• Genetic And Environmental Effects On Developmental Timing, Otolith Formation, And Gill Raker Development In Pink Salmon From Auke Creek, Alaska

      Oxman, Dion; Gharrett, Anthony; Milo, Adkison,; Cailliet, Gregor; Hagen, Peter; Smoker, William (2012)
      To determine how inheritance, environment, and hybridization influenced developmental timing, otolith formation, and gill raker development in pink salmon (Oncorhynchus gorbuscha), full and half-sibling families from Auke Creek, Alaska and third generation outbred hybrids between Auke Creek females and Pillar Creek males from Kodiak Island, Alaska (1,000 km distant) were incubated in ambient, chilled, and warmed water. Variation in development time of embryos from the odd-year broodline was primarily influenced by additive genetic factors, whereas no genetic effect was detected in the even-year run. No genotype-by environment (GxE) effects were associated with sires or families in either broodline, indicating that the observed variation in development time was likely the result of phenotypic plasticity. Hybridization (outbreeding) significantly prolonged development time in both broodlines, indicating that the phenotypic effects of outbreeding can last at least three generations. Early otolith development was genetically conserved and canalized, but the phenotypic expression of these genes is plastic and strongly influenced by environmental factors. There was no evidence that local adaptation or outbreeding influenced otolith morphology or shape. Otoliths from fish exposed to thermal stress were bilaterally asymmetrical, whereas the bilateral symmetry of otoliths from outbred fish exhibited evidence of heterosis because they were more symmetrical than their native counterparts. Unlike development time and otoliths, gill raker development was linear and consistently stable in the face of both hybridization and environmental stress. These results make it clear that different biological attributes respond to genetic control and stress in different ways.
    • Genetic diversity and population genetic structure of tanner crab Chionoecetes bairdi in Alaskan waters

      Johnson, Genevieve M.; López, J. Andrés; Eckert, Ginny L.; Hardy, Sarah M. (2019-05)
      Tanner crab (Chionoecetes bairdi) is a large-bodied species of crab harvested in commercial, personal use, and subsistence fisheries across Alaska. The commercial fisheries were highly productive until the 1980s, when most stocks faced major declines and were closed to harvest. The recovery success of stocks throughout the state has been variable throughout the subsequent decades, leading managers to question whether there are aspects of the population dynamics that are not accounted for. There is limited information on the genetic population structure of C. bairdi in Alaskan waters, which has caused uncertainty about whether established management areas align well with distribution and migration patterns for this species. I applied novel high throughput sequencing methods to measure genetic diversity and investigate the genetic population structure of C. bairdi in Alaskan waters. Genomic DNA was isolated from samples collected from Southeast Alaska, Prince William Sound, and the Eastern Bering Sea, both east and west of 166°W longitude, and processed according to a Double-Digest Restriction-Associated DNA Sequencing protocol. The final genotype assembly included 89 individuals that were genotyped at 2,740 independent, neutral single-nucleotide polymorphism (SNP) sites, and contained 3.06% missing data. The average observed heterozygosity across SNP sites within regions was significantly lower than the average heterozygosity expected for populations in Hardy-Weinberg equilibrium. An analysis of molecular variance indicated that genetic variability was mostly found within individuals (90%), 10% of variability was observed between individuals within sampling regions, and no significant amount of variation was detected between sampling regions. Furthermore, pairwise FST estimates between sampling regions were low, and thus the null model of panmixia could not be rejected. Principal components analysis was also congruent with a model of no differentiation among regions. Bayesian analysis implemented in the program STRUCTURE did not support any population partitioning above K = 1 clusters, again indicating that there is not substantial genetic differentiation among the regions sampled from across the state of Alaska. These results indicate high gene flow throughout the distribution of Tanner crab across the Alaska continental shelf. Recognized stocks are genetically indistinguishable from each other. This may indicate that stocks exchange a substantial number of migrants, and may not operate independently. This new information can provide insights as management plans are evaluated and refined.
    • Genetic linkage mapping of allozyme loci in even- and odd-year pink salmon (Oncorhynchus gorbuscha)

