these measures to differentiate among sites that vary in spawning salmon biomass. For all biota studied, stable isotopes and fatty acids indicated that MDN assimilation increased with spawner abundance. Among Dolly Varden (Salvelinus malma), larger individuals assimilated proportionately more MDN. Seasonal effects were detected for aquatic macroinvertebrates and riparian horsetail (Equisetum fluviatile), but not for Dolly Varden. Of all dependent variables, Dolly Varden [delta]¹⁵N had the clearest relationship with spawner abundance, making this a good measure for monitoring MDN assimilation. Expanding on these results, two chapters examined potential fisheries management applications. The first sought to identify spawner levels above which stream-dwelling Dolly Varden and coho salmon (O. kisutch) parr cease to gain physiological benefits associated with MDN. RNA-DNA ratios (an index of recent growth rate) and energy density indicated saturation responses where values increased rapidly with spawner abundance up to approximately 1 kg/m² and then leveled off. In coho salmon parr, energy density and RNA-DNA ratios correlated significantly with [delta]¹⁵N. These results show strong linkages between MDN and fish fitness responses, while the saturation points may indicate spawner densities that balance salmon harvest with the ecological benefits of MDN. The second application tested a quick and inexpensive method for estimating, spawning salmon abundance based on [delta]¹⁵N in stream-dwelling fishes. Estimates made with coho salmon pair were unbiased, tightly correlated with observed values, and had a mean absolute deviation of 1.4 MT spawner biomass/km. Application of this method would allow estimates of annual escapement to be made on a potentially large number of streams.
    • 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 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).
    • Straying, stress, and potential for reproductive interactions between hatchery-produced and wild chum salmon (Oncorhynchus keta) in Southeast Alaska

      McConnell, Casey John; Westley, Peter; McPhee, Megan; Atkinson, Shannon; Oxman, Dion (2017-12)
      Approximately 1.5 billion juvenile hatchery-produced Pacific salmon (Oncorhynchus spp.) are currently released each year into Alaskan waters with goals of enhancing important fisheries and minimizing detrimental impacts on wild stocks. As the abundance of hatchery-produced salmon has increased, so have concerns about hatchery-origin strays entering wild systems and interactions with wild individuals on the spawning grounds. The influx of non-native strays and their associated fitness-related traits can reduce the resilience and productivity of recipient wild stocks, and is likely to be most deleterious when disparities in population sizes and heritable phenotypic characteristics between wild and hatchery fish exist. Thus, understanding the ecological and life-history mechanisms that regulate gene flow between hatchery and wild populations is crucial for conservation and management strategies in areas where hatchery enhancement is common. Currently, the ecology of strays on the spawning grounds and proximate physiological factors associated with straying (e.g., stress) are not well known. In this thesis I examine, 1) differences and similarities in several fitness-related phenotypic traits between naturally produced (presumably wild local individuals) and stray hatchery-produced chum salmon (Oncorhynchus keta) that died on the spawning grounds of Sawmill Creek, a small watershed near Juneau, Alaska, and 2) physiological differences in cortisol concentrations and the frequency of crystalline (vaterite) structure of otoliths between straying and correctly homing salmon. Hatchery-strays comprised 51.4% of the adult chum salmon that returned to Sawmill Creek during the 2015 spawning season. Hatchery males and females returned approximately seven days later, were consistently smaller (10% for males, 6% for females) in length, and younger on average than their naturally-produced counterparts. Additionally, hatchery-produced females lived fewer days on the spawning grounds during the spawning season, and retained a higher proportion of their eggs than did naturally produced females. To explore the potential role of stress on straying, I compared cortisol samples and frequency of vaterite formation in otoliths among groups of hatchery-produced fish that homed to the hatchery, hatchery-produced fish that strayed to Sawmill Creek, and naturally produced chum salmon that presumably homed to Sawmill Creek. No significant differences in cortisol concentration were found among any groups, though differences between the sexes were detected. Males of all groups had significantly lower cortisol concentrations than did females. No differences in frequency of vaterite occurrence were found between hatchery-stray and hatchery-home groups, though both hatchery groups were higher than naturally produced groups, which is consistent with findings of other studies. Thermal marking while at the hatchery during early development was not associated with vaterite formation, and no difference in frequency of vaterite formation was observed among groups of varying mark intensities. Overall, these results revealed there was ample opportunity for reproductive interactions between stray hatchery-produced and naturally produced chum salmon in Sawmill Creek during the 2015 spawning season, and consistent differences in phenotypic traits suggests the potential for gene flow to alter population-level phenotypic variation. However, despite the potential for gene flow, these results also reveal potential barriers to introgression and indicate that at least some of the presumed locally adapted traits of the natural stock remain intact. It remains unknown what the characteristics of the wild stock were prior to regional hatchery production and the extent to which the traits of this population are reflections of genetic differences between the hatchery and wild groups or phenotypic plasticity. To the extent these results are generalizable, observed differences in fitness-related traits between naturally produced and stray hatchery-produced fish may underlie the reduced reproductive success often reported in the literature. There were no differences in cortisol concentrations and frequency of vaterite occurrence between hatchery chum salmon that strayed and those that homed correctly, and the frequency of vaterite occurrence of hatchery chum salmon did not change as thermal mark intensity increased, which suggests that thermal marking may not directly alter homing ability of adults or development of juveniles, at least via otolith formation. Despite not having an effect on straying, the consistent findings of higher frequency of vaterite occurrence in hatchery-produced fish compared to naturally produced counterparts highlight the need for future work to uncover the causal underlying mechanisms and implications of vaterite on survival of the 1.5 billion salmon released each year in Alaskan waters.
    • Using multispectral aerial imagery and GIS-based approaches to quantify juvenile salmon rearing habitat in the Kulukak River, Alaska

      Woll, Christine; Sutton, Trent; Prakash, Anupma; McPhee, Megan (2012-05)
      Monitoring the quality and quantity of freshwater rearing habitat for Pacific salmon Oncorhynchus spp. is essential for maintaining stocks of these species. Because field-based habitat monitoring in remote areas can be expensive, time-consuming, and/or subjective, new methods are desired. The objectives of this study were (1) to develop methods for using multispectral aerial imagery to classify juvenile rearing habitat and determine the accuracy of these methods and (2) to use these methods to quantify and map juvenile salmon habitat characteristics in two study areas in the Kulukak River, Alaska. I demonstrated that a decision-based fusion approach using images acquired in the visible, near-infrared, and thermal-infrared regions classified habitat classes important for juvenile salmon with accuracies of 82.5% and 67.5% in the respective study areas. In addition, I quantified and mapped habitat variables often used in juvenile salmon studies on several scales and created habitat-suitability maps for coho salmon O. kisutch, demonstrating that both my study areas differed in habitat quantity and quality and are most likely low-quality rearing areas. This study demonstrates that airborne images can be used to determine the quality and quantity of juvenile Pacific salmon rearing habitat in small streams and thus decision support in fisheries management.