• 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.
    • Factors affecting survival of Arctic-breeding dunlin (Calidris alpina arcticola) adults and chicks

      Hill, Brooke Lynne; Hunter, Christine M.; Lindberg, Mark S.; Lanctot, Richard B. (2012-05)
      Accurate estimates of, and identifying factors affecting, survival and productivity can provide insight into population trends and help determine what management actions would most benefit a population. Only limited demographic data are available for many Arctic-breeding shorebird species. I estimated survival probabilities for Arctic-breeding Dunlin (Calidris alpina arcticola); for adults between 2003 and 2010, and for chicks in 2008 and 2009. Adult apparent survival probabilities were higher for males (0.60 ± 0.04) than females (0.41 ± 0.05), were higher for individuals initiating nests earlier in the season, and yearly variation was high. These apparent survival rates appear insufficient to maintain a stable population. Daily survival rates of chicks increased as insect biomass increased across all ages and hatch dates, but the relationship with age and hatch date depended on the values of the other variables. The probability of a chick surviving to 15 days of age showed a strong relationship with hatch date, peaking in early July then declining rapidly. Chick survival was much higher for young from first nests (0.71 0.07) than early (0.23 ± 0.19) or late (0.03 ± 0.61) replacement nests. This suggests replacement nests make a much smaller contribution to annual recruitment than first nests.
    • Roles of neighboring plants and temperature on growth and survival of white spruce seedlings along elevational gradients in Alaska

      Okano, Kyoko; Bret-Harte, M. Syndonia; Mulder, Christa P. H.; Juday, Glenn P. (2018-05)
      Seedlings are the most vulnerable stage of a tree's life and their successful survival and growth are critical to support future forests. Recent rapid warming in Alaska has promoted the movement of treeline upward in elevation, while trees at low elevations have decreased their growth. Understanding the direct effects of warming and the indirect effects induced by warming, such as species interactions, on the dominant treeline species, white spruce (Picea glauca) is key to sustaining boreal forests, from low elevations to above current treeline. The objectives of my thesis were to assess the roles that warming, neighboring interaction, habitat type, elevation and season play in the survival and growth of white spruce in Denali National Park and Preserve and Fairbanks, Alaska, USA. I planted spruce seedlings where I manipulated summer temperature and neighbor plants at seven sites (forest or tundra) along an elevational gradient that crossed treeline. I measured survival after winter and summer seasons, and harvested the seedlings for biomass after the third growing season. I found that competition -- particularly light competition where seedlings were shaded -- was the most important factor for seedling growth, while along elevational gradients, temperature and season had inverse effects on their survival: more seedlings at high elevations survived in summer and under warming, but more seedlings at low elevations survived in winter and under ambient temperatures. More seedlings with neighbors survived in summer and in forests, suggesting facilitation through shading. I found some evidence for a trade-off between growth and survival. Seedlings with a high relative growth in height (RGR height) in 2012 had a lower survival rate than seedlings with a low RGR height in the following hot and dry summer of 2013. More seedlings planted with neighbors that had a small diameter in 2012 also survived in 2013, but not without neighbors. These results suggest that a trade-off between survival and growth occurred only when competition for water can be expected. No difference in survival was found after the second winter and third summer. Altogether, I concluded the most important factor affecting seedling growth in my experiment was light competition, while the most important factors for seedling survival were warming and water availability for the first two years in the subarctic montane and interior Alaska.
    • The snowshoe hare filter to spruce establishment in boreal Alaska

      Olnes, Justin; Kielland, Knut; Ruess, Roger; Juday, Glenn; Genet, Helene; Mann, Daniel (2018-05)
      Interior Alaska is a heterogeneous landscape within the circumpolar boreal forest and is largely composed of black and white spruce (Picea mariana and P. glauca). Improving our understanding of the factors affecting patterns in spruce regeneration is particularly important because these factors ultimately contribute to shaping the boreal forest vegetation mosaic. Herbivory by snowshoe hares (Lepus americanus) is one factor that likely drives patterns in spruce establishment. The interaction between spruce and snowshoe hares provides an opportunity to study how plant-herbivore interactions can affect succession, vegetation community composition, and consequently, how herbivory influences landscape heterogeneity. I explored how herbivory by snowshoe hares alters the survival and growth of spruce seedlings across Interior Alaska's boreal forest. I hypothesized that the survival and growth rate of regenerating spruce is significantly reduced by snowshoe hare herbivory and that snowshoe hare herbivory influences the pattern of spruce establishment across time and space. To address this hypothesis, I conducted research in three distinct vegetation communities across the region: productive lowland floodplains (Chapters 1 and 2), treeline (Chapters 3 and 4), and recently burned stands of black spruce (Chapter 5). Together these five chapters reveal that snowshoe hares affect spruce establishment across much of boreal Alaska. Where and when hares are abundant, spruce can be heavily browsed, resulting in suppressed seedling growth and increased seedling mortality. The results of these studies also reveal a consistent and predictable pattern in which this plant-herbivore interaction takes place. The snowshoe hare filter acts as a 'spatially aggregating force' to spruce establishment, where the potential for optimal regeneration is highest during periods of low hare abundance and where hares are absent from the landscape.