      Matsuoka, Makoto P.; Smoker, W. W. (1998)
      Genetic linkage maps of allozyme loci were constructed in even- and odd-year pink salmon (Oncorhynchus gorbuscha). The loci were mapped based on the results of gene-centromere (G-C) mapping and joint segregation analysis. For G-C mapping, 160 gynogenetic progeny families were produced, and 8,080 progeny from 74 families were analyzed using starch gel electrophoresis and histochemical stain techniques. G-C distances of 37 loci ranged from 0.5 cM at sMDH-A1* to 50 cM at sMDH-B2*. Eleven loci showed high G-C distances (>45 cM), indicating that one crossover on one chromosome arm is usual in pink salmon. Variation observed at sMDH-B1,2* in even-year families suggests that both of this loci is polymorphic and that there is possible inter-broodline chromosomal variation. Large variation was observed among families in G-C distance at several loci. Whether the variation was a reflection of difference in physical position, recombination rate, or some other factors needs clarification using a technique such as physical mapping with FISH, because this variation affects results of gene mapping based on recombination frequency. For joint segregation analysis, 320 biparental families were produced, and 13,068 progeny from 164 families were electrophoretically analyzed. Joint segregation was analyzed at over 200 locus pairs. Combined this with data from G-C mapping, 14 linkage groups involving 26 loci were constructed. The linkage maps contain eight classical linkage groups and four pseudolinkage groups. Two linkage groups found in pink salmon were conserved in widely divergent vertebrate species. Recombination frequency between linked loci were different between sexes, and it tends to be reduced in males in pink salmon. The order of loci, which probably duplicated in the recent tetraploidization event, in linkage groups I (sAAT-3 * → mAH-4*) and III (mAH-3* → sAAT-4*) was reversed. This is evidence of paracentric inversion during salmonid evolution after the duplication. Development of additional markers that are common (homologous) to many species will be necessary to examine syntenic stability and rearrangement over the evolutionary period.
    • Geomorphology and inconnu spawning site selection: an approach using GIS and remote sensing

      Tanner, Theresa Lynn; Margraf, T. Joseph; Wipfli, Mark S.; Verbyla, David (2008-08)
      This study examined the spatial components of inconnu Stenodus leucichthys spawning habitat use in the Selawik River, Alaska. Little is known about inconnu critical habitat needs; however, current studies of inconnu spawning behavior suggest a high level of habitat selectivity. This level of selectivity implies that there are specific habitat characteristics that these fish require for spawning. The purpose of this study was to build a heuristic habitat model that can be used to better understand inconnu spawning site selection in remote Alaskan watersheds. Using readily available, low- or no-cost remote sensing data layers, geographical information systems (GIS) were used in conjunction with multivariate statistics in an attempt to clarify relationships between geomorphologic features and spawning site selection. Spatial resolution of the remotely sensed data available in this study did not provide sufficient spatial detail to generate statistical correlations between spawning habitat selection and landscape characterizations. However, spawning occurred in areas of transition from high to low gradients, and in reaches typified as having very low slopes with very high sinuosity. Additionally, exploratory use of Radarsat fine beam 1 data favored its future application in fisheries investigations. This study is an initial step toward more research into inconnu spawning habitat.
    • Growth and Energetic Condition of Dolly Varden Char in Coastal Arctic Waters

