• Abundance, Recruitment, And Environmental Forcing Of Kodiak Red King Crab

      Bechtol, William R.; Kruse, Gordon H. (2009)
      Commercial harvests of red king crab Paralithodes camtschaticus around Kodiak Island, Alaska increased rapidly in the 1960s to a peak of 42,800 mt in 1965. Stock abundance declined sharply in the late 1960s, moderated in the 1970s, and crashed in the early 1980s. The stock has not recovered despite a commercial fishery closure since 1983. To better understand the rise, collapse, and continued depleted status of the red king crab stock around Kodiak Island, I conducted a retrospective analysis with three primary objectives: (1) reconstruct spawning stock abundance and recruitment during 1960-2004; (2) explore stock-recruit relationships; and (3) examine ecological influences on crab recruitment. A population dynamics model was used to estimate abundance, recruitment, and fishing and natural mortalities. Three male and four female "stages" were estimated using catch composition data from the fishery (1960-1982) and pot (1972-1986) and trawl (1986-2004) surveys. Male abundance was estimated for 1960-2004, but limited data constrained female estimates to 1972-2004. Strong crab recruitment facilitated increased fishery capitalization during the 1960s, but the high harvest rates were not sustainable, likely due to reproductive failure associated with sex ratios skewed toward females. To examine spawner-recruitment (S-R) relationships for the Kodiak stock, I considered lags of 5-8 years between reproduction and recruitment and, due to limited female data, two currencies of male abundance as a proxy for spawners: (1) all males ?125 mm carapace length (CL); and (2) legal males (?145 mm CL). Model selection involved AICc, the Akaike Information Criterion corrected for small sample size. An autocorrelated Ricker model using all males and a 5-year lag, with the time series separated into three productivity periods corresponding to different ecological regimes, minimized AIC c values. Depensation at low stock sizes was not detected. Potential effects of selected biotic and abiotic factors on early life survival by Kodiak red king crab were examined by extending the S-R relationship. Results suggested a strong negative influence of Pacific cod Gadus macrocephalus on crab recruitment. Thus, increased cod abundance and a nearshore shift in cod distribution likely impeded crab stock rebuilding.
    • Demographic components of philopatry and nest-site fidelity of Pacific black brant

      Lindberg, Mark Steven; Sedinger, James S. (1996)
      I investigated demographic components of nest-site fidelity and philopatry of Pacific black brant (Branta bernicla nigricans). My analyses included data I collected during summer 1990-1993, and also incorporated data obtained between 1986-1989. My studies of nest-site fidelity were limited to the Tutakoke River colony, Yukon-Kuskokwim River Delta, Alaska. Studies of philopatry and dispersal among colonies included observations at 7 breeding colonies of brant marked with tarsal tags (n = 20,147). I observed strong evidence that philopatry of brant was female biased. Probability of breeding philopatry, which was estimated with multi-state modeling techniques, was high (>0.9) and dispersal of adults among breeding colonies was rare. I developed an ad hoc estimator for natal philopatry that was unbiased by a confounding of homing, survival, and detection probabilities. Probability of natal philopatry for females was both age and density dependent. The density-dependent decline in natal philopatry may result from increased rate of permanent nonbreeding or increased probability of dispersal. Observed probability of natal philopatry for males was approximately equivalent to the relative size of their natal colony, suggesting that males pair at random with females from other colonies. Gene flow among populations of brant is largely male mediated, and I predict populations of brant will exhibit distinct mitochondrial DNAs if populations have been reproductively isolated for an adequate period of time. Probability of fidelity to previous nest sites for adults was high (>0.7). Probability of nest-site fidelity was affected by previous nesting success, age, and availability of nest sites. Phenology of nesting, nest-site selection, and clutch size of brant was affected by spring snowmelt. Dispersal of brant from traditional nest sites in years with late springs may represent a tradeoff between site fidelity and timing of nest initiation. Movement of young females from natal nest sites was a mechanism for colony expansion. I observed little evidence that site fidelity was advantageous, and concluded that quality of individual bird, environmental conditions, and demographic status may be more important determinants of breeding performance.
    • Diversity In The Boreal Forest Of Alaska: Distribution And Impacts On Ecosystem Services

