• 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.
    • Habitat analysis of major fishing grounds on the continental shelf off Kodiak, Alaska

      Rooney, Sean Charles; Reynolds, Jennifer; Norcross, Brenda; Heifetz, Jonathan; Kruse, Gordon (2008-12)
      "The continental shelf and upper slope of the Gulf of Alaska support diverse and commercially important communities of demersal fishes. Twenty-eight video-strip transects conducted from a research submersible, together with habitat maps based on interpreted multibeam sonar data, were used to classify distribution and abundance patterns of fishes relative to seafloor substrate type and water depth on Albatross and Portlock Banks on the Kodiak Shelf in the Gulf of Alaska. These associations were examined across spatial scales: ranging from tens of kilometer centimeters in size. A total of 5,778 fishes were recorded from 33 taxa. Fish community distribution patterns were largely correlated with depth and to a lesser extent with substrate type. Individual fish species habitat associations were also influenced by depth and substrate type; however, the spatial scale at which these factors were relevant varied by fish species. There was strong regional concordance among observed fish species habitat associations and those previously documented in studies from central California to the northern Gulf of Alaska. Although integrating substrates classified at different scales was challenging, the resulting information of scale specific habitat associations provides a more comprehensive understanding of how demersal fishes utilize benthic habitats"--Leaf iii
    • Ontogenetic considerations in the trophic level of commercial groundfish species in the Gulf of Alaska

      Marsh, Jennifer Marie; Hillgruber, Nicola; Foy, Robert; Kruse, Gordon; Wooller, Matthew (2010-12)
      "Trends in trophic level (TL) estimates of commercial fishery catches are used as ecosystem-based indicators for sustainability, but these estimates often do not incorporate species-specific interannual and ontogenetic feeding patterns. This study provides a finer resolution of ontogenetic and temporal variations in the trophic position of four groundfish species in the central Gulf of Alaska (GOA), walleye pollock (Theragra chaleogramma), Pacific cod (Gadus macrocephalus), arrowtooth flounder (Atheresthes stomias), and Pacific halibut (Hippoglossus stenolepis), using stable isotope analysis to assess TL and diet source. Samples were collected from the northeastern side of Kodiak Island, Alaska, from 2000-2004. Several Analysis of Covariance models were tested, allowing TL to co-vary with length, to detect possible variation among years and seasons and to estimate TL of catch for each study species. For each species, TL increased with length. Significant annual differences in [delta]¹³C and [delta]¹⁵N were detected for all groundfish, indicating a lower TL, pelagic diet in 2003 and a higher TL, benthic diet in 2001. Overall, TL of GOA commercial catches appeared to remain stable over 1990-2009, with the exception of walleye Pollack after 1999. This study shows that including length data could lead to an earlier detection of decline in TL estimates"--Leaf iii