      Stolarski, Jason T.; Prakash, Anupma; Sutton, Trent; Margraf, Joseph; Rosenberger, Amanda (2013-05)
      Dolly Varden char Salvelinus malma are a dominant member of the nearshore Arctic icthyofauna and support one of the largest subsistence fisheries within Arctic coastal communities in Alaska. Despite this importance, numerous aspects of Dolly Varden ecology remain poorly understood, which inhibits efforts to assess the biological consequences of anthropogenic disturbances such as hydrocarbon extraction and climate change within nearshore areas. The goal of this research was to develop and apply new techniques to measure and assess the biological integrity of Dolly Varden populations. To do so, I evaluated the precision of age determination generated from scales, otoliths, and fin rays, developed and validated bioelectrical impedance analysis (BIA) models capable of predicting non-lethal estimates of Dolly Varden proximate content, calculated and correlated retrospective estimates of Dolly Varden growth from archived otolith samples to broad-scale environmental variables, and investigated trends in whole body and tissue proximate content among years and demographics (i.e. reproductive versus non-reproductive individuals). Dolly Varden age determinations can be produced non-lethally using scales for fish up to age 5, while otoliths should be used for fish age 6 and greater. Multi-surface BIA models produced estimates of whole body proximate content with high precision. Retrospective growth analyses indicated growth increased significantly during the early 1980s, and was positively correlated to air temperature, sea surface temperature, and discharge and negatively correlated to ice concentration. Analyses of proximate content suggested that non-reproductive fish contained greater lipid concentrations than reproductive fish. Growth and condition analyses suggest that these metrics vary among years and are a function of reproductive cycles and environmental variability operating at multiple temporal and spatial scales. The adoption of scale-based aging and BIA technology will increase the precision of age-based biological statistics and aid in the detection of change within future Dolly Varden research and monitoring.
    • Growth and maturity of the Pacific razor clam in eastern Cook Inlet, Alaska

      McKellar, Jamie M.; Sutton, Trent; Iken, Katrin; Horstmann-Dehn, Lara; Hardy, Sarah; Erickson, Jack (2014-12)
      In Alaska, the only road-accessible fishery for the Pacific razor clam, Siliqua patula, is located in eastern Cook Inlet, and has been monitored by the Alaska Department of Fish & Game (ADF&G) since 1964. In recent years, a shift has been observed in size, age, and number of clam cohorts in this region, yet little is known about the early life history of razor clams in this region. This study aimed to provide information on length and age at maturity, growth rates, and spawn timing at two beaches in eastern Cook Inlet, Ninilchik and Clam Gulch, in 2009 and 2010. At Clam Gulch, only 20% of the sampled population was reproductive, compared with 83% at Ninilchik. At Ninilchik, clams were reproductive at a smaller size and younger age (p<0.05) than previously documented. The Ninilchik clams grew faster and had a larger size at age (p<0.05) than at Clam Gulch. A body condition index of clams from Clam Gulch was consistently 50% lower than at Ninilchik. Despite the relative proximity (25 km) of these locations, it is possible that environmental conditions may be different, resulting in differences in growth and reproductive output. This information is of special interest to fisheries managers as they address recent declines in the eastern Cook Inlet razor clam population and provides a benchmark for future management decisions.
    • Growth and post-harvest quality of selected Pacific oysters (Crassostrea gigas) cultured in Kachemak Bay, Alaska, and Puget Sound, Washington, in October of 2009 and June of 2010

      Thomas, Stuart Rendell; Oliveira, Alexandra; RaLonde, Ray; Eckert, Ginny; Langdon, Chris (2012-05)
      The primary objective of this project was to evaluate the growth, biochemical and fatty acid composition, physical and shell characteristics, and basic reproductive development of families of Pacific oysters (Crassostrea gigas) from the USDA-funded Molluscan Broodstock Program (MBP) planted in suspended culture in Kachemak Bay (KB), Alaska, and at an intertidal site in Thorndyke Bay (TB), Puget Sound, Washington. The MBP selects oysters to improve yields, growth, and survival, but little is known about the effects of selective breeding on other biological characteristics of selected oysters. Shell and meat characteristics of oysters from each of the seven highest-yielding MBP families were compared with those from non-selected control families at each site, which were sampled in October of 2009 and in June of 2010. Biometric and growth data, proximate compositions, fatty acid compositions, and basic degree of reproductive development were measured and compared by family, site, and sampling time. Selection improved yield, growth, and survival in MBP Cohort 20 oysters over three years of growout at KB. Colder water temperatures at KB relative to TB inhibited reproductive development, altering the biochemical composition of oysters within sites and between sampling times. Oysters grown at KB were slower growing and smaller when compared to TB, but higher in glycogen, Omega-3, and Omega-6 fatty acids (particularly docosahexaenoic acid: 22:6 Omega 3). Different latitudes and culture types were contributing factors for observed differences in growth, physiology, and composition, resulting in characteristically unique oysters from either site.
    • Growth dynamics of juvenile yellowfin sole (Pleuronectes asper) and northern rock sole (Lepidopsetta polyxystra) in the eastern Bering Sea

