• 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.
    • Migration patterns and energetics of adult chinook salmon Oncorhynchus tshawystcha in Alaska rivers

      Neuneker, Kristin R.; Falke, Jeffrey; Seitz, Andrew; Nichols, Jeff; Cox, M. Keith (2017-12)
      Adult Chinook Salmon Oncorhynchus tshawytscha undertake extensive and energetically costly migrations between food resources in the ocean and their freshwater spawning habitats, requiring them to adapt behavioral and physiological traits that allow them to successfully reach their spawning streams and reproduce. Such adaptations may be shaped by physical factors in the environment and individual- and population-specific biological characteristics. Chinook Salmon in North America are important resources for both United States and Canadian stakeholders, but relatively little is known about their freshwater migration patterns and energetic status in many rivers across their range. This research explored variation in migration timing and migration rates of Chinook Salmon in two Southeast Alaska transboundary rivers (Taku River, Stikine River), examined energetic status at multiple sampling locations in Alaska, and created and tested a predictive model for energetic status using bioelectrical impedance analysis (BIA). Migration timing was earlier for fish that spawned in more distant tributaries in both transboundary systems and the Taku River was earlier compared to the Stikine River. Migration rates decreased during periods of high flows, were slower for fish in the Taku River, and were slower in both systems in 2016 compared to 2015. Migration rates were faster for fish with spawning sites farther upstream when compared to those that spawned closer to the river mouth, but these rates decreased over time as fish swam farther upriver. Chinook Salmon (N = 129) sampled for energetic status at the beginning of their freshwater spawning migration had higher total percent lipid than those near the spawning grounds (ANOVA: F = 202.1, df = 3, P < 0.001), and total percent lipid and water were precisely predicted based on BIA measurements (R² = 0.82, RMSE = 5.33; R² = 0.78, RMSE = 2.43 respectively). The BIA model was tested to determine if it could be generalized between similar species, but this was found to be less precise than species-specific models. The BIA measurement technique was also easily implemented into an existing study on a remote Chinook Salmon population. Given threats from climate change and mining activities, this information will be useful for fisheries researchers as a benchmark for understanding migration behaviors in these Chinook Salmon populations, and indicates that integration of BIA into population monitoring may be a useful tool for creating management practices targeted at facilitating successful migration behaviors and increasing or maintaining energetic status for these fish.
    • Outbreeding depression and inheritance in three generations of geographically distinct southeast Alaska coho salmon (Oncorhynchus kisutch) populations

      Dann, Tyler H. (2009-08)
      I observed no fitness losses among F₂ hybrids of three Southeast Alaska coho salmon (Oncorhynchus kisutch) populations relative to parental controls. Marine survival did not differ among groups in one generation, but was greater for hybrids than controls in another, although the power of these tests was low. Increases in fluctuating asymmetry, which can signal losses in fitness, were not observed. Line cross analyses of length suggested additive and additive plus dominance gene action, and two of three analyses suggested epistasis. In contrast, meristic characters exhibited little variability; and in most cases tests failed to reject a simple additive model. Half- and full-sib analyses provided no evidence of quantitative genetic variation for any trait although the power to detect these effects was low. Comparisons of population divergence measured by quantitative traits (Qst) and molecular markers (Fst) that length is an adaptive trait and that bilateral meristics are highly conserved. Although we did not observe losses in fitness, the power of our tests was low, the among-population differences were unique to our experiment and so results of this study should be interpreted with caution.
    • 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.