      Young, Brian D.; Yarie, John; Chapin, F. Stuart; Greenburg, Josh; Huettmann, Falk; Verbyla, David (2012)
      Within the forest management community, diversity is often considered as simply a list of species present at a location. In this study, diversity refers to species richness and evenness and takes into account vegetation structure (i.e. size, density, and complexity) that characterize a given forest ecosystem and can typically be measured using existing forest inventories. Within interior Alaska the largest forest inventories are the Cooperative Alaska Forest Inventory and the Wainwright Forest Inventory. The limited distribution of these inventories constrains the predictions that can be made. In this thesis, I examine forest diversity in three distinct frameworks; Recruitment, Patterns, and Production. In Chapter 1, I explore forest management decisions that may shape forest diversity and its role and impacts in the boreal forest. In Chapter 2, I evaluate and map the relationships between recruitment and species and tree size diversity using a geospatial approach. My results show a consistent positive relationship between recruitment and species diversity and a general negative relationship between recruitment and tree size diversity, indicating a tradeoff between species diversity and tree size diversity in their effects on recruitment. In Chapter 3, I modeled and mapped current and possible future forest diversity patterns within the boreal forest of Alaska using machine learning. The results indicate that the geographic patterns of the two diversity measures differ greatly for both current conditions and future scenarios and that these are more strongly influenced by human impacts than by ecological factors. In Chapter 4, I developed a method for mapping and predicting forest biomass for the boreal forest of interior Alaska using three different machine-learning techniques. I developed first time high resolution prediction maps at a 1 km2 pixel size for aboveground woody biomass. My results indicate that the geographic patterns of biomass are strongly influenced by the tree size class diversity of a given stand. Finally, in Chapter 5, I argue that the methods and results developed for this dissertation can aid in our understanding of forest ecology and forest management decisions within the boreal region.
    • Dynamics of a migratory fish population with applications to the management of sablefish in the Northeast Pacific Ocean

      Heifetz, Jonathan; Quinn, Terrance J. II (1996)
      Quantitative models are developed to describe the dynamics of an age-structured migratory fish population subject to exploitation. Migration rates are quantified, alternative ways of apportioning harvest among areas are examined, and the dynamics of a migratory population is described within the general theoretical framework of a projection matrix model. Application of these modeling efforts is within the context of the sablefish (Anoplopoma fimbria) fishery in the North Pacific Ocean. A Markov model that includes natural and fishing mortality, tag reporting and shedding rates, and migration is used to quantify migration rates of tagged sablefish among fishery regulatory areas. Estimates of annual migration rates out of an area are in the range 19-69% for small (<57 cm fork length (FL)), 25-72% for medium (57-66 cm FL), and 27-71% for large (>66 cm FL) sablefish. The predominant direction of migration along the continental slope is eastward for large sablefish and westward for small sablefish. Most estimates of migration are precise, unconfounded, and robust to perturbations of input constants. An age-structured model that includes migration is constructed to examine harvest policies for sablefish. Areal estimates of yield-per-recruit depends on the geographic distribution of recruitment. In general, when evaluated under the current annual exploitation rate of 10%, apportioning harvest among areas based on areal estimates of biomass and apportionment based on the steady-state distribution of biomass give similar results. A policy of apportionment based on a weighted moving average of areal estimates of available biomass is preferred to others. This policy adapts to current information about geographic distribution of biomass, reduces the effects of measurement error, and does not require estimates of migration probabilities for implementation. The reproduction, mortality and migration of an age-structured fish population are incorporated into a projection matrix model. The model is parameterized to include areal specificity in the stock-recruitment relationship and events such as larval dispersion that is decoupled from local reproduction. For the sablefish fishery where direction of movement is age dependent, fishing at a common rate among areas may be detrimental to the population in a given area. Area-specific fishing strategies can be devised to meet management objectives such as maintenance of areal spawning potential.
    • Forecasting catches of Pacific salmon in commercial fisheries of southeast Alaska