      Williams, Benjamin Charles (2003-12)
      The first five growth zones of 744 yellowfin sole and 512 northern rock sole otoliths were measured from year-classes 1974-1989, to identify patterns of annual growth and sources of temporal variation. Growth patterns were observed graphically and temporal variation was examined by partitioning growth into year and age effects via linear models. Growth and recruitment relationships with biological and environmental variables were explored through correlation analysis and stepwise regression. Results indicate that growth of yellowfin sole and rock sole declined from the late 1970s to the mid 1980s. Yellowfin sole length at age rebounded after 1985, while rock sole length at age continued to decline until at least the early 1990s. Density-dependent factors such as competition during early growth years overshadow the impacts of environmental variables on growth for both yellowfin sole and rock sole, possibly due to the complex oceanographic and atmospheric relationships that exist in the Bering Sea. Recruitment strengths of yellowfin sole and rock sole have significant environmental components suggesting that survival rates may be influenced by environmental conditions. Also, interspecific competition with yellowfin sole may be influencing rock sole recruitment in the eastern Bering Sea.
    • Growth of chum salmon in relation to population abundance and climate in the eastern north Pacific Ocean and the recruitment of pollock in the eastern Bering Sea

      Yasumiishi, Ellen Martinson; Criddle, Keith; Helle, John; Hillgruber, Nicola (2013-12)
      Global climate change is expected to change the distribution and growth of marine species. Therefore, understanding how climate, ocean productivity, and population abundance affect the dynamics of marine species will help predict how growth and recruitment of marine species will respond to future changes in climatic and oceanic conditions. Statistically significant intertemporal correlations have been observed between a variety of environmental factors and recruitment, growth, mortality, and abundance of fish populations. However, because these correlative relationships are not reflective of the actual biophysical processes, the relationships can break down, particularly when used for forecasting. Failure of these simple correlative relationships motivates the search for biological indicators that integrate ocean productivity across ecological dimensions and through time. Measured distances along Chum Salmon (Oncorhynchus keta) scale radii and associated body morphology were used to construct time series of Chum Salmon growth and, by extension, time series of productivity of those ecological domains salmon have exploited. Seasonal and annual marine growth of Chum Salmon from Fish Creek, Alaska and Quilcene River, Washington were examined in relation to population abundances and climate indices, 1972-2004. Final body size at maturity of these Chum Salmon was associated with variation in immature growth incurred while in oceanic waters. Density-dependent effects and climate explained some of the variation in growth but did not account for the entire increase in size at maturity in the mid-1990s. In the Bering Sea, Chum Salmon growth was assessed as an indicator for the recruitment of Walleye Pollock (Theragra chalcogramma) to age-1 in an effort to support an ecosystem-based fisheries management. Chum Salmon growth and the maximum of the monthly sea surface temperature explained 85% of the variation in age-1 Walleye Pollock recruitment. Higher Walleye Pollock recruitment success was associated with the combined effect of a cool late summer and intermediate growth of Chum Salmon. The combination of a physical and biological indicator served as the best indicators for changes in the marine growth of Chum Salmon and for the recruitment of Walleye Pollock.
    • Growth of juvenile Chilkat Lake sockeye salmon in response to density-dependent and environmental factors

      Neil, Jodi C.; McPhee, Megan V.; Adkison, Milo D.; Agler, Beverly A.; Ruggerone, Gregory T. (2018-12)
      Chilkat Lake, in northern Southeast Alaska, is home to a Sockeye Salmon Oncorhynchus nerka population that is an important component in local commercial, sport, and subsistence fisheries, and has been monitored since the late 1960s. The population began declining in the late 1980s, prompting fishery managers to evaluate the production potential of Chilkat Lake to determine if it could be a candidate for enhancement efforts such as fry stocking or lake fertilization. Sockeye Salmon fry were stocked into Chilkat Lake intermittently from 1989 to 2004 in both small- (<50,000) and large-scale (2.6-5.3 million) events. The purpose of this study was to determine whether stocking of fry resulted in decreased freshwater growth due to density-dependent processes. Fish scales from the Alaska Department of Fish and Game's archived collection of adult Chilkat Lake Sockeye Salmon were measured and used as a proxy for fish growth. The objectives of this thesis were to 1) examine changes in juvenile Chilkat Lake Sockeye Salmon freshwater growth over time (1978-2012); 2) determine whether increased density of juvenile fry coupled with simultaneous climate events negatively affected freshwater growth of Chilkat Lake Sockeye Salmon; and 3) determine whether increased density of juvenile fry affected age at smoltification of Chilkat Lake Sockeye Salmon. We hypothesized that high fry density would slow growth and delay smoltification; however, these analyses produced variable results. We did not detect an effect of increased fry density on growth in the first year of fresh water, but found evidence for a subtle, negative relationship between fry density and second year freshwater growth of those fish that delayed migration. We also found that age at smoltification decreased with increasing fry density. Overall, the model results indicated that no factor or combination of factors related to stocking activity or climate consistently affected juvenile Sockeye Salmon scale growth, suggesting either unidentified, equally influential, or confounding mechanisms (e.g., high adult escapement and anomalous weather patterns).
    • Growth Of Western Alaska And Asian Chum Salmon (Oncorhynchus Keta) In Relationship To Climatic Factors And Inter- And Intraspecific Competition

      Agler, Beverly Ann; Smoker, William; Hagen, Peter T.; Kruse, Gordon H.; Mueter, Franz J. (2012)
      Ocean climate shifts and interspecific interactions with Russian pink salmon and Asian chum salmon are all believed to influence the growth of chum salmon in the North Pacific Ocean. Stepwise generalized least squares regression and Mantel's tests were used to examine factors influencing mean annual growth from adult scales collected during 1962-2008. First-year scale growth was affected by warmer regional temperatures, the North Pacific Index (NH), and reduced ice cover. Significant negative effects of Asian chum salmon abundance were found on third-year growth of five of six age 0.3 populations and three of four age 0.4 populations examined, indicating intraspecific competition. I found a negative correlation with third-year growth, North Pacific annual sea surface temperature (SST), and NM. Effects of interspecific interactions on third-year growth due to Russian pink salmon abundance were smaller than effects of Asian chum salmon abundance and SST. Warmer large-scale SSTs associated with reduced third-year growth contradicted the original hypothesis and suggested that the abundance of Asian chum salmon created a masking effect overwhelming other factors promoting growth. Strong correlations among third-year growth suggested that chum salmon experienced similar environmental conditions in the North Pacific and had overlapping distributions. More synchronous growth was observed among populations from close rivers than distant ones, indicating the importance of regional scale versus oceanwide studies. In the first year, intercircular distance declined then rapidly increased at circuli 5-9, Intercircular distance was similar by gender until the third year when male growth exceeded female growth for all populations except Japan. Back-calculated lengths indicated that fish reach ~494 mm fork length by the third year before returning as age 0.3 adults. Smolts entering the ocean during odd years had greater distances between adjacent circuli the next year, indicating reduced growth in the first year and compensatory growth during the second and third years. Overall, these results suggested possible effects on chum salmon growth due to abundance of Asian chum salmon, and this effect led to a reduction in length of approximately 42 mm, potentially affecting fecundity by 3%. These results contribute to growing evidence of competition among conspecific salmon.
    • Growth physiology of juvenile red king crab, Paralithodes camtschaticus, in Alaska