      Marshall, Robert Paul (1992)
      Data collections since 1911 and statistical methods from time series analysis are employed to forecast catches of pink, chum, coho, and sockeye salmon in Southeast Alaska. Knowledge of the spatial and temporal domains favored by Pacific salmon originating in Southeast Alaska is summarized to provide a basis for estimating environmental variation experienced by each species. Catches in northern, southern, and all of Southeast Alaska are forecast with univariate ARIMA, transfer function-noise (TFN), and vector ARMA models. Univariate models for catch in numbers and catch in weight yielded similar results for each species. Air and sea surface temperatures, freshwater discharge, and coastal upwelling enter TFN models for several species and areas. Environmental variables allow TFN models to explain a small amount of variation in the catches (average of 19%) above that explained by univariate models. Forecasts for most, but not all, species and areas are improved (average of 16%) by including environmental data in TFN models. Stock-recruit models with a parameter for density dependent mortality provide the best forecasts of pink salmon catch and are recommended for future forecasts. Winter air and sea surface temperatures enter stock-recruit models for pink salmon, and forecasts of catch and recruitment in northern and southern Southeast Alaska tend to oppose each other and cancel (1981-1985), which suggests that the salmon are caught in areas other than where they originated. Mean absolute percentage error (MAPE) for forecasts of pink salmon catch from stock-recruit models in Southeast Alaska, based on data for 1981-1990, is estimated at 49%, with first, second, and third quartiles of 10%, 23%, and 83%, respectively. Catches of Pacific salmon in Southeast Alaska are significantly correlated and are forecast jointly with good accuracy by vector ARMA models, except when effects believed to result from density dependent mortality are present in the data. Correlations indicate that coho salmon smolts might prey on young pink salmon. Also, recruitment of pink salmon in Southeast Alaska and British Columbia is correlated; regional environmental influences might thus affect catches in both areas. In Southeast Alaska, MAPE for forecasting coho and sockeye salmon catch with time series analysis is about 20%, and about 30% for chum salmon.
    • Gene-By-Diet Interactions And Obesity Among Yup'ik People Living In Southwest Alaska

      Lemas, Dominick; Boyer, Bert B.; O'Brien, Diane M.; Schulte, Marvin K.; Tiwari, Hemant K. (2012)
      BACKGROUND: Molecular approaches have expedited the discovery of human obesity genes, however the heritability explained by these loci remains low (<2%). Gene-by-environment interactions may partially account for the "missing heritability" attributed to variation in obesity phenotypes. OBJECTIVE: The specific aims of this dissertation were to (i) identify genetic polymorphisms associated with obesity-related phenotypes in Yup'ik people and (ii) evaluate how n-3 polyunsaturated fatty acid (n-3 PUFA) intake modifies associations between genetic polymorphisms and obesity-related phenotypes in a population with widely varying intake of n-3 PUFAs. APPROACH: We genotyped genetic polymorphisms in (1) candidate genes with a strong physiological role in obesity pathophysiology; (2) candidate genes identified in obesity whole-genome linkage studies that were regulated by n-3 PUFAs; and (3) candidate genes reproducibly implicated in obesity genome-wide association studies (GWAS). DATA & ANALYSES: We used Center for Alaska Native Health Research (CANHR) data collected between 2001 and 2008. We estimated dietary intake of n-3 PUFA using nitrogen stable isotope ratios (delta15N) of red blood cells (RBC) and obesity-related phenotypes were obtained by trained staff. Genotype-phenotype analyses used generalized linear models that accounted for familial correlations. RESULTS: Our analyses of candidate genes based on physiology revealed a polymorphism called P479L in carnitine palmitoyltransferase 1A (CPT1A) that was associated with elevated fasting HDL-cholesterol and all obesity phenotypes. Our investigation of candidate genes that are regulated by n-3 PUFAs and implicated in obesity whole-genome linkage studies demonstrate that polymorphisms in stearoyl CoA desaturase (SCD) and steroyl regulatory element binding protein (SLC2A4) were associated with obesity-related phenotypes; however n-3 PUFA intake did not modify associations between SCD and SLC2A4 polymorphisms and obesity phenotypes. Finally, our investigation of candidate genes reproducibly implicated in obesity GWAS demonstrated that genetic predisposition to obesity is associated with adiposity and that interactions with n-3 PUFA intake accounted for more than twice the phenotypic variation in adiposity. CONCLUSION: Taken together, results from this dissertation suggest that selecting candidate genes based on large-scale genomic analyses, such as linkage analyses and GWAS, has the potential to identify gene-by-environment interactions that partially account for the "missing heritability" attributed to obesity.
    • Heterogeneity And Bias In Abundance Estimates Of Outmigrating Chinook Salmon In The Chena River, Alaska