      Westphal, Miranda J.; Tamone, Sherry; Eckert, Ginny; Siddon, Christopher (2011-08)
      Lack of recovery, following collapse of the Alaskan red king crab, Paralithodes camtschaticus, fishery, has prompted research directed towards rehabilitating the species. To better inform rehabilitation efforts aimed at increasing survival and growth of P. camtschaticus in their first year of life, I compared individual growth of hatchery-raised and wild-caught juvenile crabs in the laboratory and then compared both sets of laboratory individuals with cohorts from the field. To understand molt cycles, hemolymph was collected from age-0 and age-3 crabs to quantify circulating molting hormones (ecdysteroids) and the duration of premolt. Size, growth increment, molt interval, and cumulative molt interval did not differ significantly between hatchery-raised and wild-caught crabs. No consistent differences existed in CL between hatchery, wild-laboratory and field-surveyed juveniles for most months, although spine lengths of hatchery-raised and wild-caught crabs were significantly longer than field-surveyed crabs most months. Patterns of circulating ecdysteroids resembled published profiles for other crustacean species. Peak ecdysteroid levels occurred regularly (approximately 17 d) prior to ecdysis despite varying molt intervals. Age-0 and age-3 juveniles spent approximately 39 % and 32 % of the molt cycle in premolt, respectively. Overall, hatchery-raised and wild P. camtschaticus were markedly similar with respect to growth.
    • Growth Rates Of Calanoid Copepods In The Northern Gulf Of Alaska, And Their Relationships To Temperature, Chlorophyll And Body Size

      Liu, Hui; Hopcroft, Russell (2006)
      The juvenile growth rate and development time of the dominant calanoid copepods in the northern Gulf of Alaska were investigated. The utility of the artificial-cohort method was successfully validated as the most practical approach for estimating copepod growth rates in this ecosystem. The underlying functional responses of growth rates to temperature, food concentration, and body size were thoroughly explored for Neocalanus flemingeri/plumchrus, Metridia pacifica, Calanus marshallae, C. pacificus and Pseudocalanus spp. These results lay the foundation for the calculation of copepod secondary production and ongoing ecosystem modeling activities for the northern Gulf of Alaska, and will contribute to the refinement of global models of copepod growth rates. In general, the rates of copepod growth were negatively size-dependent. However, a positive relationship between growth rate and body size within each stage emerged in response to food climate. The effect of temperature on growth rates was prominent, but confounded with food conditions and body sizes, which also vary with temperature conditions. Copepod growth rates were significantly related to chlorophyll a, and were frequently food-limited, particularly for later developmental stages during the summer. Compared to other co-occurring calanoid copepods, egg-carrying species (i.e. Pseudocalanus) tend to grow slowly to meet their unique life history strategy. Statistically, more variability in temperature corrected growth rates can be explained by composite nonlinear models that incorporate development stage and body size into the traditional Michaelis-Menten relationship. The species-specific comparisons of the measured growth rates with those predicted by global models of copepod growth suggested more direct measurements of copepod growth rates in various ecosystems are required for fully appreciating the global patterns of copepod growth. Caution should be used in the widespread application of those models for estimating copepod secondary production, especially in polar and sub-polar waters.
    • Growth, foraging behavior and distribution of age-0 Arctic grayling in an Alaskan stream

      Dion, Cheryl Ann (2002-12)
      I evaluated the ability of three models to relate habitat characteristics to habitat quality for age-0 Arctic grayling Thymallullus arcticus in an Alaska stream. A temperature-based growth model made accurate predictions, showing it can reliably assess thermal habitat quality. Deviations between predicted and observed growth were useful because they identified the timing of possible critical periods, when competition for food or space may cause density-dependent mortality and emigration. A foraging model consistently overestimated the mean prey size of fish, showing that such models need further work before then can accurately assess food availability from invertebrate drift. A habitat selection model accurately predicted small fish would occupy the stream margins and the ontogenetic shift into faster, deeper water, but its detailed predictions for larger fish were not very precise. These models were useful tools for assessing habitat quality and gave insight into possible interactions between habitat characteristics and population dynamics.
    • Growth-increment formation using otoliths and scales of juvenile chinook salmon

      Walker, Brian Michael; Sutton, Trent; Adkinson, Milo; McPhee, Megan (2013-12)
      Freshwater growth of juvenile Chinook salmon Oncorhynchus tshawytscha influences survival and recruitment to the adult population. Retrospective analysis is used to measure salmon growth at previous ages, with fish size and growth assumed to be accurately reflected by otolith increments and scale circuli. I conducted a 122-d laboratory experiment to validate the relationship among body size, growth, and width to daily otolith growth increments and scale circuli in juvenile stream-type Chinook salmon. Fish total length was found to be proportional to otolith axis length (r² = 0.209, p < 0.001), otolith diameter (r² = 0.667, p < 0.001), and scale radius (r² = 0.538, p < 0.001). Somatic growth was accurately reflected by growth in otolith axis length (r² 0.65, p < 0.001) and growth in scale radius (r² = 0.449, p < 0.001). My study validated the assumption that fish body size and growth are reflected by otolith and scale size and growth- increment formation. The findings of my study can be used to ascertain body size at previous ages, which will help managers detect threshold sizes, examine the strength of size-selective mortality, and determine how growth rate affects smolt migration, early marine survival, and duration of ocean residency.
    • Gulf Of Alaska Pacific Ocean Perch: Stock Assessment, Survey Design And Sampling

      Hanselman, Dana Henry; Terrance J. Quinn, II (2004)
      Pacific ocean perch (Sebastes alutus) stock size in the Gulf of Alaska has been difficult to assess because of an imprecise survey biomass index. This imprecision has been attributed to low sampling effort on a species with an aggregated distribution. In this thesis, I examined the importance of estimated survey biomass in the stock assessment and ways to improve them. First, I presented the complete stock assessment for 2003, with an analysis of uncertainty. Uncertain parameters included natural mortality, recruitment, and biomass estimates. Second, I examined adaptive cluster sampling (ACS) as a method to reduce survey uncertainty. ACS results provided lower estimates of mean abundance and lower standard errors than did simple random sampling (SRS). Bootstrapping suggested that the ACS mean may be a superior measure of central tendency. ACS results were better than SRS, but not as dramatically as suggested by previous literature. I used simulations to explore why ACS did not perform optimally. These simulations showed that it would be necessary to sample over 10% of the population to obtain large gains in precision. This is impractical for a large marine population. I explored the use of hydroacoustic data recorded on survey vessels to gain precision in biomass estimation. I used the data to (1) develop a catch prediction model based on near-bottom backscatter, (2) simulate an adaptive design, (3) apply ratio estimation in double sampling using hydroacoustic data, and (4) post-stratify survey data. Using hydroacoustic data in these designs showed gains in precision over SRS and may be useful. Finally, I used the S. alutus age structured model presented above to simulate effects of five factors: survey measurement error, catchability trends, a second biomass index, data source weighting, and sensitivity of prior distributions. Simulations showed that the stock assessment model was ineffective at high measurement error and was unable to detect trends in the data. A second biomass index yielded gains in model precision. The weight given lengths measured in the fishery was most important because of its long time series, and the prior distribution on natural mortality was most influential because it was difficult to estimate.
    • Habitat characteristics of black oystercatcher breeding territories