      Lambert, Ted Martelle (1998)
      The objective was to examine bias due to heterogeneity in capture probability (p) in an abundance estimate for chinook salmon (Oncorhynchus tschawytscha) outmigrants in the Chena River, Alaska. A higher proportion of day-marked fish (21/636 = 0.0330) compared to night-marked fish (17/1724 = 0.0098; p $<$ 0.0001, $\alpha$ = 0.05) was recaptured at the lower site in a Cormack-Jolly-Seber experiment with upper, middle and lower sites. Heterogeneity was also likely at the middle site between upper site-marked and unmarked fish. Simulations with heterogeneity confined to the middle and lower sites (i.e., due to inadequate mixing) caused small bias ($<$2.5%) in the upper site abundance estimate. With heterogeneity at all three sites (a subpopulation effect), the upper site estimate had 22.9% to 29.3% negative bias. Because heterogeneity observed in the Chena was probably due to inadequate mixing (related to daytime trap evasion), bias in the upper site estimate was probably small. <p>
    • Interrelationships of Pacific herring, Clupea pallasi, populations and their relation to large-scale environmental and oceanographic variables

      Williams, Erik Hamilton; Quinn, T. II (1999)
      Recruitment estimates for Pacific herring, Clupea pallasi, populations in the Bering Sea and Northeast Pacific Ocean are highly variable, difficult to forecast, and crucial for determining optimum harvest levels. Age-structured population models for annual stock assessments of the sac-roe fisheries rely on fishery and survey age composition data tuned to an auxiliary survey of total biomass. In Chapter 1, the first age-structured model for Norton Sound herring was developed similarly to existing models. Estimates of variability from age-structured stock assessment models for Pacific herring are often not calculated. In Chapter 2, a parametric bootstrap procedure using a fit of the Dirichlet distribution to observed age composition data was developed as a quick and easy method for computing error estimates of model estimates. This bootstrap technique was able to capture variability beyond that of the multinomial distribution. This technique can provide estimates of variability for existing population models with age composition data requiring little change to the original model structure. Recruitment time series from Pacific herring stock assessment models for 14 populations in the Bering Sea and Northeast Pacific Ocean were analyzed for links to the environment. For some populations, recruitment series were extended backward in time using cohort analysis. In chapter 3, correlation and multivariate cluster analyses were applied to determine herring population associations. There appear to be four major herring groups: Bering Sea, outer Gulf of Alaska, coastal SE Alaska, and British Columbia. These associations were combined with an exploratory correlation analysis of environmental data in chapter 4. Appropriate time periods for environmental variables were determined for use in Ricker type environmentally dependent spawner-recruit forecasting models. Global and local scale environmental variables were examined in forecasting models, resulting in improvements in recruitment forecasts compared to models without environmental data. The exploratory correlation analysis and best fit models, determined by jackknife error prediction, indicated temperature data corresponding to the year of spawning resulted in the best forecasting models. The Norton Sound age-structured model, parametric bootstrap procedure, and recruitment forecasting models serve as enhancements to the decision process of managing Pacific herring fisheries.
    • Martingales in mark-recapture experiments with constant recruitment and survival

      Humphrey, Patricia Buslee (1995)
      The method known as mark-recapture has been used for almost one hundred years in assessing animal populations. For many years, these models were restricted to closed populations; no changes to the population were assumed to occur through either migration or births and deaths. Numerous estimators for the closed population have been proposed through the years, some of the most recent by Paul Yip which make use of martingales to derive the necessary estimates. The independently derived Jolly-Seber model (1965) was the first to address the open population situation. That method as originally proposed is cumbersome mathematically due to the large number of parameters to be estimated as well as the inability to obtain estimates until the end of a series of capture events since some of the "observed" variables necessary are prospective. It also is cumbersome for the biologist in the field as individual marks and capture histories are required for each animal. Variations have been proposed through the years which hold survival and/or capture probabilities constant across capture occasions. Models based on log-linear estimators have also been proposed (Cormack 1989). This paper builds on the closed population work of Yip in using martingale-based conditional least squares to estimate population parameters for an open population where it is assumed recruitment of new individuals into the population is constant from one capture occasion to the next, and capture and survival probabilities are constant across capture occasions. It is an improvement over most other methods in that no detailed capture histories are needed; animals are simply noted as marked or unmarked. Performance of the estimator proposed is studied through computer simulation and comparison with classical estimators on actual data sets.