      McFarland, Brooke A.; Konar, Brenda; Goldstein, Michael I.; Rosenberger, Amanda (2010-05)
      Habitat use in birds is often related to forage resources and predation avoidance. The large, long-lived black oystercatcher is a shorebird that defends a composite breeding territory for foraging in the intertidal zone and nesting in the immediate upland. Predation on young is a major source of mortality for many bird species, including black oystercatcher. As these are long-lived birds with many reproductive opportunities, adult survival, associated with forage resources, is expected to be more important in habitat use than less-predictable breeding success. To identify which factors most influence black oystercatcher breeding territory use, logistic regression models were developed and tested in south-central Alaska and tested in southeast Alaska. Intertidal community composition was sampled at a subset of sites. All known breeding sites in Kenai Fjords National Park and western Prince William Sound, plus sites in southeast Alaska, were matched with available breeding sites based on substrate and exposure classifications. Two factors available breeding related to predation avoidance, greater distance to vegetation and isolation from the mainland, were the most important variables in habitat models. Intertidal community composition did not vary between known breeding and available breeding sites. This suggests black oystercatchers choose breeding territories that reduce predation risk, contrary to expectations.
    • Habitat Function In Alaska Nearshore Marine Ecosystems

      Pirtle, Jodi L.; Eckert, Ginny; Reynolds, Jennifer; Quinn, Terrance II; Tissot, Brian; Woodby, Doug (2010)
      This research demonstrates how habitat structures subtidal communities and supports individual species in Alaska nearshore marine ecosystems. This was accomplished through a case study of southeast Alaska coastal regions, and an in-depth investigation of red king crab Paralithodes camtschaticus early life stage ecology and nursery habitat. How subtidal communities reflect variation in the marine environment of southeast Alaska is poorly understood. The purpose of the first part of this body of research was to identify and compare patterns of community structure for macroalgae, invertebrate, and fish communities at shallow subtidal depths between inner coast and outer coast regions, and link patterns of community structure to environmental variability in southeast Alaska. The major hydrographic gradient of decreasing salinity and increasing temperature from the outer coast to the inner coast affected regional community structure, with greater species diversity at the outer coast. Species distribution for invertebrate communities was linked to variation in benthic habitat at local scales among sites within regions. This study improves understanding of processes that structure marine communities to better predict how environmental change will affect Alaska marine ecosystems. Many Alaska red king crab populations have collapsed and continue to experience little recovery, even for areas without a commercial fishery. Several aspects of red king crab early life stage ecology were investigated because reasons for the lack of recovery may be related to the early life history of this species. Field experiments were conducted in southeast Alaska. Settlement timing was consistent between study years (2008--09) and with historical data for this region. Local oceanographic processes that influence larval transport may be responsible for spatial variation in larval supply. In laboratory and field experiments, early juvenile crabs (age 0 and 1) demonstrated refuge response behavior to a predator threat that changed with crab ontogeny. When predators were absent, juvenile crabs preferred highly structured biogenic habitats due to foraging opportunities, and associated with any structural habitat to improve survival when predators were present. This research shows how availability of high quality nursery habitat affects red king crab early life stage success and potential for population recovery.
    • Habitat usage by flatfish (Pleuronectidae) in the Mendenhall wetlands, Juneau, Alaska

      Mattes, Lynn A. (2004-05)
      The Mendenhall Wetlands in Juneau, Alaska were sampled with a variety of gear types to determine if the wetlands were essential fish habitat for flatfish. At locations where fish were captured, water quality characteristics were recorded and stomach contents of starry flounder and yellowfin sole were examined. Starry flounder, yellowfin sole, rock sole and flathead sole were captured over the course of the sampling season, both adults and juveniles. Starry flounder were captured in all sampling locations. Starry flounder have the ability to survive in higher temperatures, lower salinities and lower oxygen content than the other species. Yellowfin sole, rock sole and flathead sole were only captured on the mudflat, not in any of the less saline or warmer locations. The flatfish had more food items in their stomachs at high tide than at low tide, with the majority of food items being benthic, such as clam siphons, whole clams, mussels and copepods. The Mendenhall Wetlands appear to provide essential habitat for starry flounder, providing both food and shelter to several life stages and marginal habitat for the other three species of flatfish observed.